Embraced by the Eerie Love of Man – On the Domestication of Dog, Sheep and Chicken

May 4, 2013 7 comments

Earlier this year a new study identified a fossil canid, excavated from Razboinichya Cave in the Siberian Altai Mountains, as a member of the dog lineage. Indeed, mtDNA of this Pleistocene specimen of the ‘Mammoth steppe fauna’ resulted most similar to that of most modern dogs.

Druzhkova et al. – Ancient DNA Analysis Affirms the Canid from Altai as a Primitive Dog, 2013

The origin of domestic dogs remains controversial, with genetic data indicating a separation between modern dogs and wolves in the Late Pleistocene. However, only a few dog-like fossils are found prior to the Last Glacial Maximum, and it is widely accepted that the dog domestication predates the beginning of agriculture about 10,000 years ago. In order to evaluate the genetic relationship of one of the oldest dogs, we have isolated ancient DNA from the recently described putative 33,000-year old Pleistocene dog from Altai and analyzed 413 nucleotides of the mitochondrial control region. Our analyses reveal that the unique haplotype of the Altai dog is more closely related to modern dogs and prehistoric New World canids than it is to contemporary wolves. Further genetic analyses of ancient canids may reveal a more exact date and center of domestication.

These results bolster previous ideas of an early appearance of domesticated dogs, though how they relate with their wolf kin remains shrouded in mystery. The resolution considerably exceeds previous results on Belgic samples thousands of miles away, where just 57 base pairs could be extracted from the mitochondrial control region of six large Pleistocene canids from Goyet cave (samples G1-6), and one from Trou des Nutons (sample TN-1), what unfortunately didn’t allow the reconstruction of much phylogenetic structure. The new results confirm the latter as a feature of Pleistocene dogs rather than a defect in previous results:

When investigating the phylogenetic informativeness of our dataset combining the Altai specimen, 72 extant dogs and 30 wolves, 35 prehistoric New World canids and four coyotes we also found low support for either a clearly resolved branching pattern or star-shaped evolution (Druzhkova et al., 2013)

Apparently dog evolution has an extremely long trajectory, and became even more complicated by the strong impact of much later, Holocene events. Their early divergence is also suggested by outstanding differences in morphology that distinguish dogs from wolves in their shortened muzzles, broader palates, crowded teeth and the broad, heavy frontal shields at the top of their skulls. The oldest (unsampled) Goyet dog, at 36,000 cal BP even older than the Altai specimen, was ‘not intermediate in form between the fossil wolves and the prehistoric dogs, but conforms to the configuration of the other Palaeolithic dogs, which are approximately 18,000 years younger’ (Germonpré et al., 2009). However, despite Goyet also supplied a representative morphological reference, Druzhkova’s team didn’t try to establish a link with this Belgium phenomenon of early dog occurrences. Even worse, the authors utterly ignored new insights that rather urge for a revision of the canid phylogenetic tree in the vein of Pilot et al. (2010). The traditional concept of a nested dog-clade, essential to the identification of Canis lupus familiaris (the domestic dog), and their putative geographical origin, already turned out incompatible with the results of Goyet. New inconsistencies may confirm the phylogenetic tree employed by Druzhkova’s team was already obsolete.

Embracing the wild progenitor of domestic breed. The start of a beautiful romance, or an enormous tragedy for the species involved?

(Embracing the wild progenitor of domestic breed. The start of a beautiful romance, or an enormous tragedy for the species involved?)

The view that dogs are the tamed descendants of the common wolf has always been the most popular one, though the scrutiny of investigators yielded ambiguous evidence. Prolific contacts between wolves and early modern humans rather tend to obfuscate early progress in the process of dog domestication:

The Palaeolithic sites yielding putative dog remains might be best described as extended-use camps or hunting sites and some of these are associated with dwellings made from mammoth bone (e.g., Germonpré et al., 2008, 489). Unambiguously identified wolf remains occur routinely in many of these sites, often at relatively high frequencies for a large carnivore. (Crockford & Kuzmin, 2012)

Incidental dog-like canids could already be distinguished in Upper Palaeolithic sites, without being sure these individual creatures could indeed be derived of tamed dogs in the periphery of human habitation rather than being the representatives of an extinct lineage of wolves. Interaction with Neanderthal may remain the only evidence that truly suits the popular preposition of the tamed wolf pur sang:

Trou de la Naulette is a famous Neanderthal site excavated by Dupont in the 1860s […]. According to the notes of Dupont, the fossil canid skull was found in the Second Horizon, the same containing the Neanderthal remains.
The Trou de la Naulette […] skulls have missing values and cannot be identified. (Germonpré et al., 2009)

Only the first appearance of dog-like features in fossils offered the opportunity to prove the acceptance of wolves as pets. For over a century Pleistocene fossils with a dog-like anatomy have been found littered over a wider area in northern Eurasia, and despite an incidental association with prehistoric human presence some reasonable doubts remain about the progress of their domestication. Dogs have traditionally been regarded the tamed version of Eurasian wolves, with the implicit assumption their differences could be fully explained by human interference and a domestic lifestyle. Earlier publications even went a lot further. Wayne et al. (1999) asserted on the basis of mtDNA that ’dogs and gray wolves may have diverged […] about 135,000 years before present’, adding that dogs ‘may have been domesticated earlier and have only recently changed in conformation with changing conditions associated with the shift from hunter-gather cultures to more agrarian societies about 12,000 years ago’. Genetic variety of dogs even exceeds the variety of the Holarctic wolf. Far from being their obvious “ancestral” counterparts, genetically speaking wolves falls within the range of genetic variety of dogs while on the basis of descend rather the opposite should be expected:

Greater mtDNA differences appeared within the single breeds of Doberman pinscher of poodle than between dogs and wolves. Eighteen breeds, which included dachshunds, dingoes and Great Danes, shared a common dog haplotype. Alaskan malamutes, Siberian huskies and Eskimo dogs also showed up in the common dog haplotype and were no closer to wolves than poodles and bulldogs. These data make wolves resemble another breed of dog. (Serpell, 1995, p.33)

Indeed, dogs are clearly the most diverse domestic species, both genetically and by morphology. Hence, Pleistocene dog domestication was traditionally considered a quite intuitive concept. Modern investigation tend to confirm the unique genetic identity of dogs in relation with wolves:

We identified 3,786,655 putative single nucleotide polymorphisms (SNPs) in the combined dog and wolf data, 1,770,909 (46.8%) of which were only segregating in the dog pools, whereas 140,818 (3.7%) were private to wolves (Axelsson et al., 2013)

However, the pendulum of scientific ‘consensus’ already tended to swing away from Pleistocene domestication in favor of still ill-understood Neolithic events when Druzhkova’s team caused considerable confusion with their published results on the Altai specimen, the second oldest Pleistocene dog. It is funny to watch great names on the scientific scene stumble in their enthusiasm, utterly unable to digest the full spectrum of conflicting information and grasp the consequences. Probably to many this new results were all too much in too short a time. Indeed, the Pleistocene Altai dog emerged genetically closer to modern dogs than to contemporary wolves, but there is more. The specimen also attested closely related with prehistoric New World canids, including both pre-Columbian domestic dogs and extinct eastern Beringian wolves, the latter being no less revolutionary for our understanding of dog evolution.

Druzhkova’s Consensus Neighbor Joining Tree incorporates an extensive mtDNA database of extinct eastern Beringian wolves, that cluster in and around main dog haplogroup A. Modern wolf mtDNA isn't derived, suggesting dog mtDNA isn't a nested haplogroup as previously assumed with this already obsolete phylogenetic representation.

(Druzhkova’s Consensus Neighbor Joining Tree incorporates an extensive mtDNA database of extinct eastern Beringian wolves, that cluster in and around main dog haplogroup A. Typical modern wolf mtDNA isn’t derived, suggesting dog mtDNA isn’t a nested haplogroup as previously assumed with this already obsolete phylogenetic representation)

One glance at Druzhkova’s Consensus Neighbor Joining Tree makes clear the mentioned New World canids don’t simply refer to the pre-Columbian dogs that Native Americans brought with them when their ancestors left Asia. This study also incorporates the extensive mtDNA database of extinct eastern Beringian wolves published by Leonard at al. (2007). In 2002, Savolainen et al. published the discovery of three wolf mtDNA haplotypes found in wolves of China and Mongolia that cluster within the main dog haplogroup or clade A (‘A total of 71.3% of dogs had haplotypes belonging to clade A’), but now also this older group of ice age wolves has its mtDNA nesting within this main dog clade. This haplotype can’t be found in current American wolves, and apparently has an age and origin that overrule any special and tight association with east Asian wolves and dogs. Moreover, the eastern Beringian wolf diverged in many ways from current Holarctic wolves, while other features were more dog-like. The sub-species was specialized to consume more carrion and differed significantly in shape from ‘both the sample of modern North American wolves and Rancho La Brea (California) Pleistocene wolves’ (Leonard et al., 2007). Contrary to their contemporary southern neighbors and modern wolves, ‘[e]astern Beringian wolves tend to have short broad palates, probably adapted for producing relatively large bite forces suggesting the killing of bulky prey, such as bison and horse’ (Leonard et al., 2007). Apparently holarctic wolf subspecies were once distinguished along ecological lines that ceased to exist:

Notably, the Pleistocene C. lupus from eastern Beringia by the skull shape, tooth wear, and isotopic data is also reconstructed as specialized hunter and scavenger of extinct North American megafauna (Leonard et al., 2007). In addition, East-Beringian wolves genetically differ from any modern Northern American wolf, and instead they appear most closely related to Late Pleistocene wolves of Eurasia. This uniquely adapted and genetically distinct wolf ecomorph suffered extinction in the late Pleistocene, along with other megafauna.(Baryshnikov et al., 2009)

For sure the origin of the modern ‘Holarctic’ grey wolves lays in more southern latitudes, without much certainty if the wolf that ultimately replaced the variety of more northern ‘ice age’ latitudes was already part of a single wolf population that encompassed the southern glacial borderlands and refuges of Eurasia and North America, or that they expanded from any place in particular. Most likely the cradle of modern wolf evolution was somewhere south of the glacial habitat. Ancient strains of the grey wolf are nowadays recognized in the Egyptian jackal, otherwise often considered transitional to the golden jackal, that reveal mtDNA divergence with grey wolves up to about 800 kya. The Indian subcontinent still includes three diverse, distinct wolf lineages — Indian wolf, Tibetan wolf and Eurasian wolf. Mitochondrial DNA analysis suggests the Himalayan wolf is distinct from the Tibetan wolf, and represents the most divergent wolf lineage. Such genetic diversity is generally considered indicative of origin. We need to be cautious, though, since we don’t know the hybridization record of South Asian wolves, that shared their habitat for thousands of years with other canids. The recent detection of gray wolf mtDNA in the golden jackal of Senegal even ‘brings the delineation between the African wolf [Canis lupus lupaster] and the golden jackal [Canis aureus] into question’ (Gaubert et al., 2012). But even the Golden Jackal is genetically closer related than the coyote (Rueness et al., 2011, based on 726 bp of the Cyt b gene: a region of mitochondrial DNA commonly considered useful to determine phylogenetic relationships between organisms and within families and genera due to its sequence variability), hence its western distribution could eventually imply a southwestern Eurasian origin of the wolf. This location of origin may be further elaborated and even extended to the Holarctic wolf by the phylogenetic investigation of Pilot’s team (2010). Their results distinguished a single major subdivision of Holarctic wolves based on 230 bp mtDNA control region sequences of 947 contemporary European wolves that – contrary to Indian and Himalayan wolves – also applies to the worldwide wolf population:

Based on the phylogenetic trees and networks constructed, we defined two haplogroups, 1 and 2
The two haplogroups were separated by five mutational steps: three transitions, one transversion, and one insertion/deletion.
In all the trees and networks constructed, haplotypes from the two groups were clearly separated, although they did not always constitute two monophyletic clades
Haplotypes of Indian and Himalayan wolves were separated from all the other haplotypes by more than 6 mutational steps
In ancient European wolves, haplogroup 2 was predominant. All ancient samples from Belgium, Germany, Czech Republic, Hungary, and Ukraine, ranging in age from 44,000 to 1,400 years B.P., belonged to this haplogroup. Only one haplotype of ancient wolf (w7), sampled in western Russia and dated from 2,700 – 1,200 years ago, belonged to haplogroup 1
Our results are consistent with Germonpré et al. [2009], who showed that the ancient European haplotypes are placed in one part of the wolf haplotype network rather than being scattered across the complete network.

[…] contemporary data may suggest substantial changes in haplogroup frequencies over the last 40,000 years from the predominance of haplogroup 2 to the predominance of haplogroup 1.

[…] mtDNA haplotypes of Pleistocene wolves from eastern Beringia belonged to a distinct haplogroup that does not occur in contemporary North American wolves. This haplogroup corresponds to haplogroup 2 in our study […] and some of the ancient European and Beringian wolves even shared a common haplotype (Pilot et al., 2010)

(Contrary to previous results, Pilot's team found that current Holarctic wolves fall in two different haplogroups. Transitional forms are found in the Balkans. Haplogroup 1 appears to be a new development, while haplogroup 2 remained closer to dogs)

(Contrary to previous results, Pilot’s team found that current Holarctic wolves fall in two different haplogroups. Transitional forms are found in the Balkans. Haplogroup 1 appears to be a new development, while haplogroup 2 remained closer to dogs)

The ambiguous assignment of only one haplotype (w20, from Turkish Trakia) and the intermediate position of Balkan wolves in general (figure 1 in Pilot et al., 2010) is in agreement with the aforementioned southwest Eurasian origin of Holarctic wolves, and even more specific to the origin of modern wolves whose mtDNA cluster in haplogroup 1. Instead, dogs cluster to ancient European wolves and their relatives in the Pleistocene arctic region, whose mtDNA cluster in haplogroup 2. The ancient predominance of dog-like mitochondrial DNA in wolves thus can’t be exclusively associated with some ‘Beringian-like’ tendencies in the Pleistocene Eurasian wolf phenotype, that otherwise has all appearance to be intrusive from the east. This counter-intuitive geographic separation of ancestral Holarctic wolves in the west, nearby old centers of human occupation, and dog-like haplotypes far away from any human interference at all, isn’t necessarily irreconcilable to dog domestication. Actually, wild animals that had the opportunity to co-evolve with humans never experienced the same magnitude of extinction that happened e.g. in the Americas: ‘It has long been thought that extinctions in Africa were less severe than in other regions of the world due to the long term coevolution of humans and megafauna’ (Louys et al., 2006). In general, such animal populations being situated closer to the known centers of human evolution turned out less prone to domestication as well. Coevolution apparently involved wild animals getting wilder and less prone to domestication. Animals that remained curious and less cautious for humans met their end during and after the great megafaunal extinctions. The Beringian wolf phenotype may have belonged to the latter category, and became extinct. However, before this happened some individuals were attested to have already mixed with western wolf populations. Probably it was no coincidence this phenotype emerged as the prime target of human interaction and, eventually, domestication.
The nature of Holocene extinction, that started at the end of the last Ice Age, is contested, though generally considered due to both climate change and the proliferation of modern humans. The impact of this phenomenon was not limited to the extinction of numerous species. Hofreiter (2010) stressed that ‘studies like that by Pilot et al. are starting to reveal that at least some surviving species are also depleted in genetic diversity compared with their Pleistocene ancestors.’ Somehow the dogs were exempted from this depletion, for they still are ‘a genetically diverse species that likely originated from a large founding stock possibly derived from wolf populations existing in different places and at different times’ (Vilà et al., 1999) – even though most of these ancestral wolf populations are now extinct, and replaced by new wolf populations that are not representative to the founding stock. The effect of this Late Pleistocene change of grey wolf populations was huge. Meachen’s team (2012) ‘suggest that Pleistocene coyotes may have been larger and more robust in response to larger competitors and a larger-bodied prey base’, being consistent with the view that even the early American grey wolves in the tar pits could thrive in their niche only after this post-megafaunal development of the coyote evolving away from wolf-like forms. Leonard et al. (2007) relied ‘on an early arrival of the more gracile wolf from the Old World and migration to areas below the Wisconsin ice sheet’ to explain the presence of two distinct Pleistocene gray wolves in North America, though actually the southern type is rare or problematic before 10,000 BP while eastern Beringian wolves attest too many infinite dates and genetic diversity to have simply evolved locally and derive from this hypothesized population of immigrant American common ancestors. Instead, sudden grey wolf competition may have supplied an additional reason for the sudden post-Glacial downsizing of the coyote, while also current hybridization patterns in North America tend to confirm the modern grey wolf’s more recent introduction from Eurasia:

[…] extensive admixture zones in North America, where four morphologically distinguishable wolf-like canids can potentially interbreed: the gray wolf of Old World derivation, the coyote and red wolf (both of which originated in North America), and the Great Lakes wolf. (VonHoldt et al., 2011)

Meanwhile, the genetic tie of eastern-Beringian wolves with Eurasian gray wolves – and early dogs! – discourages premature conclusions on dog domestication in the Americas, not in the least because this tie considerably precedes the attested Native American immigration ~15,000 years BP. More likely, eastern Beringian wolves managed to preserve their dog-like genetic legacy longer than elsewhere on the northern hemisphere, until worldwide disaster struck the ice age megafauna:

the eastern-Beringian ecomorph was hypercarnivorous with a craniodental morphology more capable of capturing, dismembering, and consuming the bones of very large mega-herbivores, such as bison. When their prey disappeared, this wolf ecomorph did as well, resulting in a significant loss of phenotypic and genetic diversity within the species. Conceivably, the robust ecomorph also was present in western Beringia in the Late Pleistocene, but specimens were not available for this study. (Leonard et al., 2007)

The ecological and derived morphological segregation of Pleistocene wolves in a northern ice age subspecies and the subspecies of southern ice age refuges appears to have had a genetic component that survives in dogs and wolves respectively:

According to Hofreiter [2007], this may imply that Pleistocene wolves across Northern Eurasia and America may have represented a continuous and almost panmictic population that was genetically and probably also ecologically distinct from the wolves living in that area today. (Pilot et al., 2010)

The southern subspecies may have comprised several isolated gray wolf populations in Eurasian and American ice age refuges, not all of which necessarily survived the global wave of post-glacial loss of diversity, or extinction. Indeed, ‘[…] most of the genetic diversity of megafaunal animals may have been lost at the end of the Pleistocene, even in surviving species’ (Hofreiter 2007). Some of the general post-glacial loss of diversity may be due to more recent expansions and replacements, and since most of the sampled eastern Beringian wolves attest ‘infinite dates’ (Leonard et al., 2007 sup.) it is likely their stock was already present in the region for a longer time. However, at least the northern subspecies is strongly indicated to have been a single Pleistocene population that was also genetically distinct:

[Leonard et al., 2007] found evidence that the Beringian wolves were morphologically different from modern North American wolves and from Pleistocene wolves from more southern regions. Moreover, the differences in morphology suggest that the Pleistocene Beringian wolves were adapted to hunting and scavenging members of the now extinct megafauna, a conclusion supported by isotope analysis. Finally, these wolves not only represented a different ecomorph, they were also genetically distinct. Not a single sequence of their mitochondrial DNA haplotypes exactly matched sequences found in modern and historical wolves identified to date. However, some of the sequences perfectly matched, albeit only for short stretches, sequences obtained from Eurasian Pleistocene wolves, from as far west as the Czech Republic. Thus, Pleistocene wolves across Northern Eurasia and America may actually have represented a continuous and almost panmictic population that was genetically and probably also ecologically distinct from the wolves living in this area today. Despite their high mobility, these wolves did not escape the megafaunal extinctions at the end of the Pleistocene, even though the causes of their extinction are unclear. The specialized Pleistocene wolves, thus, did not contribute to the genetic diversity of modern wolves. Rather, modern wolf populations across the Holarctic are likely be the descendants of wolves from populations that came from more southern refuges as suggested previously for the North American wolves (Hofreiter, 2007)

Germonpré (2009) noted similar trends like Beringian wolves in skulls from Trou Baileux, Trou des Nutons, Mezin 5469, Mezin 5488 and Yakutia, that all are considered to be from fossil wolves. Leonard et al. (2007) analyzed the eastern Beringian wolves genetically and attributed the disappearance of this robust prehistoric ecomorph to ecological changes that occurred after the Last Glacial Maximum. Even though her team also based themselves on a database of pre-Columbian dogs when they rejected domestication of modern North American wolves for the dogs of Native Americans, only Druzhkova’s team combined both data sets to make a genetic comparison between Beringian wolves and dogs. His unfortunate inadequacy to compare his results on the Altai dog with Germonpré, whose results on Pleistocene Belgian dogs of comparable age and morphology were hampered by the low resolution of just 57 bp of the mitochondrial control region, may be solved by the results of Pilot’s team he was not acquainted with. Like the Pleistocene Belgium dogs of Goyet Cave, Altai dog of Razboinichya Cave clearly cluster with ancient Holarctic wolves rather than modern wolves, but their close genetic relationship with modern dogs is based on the virtual extinction of the Holarctic wolf source population rather than some advanced stage of dog domestication. As such, criticism against the existence of Pleistocene ‘dogs’ is still valid:

One of the features that M. Germonpré et al.’s so-called ‘Palaeolithic dogs’ (and the Razboinichya specimen) have in common is that they represent one or a few dog-like individuals found amongst many typical wolf individuals.

[…] the ‘Palaeolithic dogs’ […] may simply be rather ‘short-faced’ wolf individuals that lived within a population of typical wolves that interacted in various ways with human hunters. While the dog-like morphology of some Late Pleistocene wolves may have arisen due to persistent interactions with people over varying lengths of time, it is misleading to call this relationship ‘domestication.’ (Crockford & Kuzmin, 2012)

The similarity of Pleistocene dogs with certain types of Pleistocene wolves may be deceiving. Not unlike Beringian wolves, the Paleolithic dogs tend to have short, broad palates with still large carnassials:

Compared to wolves, ancient dogs exhibit a shorter and broader snout (Lawrence, 1967; Olsen, 1985; Sablin and Khlopachev, 2002). All Palaeolithic dogs in our study conform to this pattern. (Germonpré et al., 2009)
European Palaeolithic dogs, characterized by, compared to wild wolves, short skulls, short snouts, wide palates and braincases, and even-sized carnassials (Germonpré, 2012a)

There exists an older notion of a late Pleistocene lineage of dag that might have existed during the late Pleistocene until these became globally extinct during the last 20,000 years. This possibility of ‘an aberrant lineage of dog-like canids might have existed throughout the northern hemisphere during the late Pleistocene’ was recently explored by Thalmann, to the somewhat unsettling result that no exact mtDNA matches could be retrieved in modern dogs or modern wolves. At least the sudden Neolithic reduction of the carnassials in the perceived dog lineage may indicate a recent bottleneck that could explain such an extinction of mtDNA lineages for dogs, while the extinction of these mtDNA lineages in wolves has already been cited as a typical post-Glacial phenomenon: also ‘the mtDNA of the Belgian fossil wolves shows a large amount of genetic diversity that has not been described for modern wolves’ (Germonpré et al., 2009).
This ‘aberrant lineage of canids’ probably existed in the ecomorph stock that had its gravity in NE Asia and northern America, and incidentally reached far into the west. Being closely related with Eurasian wolves, an early tendency towards speciation was arrested by the Late Glacial events that led to the predominance of the Holarctic wolf. Mere extinction may have been the result, or advanced hybridization processes that eventually lead to ‘the fusion of the parent species’ gene pool and a loss of species.’ (Reece et al., 2011), not unlike the ABC Island brown bears that are recently identified as the descendants of a polar bear population that was gradually converted into brown bears via (male-dominated) brown bear admixture: ’This process of genome erosion and conversion may be a common outcome when climate change or other forces cause a population to become isolated and then overrun by species with which it can hybridize’ (Cahill et al., 2013). By the time the Eurasian ice age wolf ecomorph became extinct, human interaction or ‘dog domestication’ was already ongoing, leading to the preservation of much of the genetic diversity that has disappeared in wolves. The now attested genetic continuity in the Pleistocene Altai dog supplies evidence it didn’t take such a long time since the Pleistocene to get nowhere. On the contrary, the origin of dogs can now be perceived firmly rooted in the Pleistocene whatever the type of domestication applicable to the earliest interactions with humans. Germonpré (2012b) announced a forthcoming investigation of stable isotopes on Pleistocene dogs to verify if their diet can be related to that of prehistoric humans from the same time and region. Instead, Belgian Pleistocene wolves were already attested to consume the same kind of bulky prey that Leonard et al. (2007) deduced for eastern Beringian wolves based on their bite, such as horse and large bovids. Could the Pleistocene abundance of meat offer an alternative explanation for the unaltered size of the carnassials of Pleistocene dogs? If so, would there exist any other criteria that suffice to prove the veracity of Pleistocene dog domestication at all?
The persistence of large carnassials up to Neolithic times would also imply a dependency of fresh meat that may have been ever harder to obtain. On the eve of the Neolithic transition, when increased population pressures virtually forced human culture into the direction of food production, a dog must have been an expensive asset only a few could afford. Until recently everywhere in Polynesia starch-rich poi from the taro corm was used to fatten the dogs for use as food because meat was too valuable to be used as dog food. This transition of breeds like the Hawaiian Poi dog and the Maori Kuri dog, both extinct, from predators to fattened up food resources, was only possible in a Neolithic society with an abundance of starch-rich products. The Neolithic change to starch-rich diets induced some dogs to adapt genetically (Axelsson et al., 2013). This important event in dog evolution apparently caused an explosion of population growth and genetic replacement – until very recently confused with a one and only domestication event in the Neolithic rather than already during the Pleistocene.
Only nowadays dog domestication is being appreciated as a true evolutionary process. Their divergence from wolves wasn’t just a superficial accumulation of qualities favored by human preferences, such as color and character, hardly worthy of major biological interest. Instead, novel adaptations including brain functions, starch digestion and fat metabolism indicate more fundamental changes, each having evolutionary advantages all of their own that tend to set dogs apart from wolves. One amazing result of current investigation is these changes must have been closely associated with dog populations in Southeast Asia, even to the point that dogs were hypothesized to originate from an otherwise unspecified Asiatic wolf, albeit ‘with minor genetic contributions from dog–wolf hybridization elsewhere’ – for this occasion assumed to have inhabited eastern Asia south of the Yangtze River (Ding et al, 2011). Actually, there is no shred of evidence wolves or other members of the “Canis” genus were present in this area, thus adding up to a major inconsistency in dog evolution:

The earliest archaeological evidence of ancient dogs was discovered in Europe and the Middle East, some 5–7 millennia before that from Southeast Asia. However, mitochondrial DNA analyses suggest that most modern dogs derive from Southeast Asia, which has fueled the controversial hypothesis that dog domestication originated in this region despite the lack of supporting archaeological evidence. (Sacks et al., 2013)

Once again high genetic variability emerged as a poor advice to pinpoint the geographic origin of a species. Not unlike the results on human DNA, for dogs the archeological record is all out of tune with genetic evidence, or the way it is currently interpreted. Also for dogs scientific efforts to understand the origin were increasingly directed away from observations considered inconvenient to the traditional ‘scientific’ scenarios, and aberrated in the realm of increasingly unintelligible constructs. Intriguing parallels with the Recent Out of Africa (ROA) paradigm may be elucidated, where high human genetic variability of the purported African homeland is alternately considered evidence for a recent origin of modern humans – or the result of archaic hybridization (Hammer et al., 2011). Likewise, modern science erroneously sought the putative center of dog domestication where genetic variability reaches peak values, that for dogs could be found in Southeast Asia. Dogs even mimic the genetic signals of change in modern humans:

Sets of functionally related genes show highly similar patterns of evolution in the human and dog lineages. This suggests that we should be careful about interpreting accelerated evolution in human relative to mouse as representing human-specific innovations (for example, in genes involved in brain development), because comparable acceleration is often seen in the dog lineage. (Lindblad-Toh et al., 2005)

Rather than being deterred by the lack of archeological evidence, modern investigation contented itself with pursuing false positives to discard Pleistocene dogs like this Altai canid as an incipient dog that did not give rise to late Glacial – early Holocene lineages and probably represents wolf domestication disrupted by the climatic and cultural changes associated with the LGM (Ovodov et al, 2012). For convenience of the naysayers this fate was shared by an abundance of other ‘incipient dogs’ allegedly up to 36,000 BP whose remains were found littered over a wide area, not only including the canid skulls from Goyet (Belgium), that so far counts as the oldest specimen, but also from disparate places like Predmostí (the Czech Republic), and Mezin and Mezhirich (the Ukraine). Four out of thirteen ambiguous finds fished from the bottom of the North Sea (Southern Bight), were firmly identified as Pleistocene dogs in the thesis of Datema, 2011. In the deepest part of the famous Chauvet cave, France, a track of footprints from a large canid could be associated with the one of a child (Garcia, 2005), whose torch wipes were dated at c. 26,000 BP. Still other investigators remained to even discard the notion of these Pleistocene dogs being incipient at all – to the chagrin of Germonpré’s team that as late as 2012 felt obliged ’ to remedy some errors, misunderstandings and misrepresentations’ on the case. Now, the results of Druzhkova’s team blow away this apparent prevalence of a Southeast Asian origin of dog domestication in more recent scientific investigation, that not unlike the Recent Out of Africa paradigm became genetically supported by unfortunate conclusions on variability of mtDNA (Savolainen et al., 2002) and of Y-DNA (Ding et al., 2010) respectively. However, unlike ROA, archeological and fossil evidence that a common ancestor was present in the putative geographic origin, i.e. traces of early domestication and a habitat for prehistoric wolves in Asia South of Yangtze River (ASY) as proposed by Pang et al. (2009), is still dearly missing.
The study of VonHoldt et al. (2010) had already revealed disproportionate hybridization especially for the ancient breeds in east- and southeast Asia by Chinese and Middle Eastern wolves (supplemental Figure 5 at k=5). Apparently hybridization inflated heterozygousity of south-east Asian nuclear DNA and lured the scientific community into an “Out of Southeast Asia hypothesis. Instead, Sacks et al. (2013) introduced a new interpretation of this Southeast Asian hypothesis by stating that ‘isolation of Neolithic dogs from wolves in Southeast Asia was a key step accelerating their phenotypic transformation’, to offer a scenario where a new type of dog emerged in the Neolithic that virtually pushed earlier Palaeolithic dogs into extinction:

Archaeological and ancient DNA evidence suggesting that late Palaeolithic dogs were replaced by Neolithic immigrants in regions as disparate as Japan, the Middle East, and North America
The apparent origins of most modern dog matrilines from Southeast Asia has been interpreted as evidence that dogs were first domesticated in this region (Savolainen et al. 2002; Pang et al. 2009). However, the lack of archaeological evidence of dogs in Southeast Asia until some 5,000–7,000 years later than in central and western Eurasia, suggests either that the single genealogical history reflected in mtDNA could be misleading (e.g. VonHoldt et al. 2010) or that most modern dogs trace their ancestry proximately to Southeast Asia, but as a secondary center of diversification associated with Neolithic rather than Palaeolithic peoples (Brown et al. 2011).

[…]our findings support the hypothesis for a massive Neolithic expansion of dogs from Southeast Asia rather than a Palaeolithic origin of dogs from this region. (Sacks et al., 2013)

Thus accelerated Neolithic evolution and the absence of wolves in Southeast Asia to mate with, are now considered the main agents for the rapid change of Palaeolithic dogs into modern dogs, the latter being especially successful in increasing their numbers on a worldwide scale.
Inadvertedly, hybridization was here mentioned as a factor to be dealt with. Actually, recurrent hybridization events already prevented Canis evolution to be a straightforward linear succession towards present-day species. This process should also have blurred out the nascent differences typical of a more detailed branching tree full of evolutionary dead-ends, as traditionally employed also for canid evolution. Again, not unlike human evolution, mosaic evolution was a feature also for canids that can be traced back even to the early divergence of wolves and jackal:

considering C. etruscus and C. arnensis as wolf-like and jackal-like dogs, respectively, is an oversimplification not always valid, because C. arnensis is more similar to C. lupus than C. etruscus regarding some cranial characters (e.g., Fig. 1b), while C. etruscus seems to exhibit a broader set of peculiar features. Recent genetic studies confirm this hypothesis, as jackals do not constitute a homogeneous genetic group despite their great morphological affinity, albeit different analyses do not fully agree on their phylogenetic relationships (Cherin et al., 2013)

Some prehistoric canid characteristics are simply ancestral, what back in time can be illustrated by some degree of convergence to rather coyote-like forms, suggesting even jackals evolved partly parallel with the ancestors of the gray wolf:

This paper reports a new species of dog (Canis accitanus nov. sp.) from the Fonelas P-1 site (dated close to the Plio-Pleistocene boundary) in Granada, Spain. This new taxon shows cranial features more similar to coyote-like dogs (C. lepophagus, C. priscolatrans, C. arnensis or C. latrans) than to wolf-like dogs (C. etruscus, C. mosbachensis or C. lupus), such as a long and narrow muzzle, a little-developed sagittal crest and frontal bones raised only a little above the rostrum. (Garrido & Arribas, 2008)

As raised in a previous blog, in some cases mosaic evolution may be the result of hybridization events or cross-species gene flow during some extended period during speciation, or even afterwards as long as cross-breeding may still result in viable offspring. According to Gaubert et al. (2012) ‘hybridization among Canis taxa has proved to be common and to involve significant phenotypic changes in hybrid generations, reaching fixation in several cases’.
Naturally, cross-breeding may result in increased variability – as long as the elimination of deleterious hybrid fitness components by selection doesn’t purge most of the polymorph alleles. However, admixture with modern wolves can’t fully explain the genetic deviation of modern dogs since much of their polymorph alleles simply can’t be found in wolves. This does not contradict wolf admixtures in a later stage, what apparently occurred in the ancestors of Neolithic dogs. Since ‘[…] the European and American breeds clustered almost entirely within the Southeast Asian clade, even sharing many haplotypes, suggesting a substantial and recent influence of East Asian dogs in the creation of European breeds’ (Brown et al., 2011), it shouldn’t come as any surprise that ‘morphologic comparisons suggest that dogs are closest phenotypically to Chinese wolves’ (Wayne et al., 1999). The evolution of Neolithic dogs must have been highly impacted by Pleistocene dogs near East Asia, what suggests late-Pleistocene admixture to explain that ‘one osteological feature diagnostic of dogs is also found among Chinese wolves’ (Savolainen et al., 2002). However, the more complex hybrid character of all descendant dog breeds may be illustrated by the ‘higher proportion of multi-locus haplotypes unique to grey wolves from the Middle East, indicating that they are a dominant source of genetic diversity for dogs rather than wolves from east Asia, as suggested by mitochondrial DNA sequence data’ (VonHoldt et al., 2010).
Hybridization between dog breeds require a broad genetic base to start with. However, the direct ancestors of modern wolves and their deduced range of genetic variability don’t supply a sufficient source for the total range of dog variability. Still, an abundance of other traits attest the impact of hybridization processes. Neoteny, the retention of juvenile characteristics into adulthood, is often considered an important characteristic of dogs. Serpell considered this a result of hybridization:

Our feeling on the development of breeds is expressed by Haldane (1930, pp. 138), writing about the evolution of species, when he stated that there is ‘every reason to believe that new species may arise quite suddenly, sometimes by hybridization, sometimes perhaps by other means. Such species do not arise, as Darwin thought, by natural selection. when they have arisen they must justify their existence before the tribunal of natural selection’. (Serpell, 1995, p.42)

Brown’s team (2011) does a remarkable job in distinguishing a Southeast Asian development in recent dog evolution, though his classification doesn’t suffice to reveal the origin of dog Y chromosome haplotypes. Genomic analysis of prehistoric canids, modern dogs and wolves indicate a basal placement of some dog haplotypes in the phylogeny. One middle-eastern haplotype actually resulted “ancestral”, being attested also in Dhole, black-backed jackal and a wolf from China (haplotype 12). Middle-eastern dog Y-chromosome haplotypes resulted shared with wolves and/or Southeast Asian dogs (haplotypes 8, 10 and 11) or none (haplotypes 7 and 9, though both being rather distantly related with wolves). Only Southeast Asian dogs were easily distinguished from all other related canines combined. Despite alignment bias being possibly the prime reason for these results, more recent wolf admixture and even cross-species hybridization can’t be ruled out. Indeed, the most basal members of Canis tend to be more “doggish” in looks and behavior, while the more “wolfish” phenotype of the northern hemisphere seems to have made its appearance only about 300,000 years ago. In other words, canids are increasingly “doggish” with their genetic distance from true grey wolves, what can be illustrated by the incremental series Indian wolves; Egyptian wolves; Golden jackal; coyote; Ethiopian wolf (Charles Darwin equivocally hypothesized this species gave rise to greyhounds); “the other jackals” (a polyphyletic group that despite great morphological affinity miss any further taxonomic integrity); and Dholes respectively, the latter having a phenotype most similar to the dingo while being of the genus “Cuon,” and as such not even part anymore of genus “Canis.” The wide-spread “doggish” appearance among non-wolf canids might indeed raise the question of ancient attempts to achieve interspecies hybrids.

The confusion extends to other domesticated animals: also the domestication of sheep, amongst the first species to be domesticated by man, is characterized by considerable genetic variability and a certain lack of wild matches. Kijas et al. (2012) state that despite a common origin of all domestic breeds of sheep, their ‘analysis revealed this domestication process must have involved a genetically broad sampling of wild stock.’ Moreover, like with dogs, the genetic variability of sheep has a weak global population structure and lack of association between genetic diversity and distance from the perceived domestication center, interpreted thus:

This suggests a highly heterogeneous predomestication population was recruited, and the genetic bottleneck which took place was not as severe during the development of sheep as for some other animal domesticates. It is also possible that cross-breeding with wild populations persisted following the initial domestication events to generate the diversity observed. (Kijas et al. (2012)

However, a purported single origin certainly contradictory with a broad genetic base. The possibility of cross-breeding with wild populations, as raised by Kijas’ team, virtually depends on the assumption that ‘high levels of gene flow have occurred between populations following domestication’. However, admixture appears contradictory with the observed homogeneity:

For SNP pairs separated by 10 kb or less, a high degree of conservation of LD phase was observed between all breeds […] Given that LD at short haplotype lengths reflects population history many generations ago, this also supports a common ancestral origin of all domestic breeds of sheep. The result is in contrast to cattle, where two distinct groups emerge from a similar analysis, even at haplotype lengths of 0–10 kb, reflecting the Bos taurus taurus and Bos taurus indicus sub-species and their separate domestication events (Kijas et al., 2012)

Instead, Pedrosa’s team rather adhered to the view that ‘introgression is generally ruled out as the cause of clearly differentiated maternal lineages in livestock, since introgression via females seems quite improbable.’ Indeed, just like with dogs, hybridization can’t be easily assumed just because of the theoretic possibility offered by closely related species or sub-species in the wild.
The center of sheep domestication currently encompasses the natural environment of at least three subspecies of Ovis, whose genetic boundaries are sometimes difficult to conceive: Argali (O. Ammon), Urial (O. Vignei), and Mouflon (O. Orientalis), the most western variety. Mitochondrial DNA of sheep doesn’t show any close relationship with argali or urial sequences (Pedrosa, 2006), what is remarkable since hybridization between the various subspecies has been observed in the wild. However, if hybrid admixture was limited to the domestication event this would almost insinuate a domestication purpose! For sheep cross-breeding may have been recognized from the start as predominantly detrimental to their specific qualities in the process of domestication, what should be a compelling argument to discard the persistence of cross-breeding with wild populations as a valid explanation for the observed genetic diversity of the domesticated form. On the contrary, the existence of widely spread and divergent mtDNA lineages without any current match in wild populations rather seems to indicate ancient hybridization events that preceded the fixation of domesticated sheep:

Time since divergence of types B and A estimated from the Cyt b gene [for sheep lineages] (around 150 000 to 170 000 years ago) agrees with the values obtained from Cyt b for goat lineages by Luikart et al. (2001; around 200 000 years ago) as well as those obtained for cattle (Bradley et al. 1996). Lineage C proved to have diverged earlier (between 450 000 and 700 000 years ago). (Pedrosa, 2006)

Another positive for early hybridization “by design” involves the domestication of chicken, that may descend from up to four Gallus species and their subspecies:

Four species of genus Gallus inhabit Southeast Asia: […] Red junglefowl has a strong sexual dimorphism with males having red fleshy wattles, and it is most widely distributed over the area. La Fayette’s junglefowl morphologically resembles red junglefowl, but it inhabits only Sri Lanka. Gray junglefowl has body plumage on a gray background color and is distributed from southwest to central India. Morphologically distinct green junglefowl is limited to Java and its immediate vicinity, Bali and Lombok [corr.: the Lesser Sunda Islands]. It has been debated whether any single species of the four, especially red junglefowl, predominantly contributed to the genome of domestic chickens (a single-origin hypothesis) or whether multiple species of the four made a substantial genetic contribution to domestic chickens (a multiple-origin hypothesis). (Sawai et al., 2010)

Actually, the Green junglefowl has a lot more eastern penetration into the Lesser Sunda islands, what somewhat invalidates Sawai’s ‘Javan’ origin hypothesis for this species. However, its unique isolation resulted in a genetically divergent species whose ability to hybridize with chicken is highly restricted.

(On the left: Green junglefowl (above) and Grey junglefowl; in the middle the Bekisar hybrid (above) and an Araucana rooster; Blue Araucana eggs can be easily distinguished in the upper right; The map (Storey et al., 2012) displays the current distribution of Red junglefowl, the accepted progenitor of chicken, and the current distribution of some chicken mtDNA haplogroups. However, the oldest chicken were found in cultural contexts of northern China on the dividing line between the Palaeolithic and the Neolithic)

(On the left: Green junglefowl (above) and Grey junglefowl; in the middle the Bekisar hybrid (above) and an Araucana rooster; Blue Araucana eggs can be easily distinguished in the upper right; The map (Storey et al., 2012) displays the current distribution of Red junglefowl, the accepted progenitor of chicken, and the current distribution of some chicken mtDNA haplogroups. However, the oldest chicken were found in cultural contexts of northern China on the dividing line between the Palaeolithic and the Neolithic)

Evidence abounds that Red junglefowl is the prime progenitor of domesticated chicken:

Haplogroup E is predominant among Indian, Middle Eastern, and European chickens and is an indication that the roots of European chickens lie within the Indian subcontinent. (Gongora, 2008b)

However, not unlike dogs, the calculated mtDNA divergence date with this purported progenitor by far exceeds archeological evidence of domestication:

According to archeological findings, the divergence time of domestic chickens from junglefowls is estimated to be on the order of 10,000 years. The MCMC method reveals, however, that the extent of nucleotide divergence after the split of red junglefowl from the chicken ancestor is […] 58,000 +/- 16,000 years ago. This dating is nearly six times older than what the archeological remains suggest. (Sawai et al., 2010)

Like with dogs it is tempting to attribute this divergence discrepancy to an ‘aberrant wild subspecies’ as the progenitor of the domestic form. Despite the historic distribution of Red junglefowl is limited to Southeast Asia in the range between the Indus valley, Yunnan (southern China) and Lombok, the oldest undisputed domestic chicken remains, dated 5400 BC, have been recovered from archaeological sites in northern China. Though chicken near that age (5000 BC) were also attested in cultural contexts in the Ganges region of India, this has led to debate about whether the natural range of Red Junglefowl reached much further north in prehistory. However, unlike dogs, this genetic diversity doesn’t extend to mtDNA, despite the lack of a major mismatch between the mtDNA haplotypes of domesticated and wild subspecies.
Only 56 out of all 206 Red junglefowl mtDNA sequences, recovered from the control region (CR) and available to a 2013 study of Miao’s team, were not found in domestic chicken. Of these, only seven from Yunnan and the island of Hainan (China) could be accommodated as new haplogroups W-Z within the monophyletic tree of domestic chicken, thus probably confirming rather Chinese roots of domesticated chicken (in the vein of Liu and Oka). An additional unclassified 21 haplotypes from Vietnam, Sumatra and Haryana (Northern India) appear not too distantly related, while 28 other haplotypes from Haryana and Indonesia could only be classified as ‘divergent’:

As for the red junglefowl, 76.2% (157/206) of the CR haplotypes were assigned to haplogroups in this genealogy (Figure 4; see Supplementary dataset 1). Apart from the common haplogroups A–G, the wild fowl harbored haplogroups W–Z, which were not detected in domestic chickens. Of the remaining sequences (49/206) not classified in the genealogy, 28 haplotypes from India and Indonesia (for example, ‘outgroups’ in Figure 1) had too many variants to be assigned; variation included many transversions (see Supplementary dataset 1). This suggested that they were remotely related to the other chickens (Miao et al., 2013)

This sequence divergence is such that natural hybridization with grey and green junglefowl respectively has been the suggested source of these divergent mtDNA lineages, though Miao’s team justly stresses this hypothesis requires a more comprehensive survey.
In Bangladesh the ‘phylogenetic tree showed low genetic distance and close relationship within and between the chicken populations of Bangladesh, which were closely related with G. g. murghi of Indian origin’ while a minority of domestic chicken and one red junglefowl were related with G. g. bankiva and G. g. gallus, ‘implying the origin of gene flow to Bangladesh’ (Islam & Nishibori, 2012).
This shocking lack of evidence for a truly unadmixed wild ancestral population has severe repercussions on the origin question of domestic chicken. The first three Gallus g. Bankiva accession numbers ever investigated (AB009430, AB009431 and AP007718) were found sufficiently different to originally exclude the Javanese wild subspecies from the group of domesticated chicken ancestors altogether:

On the whole, the analyzed data fit into two main clades […]: one formed by the continental red jungle fowl subspecies and all domestic chicken samples, which we named the continental clade, and another exclusively constituted by G. g. bankiva samples from Java that we named the island clade. (Liu et al., 2006a)

However, Oka et al. (2007) modified the interpretation of AP007718, and attributed a subsequent bankiva sample (AP003323) to one of the known chicken haplogroups, thus bringing also the Gallus g. bankiva subspecies into the fold of ancestral chicken:

G. g. bankiva [~Javanese red junglefowl] sequence ([AP007718, corr.]), which is distantly related to domestic chickens, was located on the outside of the Type C clade. However, another G. g. bankiva sequence ([AP003323, corr.]) and two G. g. gallus sequences [AP003322 and AB007725] were included in Type C. One G. g. spadiceus [~Burmese red junglefowl] sequence (AB007721) was close to the domestic chicken and very similar to Type A. The other G. g. spadiceus sequence (AP003323) was included in Type E. (Oka et al. – 2007).

Despite a genetic distance of no less than 30 mutation steps (Figure 3, Oka et al. 2007), AP007718 is slightly closer related with haplogroup C as defined by Oka’s team. It was not too farfetched to attribute an ancestral status to this chicken haplogroup:

[…] it is suggested that Types D, F and G diverged from Type C, and that Type E diverged from Type B.
[…] we suggest that Type F was derived from a group of Indonesian native chickens
It is suggested that Types A and B chickens (i.e. chickens of Chinese and Korean origin) were derived from Type C (i.e. they are of Southeast Asian origin) – Oka et al. (2007)

Such an all-encompassing phylogenetic system for chicken mtDNA, that includes ~75% of all wild specimen, seems irreconcilable with the extant picture of low genetic distances for chicken mtDNA:

It should be noticed that all the haplotypes that shared by or restricted to the red jungle fowls in clades A, B, E, and F diverged from the potential root in each clade by no more than 4-mutation distance, which was within the mutation distance observed between the domestic chicken and the potential wild progenitor G. g. gallus (Liu et al., 2006a)

Apparently, for all chicken and continental Red junglefowl together, the calculated mtDNA age is far less than nuclear DNA would suggest. However, since the monophyletic tree of chicken mtDNA can’t convincingly reflect the evolutionary history of the Gallus parent species, this should imply that current Red junglefowl populations simply lost their original mtDNA diversity quite recently due to introgression from feral chicken.
Better survival of ancestral mtDNA haplogroups in sheep and dogs could be due to evolutionary strain elsewhere that applied exclusively on their wild progenitors after the domestication events. Currently, gene flow between wolves and dogs, or between sheep and their wild progenitors, virtually doesn’t happen in the wild. Wolves would rather eat than mate a dog, and sheep don’t even survive to meet a wild partner in its habitat. Red junglefowl didn’t experience or acquire such an efficient natural barrier against gene flow from feral domesticated forms. Up to modern times this situation still didn’t affect the competitiveness of Red junglefowl populations in the wild. In general, in a natural habitat admixture of wild animals with their domesticated kin tends to compromise the competiveness of their feral offspring. Genetically there is few to gain and much to lose from domestic chicken that e.g. lost their ability to fly; feral sheep don’t even exist and only wolves evolved to abstain from cross-breeding with feral domesticated kin – even without strict biological barriers. However, since modern wolves predominantly attest another mtDNA clade, it is more than likely that evolutionary adaptation included less vulnerability to gene flow and ultimately led to the extinction of dog-introgressed wolves that were purportedly available in the Pleistocene (Germonpré et al., 2012a). The current vulnerability of Red junglefowl is unknown, but all indicates gene flow and introgression from domesticated chicken is rampant. The success of Green junglefowl west of the Wallace biogeographic division where they share the habitat with Javan Red junglefowl, while the latter hardly penetrated further east than Lombok (except for some unreliable observations). Wallace’s Line is the western border of a transitional region between Asiatic and Australian floras and faunas, where organisms show a high degree of isolation and endemism. Here, the Lesser Sunda Islands chain was definitely accessible from the west in the Pleistocene, what is attested even by the elephant that made an appearance up to Timor. West of this line, Java never ceased to be part of the Asian ecozone and hence was never truly isolated to justify Green junglefowls divergence from Red junglefowl populations. Instead, current cohabitation in Java together with the local subspecies of Red junglefowl could be indicative of future replacement tendencies for Gallus that mimic the gray wolf divergence from dogs towards the modern Holarctic wolf.

(Wallace's Line is the western border of a transitional region between Asiatic and Australian floras and faunas, where organisms show a high degree of isolation and endemism. The success of Green junglefowl also west of this region, wherein Javan Red junglefowl could hardly penetrate, could be indicative of introgression-driven weakness of the latter with respect to domestic chicken and future replacement tendencies for Gallus that mimic the gray wolf divergence from dogs towards the modern Holarctic wolf)

(Wallace’s Line is the western border of a transitional region between Asiatic and Australian floras and faunas, where organisms show a high degree of isolation and endemism. The success of Green junglefowl also west of this region, wherein Javan Red junglefowl could hardly penetrate, could be indicative of introgression-driven weakness of the latter with respect to domestic chicken and even future replacement tendencies for Gallus)

However, chicken introgression could even be indicated for the vastly divergent Green junglefowl, on the basis of nuclear DNA, attesting that ‘shared haplotypes are evenly distributed over all samples of red junglefowl, whereas this is not the case for those of green junglefowl’ (Sawai et al., 2010).
Purportedly introgressed chicken haplotypes in the green junglefowl were found to significantly increase Green junglefowl nucleotide diversity. This result is remarkable, since green junglefowl allegedly diverged 3.6 million years ago from the common ancestor of chicken and red junglefowl (Sawai et al., 2010), and first generation female hybrids were found notably infertile. Introgression of mtDNA would thus be close to impossible here. To break natural barriers in the forests, introgression of nuclear DNA may only be achieved for next generation hybrid offspring, that indeed must be readily available on a local basis in feral chicken populations. Indeed, Green junglefowl hybrids are still around being in high demand and part of an old Indonesian tradition.
Meanwhile, ‘attempts to investigate domestication and dispersal using mtDNA data from modern chickens have been confused by the tangled phylogenies which reflect millennia of overlapping dispersals and over a century of interbreeding for both commercial lines and show breeds’ (Storey et al,. 2012). Hence, only nuclear DNA remains to offer more insight into the origin of genetic diversity in domesticated chicken, while mtDNA diversity may only supply information on the world-wide history of the domestication process itself. Interestingly, ‘regional distribution of the clades was observed, which indicates some geographic structuring in chicken populations’ (Liu et al., 2006a). Structure, that thus should tell us the tale of domestic chicken from a single source rather than multiple domestication events. Also this feature is structurally different from domesticated animals like dogs and sheep, where high mtDNA diversity was preserved. This may be explained by a quite distinguished purpose of chicken domestication, as ‘it has also been proposed based on comparative morphology, historical depictions, and genetic relatedness that egg type chickens are the most ancient breed […] Therefore, the phylogeographic assumption that females have greater geographic inertia may be violated in the study of chickens by the widespread use of eggs’ (Storey et al., 2012). No other domestic vertebra experienced selective processes that applied so exclusively on females, what inevitably contributed to the severe reduction of mtDNA diversity as being observed.
The original proposal that haplogroup C ultimately derives from China, where prehistoric Red junglefowl populations could merely be assumed, might be as good as any, and actually reminds to the proposal of an ‘aberrant lineage of wolf’ for the ancestor of domestic dogs:

Although Japanese chickens displayed the highest nucleotide diversity […] for the clade C (Fig. 2D), the absence of red jungle fowl samples in clade C favors that this clade originated from South China. A recent domestication of clade D or gene Xow from domestic into the wild red jungle fowl population are two possible explanations for the fact that clade D mainly contained of red jungle fowl and gamecocks. These distinct patterns combined with archaeological records as well as with the geographic distribution of G. gallus are consistent with clades C and D originating relatively recently, perhaps in South and Southwest China and/or surrounding areas (Liu et al., 2006a)

Deviation from a simple star-like distribution pattern of this geographically restricted grouping may be due to the success of more recent breeds that instead propagated the few international mtDNA lineages, such as Haplogroup E. Due to the selective forces of human intervention such perpetual replacements completely obfuscated, for instance, the debate on early Polynesian arrivals in the Americas, where allegedly pre-Columbian chicken and their potential offspring happen to group predominantly with international mtDNA rather than the Polynesian haplogroups of more limited distribution:

The single ancient sequences reported from Tonga Mele Havea and Ha’ateiho, Samoa Fatuma Futi, Hawaii Kualoa, Niue Paluki, one sequence from Easter Island Anakena (early settlement phase Cal AD 1270–1400), and the putatively pre-Columbian (Cal AD 1304–1424) Chilean El Arenal-1 sequence belong to haplotypes 8 and 5 within haplogroup E (Fig. 1). Haplotype 8 equates to the E1 haplotype reported in Liu et al. [2006a], which is ubiquitous worldwide and 100% identical to haplotypes from European Barred Plymouth Rock, White Plymouth Rock, White Leghorn, and New Hampshire as well as native chicken sequences from [India, corr.], Central Asia, and China. In contrast, five of the other contemporaneous archaeological chicken sequences from Easter Island cluster with haplotypes 145 (n = 4) and 148 (n = 1), which are part of an uncommon group comprising mostly Indonesian chickens within haplogroup C (Fig. 1). Ancient Easter Island haplotype 145 is identical to one sequence of Red Junglefowl from the Philippines. Within other modern chickens, the closest related sequences have been recorded from Lombok and Java in Indonesia and the Philippines. Given their unique phylogenetic position and their pre-European contact dates, haplotypes 145 and 148 presumably represent a record of early Polynesian chicken transport, potentially overwritten subsequently in the western Pacific. The noticeably less star-like pattern of haplogroup C, centered on the less frequent haplotypes 91 and 95, is likely to be an artifact of incomplete sampling or a different population history. (Gongora et al., 2008a)

Nowadays, the haplogroup C denomination is confined to a much smaller group of continental chicken, while Oka’s and Gongora’s haplogroup C definition has been currently passed over to Liu’s (ancestral) haplogroup D, once tentatively proposed by Liu’s team for a loose group of cock-fighting chicken and Red junglefowl though currently thought to be closely associated with an Austronesian legacy in Indonesia, Madagascar and (hence?) Africa, and Polynesia:

Among the three Guamanian haplogroup D samples, three lineages were observed. One matched contemporary samples from the Philippines, Indonesia, and Japan. The other lineages were unique, but were closely related to contemporary samples from Indonesia, Japan, the Philippines, and China as well as India, Sri Lanka, Thailand, and Madagascar. Among the 40 haplogroup D samples from Vanuatu, seven lineages were observed. Four were exact matches to contemporary samples from Indonesia, Japan, the Philippines, and Southern China, as well as prehistoric Easter Island samples. The major Vanuatu lineage (n = 17), also found in a Red Jungle Fowl from the Philippines, was distributed across all four islands sampled (Dancause et al., 2011)

Conceivably the oldest ‘chicken’ haplogroup, the Indonesian hotspot of mtDNA haplogroup D distribution opens up an entirely new perspective on chicken domestication. Near the Island Southeast Asian origin of Polynesian Haplogroup D chicken, Bekisars are still the first generation (F1) hybrid offspring with Green junglefowl. Bekisars, whose colorful roosters have a glossy blackish green plumage, were the mascots of the original inhabitants of the Sunda Islands. Indeed, fresh chicken hybrids of the green junglefowl are still in demand. Seafaring cultures in the neighborhood allegedly took advantage of their unique crowing sound, loud enough to be heard for two miles over the sea, and consequently hybrids were part of their traveling gear. Because of the location, results of hybridization experiments on local chicken may be most noticeable in chicken populations whose history was especially related to mtDNA haplogroup D.
Currently, the role attributed to green junglefowl hybrids in the earliest Polynesian explorations is a popular theme. This has everything to do with the radiocarbon dating of apparently pre-Columbian chicken of El Arenal, Chile, that allegedly lived sometime between ad. 1321 and 1407 (Storey et al., 2007), and its purportedly ancestral relation with a peculiar local breed:

It has been suggested that the unique type of chicken known as the Araucana, which has no tail and lays blue eggs, is descended from pre-European stock bred by the Mapuche (formerly called Araucanos) people of Southern Chile (Storey et al., 2007)

An Oceanic origin, still contested, has been partly substantiated:

All ancient West Polynesian samples, early samples from Anakena, Easter Island and Kualoa, Hawaii, and the El Arenal sample share a single unique point mutation (a T to C transition) at site 214. One of the modern Araucana feather samples also shares this unique mutation. Three other SNPs (all transitions) at sites 278, 303, and 339 are shared by these West Polynesian, early Anakena and Hawaii, and the Chilean bone samples and sequences reported from modern chickens in Southeast Asia, specifically samples from the Yunnan region of China and Vietnam (Storey et al., 2007)

Indeed, in 1532, Spanish conquistador Francisco Pizarro recorded the presence of chickens in Peru, where the Inca used them in religious ceremonies. ‘That suggests chickens had already been there for a while’ (Storey in Archeology, Volume 61 Number 1, 2008).
However, all (meanwhile) three purported Pre-Columbian chicken remains turned out to have their mtDNA in the most common haplogroup E. But, in accordance with ‘modern Chilean sequences [that] cluster closely with haplotypes predominantly distributed among European, Indian subcontinental, and Southeast Asian chickens, consistent with a European genetic origin’ (Gongora et al., 2008a), this common haplotype (mtDNA E) was also present in ancient Polynesian chicken. Prehistoric chicken remains from Easter Island stand out for the dominant presence of mtDNA D, however, so ‘the two lineages may have converged before they were dispersed, as a polymorphic population, to Hawaii and Easter Island. Both haplogroups appear in early period archaeological sites in East Polynesia’ (Storey et al., 2012).
The search for haplogroup D in the Americas was not all in vain:

Haplogroup D has not yet been detected in any ancient chicken bone samples from Europe or from Thailand. Thus far it has only been identified in ancient Polynesian and Micronesian chicken remains as well as a single Peruvian sample. Haplogroup D has not yet been detected in any ancient chicken bone samples from Europe or from Thailand. Thus far it has only been identified in ancient Polynesian and Micronesian chicken remains as well as a single Peruvian sample. The available sample size for this study is too small to be representative
The early date of the Peruvian assemblage from which this haplogroup D sample was recovered raises the possibility that it could represent a descendant of a chicken haplogroup introduced from Polynesia. The fact that the sequence from the chicken bone from the Torata Alta site in Peru is identical to one from Fais in Micronesia also may support a possible Pacific connection. (Storey et al., 2012)

The Green Junglefowl is the only species of junglefowl that produces grey tinted eggs, indeed a possible forerunner of the bluish Araucana eggs. Instead, Red junglefowl miniature eggs vary between pure white and a deep creamy-buff. Ancient breeds often have tinted eggs (Silkies, Sussex) that approximate Gray junglefowl, whose eggs vary from very pale cream to rich warm buff, though the latter are often freckled and even spotted. The brownish red spotted eggs of the Singhalese Gallus Lafayette, or Ceylon junglefowl, appear profoundly out of range though reminds the French marran breed. Funny detail is that brown eggs, commonly associated with ‘natural’, are actually without equivalent in natural gallus species.
Nishibori et al. (2005) elaborated molecular evidence of Gallus hybridization except for the Green junglefowl. Plain hybridization has been well substantiated with the Grey junglefowl (India):

Our data imply that carotenoids are taken up from the circulation in both genotypes but are degraded by BCDO2 in skin from animals carrying the white skin allele (W*W). Surprisingly, our results demonstrate that yellow skin does not originate from the red junglefowl (Gallus gallus), the presumed sole wild ancestor of the domestic chicken, but most likely from the closely related grey junglefowl (Gallus sonneratii). This is the first conclusive evidence for a hybrid origin of the domestic chicken, and it has important implications for our views of the domestication process (Eriksson et al. – 2008)

Thus, the most common chicken being yellow-legged, modern chicken should be descendants of hybrids that originate predominantly from India, home of both the Grey junglefowl and an Indian subspecies of Red junglefowl: ‘Recently, […] molecular data also show that Indian Red junglefowl (G. g. murghi) also contributes to the domestication’ (Sawai et al., 2010).
The wide distribution of this hybrid form may be tempting to assume also a hybrid origin of domestic chicken. However, the ancient Sussex breed, though their large lightly tinted tan eggs might still suggest Gray junglefowl influences, also has white legs and skin in every variety. Brahmas, one of the largest breeds of chicken having fully feathered, white legs, derive from Shanghai, China. Such breeds far outside the range of red junglefowl tend to corroborate to the evidence that on a world-wide scale yellow legged hybrids were not part of the oldest introduction of domesticated chicken, or that successive waves of hybrids introduced different expressions of a hybrid nature.

How come early hybridization of domestic stock still receives so little attention? Faunal interference before the successful Neolithic domestication events may be deduced from biogeographic evidence. Some animals are thought to have translocated by humans already in prehistoric times. For instance, the natural range of Asian wild dogs (or Dholes) may reached much further than nowadays, still genetic evidence also insinuates a human role in their current distribution:

the grouping of Sumatran and Javan haplotypes with those from India (south of the Ganges) and Myanmar, as opposed to those from Malaysia and Thailand, should be noted.
Further studies are required to clarify these results but in the absence of alternative explanations, these results may be suggestive of human translocation of dholes from one of these regions into Sumatra and/or Java. But since there is no documented evidence for such translocation(s), and given that dholes have been long considered vermin (and not hunted for sport, cf. red fox introductions to Australasia), this hypothesis must remain highly speculative (Iyengard et al., 2005)

(The interior-most node of the Middle Eastern clade in the study of Brown's team (2011) corresponds to the new haplotype 12, recognized as ancestral and also shared with Asian Wild Dogs or Dhole. In appearance Dholes are not unlike shepherd dogs, that purportedly resemble Pleistocene dogs most. On morphologic grounds they belong to another genus (Cuon), though some of their distinguished traits fall within dog variability. Despite having the same number of chromosomes (78) as dogs, hybridization has not been recorded in any scientific investigation)

(The interior-most node of the Middle Eastern clade in the study of Brown’s team (2011) corresponds to the new haplotype 12, recognized as ancestral and also shared with Asian Wild Dogs or Dhole. In appearance Dholes are not unlike shepherd dogs, that purportedly resemble Pleistocene dogs most. On morphologic grounds they belong to another genus (Cuon), though some of their distinguished traits fall within dog variability. Despite having the same number of chromosomes (78) as dogs, hybridization has not been recorded in any scientific investigation)

At least the genetic results of Brown’s team (2011) cited above into the direction of Dhole or other admixture in domestic dogs was hastily swept under the carpet, when they found the novel Y-chromosome haplotype 12 that besides being recognized as ‘ancestral’ was also shared by Dhole, black-backed jackal, and a wolf from China. The Dhole (Cuon alpinus), also called the Asiatic wild dog, red dog, red wolf, or whistling dog, was widespread across North America, Europe and Asia during the Pleistocene. The species’ range, however, became restricted to Asia after the late Pleistocene mass extinctions c. 12 000–18 000 bp, when it became extinct across North America and Europe, along with several other large species such as mammoths and dire wolves. Like the African wild dog, they have the same number of 78 chromosomes like dogs, as do wolves, coyote and the golden jackal. However, hybridization with any of them has been attempted nor recorded. In appearance Dholes are not unlike shepherd dogs, that purportedly resemble Pleistocene dogs most:

In the PCA and DFA plots, the Palaeolithic dogs are situated near the Central Asian Shepherd dog, which was assigned in the DFA to the prehistoric dog group. This suggests that their skull shape resembles that of the latter breed which was originally used as a flock guardian and as a protector against predators such as bears, striped hyenas and wolves (Labunsky, 1994). The latter property in a dog could also have been useful for Palaeolithic people (Germonpré et al., 2009)

More features of modern dogs are intermediate between Dholes and wolves. Female dogs have 8 to 12 teats, while wolves have only 4 to 8. Female Dholes are on the other end of the spectrum having 12 to 14 teats rather than 10.
Dholes can be recognized in the fossil record by their reduced number of teeth: 40 instead of 42, due a missing molar (M3) in the lower jaw:, against dogs: However, the number of teeth for dogs is known to vary, and in his thesis Datema (2011) uses two reference cranials of dog (Canis lupus familiaris) with exactly this Dhole-like dental formula to investigate whether some dog-like remains recently fished up from the bottom of the North Sea (Southern Bight) really belonged to Pleistocene dogs or rather to “Cuon alpinus”. Was the Dhole indeed a member of the Mammoth Steppe Fauna?
One of Datema’s fossil Canidae specimen, labeled NMR90, was suspected to belong to Cuon alpinus. In this sample M3 is missing, like in Dholes. However, at least with respect to mandible lengths a-b and c-b this specimen was rather intermediate between wolf and Dhole and most similar to dogs:

NMR90, a recently found posterior half of an extremely small jaw (with P4 and M1) of estimated Late Pleistocene age) is suspected, due to its apparent small size and dental formula, that it most probably belongs to neither wolf nor dog (nor fox, which is considerably smaller), but to Cuon alpinus
The specimen range of NMR90 falls entirely outside [below] the population range of C. l. lupus and also entirely outside [above] the population range of Cuon alpinus, but well within the range of C. l. familiaris for a-b (table 4.2 and fig. 4.2). For c-b the specimen range of NMR90 falls entirely outside [above] the population range of Cuon alpinus, entirely within the C. l. familiaris range and overlaps slightly (1.36 mm) with the C. l. lupus population range, although most of the specimen range of NMR90 (2.75 mm) falls outside [below] the C. l. lupus range. (Datema, 2011)

Even though the sample was ultimately classified as a Dutch Dhole from the Southern Bight, this comparative study reveals how tentative such results may be. On the contrary, it has all appearance that Pleistocene dogs represented much more than an aberrant species of wolf. They were close relatives to the ice age ecomorph and probably all other Holarctic Pleistocene wolves that couldn’t resist the ‘human kiss of death’, and ‘hence’ became utterly outcompeted by an aggressive new type of wolf from the south that could. And Pleistocene dogs, embraced by the eerie love of humans, might have diverged even further for being purposely hybridized from the start!

(The famous Aurignacian "Venus and the Sorcerer" rock painting in Chauvet cave, Ardeche, depicts an anthropomorphic steppe bison and a female lion, sexually united by a black female pubic triangle. Genuine fascination for cross-species mating is related with a huge body of mythological themes, including shapeshifting, and may have triggered early hybridization experiments)

(The famous Aurignacian “Venus and the Sorcerer” rock painting in Chauvet cave, Ardeche, depicts an anthropomorphic steppe bison and a female lion, sexually united by a black female pubic triangle. Genuine fascination for cross-species mating is related with a huge body of mythological themes, including shapeshifting, and may have triggered early hybridization experiments)

Indeed, hybridization is one of the first recorded obsessions of modern humans. The famous Aurignacian “Venus and the Sorcerer” rock painting in Chauvet cave, Ardeche, already depicts the cross-species mating of an anthropomorphic steppe bison and a female lion, sexually united by a black female pubic triangle. Bull-related fertility and the procreation of hybrid monsters remained a recurrent theme in mythology up to the Greek Minotaur and the Frankish Quinotaur. There could be more. When the Sumerian Enkidu killed the Bull of Heaven, and hence was doomed to die, his friend Gilgamesh was in great grief and swore: “I will wander through the wilderness in the skin of a lion”. We might think this was a strange way to please the gods, though Chauvet Cave would suggest a rich mythology preceding Gilgamesh being based on this bond between species. We can’t dismiss this genuine fascination of early modern humans as purely theoretical. Actually, even the huge body of mythological themes related to shapeshifting has all appearance to be closely connected to an early human fascination for cross-breeding. We simply can’t exclude the possibility that hybridization experiments were already attempted long before the Neolithic.


  • Aggarwal et al. – Mitochondrial DNA coding region sequences support the phylogenetic distinction of two Indian wolf species, 2007, link
  • Albert et al. – A Comparison of Brain Gene Expression Levels in Domesticated and Wild Animals, 2012, link
  • Avian Information System of India – On Ceylon junglefowl, Grey junglefowl and Red junglefowl.
  • Axelsson et al. – The genomic signature of dog domestication reveals adaptation to a starch-rich diet, 2013, link
  • Baryshnikov et al. – Finding of the Late Pleistocene carnivores in Taimyr Peninsula (Russia, Siberia) with paleoecological context, 2009, link
  • Bay-Petersen – Competition for resources : the role of pig and dog in the Polynesian agricultural economy, 1983, link
  • Brown et al. – Phylogenetic Distinctiveness of Middle Eastern and Southeast Asian Village Dog Y Chromosomes Illuminates Dog Origins, 2011, link
  • Cahill et al. – Genomic evidence for island population conversion resolves conflicting theories of polar bear evolution, 2013, link
  • Camerini – Evolution, Biogeography, and Maps: An Early History of Wallace’s Line, 1993, link
  • Cherin et al. – Re-Defining Canis etruscus (Canidae, Mammalia): A New Look into the Evolutionary History of Early Pleistocene Dogs Resulting from the Outstanding Fossil Record from Pantalla (Italy), 2013, link
  • Crockford & Kuzmin – Comments on Germonpré et al. […] “Fossil dogs and wolves from Palaeolithic sites in Belgium, the Ukraine and Russia: osteometry, ancient DNA and stable isotopes”, and […] “Palaeolithic dog skulls at the Gravettian Predmostí site, the Czech Republic”, 2012, link
  • Dancause et al. – Characterizing Genetic Diversity of Contemporary Pacific Chickens Using Mitochondrial DNA Analyses, 2011, link
  • Datema – Was Cuon alpinus a member of the Mammoth Steppe Fauna? Comparative morphological and osteometrical study on recent and fossil Canidae hemimandibles, 2011, link
  • Ding et al. – Origins of domestic dog in Southern East Asia is supported by analysis of Y-chromosome DNA, 2011, link
  • Dhole Fact File, link
  • Druzhkova et al. – Ancient DNA Analysis Affirms the Canid from Altai as a Primitive Dog, 2013, link
  • Eriksson et al. – Identification of the yellow skin gene reveals a hybrid origin of the domestic chicken, 2008, link
  • Garcia – Ichnologie générale de la grotte Chauvet, 2005, link
  • Garrido & Arribas – Canis accitanus nov. sp., a new small dog (Canidae, Carnivora, Mammalia) from the Fonelas P-1 Plio-Pleistocene site (Guadix basin, Granada, Spain), 2008, link
  • Gaubert et al. – Reviving the African Wolf Canis lupus lupaster in North and West Africa: A Mitochondrial Lineage Ranging More than 6,000 km Wide, 2012, link
  • Germonpré et al. – Fossil dogs and wolves from Palaeolithic sites in Belgium, the Ukraine and Russia: osteometry, ancient DNA and stable isotopes, 2009, link
  • Germonpré et al. – Palaeolithic dog skulls at the Gravettian Predmostí site, the Czech Republic, 2012a, link
  • Germonpré et al. – Palaeolithic dogs and the early domestication of the wolf: a reply to the comments of Crockford and Kuzmin, 2012b, link
  • Gongora et al. – Indo-European and Asian origins for Chilean and Pacific chickens revealed by mtDNA, 2008a, link
  • Gongora et al. – Reply to Storey et al.: More DNA and dating studies needed for ancient El Arenal-1 chickens, 2008b, link
  • Hammer et al. – Genetic evidence for archaic admixture in Africa, 2011, link
  • Hofreiter – Pleistocene extinctions: haunting the survivors, 2007, link
  • Hofreiter & Barnes – Diversity lost: are all Holarctic large mammal species just relict populations? 2010, link
  • Hooijer – Indo-Australian Insular Elephants, 1967, link
  • Iyengard et al – Phylogeography, genetic structure, and diversity in the dhole (Cuon alpinus), 2005, try here
  • Islam & Nishibori – Phylogenetic Analysis of Native Chicken from Bangladesh and Neighboring Asian Countries Based on Complete Sequence of Mitochondrial DNA D-loop Region, 2012, link
  • Kays et al. – Rapid adaptive evolution of northeastern coyotes via hybridization with wolves, 2010, link
  • Kijas et al. – Genome-Wide Analysis of the World’s Sheep Breeds Reveals High Levels of Historic Mixture and Strong Recent Selection, 2012, link
  • Larson et al – Rethinking dog domestication by integrating genetics, archeology, and biogeography, 2012, link
  • Leonard et al. – Ancient DNA evidence for Old World origin of New World dogs, 2002, link
  • Leonard et al. – Megafaunal Extinctions and the Disappearance of a Specialized Wolf Ecomorph, 2007, link
  • Lindblad-Toh et al. – Genome sequence, comparative analysis and haplotype, structure of the domestic dog, 2005, link
  • Louys et al. – Characteristics of Pleistocene megafauna extinctions in Southeast Asia, 2006, link
  • Liu et al. – Multiple maternal origins of chickens: out of the Asian jungles, 2006a, link
  • Liu et al. – Genetic relationship of Chinese and Japanese gamecocks revealed by mtDNA sequence variation, 2006b, link
  • Meachen & Samuels – Evolution in coyotes (Canis latrans) in response to the megafaunal extinctions, 2012, link
  • Miao et al. – Chicken domestication: an updated perspective based on mitochondrial genomes, 2013, link, or try here, supplemental information here
  • Moss & Wilson – Biogeographic implications of the Tertiary palaeogeographic evolution of Sulawesi and Borneo, 1998, link
  • Napierala – A ‘new’ Palaeolithic dog from central Europe, 2010, link
  • Nishibori et al. – Molecular evidence for hybridization of species in the genus Gallus except for Gallus varius, 2005, link
  • Oka et al. – Analysis of mtDNA sequences shows Japanese native chickens have multiple origins, 2007, link
  • Ovodov et al. – A 33,000-year-old incipient dog from the Altai Mountains of Siberia: evidence of the earliest domestication disrupted by the Last Glacial Maximum, 2011, link
  • Pang et al. (2009) – mtDNA data indicate a single origin for dogs south of Yangtze River, less than 16,300 years ago, from numerous wolves, 2009, link
  • Pedrosa et al. – Evidence of three maternal lineages in near eastern sheep supporting multiple domestication events, 2006, link
  • Pilot et al. – Phylogeographic history of grey wolves in Europe, 2010, link
  • Reece et al. – Campbell Biology, ninth edition, 2011, ISBN 9780321558237
  • Rueness et al. – The Cryptic African Wolf: Canis aureus lupaster Is Not a Golden Jackal and Is Not Endemic to Egypt, 2011, link
  • Sacks et al. – Y chromosome analysis of dingoes and Southeast Asian village dogs suggests a Neolithic continental expansion from Southeast Asia followed by multiple Austronesian dispersals, 2013, link
  • Savolainen et al. – Genetic evidence for an East Asian origin of domestic dogs, 2002, link
  • Sawai et al. – The Origin and Genetic Variation of Domestic Chickens with Special Reference to Junglefowls Gallus g. gallus and G. varius, 2010, link
  • Serpell – The Domestic Dog: Its Evolution, Behaviour and Interactions with People, 1995, link
  • Sharma et al. – Ancient wolf lineages in India, 2004, link
  • Storey et al. – Radiocarbon and DNA evidence for a pre-Columbian introduction of Polynesian chickens to Chile, 2007, link
  • Storey et al. – Pre-Columbian chickens, dates, isotopes, and mtDNA (Reply to Gongora et al., 2008a), 2008, link
  • Storey et al. – Mitochondrial DNA from 3000-year old chickens at the Teouma Site, Vanuatu, 2010, link
  • Storey et al. – Investigating the Global Dispersal of Chickens in Prehistory Using Ancient Mitochondrial DNA Signatures, 2012, link
  • Thalmann et al. – Inferences on dog domestication – genetic analysis of the most ancient dogs utilizing DNA capture arrays, SMBE 2012, extract
  • vonHoldt et al. – Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication, 2010, extract
  • VonHoldt et al. – A genomewide perspective on the evolutionary history of enigmatic wolf-like canids, 2011, link
  • Vilà et al. – Multiple and ancient origins of the domestic dog, 1997, link
  • Vilà et al. – Phylogenetic Relationships, Evolution, and Genetic Diversity of the Domestic Dog, 1999, link
  • Wayne et al. – Origin, genetic diversity, and genome structure of the domestic dog, 1999, link

The Mesolithic Blind Spot

January 26, 2013 4 comments

Two 5000 BC Mesolithic individuals from the La Braña-Arintero site in León (Northwestern Spain), may have bolstered undue confidence in a forlorn Mesolithic continuum of native hunter-gatherers from Iberia to Finland. Despite genomic data revealing they were apparently most similar to current Northern European types, in depth assessments of migrational possibilities were conspiciously missing:

The mitochondria of both individuals are assigned to U5b2c1, a haplotype common among the small number of other previously studied Mesolithic individuals from Northern and Central Europe. This suggests a remarkable genetic uniformity and little phylogeographic structure over a large geographic area of the pre-Neolithic populations.
The generated data covered 41,320,020 nucleotide positions for La Braña 1 and 16,876,146 for La Braña 2; thus, about 1.34% and 0.53% of the La Braña 1 and 2 genomes were retrieved, respectively […]
A worldwide genomic principal component analysis (PCA) with data from the 1000 Genomes Project places La Braña 1 and 2 near, but not within the variation of current European populations (Figure S2). However, when compared exclusively to European populations, La Braña 1 and 2 fall closer to Northern European populations such as CEU and Great Britons than Southern European groups such as Iberians or Tuscans (Sánchez-Quinto et al., 2012)

The Sardinian Prehistoric Altar of Monte D’Accoddi, older that the Egyptian pyramids and the Middle Eastern ziggurat, may as well represent native European diversity.

The Sardinian Prehistoric Altar of Monte D’Accoddi, older that the Egyptian pyramids and the Middle Eastern ziggurat, may as well represent native European diversity.

Sánchez-Quinto et al. went into some effort to declare this particular early ‘northern’ genotype virtually “without issue” in Southern Europe:

In the genomic analysis, it is interesting to see that the La Braña individuals do not cluster with modern populations from Southern Europe, including those from the Iberian Peninsula.
The position of La Braña individuals in the 1000 Genomes Project data and the 1KGP omni [2.5M] chip PCAs suggests that the uniform Mesolithic substrate could be related to modern Northern European populations but may represent a gene pool that is no longer present in contemporary Southern European populations (Sánchez-Quinto et al., 2012)

Others are keen to warn against premature generalizations. Martin Richards: ‘Unfortunately, some ancient DNA researchers seem unable to resist making sweeping claims about the ancient genetic structure of whole regions’ (Balter, 2012). “Only half” of the few current Mesolithic samples are in the mtDNA U5b group, indicating Mesolithic peoples were more diverse than many so far chose to perceive. Moreover, south of the Alps there was also an entirely other element that before Ötzi the Iceman we only knew from the isolated Sardinian island. D-statistic analysis indeed confirmed that ‘the Iceman and the HGDP Sardinians are consistent with being a clade’ (Patterson et al., 2012). Ancient DNA data from an early Iron Age individual from Bulgaria showed close affinity with Sardinians as well, indicating the “Sardinian clade” must have closely resembled populations present in the Southern Alpine region around 5000 years ago. Currently there exists some prevalence to cluster this “southern flavor” apart from the mentioned Mesolithic group, while geographically there is some overlap. The jury is out on the question whether or not the Sardinian cluster is autochthonous in Europe. The “pan-Mesolithic” simplification could thus easily be due to erroneous modeling, poor resolution and insufficient sampling of the prehistoric situation.
Another issue may be the current genetic landscape of Europe. Due to Neolithic and post-Neolithic population movements the ‘southern flavor’ was apparently overrun or out bred except for Sardinia, while the ‘northern flavor’ diluted slightly in the north but otherwise expanded considerably. This is evidenced by an almost devastating retreat of the southern “Ötzi-like” genotype ever since the time of Ötzi about 3300 BC, in favor of a more Northern European-like genotype. The retreat of this “Sardinian” genomic element fully postdated the southern Mesolithic expanse evidenced by the La Braña-Arintero individuals, as well as the 4600 BC Mesolithic skeletons found in Aizpea, Navarra (Spain), for that matter, also carrying U5b. The retreat of both types may be interrelated and contemporaneous. Indeed, the early Mesolithic predominance of mtDNA U5b is hardly reflected by the modest contribution of mtDNA U5b in modern European populations. This mtDNA haplotype nevertheless strongly suggests an expansive northern origin as they share U5b with mtDNA samples recovered from present day Lithuania (Donkalnis and Kretuonas sites), Poland (Dudka site), Germany (Hohlenstein-Stadel individuals and Falkensteiner Höhle sites; and arguably (according to Sánchez-Quinto) from the 4000 BC Reuland-Loschbour site in Luxembourg as well as from the “Cheddar Man” skeleton found in Gough’s Cave, England. Also here Sardinia is remarkable for having preserved some unique mtDNA U5b3, whose possible relation with stone tool innovation may only be suspected: ‘The root of U5b3a1 originated probably in the Mediterranean coast of southern France and the same haplotype then went into Sardinia some 7–9 kya, possibly as a result of the obsidian trade that linked the two regions.’ (Pala et al., 2009)
Hence, Patterson’s (2012) high Z-scores with UK, Ireland and especially Russia, could be expected to link Sardinia to a conservative early Mesolithic influx. Unfortunately, Patterson’s team preferred to extrapolate the Russian evidence from a rather hypothetical Middle East signature, otherwise dearly missing in their dataset. Their hypothesis nevertheless triggered them to (weakly) link the southern component to the arrival of Neolithic farmers “probably from the Middle East”. Also in other ways the intermediate role they assign to some would-be “exclusive” Eastern European association, actually due to a lack of resolution, fails to supply proxy-evidence for the genetic link with the Middle East they apparently expected:

An alternative history that could produce the signal of Asian-related admixture in northern Europeans is admixture from steppe herders speaking Indo-European languages, who after domesticating the horse would have had a military and technological advantage over agriculturalists (Anthony 2007). However, this hypothesis cannot explain the ancient DNA result that northern Europeans today appear admixed between populations related to Neolithic and Mesolithic Europeans (Skoglund et al. 2012), and so even if the steppe hypothesis has some truth, it can explain only part of the data. (Patterson et al., 2012)

Patterson’s team asserts that the Sardinian clade corresponds to the genotype of Europe’s Neolithic settlers, and finds some support in Neolithic farmer’s DNA of about 5000 years ago in what is now Sweden (Skoglund et al. 2012) that ‘shows a signal of genetic relatedness to Sardinians that is not present in the hunter–gatherers who have much more relatedness to present-day northern Europeans’. Hence they hypothesize that:

[…] agriculturalists with genetic ancestry close to modern Sardinians immigrated into all parts of Europe along with the spread of agriculture. In Sardinia, the Basque country, and perhaps other parts of southern Europe they largely replaced the indigenous Mesolithic populations, explaining why we observe no signal of admixture in Sardinians today to the limits of our resolution. (Patterson et al., 2012)

Their observations are indeed due to the limits of doing a 3-population test. Loh et al. (2012): ‘The 3-population test loses sensitivity primarily as a result of drift since splitting from the references’ lineages. […] Small mixture fractions also diminish the size of the admixture term […] and we believe this effect along with post-admixture drift may be the reason Sardinians are detected as admixed only by [linkage disequilibrium (LD)-based] ALDER.’ On the other hand, since ‘LD breaks down [proportional to] the age of admixture, there is nearly no LD left for ALDER to harness beyond the correlation threshold’, that Loh apparently has below ‘7,000-9,000 years ago when agriculture arrived [in] Europe’. Using this method, Loh could relate Sardinians unequivocally to northern Africa instead:

Our findings thus confirm the signal of African ancestry in Sardinians […] The date, small mixture proportion, and geography are consistent with a small influx of migrants from North Africa, who themselves traced only a fraction of their ancestry ultimately to Sub-Saharan Africa (Di Gaetano et al., 2012)

However, Di Gaetano (2102) ran ADMIXTURE software in a different way, using Identity-by-state (IBS) sharing between and within populations for 126K autosomal SNPs. Applying a cross-validation procedure to validate results for each number of clusters, K, from 2 to 10, he ‘obtained at K= 4 the lowest cross-validation error.’ Thus their data set could be restricted to four clusters (K=4) or regional common denominators, painted purple (Northern Africa), blue (Middle East), light green (Northern Europe) and crimson (Italy) in their figure 3. Now the results indicated something completely else:

The HapMap CEU individuals showed an average Northern Europe (NE) ancestry […] of 83%. A similar pattern is observed in French, Northern Italian and Central Italian populations with a NE ancestry of 70%, 56% and 52% respectively (Figure 3). According to the PCA plot, also in the ADMIXTURE analysis there are relatively small differences in ancestry between Northern Italians and Central Italians while Southern Italians showed a lower average admixture NE proportion (43,6%) than Northern and Central Italy, and a higher Middle East ancestry (light blue) of 28%. (Di Gaetano et al., 2012)

Thus could be established by Di Gaetano’s team that the average admixture proportions for Northern European ancestry within the current Sardinian population is 14.3%, with some individuals exhibiting very low Northern European ancestry (less than 5% in 36 individuals on 268 accounting the 13% of the sample) – probably indicating an uneven and complicated population history for this component. This kind of patchy distribution has also been noted for the Sardinian mtDNA U component, that was dearly missing in 16 ancient Nuragic individuals of Central Sardinia (~2,700-3,430 yBP) whose mtDNA were T, H1, K, V, J, X. mtDNA has a total of 9.2% in modern Sardinia, well within common European values (8.1%-10.3%). The highest percentages in modern Sardinia for U5a, U5b, U8 and Uother were measured in the north, reaching a significant 15.1% over 106 samples. (Der Sarkissian, 2011) Could we tentatively assume an ancient substructure of coexisting populations, where a northern Mesolithic element was not necessarily native in Europe’s south? Simultaneously, Di Gaetano’s team confirmed the Sardinian clade was deeply rooted in Sardinia – and probably elsewhere as well:

An intriguing result of the ADMIXTURE analysis was the proportion of ancestry in Sardinia, an ancestry shared with all the European and Northern African populations included in this analysis but with the highest level in Sardinia (Figure 3 crimson colour).
This average admixture proportion is widespread across all over the Sardinia island, with no geographic clustering, underlining an internal genetic homogeneity among the Sardinians. At the same time, this admixture proportion could be the signature of a common ancient genetic background of all the continental European populations but the isolation of the Sardinians has preserved this ancestry. The recent sequencing of the Iceman’s genome, argues strongly in favor of the hypothesis that at least continental Europeans, living 5,300 years ago, were more similar to the current Sardinians.

Di Gaetano’s cross-validation analysis sets his admixture analysis apart from the murky assessments that prevail on the internet, where interest groups tend to invent their own clusters of choice, suppressing others they dislike, and typically display results meant to boost fancy Kurganist or Orientalist scenarios. Instead, we have now at our disposal an ancestral genetic configuration that is truly relevant to the Mediterranean ethnogenesis, having a northern component predominantly shared with northwestern Europe rather than northern Europe as a whole – due to the close correlation with a “CEU” reference population of Utah residents with ancestry from Northern and Western Europe. For sure this particular northern correlation is bound to be completely different from one including random northern reference samples that for instance may predict a rather Finnish affinity, knowing Finland is an outlier within the northern hemisphere all by itself whose specific historic or prehistoric influence in the Mediterranean should be dealt with separately. For instance, the significant Mesolithic burial site ‘Yuzhnyi Olenii Ostrov’ in Karelia, NW Russia, dated at 7500-7000 YBP, surprisingly yielded mongoloid influences and Siberian mtDNA C1. The haplogroup has virtually disappeared from the region, though apparently this was part of a huge Siberian genetic interchange between west and east that also involved “European” mtDNA (eg. U5a in the peri-Baikal region, Van Sarkissian 2011). This Mesolithic integration may have been at the base of long-range linguistic integration that ultimately formed Uralic and Altaic languages, but most of all supplied a new genetic component in North Eastern Europe, that already could have had some impact on the genetic composition of Skoglund’s three Mesolithic samples (Ajv52, Ajv70 and Ire8) on the island of Gotland (5300 to 4400 cal yr B.P.). If Finnish-like genetic proximity just off the radar indeed already affected Skoglund’s Scandinavian samples this essentially detaches Mesolithic Scandinavia from the northern European horizon “pur sang” – potentially shatters current ideas on a much later bronze- or iron age Uralic arrival in the region.

Having recent admixtures successfully filtered out, Nelis' team (2012) presented Europe's genetic landscape in the form of a triangle, with the Finnish, Baltic and Italian samples as its vertexes.

Having recent admixtures successfully filtered out, Nelis’ team (2012) presented Europe’s genetic landscape in the form of a triangle, with the Finnish, Baltic and Italian samples as its vertexes.

Such old substructure for northern European populations has rarely been dealt with and runs counter to the traditional assumption of an extended period of steady gene flow between southern and northern populations, followed only by a fairly recent immigration of “the Finnish” component. In 2009 Nelis’ team already noted his scatter plot took ‘the form of a triangle, with the Finnish, Baltic and Italian samples as its vertexes’, what indeed implies a much more complicated substructure for northern populations whose generalization is bound to introduce irrecoverable errors.
Point of contention about a more general Sardinian-clade ancestry in Europe may be it remains low or hard to conceive north of the Alps, where a different clustering dominates. Naturally, adopting all-inclusive variability in the whole of Mesolithic Europe potentially shatters the concept of any kind of Mesolithic hunter-gatherer continuum and would instead define the Mesolithic La Braña-Arintero specimen to represent an early Northern intrusion.
Scrutiny of the Sardinian Northern admixture doesn’t really confirm Sánchez-Quinto’s team assertion the old Mesolithic substratum is by now seriously diminished in southern Europe, unless it retreated together with the Sardinian clade. But, apparently the current European genotype is again strongly admixed by a Northern European component, doesn’t this imply at least two different expansion periods for genes of the Northern European type in Southern Europe?
Altogether, the current scope of investigation supplies ample evidence of northern expansion within the European gene pool, and a rather poor case for an oriental Neolithic intrusion if compared with the current oriental composition.
Rather than recurring to the hypothesis that the current Near Eastern genotype “thus” must have changed beyond recognition in order to fit the evidence of a very different “Ötzi-like” genotype, I consider it more parsimonious to seek the origin of this Southern European genotype in the southern local Mesolithic.
The purported “oriental” affinity for European autosomes of this southern component is far from obvious. Modern populations in the near east have a quite different signature, what makes an oriental origin of an Ötzi-like component in European populations highly hypothetical and problematic. So far there is not any indication modern populations east of the Mediterranean somehow “lost” their tentatively hypothesized Ötzi-like component due to post-Neolithic immigration, so all attempts to attribute an “Oriental” Neolithic identity to Europe’s Ötzi-like southern component appear futile and rather of the category “ideological reactionism” as far it concerns the fashionable adherence to a flourishing multitude of post-war or semi-biblical hypotheses on Indo-European and Neolithic origins. Actually, improved technology and methods show ever less non-European identity or admixture in the Sardinian clade, except for small non-European affinities being “north African” rather than Asian. Simultaneously, the “northern” affiliation of most European populations appear firmly rooted in the Northern Mesolithic, and includes a significant ancient affinity with Amerindian populations apparently poor or absent in the representatives of the Sardinian clade like Ötzi and the Neolithic farmer of Gokham (Gok4). According to Dienekes the Iberian hunter-gatherer of La Braña 1 is of the ‘non-Amerindian’ affiliation and African-admixed, what indeed could confirm a longer local history of this Mesolithic presence in the south. One way or the other, current admixture analyses thus reveal the European north-south diversity deeply rooted in prehistory. As such, Patterson’s global ethnical division of prehistoric Europe on cultural grounds in separate Mesolithic and a Neolithic entities is build on thin air.
The European North-South differentiation is real enough. Jay et al. (2012) found that the major orientations of genetic differentiation are north-south in Europe, where ‘the precise NNW-SSE axis of main European differentiation can not be explained by a simple Neolithic demic diffusion model without admixture with the local populations because in that case the orientation of greatest differentiation should be perpendicular to the direction of expansion.’
Investigating to what extent the results are changed when perturbing the geographical sampling locations of the sampled populations:

If Cyprus and Turkey, the two most Southeastern populations, were removed, the axis of maximum differentiation shifted from a NNW-SSE orientation towards a N-S orientation […] If all other Southeastern populations […] were removed, the orientation of maximum differentiation hardly changed, going from 167 to 161 [degrees]. However, if Cyprus, Turkey and all other Southeastern populations were excluded the anisotropic terms ceased to be significant (Jay et al., 2012)

Apparently, the Balkan populations add some more weight to Europe’s N-S differentiation, but don’t really change the genetic landscape south of the Alps. Actually, the SE European impact on the N-S differentiation can be interpreted as a discontinuity arising from a barrier to dispersal, ie. not exactly what one has in mind with an extensive Oriental Neolithic invasion. Hence, most important in Europe remains the N-S differentiation. What could have caused this?

Diamond (1997) proposed that because populations at the same latitude experience the same climate, technological diffusion was more easy and rapid in the E-W direction than in the N-S direction. If the spread of technology accompanied the spread of people as assumed by the demic diffusion models (Diamond and Bellwood 2003), the level of genetic differentiation should then be the greatest along the N-S orientation. (Jay et al., 2012)

In a previous article I already dismissed as probably invalid the underpinning believe in a tremendous genetic impact of agricultural immigrants. The active role of prepottery neolithic groups in SE Europe in the development and expansion of local forms of Neolithic culture may have supplied another reason for this observation. Actually, in several genetic diagrams it isn’t so very hard to perceive a native Southern European genotype that is definitely distinct and defies all similarity to current Near Eastern genotypes. The Ötzi-like southern element neither descents unequivocally of “Neolithic invaders” nor is it culturally confined in any other generic way. Actually, it isn’t necessary to equate the early Neolithic inhabitants of the Mediterranean with oriental immigrants at all now we know these islands were already inhabited long before Neolithic culture arrived:

Discoveries on Cyprus, Crete, and some Ionian islands suggest seafaring abilities by pre-Neolithic peoples, perhaps extending back to Neanderthals or even earlier hominins. (Simmons, 2012b)

Being utterly unrelated with oriental genotypes and affiliated instead to current Sardinian genotypes, an oriental Neolithic identity of the Sardinian clade isn’t even imperative:

Pre-Neolithic sites on some western Mediterranean islands, such as Sardinia, are controversial […], although they appear well established for Corsica (Simmons, 2012a)

If derived of Neolithic immigrants anyway, these immigrants must have been close European neighbours whose hypothetic oriental origin had already diluted beyond recognition by local admixture. There even exists growing uncertainty about a prefabricated oriental origin of the European Neolithic at all, now even the earliest Neolithic Pre-Pottery stage (PPNA) has been confirmed in Greece and the Mediterranean island of Cyprus (~11,700 – 10,500 BP).
It is likely that full-scale colonization of Cyprus occurred during the Cypro-PPNB, that itself is sometimes difficult to distinguish from PPNA, for convenience considered the very earliest Neolithic stage that includes villages but does not yet contain morphologically domesticated plants and animals – ie. actually a period of hunter-gatherers that barely entered a Mesolithic stage.

Recent research has documented […] an interior PPNA site (Ayia Vavarva Asprokremnos) dating to ca. 9000 CAL B.C. […] and entities near the coast, including PPNA or early PPNB Ayios Tihonas Throumbovonos […] and PPNA Ayios Tihonas Klimonas […]. This has prompted some […] to coin the term “Early Aceramic Neolithic” to include both the PPNA and Cypro-PPNB. (Simmons, 2012a)

Already the earliest prepottery period in Cypus attested the management of wild boar, an intermediate stage between “hunting” and “breeding.” Actually, there is no record of suids on any of the isolated Mediterranean islands before Neolithic introduction, including Cyprus. The small size of Cyprus’ PPNA suids, dated to ca. 12,500 cal. B.P. at the Cypriot site of Akrotiri Aetokremnos, doesn’t correspond to any known wild population living on the continent, and even predates domestic downsizing elsewhere. They are ‘the same size as the Early and Middle Neolithic domestic pigs of Corsica, which are among the smallest known Holocene suids from a Mediterranean island’, adding up to the possibility this earliest attested domestication-like downsizing of suids in Cyprus may actually be part of a common phenomonon often observed on islands. Pig domestication was first evidenced in the upper Euphrates basin, at Nevali Cori, where ‘a rapid decrease in animal size ca. 10,500 calibrated radiocarbon date (cal.) B.P. suggests an abrupt event and a constant and intensive breeding pressure’. This is almost contemporary to ‘small-sized suid bones on the Aegean islands of Youra and Kythnos during the 10th and 11th millennia cal. B.P’, suggesting that ‘managed wild boar predated domestic pigs in this area by at least 1 millennium’.
Human introduction of suids to Cyprus during the 12th millennium cal. B.P. implies that wild boar were already managed on the continent at that time (i.e., 1,500 years before the earliest attested domestication), but also attest the importance of seafaring for cultural expansion during the earliest stages of the Neolithic:

First, it is possible that genetically differentiated wild boar populations in eastern and western Anatolia were domesticated independently. Perhaps more likely, however, is a scenario in which eastern Anatolian wild boar were initially domesticated and subsequently transported west out of the Neolithic ‘core zone’ […] The route along which domestic pigs traveled to arrive in western Anatolia remains unknown. The presence of domestic pig remains by the 7th millennium BC (Pottery Neolithic layers) at the site of Yumuktepe, in south-central Turkey […], and the general dearth of pigs during the same period in central Anatolia […], however, suggests that one of the possible routes was along the Mediterranean coast. (Ottoni et al., 2012)

Seafaring between Greece and the Greek islands was evidenced by ‘the occurrence of obsidian from the Aegean island of Melos at the mainland Greek coastal site of Franchthi cave, beginning from the 11th millennium before the present (B.P.)’ , what certainly is in agreement with some importance of eg. Cyprus as a Neolithic nexus that links east and west together:

The Neolithic transformation initially occurred in the Near East, but then spread to adjacent areas. This transmission is often thought to have been through Anatolia, but the new research also suggests maritime routes, with the Cypriot evidence indicating a substantial level of mainland interaction. (Simmons, 2012b)

Continuity up to the relatively homogeneous preceramic Khirokitia culture (KC) may be illustrated by the site Ais Giorkis, that ‘has two aceramic phases and is possibly transitional into the KC’ (Simmons, 2012a). By then, the Cyprus Neolithic ‘showed few parallels with the [Levantine] mainland, having only the basic economic suite of key domesticated plants and animals’. This local transition must have marked the end of the hypothesized maritime rute of the Levantine Neolithic into Europe. Mainland Levantine influence dwindled, and KC developed further in virtual isolation – except for the use of non-native flakes of obsidian – only to follow the extinction of earlier introduced cattle at about 6000 BC. This date corresponds with the surge of a ceramic Neolithic in the mediterranean, when pottery became important. Especially the Cardium pottery culture expanded in the mediterranean, to the west as far as Iberia, but this culture had its earliest sites, dating to 6400-6200 BC, in Epirus and Corfu, not in the Levant. Apparently, the Levantine influence on European populations was considerably constrained in time and space, what may explain the lack of a much closer Levantine affiliation with European populations, including the southern “Neolithic” Ötzi-type genotype. If related to Neolithic genotypes at all, Ötzi should cluster with contemporary Greek populations rather than oriental populations. Indeed, this is already strongly suggested by the DNA of a sampled iron-age Bulgarian individual.

Behar's (2010) plot detailing the Levantine genetic structure in relation with Europe.

Behar’s (2010) plot detailing the Levantine genetic structure in relation with Europe.

A popular method in genetic investigation uses Fst (Fixation Index) diagrams to quantify long-term gene flow between neighboring populations. Thus, by now a multitude of Fst diagrams is available that most of all attest a genetic continuum between neighboring populations all over the world, at different levels of detail. Typically, sets of genes are used that predominate on each side of a geographic continuum, on the assumption that basic genetic history or divergence by isolation over time superseded genetic convergence by gene flow. Fst increases proportionally with distance rather than anything else, suggesting the importance of an underpinning process of genetic divergence rather than deep genetic history. The relationship between FST and geographic distance is most of all consistent with an equilibrium model of drift and dispersal. Equilibrium models of isolation by distance predict an increase in genetic differentiation with geographic distance. On a world-wide scale, the results of Rosenberg et al. (2002) features a global linear increase of Fst with geographic distance from Africa up to South America, almost exclusively due to Holocene or Epi-paleolithic genetic divergence.
In Behar’s (2010) FST diagram (Figure 2) a clear genetic continuum may be discerned in the middle east, but in relation with Europe this same diagram attests a discontinuity or dichotomy between both Eurasian continents. A vestige of some old Mediterranean genetic continuum may be discerned between the Levant via Cyprus into the direction of Sardinia. Another vestige of gene flow may be discerned through Anatolia into the direction of Romania. Strange enough, the genetic leap of Cyprus with Europe is considerable and despite Cyprus’ historic association with especially Greece, the island belongs genetically rather to the Near East. Most unfortunate to the Oriental case for Europe’s Neolithic population origins, the genetic trail of Neolithic genotypes has another dead-end in Anatolia (Turkey) – according to Skoglund (2012) ‘possibly due to gene flow from outside of Europe’. This evidence for an apparently quite effective genetic barrier is the more remarkable now Skoglund’s team (2012) asserts the Neolithic farmer (typed Gök4)sampled in Sweden ‘shared the greatest fraction of alleles with southeastern European populations (Cypriots and Greeks) and showed a pattern of decreasing genetic similarity to populations from the northwest and northeast extremes of Europe’, while Turkish reference samples ‘stand out because of low levels of allele sharing’. This latter behaviour is contradicted by the graph (3B) where Skoglund apparently refers to, raising questions about its accuracy – especially across the Bosporus. Gök4’s association with western Europe is taken for granted.
Few of the purported Neolithic derived “grand division” is left nowadays in Europe. Already in 2009 Nelis et al. decribed a gradient between modern European populations that is rather “south-north” and hardly influenced by an eastern source. Southern Italy, according to Nelis’team at one extreme side of the genetic spectrum, is known for a disproportionate “oriental” element (28% according to Di Gaetano), but it remains hard to accept Southern Italy should be more “oriental” in Nelis’ graph than eg. Bulgaria. This east-west discrepancy thus reveal the oriental admixture in the European gene pool is predominantly a recent phenomenon that could still easily be filtered out. Instead, Nelis’team couldn’t filter out the Finnish element – probably because this element was already introduced in the Mesolithic, as already described above. Thus the filtering applied by Nelis apparently removed recent introgression successfully, making his graph a reliable representation of ancient European substructure.

The origin of modern Europeans is still a mystery. They didn’t derive unequivocally from any generalized concept of the European Mesolithic, nor from the “Ötzi-like” element of central and southern Europe, and even less from oriental types being ambiguously dubbed “Neolithic”. The late- or post-Neolithic “Beaker” migrations may have played an important role in reshuffling groups that already had a strong foothold in Europe, but so far attempts to relate eg. Corded Ware or Bell Beaker and derivative cultures to external groups were unconvincing. At least here we can find part of the solution on why post-Ötzi Europe emerged so extensively Northern-European admixed:

We applied rolloff to Spain using Ireland and Sardinians as the reference populations.
We have detected here a signal of gene flow from populations related to present-day northern Europeans into Spain around 2000 B.C. […] At this time there was a characteristic pottery termed “bellbeakers” believed to correspond to a population spread across Iberia and northern Europe. (Patterson et al., 2012)

In this article I will adhere to the current archeological insight that reconstruct a continued Mesolithic presence in some key regions that coexisted with distinguished Neolithic groups. That is, the native hunter-gatherer groups that evolved into the main cultural bearers of the Middle Neolithic don’t necessarily represent the complete legacy of earlier Mesolithic expansions. Those Mesolithic groups that had already fully adapted to the Neolithic way of life may have become bottlenecked together with the Danubian population they merged with, while the Mesolithic groups of many geographic other locations that didn’t adapt may have disappeared altogether. However, a growing body of evidence indicates the dramatic population crash that terminated the “Danubian” Early Neolithic was survived by some groups of Late Mesolithic origin that continued to thrive and ultimately entered a new (Middle-) Neolithic phase several centuries later, that in turn evolved more gradually into the pan-European Late Neolithic Beaker groups.

The existence of such hiatus is of importance for understanding the regional transition process, and implicitly also for understanding the relationship between local hunter-gatherers and the incoming Neolithic in general. (Vanmontfort, 2007)

Indeed, a deep gap separates two important Neolithic periods in Europe, but the gradual transition to a Neolithic way of life quite different from that of the Danubian settlers can best be appreciated in regions where the retreat of Danubian influence was most obvious. The Danubian collapse was a regional phenomenon from the Paris Basin in the west to Germany and Poland in the east, but can only be related with a continuation of traditional hunter-gatherer communities in a few places. This event delayed the advent of the Neolithic to the northernmost part of the North European Plain, that includes the Low Countries north of the Rhine and Scandinavia, for another millennium. Especially some western regions witnessed a Neolithic retreat, like in Belgium:

It is the westernmost region settled by Linearbandkeramik (LBK) communities and their cousins of the Groupe de Blicquy (BQY) during the late 6th and early 5th millennium calBC. With the sudden disappearance of these communities, however, the Neolithic as a whole seems to have vanished as well. The region was not occupied by Hinkelstein/Grossgartach and Roessen, the post-LBK Danubian cultures that can be found to the east and south, nor by a local Neolithic similar to the Cerny in Northern France. Only during the last centuries of the 5th millennium calBC, at the beginning of the ‘Michelsberg Culture phase’, does the Neolithic take up its thread (Vanmontfort, 2007)

However, such a Middle Neolithic “revival” happened in situ, at least on the continent, without clear migrational evidence other that the preference for new settlement locations that typically don’t relate to those of their Danubian forerunners. Migrational was the Neolithisation of Britain, that never knew a Danubian phase and directly derive from continental representatives of the Middle Neolithic. This involved several distinct strands of the earliest Neolithic activity in Britain and Ireland: one linking north-west France (probably Normandy) with southwest England during the first quarter of the fourth millennium; one Breton strand, which is found along the Atlantic/Irish Sea façade that appeared first between ~ 4200 and 3900 cal BC.; an even earlier, short-lived episode of ‘Neolithisation’ c. 4300 cal BC or earlier may have linked the west of France and south-west Ireland; and especially the Carinated Bowl (CB) tradition, that came to encompass much of Britain and much of Ireland, dated between ~3950/3900 and 3700 cal BC and also rooted in the westernmost extension of the Middle Neolithic on the continent:

Middle Neolithic ceramic traditions—i.e. the Northern Chassey, the Belgian and Northwest Michelsberg, and Michelsberg-affiliated traditions in the Scheldt Basin—offer some parallels with the CB tradition.
[…] neither the Northern Chassey nor the Northwest Michelsberg and its affiliated ‘cultures’, as currently known, offers an exact parallel for the ‘CB Neolithic’.
Despite the current absence of proof, it remains a reasonable possibility that ceramic assemblages that more closely match CB pottery (and the accompanying elements of the CB Neolithic ‘package’) remain to be found in Picardie and/or Nord-Pas de Calais.(Sheridan, 2007)

Thus it can be established that the bearers of Middle Neolithic culture were certainly flexible enough to organize migrations to new territories, but still this pattern is missing in most of Continental Europe: ‘the spatial distribution of Late Mesolithic, Early and Middle Neolithic sites, suggest a local development of the Middle Neolithic on top of a native, Mesolithic-rooted substratum’ (Vanmontfort, 2008b).
However, this model requires a mobile Mesolithic source population that remained able to move freely within territories commonly considered exclusively “Neolithic”!

Current archeological insights indeed tend to attribute much more importance to the role of the transitional “Mesolithic” populations of just before or contemporary with the Neolithic, while expanding early Neolithic settlers often hardly outgrew their Mesolithic identity themselves. Holocene migrational mobility must have been a worldwide phenomenon, as recently confirmed in genetic datasets as far away as Australia. Phenotypic similarities between Australian Aboriginal People and some tribes of India were already noted by T.H. Huxley during the voyage of the Rattlesnake (1846–1850), but were neglected until now we know 11% of the autosomal DNA of northern Australians can be related to prehistoric Indian hunter gatherers (assumed most similar to Chenchu, Kurumba reference populations and to the South Indian nontribal Dravidian speakers) that crossed the Indian ocean, while a tremendous 60% of Australian YDNA (virtually all this being Hg C4) now apparently derive from a related single admixture event of Indian ancestry. This even affected the more archaic Riverine group of SE Australia, that rather cluster with Melanesians (Bouganville) and Papua New Guineans: ‘An Australian and New Guinea link is quite clear through the mitochondrial P haplogroups, their common ancestors apparently entering Sahul from south-east Asia’ (Van Horst-Pelikaan), even though here new YDNA replacements of European origin are speeding up that already tend to obscure the past.

Assuming a generation time of 30 y, our results indicate that the gene flow from India into Australia occurred around 4,230 y ago, consistent with a previous estimate based on a small number of Y-STR (short tandem repeats on the Y-chromosome) loci.
Interestingly, at around this time, several changes take place in the archaeological record of Australia. There is a sudden change in stone tool technologies, with microliths appearing for the first time (Pugach et al., 2013)

At this time the dingo made its first appearance in the Australian fossil record, and people started to process plants differently. Certainly the apparently Veddoid immigrants from India must have brought their time capsule with them, but except for the dogs they came with empty hands and confident to find their needs “on the road”, ie. in Australia. By then the Neolithic level of civilization was not a shared commodity for all of South Asia, and possibly much of India was even far behind in the aspects of horticulture in comparison with much closer neighbours of Australia. The earliest evidence for banana (M. acuminata ssp. banksii, 22 chromosomes) cultivation derives from Kuk Swamp at 7000-6500 years ago in highland New Guinea, but hadn’t reached South Asia nor mainland East Asia yet. There exists ample evidence for maritime interactions from the early Holocene in western New Guinea and eastern Indonesia. The sago palm reached the Philippines and Indonesia from further east. Possibly taro originates from New Guinea, as well as sugar cane and Australimusa bananas (20 chromosomes). Australia, including the anthropological conservative parts further down SE, could very well have been already on the same “Neolithic” level of New Guinea at the time of the Indian immigrants:

[…] more sedentary groups in places with rich food sources such as the central and lower Murray valley […] had many of the characteristics of similar complex foraging societies. […] They also practiced what can properly be described as effective horticulture.
The diet of these people was so similar to that of New Guinea agriculturists that their tooth pathologies are virtually identical
(Barker, 2006)

The expansion happened only a few centuries before rice cultivation reached the advanced Indus Valley Civilization:

Depending on how the researchers calibrated their clock, they pinpointed the origin of rice at possibly 8,200 years ago, while japonica and indica split apart from each other about 3,900 years ago. The study’s authors pointed out that these molecular dates were consistent with archaeological studies. Archaeologists have uncovered evidence in the last decade for rice domestication in the Yangtze Valley beginning approximately 8,000 to 9,000 years ago while domestication of rice in the India’s Ganges region was around about 4,000 years ago. (May 3, 2011 in ScienceNewsline.com)

This may collaborate to the explanation why this immigration event didn’t bring Australia immediately to the contemporary level of regional civilization as we perceive this today. Even the dingo may have been more island East Asian than Indian. Instead, prehistoric Indian immigration may have been much more important for bringing new tool technologies and – the introduction of highly successive new genes.

This must be an eye-opener for those that still disregard the Mesolithic as “competitive” and “modern”. Increased evidence and new insights reveal the technological impulse, that triggered the tremendous population changes conceived to have repatterned the world, as “Mesolithic” rather than “Neolithic”. The Mesolithic refining of stone tools supplied a varied tool kit for a competitive, wide spectrum economy, with native stone products sometimes even being in high demand in the Neolithic world; Gobekli Tepe, currently dated to the PPNA/early PPNB and starting in the second half of the tenth and ninth millennia cal BC., was actually a wonder of Mesolithic architecture well before the Neolithic revolution in Anatolia: only the most recent layer consists of sediment deposited as the result of PPNB-level agricultural activity (Dietrich et al. [2012]: ‘Since neither domesticated plants nor animals are known from the site, it is clear that the people who erected this monumental sanctuary were still hunter-gatherers, but far more organised than researchers dared to think 20 years ago’); and the development of Neolithic agriculture would not have made any sense without the Holocene appearance of plant-processing technologies. Apparently, at least some great expansion events were rather linked to the technological improvements that immediately preceded or were contemporaneous to the Neolithic, eg. concerning the use of microliths – small stone tool commonly used to form the points of hunting weapons, such as spears and arrows. Still, the general narrative of incoming farmers, bearing an evolved Neolithic package, that replaced previous populations according to a simple model of migration, demographic growth and the dispersals of the world’s main language phyla, being all driven by the invention of agriculture, remains enormously influential, and continues to be vigorously defended. Concerning migrational processes, genetic investigation and population history, however, the Neolithic agricultural revolution increasingly emerges as a non-unique phenomenon that at most marks the temporary success of an expansive period:

One of the prehistoric events that has been considered as a plausible device to fuel both demographic and cultural spread is the shift from a hunter-gatherer to an agricultural mode of subsistence thought to have occurred independently in only a few places in the world […] However, the attempt at explaining the success of the ten most widely spoken language families of the world in terms of the Neolithic demic diffusion model —that is, by linking the spread of languages, genes, and economy—has been challenged in almost every single case (Chaubey et al., 2010)

The expansion of Indian hunter-gatherers to Australia, albeit already on the Mesolithic level of development, magnificently outclassed the migratory achievements of their Neolithic contemporaries. Most likely the migrational irrelevance of Neolithic settlers was a tendency that applied all over the world. In SE Asia, it is doubtful rice cultivation was part of the original ancestral subsistence package in the Austroasiatic expansion:

One claim made by Diffloth (2005) appears to us to be uncontroversial; that Austroasiatic speakers typically spread along river valleys, seeking swampy ground to cultivate taro
Generally the indications are strong that taro was the original crop and that rice was superimposed upon it. The extension of rice agriculture into new niches over time, such as the steep hillsides, would have greatly extended to potential range of those early communities. (Sidwell & Blench, 2009)

As such, it would be premature to classify the original Austroasiatic horticulture as primarily Neolithic, although the quest for humid valley bottoms suitable for taro is considered ‘one of the “engines” of the Austroasiatic expansion’ (Blench 2011). Linguistic evidence is ‘consistent with the idea that methods of farming and preparing harvested rice for consumption were relatively new to proto-Austroasiatic speakers. [Example] words could even have been coined, and diffused through the speaker community, after the linguistic break-up had begun, but while speakers were still in contact (the dialect chain stage)’ (Sidwell & Blench, 2009).
This chain spans a geographic and linguistic continuum without nesting, whose most northerly and southerly extremities ultimately became the Manda and Nicobaric branches respectively. The centre of that chain remained located on the middle Mekong. On their zenith Austroasiatic settlers may have reached pre-Austronesian Indonesia in the east, where the main Austroasiatic YDNA haplogroup O2a-M95 is still dominant on many islands; the Indus Valley to the west, just before the arrival of the Indo-Aryans; and north as far as the borders of Bronze Age China at the Yangzi river. High percentages of O2a for Hmong (Miao) and Mien (Yao) people (up to 45.16% in the Yao lowland), otherwise without doubt ancient inhabitants of the East Asian area and “intermediary” between Southeast Asians to East Asians (Cai, 2011), may be one of the many relicts of forlorn Austrasiatic presence in the north. It has been widely claimed that the name of the Yangtze itself is of Austroasiatic origin. When Austroasiatic hegemony collapsed, much of its territory was overrun by their neighbours far and wide, such as the Austronesians – predominantly YDNA Hg O1a1 (O-P203) O1a2 (O-M110) – and the Tai-Kadai people, (originally) from the northeast, and Tibeto-Burman people from the northwest.
The subsequent Austronesian expansion was culturally Neolithic whose origin is usually pinpointed in Taiwan, but according to Blench much of its tremendous cultural diversity was borrowed from the Austroasiatic speakers that reached western Borneo and Papawan before them: the Austronesian speakers assimilated them and adopted taro cultivation before they continued their expansions.

In recent years there has been a rising chorus of discontent from archaeologists who are increasingly claiming that the data does not fit the simple demographic expansion model. The claim, put simply, is that assemblages seem to be rather diverse and complex and do not correspond to a simple model of incoming Neolithic farmers replacing foragers. Rather, the patterns of material culture in prehistory seem to point to earlier and more complex inter-island interactions than the Austronesian expansion model would seem to imply. (Blench, 2011)

Instead of a simple substitution of Austro-Melanesian foragers by Austronesian newcomers (predominantly falling into YDNA haplogroup O1a, whose currency is rather poor among modern Austronesian speakers), a picture emerges of intense cultural and ethnical integration to the effect that ‘Neolithic incursions make only a minor impact on the paternal gene pool, despite the large cultural impact of the Austronesian expansion’ (Karafet et al., 2010).
Another part of the Austroasiatic speakers migrated west. Especially the Munda group penetrated deep into the racially distinct regions of India. Sidwell & Blench deny great antiquity for the Austroasiatic group, and consider Munda’s profound change the result of rapid restructuring in a bottle-neck event at the arrival of a small population of emigrants, at most 4000 years ago. Michael Witzel, a German-American philologist, asserts that Indo-Aryan of the earliest Rig Vedic period (~ 1700-1500 BC) received influences of a linguistic substratum similar to Munda, as he found – besides an utter lack of Dravidian loans in the early Rig Vedic period – ‘some three hundred words from one or more unknown languages, especially one working with prefixes. […] close to, or even identical with those of Proto-Munda’.
Though ancient Austrasiatic presence in the Indus Valley may be tentatively assumed, especially since the dates are consistent with the pre-Vedic arrival of rice cultivation in the area and the acceptance of an Austroasiatic word for rice in southern India, from where this word conquered the world, we have to be weary. Compared to the paleolithic situation, generally assumed to have been the scene of thousands of small, virtually unrelated languages, the current classification of most languages into just a few phyla is disproportionate. Only Papua New Guinea – having 850 languages, proposed to fit in 23 Papuan language families and leaving 9–13 isolates – echoes the Paleolithic situation. A fair degree of linguistic diversity was preserved in the Americas, and also the 12 extinct languages that group in five possibly unrelated clusters on a tiny island like Tasmania, may help to see the current situation in proportion. Virtually everywhere else the almost contemporaneous expansion of just a few language families in the world, inevitably at the expense of thousands of other languages between Cape town and Dublin and Tokyo, can only be taken diagnostic of sudden, unprecedented cultural change. There is no alternative than to assume at most a Holocene origin for all main current language families, what also implies we should be ready to accept the extinction of linguistic groups that only survived long enough to have left traces in the languages we know, being otherwise completely unrelated with any extant group. Still attempts abound to link barely known and unidentified languages of some old civilizations to extant language groups: Sumerian to Finnish, Elamite to Dravidian, Cretan to Semitic, Etruscan to an Altai-Ugrian mix – and now Harappan to Austrasiatic? The latter may at most apply to just the ultimate phase of the Indus Valley civilization. What matters here are Munda groups that survived in central India, as a relict of Neolithic immigration from the east whose SE Asian origins are genetically confirmed:

The presence of a significant (approximately one-quarter) southeast Asian genetic component among Indian Munda speakers is […] implying their recent dispersal from southeast Asia followed by extensive admixture with local Indian populations. The strongest signal of southeast Asian genetic ancestry among Indian Austroasiatic speakers is maintained in their Y chromosomes, with approximately two-thirds falling into haplogroup O2a. Geographic patterns of genetic diversity of this haplogroup are consistent with its origin in southeast Asia approximately 20 KYA, followed by more recent dispersal(s) to India. (Chaubey et al., 2010)

This age estimate of Hg O2a is the hypothetic upper boundary for any Austrasiatic dispersal event into India that involve the O2a lineage, with the assumption that this YDNA haplogroup already originated somewhere near the Austroasiatic homelands. ADMIXTURE analyses of Chaubey et al. at K=7 reveals the dominance of a Dai-like “Southern East Asian” genetic component for Austrasiatic speakers in general. Austroasiatics have also picked up some South Asian (or “Dravidian”) influence – what may tell us something about either admixture of nearby pre-Indo Aryan populations, or reveal a possible pre-mongolid native population closely related to neigbouring South Asian populations in the west. Remarkable is the omnipresence of this “Southern East Asian” element, as it is represented all over East Asia, with percentages getting smaller towards the north. A SE Asian expansion so far to the mongolid north is hard to accept, so I figure this feature must be due to incomplete lineage sorting, reminiscent of an eventually northern mongolid origin of most of the SE Asian genetic component. Another “mongolic” component that reached south appears more pronounced in Sino-Tibetan populations, what should be the result of a much more recent genetic association linking SE Asia to the north. This second element may be correctly represented – ie. conform the k=7 reference groups – in its purest form by north-east Asian Hezhen and Xibos people. The Xibos may be described as a Tungusic-speaking offshoot of the ancient Shiwei people, that inhabited far-eastern Mongolia, northern Inner Mongolia and northern Manchuria. The origin of the Hezhens or Nanai, sometimes also referred to as “fish-skin people”, is Manchuria. Especially the latter region is characterized by extreme seasonal contrasts, ranging from humid, almost tropical heat in the summer to windy, dry, Arctic cold in the winter. The Nanai economy was based on fishing, and agriculture entered their lands only slowly. Naturally, none of those purported mongolid migrations from the north are related to the Neolithic way of life in any way.
Some genetic peculiarities, and the absence of clear linguistic ties, may confirm this latter “Manchurian” expansion south into SE Asia to have predated the ‘Neolithic’ Austroasiatic and Austronesian expansions. For instance the EDAR 1540C allele is a major genetic determinant of hair thickness, which shows high frequencies in populations of East Asian and Native American origin but is essentially absent from European and African populations. The EDAR component reaches saturation in north-east Asia, and supply a clear distinction of Austroasiatic and Austronesian ethnicities with both South Asians (Indians), the “negrito” people of Upper Paleolithic descend in island SE Asia, and Sahul (Australia, New Guinea) where the lowest regional percentages so far measured was among the Gidra people. Though positive selection has been cited as a prime explanation for its expansion, this has not been substantiated and actually simple pre-neolithic expansion from the north may have played a more important role:

Since hair can play an important role in the protection of the head against coldness by preventing heat exhalation, the thicker hair of 1540C carriers may have been advantageous in cold climates in the north part of Asia. An alternative possibility is that functional changes on EDAR may affect another trait. For example […] it is possible that the functional change between 1540T and C also have an influence on teeth morphology (Fujimoto et al.)

The EDAR allele extend to Tibeto-Burman ethnicities, and remains significant or reminiscent in Austroasiatic ethnicities as the Khasi and Munda that ventured far more west:

Tibeto-Burman speakers of India have the highest (~61%) 1540C allele frequency in south Asia, consistent with their predominantly East Asian ancestry inferred from autosomal and uniparental loci. Meanwhile, the Khasi population is characterized by a 40% frequency of the allele (table 3). Munda speakers also show detectable presence, with a ~5% average, in contrast to its complete absence among Indo-European and Dravidian speakers […] These results are in line with the models suggesting gene flow from southeast Asia to India, albeit more significant among Khasi- than Munda-speaking populations. (Chaubey et al., 2010)

This somewhat extented excursion to Asia shows some of the current concepts about the “Neolithic advance” are incomplete or just completely wrong. The Austrasiatic expansion wasn’t triggered by some adyacent Neolithic trigger, it didn’t originate in the Near East in any way, and instead was rooted in the local Mesolithic of the Mekong river area. According to current insights, rather than being geographically on the cultural or genetic wave of advance that purportedly started in the Near Eastern cradle of Neolithic culture, the Austrasiatic expansion triggered a Neolithic wave all by itself. Both Neolithic waves apparently met rather peacefully somewhere in between, possibly near or in the Indus Valley, where after both Neolithic impulses petered out. Rather than being the source of flourishing linguistic phyla, the initial participants of both Neolithic waves failed to consolidate their early advantage and dwindled. Their brilliantly acquired agricultural niches were soon to be taken by less advanced groupings, that nevertheless seem to have derived much of their strength and abilities to their Neolithic forerunners. In India all the Neolithic “avant guarde”, whether or not originally from the west or from the east, succumbed to the belligerent Indo-Aryans that themselves most likely didn’t participate in the Neolithic advance. At most the genetic heritage of those early Neolithic participants can still be traced abundantly close to their origin, but it didn’t achieve to dominate the modern world. Those Neolithic phyla that didn’t disappear altogether only survived as small, often disparate groups.
All this indicates something else about the great changes that innovated the world at the dawn of history: these didn’t start exactly from a single Neolithic impulse somewhere in time and space, and didn’t evolve further on a single track of advance. Instead, those changes have all appearance to be rooted in generic Mesolithic – or Epi-Paleolithic – culture far and wide, whose mobility was vastly superior to what we know of their Neolithic counterparts. The Veddoid migration to Australia is only one example where Neolithic societies failed and Mesolithic societies expanded instead almost beyond imagination. Indeed, this common Mesolithic heritage may link disparate and almost contemporary Neolithic developments together, and possibly supply a much better reference for the cultural trigger that set the Neolithic developments in motion.
Above I hinted at an ultimate origin of the SE Asian impetus in Manchuria.
Recently sequenced sequenced nuclear and mitochondrial DNA that had been extracted from the leg of an ~40,000 years old “relative” from Tianyuan Cave near Beijing, China (ie. Tianyuan-1), seems to confirm the important role of already differentiated early modern humans of NE Asia since their genes revealed they shared a common origin with the ancestors of many present-day Asians and Native Americans. Firmly classified within haplogroup B, one of the main defining mitochondrial DNA mutations is T16189C. This is an otherwise recurrent polymorphism of the mtDNA phylogenetic tree and possibly subject to negative selection, since it was found associated with higher incidence of coronary artery disease type 2 diabetes mellitus. Strikingly, this polymorphism and adyacent basepairs (atcaacccccccCccccatg) fully correspond with – guess what! – the Neanderthal outgroup: another argument to revise the whole classification system for mtDNA and its undue dependence on apert misconceptions that depart from allele-dependent mutation rates. More than ever, ‘the presence of several archaic features, lost or rare in the [Middle Pleistocene Modern Human] sample, implies that a simple spread of modern human morphology eastward from Africa is unlikely’ (Shang et al,. 2007). The “modernity” of Tianyuan-1 may be thus be less “African” than now – on genetic grounds – may be assumed “by default”. Instead I conceive an important, recurrent expansion node that eventually even contributed to the Mesolithic seeds that were essential to the contemporaneous development of Neolithic culture all over the world. An expansion node “slightly” different, by the way, from the ancestral population discovered by Patterson et al. (2012) that contributed closely related genes find in Amerindians (having the Brazilian Karitiana as a reference population) and Northern Europeans; and most probably also “slightly closer” to a more recent “mongoloid” influx of the Arctic and the Americas that caused current NE Asiatic populations (having the Beringian Chukcha as a reference population) to diverge sightly:

One possible explanation for these findings is that the ancestral Karitiana were closer genetically to the northern Eurasian population that contributed genes to northern Europeans than are the Chukchi. (Patterson et al., 2012)

In my blog “The European Mesolithisation of a Caucasian Neolithic, or the Origin of the Indo European Language family” I hinted at a central Asiatic (?) “Dene-Caucasian” origin of the Anatolian Neolitic wave of advance that reached as far as the Danubian Neolithic in the west and the Indus Valley in the east, being possibly also at the root of contemporary developments in China and the Americas. There may be a third line of cultural events that originated in the northern arctic, whose ring-built pottery techniques may have travelled for thousands of years and thousands of kilometers from east to west before they established a Ceramic Mesolithic right in the backyard of the Danubian Neolithic. These people originated in the Maglemose and Tardenoisien that descended of the early Mesolithic Seuveterrien culture, that had already disinguish itself from the Paleolithic Magdalenien by using microliths in their toolbox. By now they were preparing for the Middle Neolithic transition that was due to supersede the Danubian Neolithic. Their Mesolithic expansionism was essential for the profound genetic changes that made modern Europe so different from how it was before.
Until it reached the wetlands of northern Europe, the Neolithic advance in Europe was pretty straightforward once it had entered the Balkan. Before the Danubian acculturation Neolithic expansion was pretty slow and often accompanied by an increased gene flow into bordering Mesolithic populations once the people involved were eager to enter the Neolithic way of life. Also the Danubian Neolithic essentially started as a Mesolithic development of local populations, albeit not entirely autochthonous. Pottery techniques and apparently much of their YDNA male lineages carrying the Hg G2a marker derived from more southern Neolithic entities:

Due to the latest research, the LBK formation in Transdanubia must have involved an essentially Mesolithic subsistence, complemented by certain elements of the Neolithic package brought here by migrant late Starcevo groups. Many small sites were located in marshy areas, unsuitable for food production as a basis of livelihood. The currently available evidence suggests that there was a 4–5 generations long period, when it was not self-evident that the sedentary way of life would be fully accepted and adopted. (Oross & Bánffy, 2009)

In this period the Danubians also switched to timber-framed houses, while up to then the Mesolithic people in the region predominantly used tents – although timber was already for permanent dwellings dated 5,800 BCE at Lunt Meadows, Sefton (Merseyside, England). The formative phase for the Danubian Neolithic spanned a roughly 150–200 year period between 5600/5500 and 5400/5350 calBC. This was probably long enough for profound changes that may have affected language and genetic composition, but most importantly – the transition set the Danubian people apart from their Mesolithic neighbours, whether or not they originally spoke related languages. At the end the LBK phenomenon emerged as a homogenous people, superseding their southern inspirators and able to expand quick as lightning, searching for arable lands that they invariably sought in the fertile loess grounds somewhat inland from the coastal areas of continental Northern Europe. Their main expansion happened during the Earlier LBK (5450–5300/5250 calBC).

The [Earlier] period’s Transdanubian sites are rather uniform, with no trace of the south-north division characterizing the formative phase, when the terminal Starcevo sites in southern Transdanubia were still occupied. It should at this point be recalled that the LBK spread over large areas of Central Europe exactly during this period, and that its settlements in southern and central Germany […] became firmly established at this time. (Oross & Bánffy, 2009)

Despite their still fresh Mesolithic roots, there is ample evidence the LBK people and native populations in the neighbourhood kept apart, probably being two quite different ethnicities. Vanmontfort (2007) proposed a working hypothesis on native populations that – induced by the leapfrogging arrival of early Neolithic settlers from the Danube region – evolved their way of life gradually into a Middle Neolithic that was quite different from the Danubian. In this view, the Danubian settlers were never dominant but rather “tolerated” when they settled in areas only marginally exploited by hunter-gatherers. On the western limits of their expanse, some Earlier LBK settlements got intertwined with an apparently native La Hoguette pottery tradition. This did not happen in the Hainault region, but in the Limburg area the makers of this pottery were apparently integrated in LBK culture, to the result that purportedly derived Limburg pottery became part of the local (phase II) LBK culture – also in Hainaut. Remarkable is its total absence in the Mesolithic sites of the Hesbaye sector and the Dutch Limburg, nor in the Mesolithic Tardenois and Somme sites. Some of the LBK arrowheads show ‘precise analogies with certain late/final Mesolithic arrowheads (asymmetrical trapezes and triangles with flat inverse retouch and the microburin technique)’. In the process of expansion into the Paris Basin, LBK even accepted two chronologically different types of assymmetrical arrowhead lateralisation from their Mesolithic neighbours, that globally follows the other chrono-spatial division of LBK association with La Hoguette (~left-lateralisation) and Limburg pottery styles(~right-lateralisation). In the Mesolithic Somme region (where we have more ‘native’ information) asymmetrical trapezoidal arrowheads appeared at 6500 cal BC, and probably this type was also common more to the east when LBK could accept this feature already in the Moselle and Alsace regions at an early stage. The subsequent change in the Somme region to right lateralization was probably a more general phenomenon of the Mesolithic in the west, that was first accepted by the LBK in Belgium. Like Limburg pottery, the arrowhead techniques became fixed in the LBK before expanding further into the territory of Mesolithic populations in the northern Paris Basin, to the result that divergent patterns began to occur:

it is significant that the Rubané arrowheads of the northern Paris Basin present technical differences from those of the local Mesolithic. They are in fact much more similar to the arrowheads of the Belgian Rubané. Likewise, oblique truncations disappeared and the symmetrical points of the Rubané of Champagne are totally unknown in the local Mesolithic. Thus one has to accept the idea that the Danubian asymmetrical arrowheads were already an integral element of the lithic industry of the western LBK, which developed in the Rhine-Meuse region during a phase earlier than that of the Paris Basin Rubané. (Allard, 2007)

Interesting is the Mesolithic tradition in the use of Wommersom quartzite and Phtanite, that was another element accepted in LBK culture.

An LBK pit at Maastricht-Klinkers contained several pieces of Wommersom quartzite. This raw material was frequently used by late Mesolithic hunter-gatherer groups (Caspar 1984), but not by the LBK farmers. (Amkreutz et al., 2008)

Only rarely attested in LBK contexts, it ‘remains questionable if they are actually part of the LBK stone tool production’ – suggesting the exploitation and especially, the continuation of Wommersom use after the retreat of LBK in the region is diagnostic for the irrefutable presence of a Mesolithic population within what is commonly assumed LBK territory. Indeed, one hypothesis asserts the near archeological invisibility of native populations ‘due to their undiagnostic toolkit or taphonomical reasons’ (Vanmontfort, 2007). At first contact the newly arriving LBK population, or family groups, appreciated some of the native know-how and methods, and this is where we receive a clear snapshot of the Mesolithic presence through LBK. There is evidence the native hunter-gatherers remained in the area in a mutual conflict-avoiding situation. Ever since, the development paths of both ethnicities diverged again and apparently they even became increasingly indifferent towards each other:

Despite the indications of contemporaneity and interaction, the data confirm the difference between hunter-gatherers and LBK. There is no data supporting the idea of symbiosis.

Only last year the Venus of Geldrop was recognized as a true example of Dutch stone age art, dated over 10,000 years old.

Only last year the Venus of Geldrop was recognized as a true example of Dutch stone age art, dated over 10,000 years old.

Eventually, the collapse of the Danubian Neolithic left an archeological wasteland between the Mesolithic Swifterbant culture in the northwestern wetlands, that expanded to the Lower Scheldt and ‘perhaps even more to the south’, and the Neolithic hinterland to where Neolithic culture bided more time – until in a next stage also the Danubian derived BQY/VSG communities suddenly disappear, leaving a chronological hiatus of Neolithic exploitation between 4850-4300 cal.BC.. In the coversand regions and the southern loess ‘a Mesolithic presence is mainly attested by small surface scatters or isolated microliths’. However, despite their continued presence, ‘it remains difficult to link the evolution with the Mesolithic-Neolithic transition.’
During this hiatus there was no notable expansion, probably because the Mesolithic people that co-inhabited the region already dominated long before. From here on the NW European archeological cultures developed polycentrically, most globally represented by the Rhineland Michelsberg Culture and northern French traditions in Chasseén Septentrional, where the Scheldt basin occupied an intermediate position “in between”. The subsequently emerging second Neolithic phase is ‘clearly different from the first “Danubian” one in almost all its archeological aspects […] The lack of large dwelling structures with deeply planted posts signals a more mobile settlement.’
The ensuing population of NW Europe was neither Danubian nor “Mesolithic” anymore in the pre-Neolithic sense. Instead, much of Europe entered a Middle Neolithic were native groups inherited strongly from a subset of an older Mesolithic that was different from earlier Mesolithic expansion groups. Michelsberg and TRB draw from the same Mesolithic source, and the influence of this or similar cultural groups was soon to expand over much of Western, Northern and even Eastern Europe. Maritime expansion to the Mediterranean and mainland expansion further east still had to wait to the Beaker cultures, that emerged not so very much later in a process of consolidation and accelerated development and commerce. Only once those people entered the full light of history we know their identity, and actually there is no doubt even the current populations are still essentially the same as those that once allowed the Danubian Neolithic to enter their lands – only to be dispatched again later. For understandable historic reasons this is still a blind spot for an elder generation that engaged in teaching the catechism of the archeological bible. It grows harder every day to conform a rapidly growing body of evidence to obsolete views, and there is a growing dearth of parsimonious models to explain what we see. The genetic changes that made modern Europeans the way they are now are still there, and all indicates these are due to Mesolithic events in northwestern Europe.


  • Balter – Ancient Hunter-Gatherers Kept in Touch, Science 2012, link
  • Barker – The Agricultural Revolution in Prehistory: Why Did Foragers Become Farmers? 2006, link
  • Behar et al . – The genome-wide structure of the Jewish people, 2010, link
  • Blench – Stratification in the peopling of China: how far does the linguistic evidence match genetics and archaeology? 2004, link
  • Blench – Was there an Austroasiatic Presence in Island Southeast Asia prior to the Austronesian Expansion? 2011, link
  • Blench – Archaeology and Language II: Correlating archaeological and linguistic hypotheses, 1998, link
  • Bowern – The riddle of Tasmanian languages, 2012, link
  • Cai et al. – Human Migration through Bottlenecks from Southeast Asia into East Asia during Last Glacial Maximum Revealed by Y Chromosomes, 2011, link
  • Chaubey et al. – Population Genetic Structure in Indian Austroasiatic Speakers, 2010, link
  • Denham et al. – Pre-Austronesian dispersal of banana cultivars West from New Guinea: linguistic relics from Eastern Indonesia, 2009, link
  • Der Sarkissian – Mitochondrial DNA in ancient human populations of Europe, 2011, link
  • Di Gaetano et al. – An Overview of the Genetic Structure within the Italian Population from Genome-Wide Data, 2012, link
  • Dienekes – Ancient European DNA assessment with ‘globe4’, October 21, 2012, link
  • Dietrich et al. – The role of cult and feasting in the emergence of Neolithic communities. New evidence from Göbekli Tepe, south-eastern Turkey, 2012, link
  • Donohue et al. – Banana (Musa spp.) Domestication in the Asia-Pacific Region: Linguistic and archaeobotanical perspectives, 2009, link or try here
  • Fujimoto et al. – A scan for genetic determinants of human hair morphology: EDAR is associated with Asian hair thickness, 2008, link
  • Hudjashov et al. – Revealing the prehistoric settlement of Australia by Y chromosome and mtDNA analysis, 2007, link
  • Jay et al. – Anisotropic isolation by distance: the main orientations of human genetic differentiation, 2012, link
  • Karafet et al. – Major East-West Division Underlies Y Chromosome Stratification Across Indonesia, 2010, link
  • Kennedy – Stone age nomads settled down in Merseyside, flints and timber suggest, in: The Guardian, Monday 19 November 2012, link
  • Loh et al. – Inference of Admixture Parameters in Human Populations Using Weighted Linkage Disequilibrium, 2012, link
  • Mueller – The Mitochondrial T16189C Polymorphism Is Associated with Coronary Artery Disease in Middle European Populations, 2010, link
  • Nelis et al. – Genetic Structure of Europeans: A View from the North–East, 2009, link
  • New York University – Rice’s Origins Point to China, Genome Researchers Conclude, Published: May 3, 2011 in ScienceNewsline.com, link
  • Oross & Bánffy – Three successive waves of Neolithisation. LBK development in Transdanubia, 2009, link
  • Ottoni et al. – Pig domestication and human-mediated dispersal in western Eurasia revealed through ancient DNA and geometric morphometrics, 2012, link
  • Pala et al. – Mitochondrial Haplogroup U5b3: A Distant Echo of the Epipaleolithic in Italy and the Legacy of the Early Sardinians, 2009, link
  • Patterson et al. – Ancient Admixture in Human History, 2012, link or try here
  • Pugach – Genome-wide data substantiate Holocene gene flow from India to Australia, 2013, link
  • Qiaomei Fu et al. – DNA analysis of an early modern human from Tianyuan Cave, China, 2013, link
  • Redd et al. – Gene Flow from the Indian Subcontinent to Australia: Evidence from the Y Chromosome, 2002, link
  • Rosenberg et al. – Genetic Structure of Human Populations, 2002, link
  • Shang – An early modern human from Tianyuan Cave, Zhoukoudian, China, 2007, link
  • Sharrock – Diversity in the genus Musa, Focus on Australimusa, 2001, link
  • Sheridan – From Picardie to Pickering and Pencraig Hill? New information on the ‘Carinated Bowl Neolithic’ in northern Britain, 2007, link
  • Sánchez-Quinto et al. – Genomic Affinities of Two 7,000-Year-Old Iberian Hunter-Gatherers, 2012, link
  • Sidwell & Blench – The Austroasiatic Urheimat: the Southeastern Riverine Hypothesis, 2009, link
  • Simmons – Ais Giorkis: An unusual early Neolithic settlement in Cyprus, 2012a, link
  • Simmons – Mediterranean Island Voyages, 2012b, link
  • Skoglund et al. – Origins and Genetic Legacy of Neolithic Farmers and Hunter-Gatherers in Europe, 2012, link
  • Vanmontfort – The Mesolithic-Neolithic transition in a frontier zone, 2007, link
  • Vanmontfort – Forager–farmer connections in an ‘unoccupied’ land: First contact on the western edge of LBK territory, 2008, link
  • Vanmontfort – A southern view on north-south interaction during the Mesolithic-Neolithic transition in the Lower Rhine Area – Between Foraging and Farming chapter 8, edited by Fokkens, 2008, link
  • Van Holst Pellekaan – Genetic evidence for the colonization of Australia, 2013, link
  • Vigne et al. – Pre-Neolithic wild boar management and introduction to Cyprus more than 11,400 years ago, 2009, link
  • Witzel, Early Sources for South Asian Substrate Languages, 2007, link
  • Yong – Genomes link aboriginal Australians to Indians, Mingling of genes four millennia ago suggests continent was not isolated after all, Science 14 january 2013, link

Expanding Hybrids And The Rise Of Our Genetic Common Denominator

September 29, 2012 10 comments

With the attestation of Neanderthal and Denisova DNA in the human genome, and strong indications for the genetic contribution of also other archaic hominines previously considered ‘extinct without issue’, the simple model of prefabricated, homogenous modern humans that moved ‘out-of-Africa’ to replace the human evolutionary residue all over the world in a single blow, failed dramatically. Now, the scientific community is literally forced to pay attention to decades of accumulated counter-evidence and criticism.

Average Joe replacing Average Joe: A new genetic common denominator rises up from the earth, combining the best of all available biological elements to adapt to a new way of life. Average Joe is a Hybrid!

One issue concerns the implied range expansions of a single ‘bottlenecked’, homogenous population that extended its African habitat to entirely new environments and climates. This should have been attested by selective sweeps in the genome – but it doesn’t.

While most people assumed that the out-of-Africa expansion had been characterized by a series of adaptations to new environments leading to recurrent selective sweeps, our genome actually contains little trace of recent complete sweeps and the genetic differentiation of human population has been very progressive over time, probably without major adaptive episodes.
[…] if some introgressed genes were really advantageous, they should have spread and fixed in the human population, but […] there is no widespread signature of strong selective sweeps in Eurasia. (Alves et al., 2012)

Selective sweep can be recognized by a large reduction of genetic variation near a favorable gene on the chromosome, caused by a quick expansion within a population of the gene by natural selection. Only a few complete sweeps and near-complete sweeps could be found, ‘suggesting that there was relatively little directional adaptive evolution associated with the “origin of modern humans.” Measuring by genetic change, agriculture was many times more important than the appearance of modern humans throughout the world’ (Hawks, 2012-07-20). Does this imply that genetic change of modern humans was predominantly not the result of sudden adaptive mutations? Possibly humans acquired their genetic adaptations to their respective extant environments in a different way:

[…] there are precious few genetic changes shared by all (or even most) humans today, that are not also shared with Neandertals, Denisovans, or plausible other archaic human groups (such as archaic Africans).
That of course follows from the fact that a fraction of today’s gene pool actually comes from those ancient groups. Their variation is (by and large) human variation. (Hawks, 2012-07-20)

Apparently, there was a host of archaic hominines out there, previously considered the evolutionary ‘dead ends’ from all over the world, whose traces can still be perceived as superimposed variability in the modern human genome. That is, up to now investigation on archaic admixture is mainly focused on the differences between modern populations, that increasingly emerge as the relicts of intense ‘archaic’ hybridization processes. ‘Neandertals and Denisovans fall within the variation observed for human nuclear sequences. Thus, only few fixed differences can be identified’ (Meyer et al., 2012). This way, out of 3.2 billion sequenced Neanderthal base pairs only about 600 Mb could be unambiguously attributed to Neanderthal introgression, what is low in comparison with Meyer’s estimation that 6.0% of the genomes of present-day Papuans derive from Denisovans. But, archaic hominines also shared a considerable genetic common denominator with modern humans, whose possible incorporation remains poorly analyzed. A variable portion of archaic DNA actually being shared with modern humans could affect the observed magnitude of introgression, but earlier assertions that Denisovans were indeed more divergent were never confirmed. Without clear traces of selective sweep, the true origin of ambiguously shared and distinctly archaic portions of the genome are impossible to tell apart. Reported examples of selective sweep remain rare:

We also identify over 100 Neandertal-derived alleles that are likely to have been the target of selection since introgression. One of these has a frequency of about 85% in Europe and overlaps CLOCK, a key gene in Circadian function in mammals. This gene has been found in other selection scans in Eurasian populations, but has never before been linked to Neandertal gene flow. (Sankararaman et al., 2012)

The circadian function refers to a chrono-biological adjustment to an external rhythm like daylight, what logically implies a genetic adaptation to the northern Neanderthal habitat with an exclusive advantage for northern populations. Such an introgressed innovation that apparently behaves like a new favorable mutation remains an exception, since hybrid incorporation and repatterning of whole chunks of introgressed DNA doesn’t require selective sweep.

These days many investigators try to reconstruct the past demography in their own way, though often the effort remains haunted by some remarkably conservative out-of-Africa assumptions. A wealth of newly published information on the subject is currently waiting for a proper interpretation to close the gap between our modern genome and the sequenced data retrieved from some of our ancestors. Conflicting perspectives often result in contradictory assertions that may be counter-intuitive and in need of reconciliation one with the other. The following investigation belongs to this category:

Science DOI: 10.1126/science.1224344

Meyer et al. – A High-Coverage Genome Sequence from an Archaic Denisovan Individual, 2012, link


We present a DNA library preparation method that has allowed us to reconstruct a high-coverage (30X) genome sequence of a Denisovan, an extinct relative of Neandertals. The quality of this genome allows a direct estimation of Denisovan heterozygosity, indicating that genetic diversity in these archaic hominines was extremely low. It also allows tentative dating of the specimen on the basis of “missing evolution” in its genome, detailed measurements of Denisovan and Neandertal admixture into present-day human populations, and the generation of a near-complete catalog of genetic changes that swept to high frequency in modern humans since their divergence from Denisovans.

This study has several interesting results worth mentioning: an extremely low genetic diversity of Denisova humans that can’t be observed in any modern population; the observation that Europeans have 24% less Neanderthal admixtures (“not being shared by Africans”) than Asians; and apparent indications of some hybridization event in the past, still noticeable in the chromosomes of all modern Denisovan descendents.

Low genetic diversity of Denisovans puts the asserted homogeneity of the modern human species in a new perspective. Despite all earlier speculation on an African bottleneck, designed to explain modern genetic homogeneity from a phylogenetic perspective, current genetic variability is now found to exceed the attested variability of ancient Denisovans for all modern ‘phyles’, or ethnicities:

Several methods indicate that the Denisovan hetero-zygosity is about 0.022%. This is ~20% of the heterozygosity seen in the Africans, ~26–33% of that in the Eurasians, and 36% of that in the Karitiana, a South American population with extremely low heterozygosity. Since we find no evidence for unusually long stretches of homozygosity in the Denisovan genome, this is not due to inbreeding among the immediate ancestors of the Denisovan individual. We thus conclude that genetic diversity of the population to which the Denisovan individual belonged was very low compared to present-day humans. (Meyer et al., 2012)

Nevertheless, Denisovans lack any relevant African affiliation. Their ‘phyle’ should have been separated long enough from the other branches of human evolution to have reached a genetic diversity comparable to Africans. Apparently, since this didn’t happen, genetic variability doesn’t simply translate to the age of an otherwise isolated population. Investigators may now dedicate their diligence to duplicate their calculations for a purported recent African bottleneck, and design a corresponding recent Denisovan bottleneck. Or they could just admit the geographic maxima of modern variability in Africa may rather represent archaic admixture than the age of a single human phyle.
Unfortunately, the Meyer study doesn’t mention the Neanderthal-like admixtures of Africans, except by saying that the ‘genetic contribution from Neandertal to the present-day human gene pool is present in all populations outside Africa’. It is important to keep this voluntary restriction in mind in reading their most remarkable assertion: ‘We estimate that the proportion of Neandertal ancestry in Europe is 24% lower than in eastern Asia and South America’ (Meyer et al., 2012).
This runs contrary to more detailed genetic analyses that previously revealed slightly higher levels of Neanderthal admixture in Europe. John Hawks counted derived SNP alleles of the 1000 Genomes Project being shared with the (Neanderthal) Vindija Vi33.16 genome, and found the surpluses in Europe and East Asia where rather comparable:

The Europeans average a bit more Neandertal than Asians. The within-population differences between individuals are large, and constitute noise as far as our comparisons between populations are concerned. At present, we can take as a hypothesis that Europeans have more Neandertal ancestry than Asians. If this is true, we can further guess that Europeans may have mixed with Neandertals as they moved into Europe, constituting a second process of population mixture beyond that shared by European and Asian ancestors. (Hawks, 2012-02-08 )

Unfortunately, the attested agreement between non-African and Neandertal genomes, and between Melanesian and Denisova genomes for that matter, didn’t result yet in the full identification of all specific genetic loci involved. Basically, the observed agreement was initially based on the differences between Africans and non-Africans in comparison with the archaic genome being investigated. Hence, the overall picture of archaic ‘differences’ may be distorted by shared components within the African reference group, that Meyer’s team didn’t include in their investigation and that Hawks didn’t quantify for his modern genomes that share derived SNP alleles with the (Neanderthal) Vindija Vi33.16 genome. In other words, this Neanderthal ancestry in Europe allegedly being 24% lower than Asia (according to Meyer et al.) is essentially meaningless without additional information that quantifies sharing:

My initial reaction to this difference is that it reflects the sharing of Neandertal genes in Africa. Meyer and colleagues filtered out alleles found in Africa, as a way of decreasing the effect of incomplete lineage sorting compared to introgression in their comparison. But if Africans have some gene flow from Neandertals, eliminating alleles found in Africans will create a bias in the comparison. If (as we think) some African populations have Neandertal gene flow, that probably came from West Asia or southern Europe. So as long as the present European and Asian (and Native American) samples have undergone a history of genetic drift, or if (as mentioned in the quote) they mixed with slightly different Neandertal populations, this bias will tend to make Asians look more Neandertal and Europeans less so.
Anyway, this demands further investigation. (Hawks, 2012-08-30)

Apparently, the legacy of the Out-of-Africa dogma caused Meyer et al. to take the African part for granted and just to look at the non-African part. We are lucky to have some additional information already at hand to more or less visualize how the Meyer et al. results could still be in tune with earlier results, that rather emphasized a closer match of Neanderthal admixtures with Europeans. The Austrian study of Hochreiter et al. (2012) actively incorporates the internationally shared Neanderthal and Denisova alleles in their calculations to measure the probability of uneven distribution (Fisher’s exact test) and to obtain the corresponding odds ratios, that give a symmetrical representation of the relative genetic enrichment for each type of admixture. From here on, all depends on how we perceive the human genome and what part of it we are willing to recognize as true Neanderthal or Denisova admixture, or something else.
Hochreiter’s study retrieved data from the Korean Personal Genome Project (KPGP) combined with those from the 1000-Genomes-Project:

Genotyping […] 1,131 individuals and 3.1 million single nucleotide variants (SNVs) on chromosome 1 […] identified 113,963 different rare haplotype clusters marked by tagSNVs that have a minor allele frequency of 5% or less. The rare haplotype clusters comprise 680,904 SNVs; that is 36.1% of the rare variants and 21.5% of all variants. The vast majority of 107,473 haplotype clusters contains Africans, while only 9,554 and 6,933 contain Europeans and Asians, respectively. (Hochreiter et al., 2012)

According to this data, only 6,490 (113,963 minus 107,473) of the rare haplotype clusters on chromosome 1 were exclusively non-African. The vast majority of all rare haplotypes, however, are shared with Africans one way or the other:

We characterized haplotypes by matching with archaic genomes. Haplotypes that match the Denisova or the Neandertal genome are significantly more often observed in Asians and Europeans. Interestingly, haplotypes matching the Denisova or the Neandertal genome are also found, in some cases exclusively, in Africans. Our findings indicate that the majority of rare haplotypes from chromosome 1 are ancient and are from times before humans migrated out of Africa. (Hochreiter et al., 2012)

The 9,554 and 6,933 European and Asian haplotypes thus per definition include a considerable overlap with extant African rare haplotypes. Moreover, the size of such an African overlap is proportional with the total count of shared Eurasian haplotypes. Mathematically it could be deduced that at the very least, 3,064 (ie. 9,554 minus 6,490) out of 9,554 ‘European’ haplotypes, and 443 out of 6,933 ‘Asian’ haplotypes should be also African. The maximum count of African rare haplotypes, however, that made it ‘Out-of Africa’ and are currently shared with non-Africans, remained well below 10%. Since over 90% of the African rare haplotypes are thus not shared with Neanderthals and Denisovans, in an Out-of-Africa scenario this would mean that a similar proportion of the European and Asian rare haplotypes could be expected to be non-Neanderthal and non-Denisova. Could we really rely on the ancestral origin of so many shared haplotypes? Just being shared African doesn’t make these haplotypes ancestral all of a sudden, and less without a proper quantification.
Let’s first try to quantify the potential Neanderthal admixtures a bit. Hu’s analyses of archaic segments should give an adequate peek inside the various admixtures for an educated guess:

Archaic hominin admixture with modern non-Africans was detected by genome wide analysis of Neanderthal and Denisovan individuals.
To gain better understanding in demographic and evolutionary significance of archaic hominin admixture, […] we identified 410,683 archaic segments in 909 non-African individuals with averaged segment length 83,460bp. In the genealogy of each archaic segment with Neanderthal, Denisovan, African and chimpanzee segments, 77~81% archaic segment coalesced first with Neanderthal, 4~8% coalesced first with Denisovan, and 14% coalesced first with neither (Hu et al., 2012)

Considering the above, apparently very few (or none?) of all the non-archaic haplotypes that made it out of Africa became rare. Such results, naturally, would imply one enormous problem about the construct Homo Sapiens Sapiens (HSS). Instead, the lack of rare haplotypes outside Africa that could be safely assigned unambiguously to what is generally considered the constituent forerunner of modern humans, indeed echoes much earlier claims of ancestral homogeneity. As already referred to above, population geneticist are very much acquainted with the concept of an early HSS bottleneck, since this was once designed to explain away all evidence of this kind. Hence, I appreciate the reasons why Hochreiter et al. prefer to consider the rare Denisova- and Neanderthal-like rare haplotypes in Africa ‘ancestral’, even those being exclusively African, but this preposition logically implies the existence of allegedly HSS ancestral haplotypes in Eurasia that are neither rare nor absent in Neanderthal and Denisova. Combined with the ever more unpopperian association of frequent haplotypes with HSS per definition, it has now all appearance Homo Sapiens Sapiens is nothing but the current genetic common denominator in disguise.
As for now, apparently the Neanderthal admixtures indeed account for the greater part of the Eurasian archaic components. The discovery of the Denisova component was just mere luck, and the odds are high that more archaic hominines contributed to the Eurasian admixtures. For all we know, on the eve of the transition to modern humans Europe was only inhabited by Neanderthal. However, the likelihood of additional archaic admixture in South East Asia are being widely discussed. Moreover, Hu’s results almost exclude the possibility that substantial African archaic admixtures, at least those not yet being fully incorporated in the ‘bottlenecked’ HSS population, expanded out of Africa. Altogether, it wouldn’t be farfetched to consider most of the 14% Eurasian remainder to be essentially archaic Asian. Actually, Hu’s 14% Eurasian admixtures currently unaccounted for could easily correspond to the genetic contribution of up to four Asian archaic hominines like Denisovan’s – wherever those may have existed in isolation from Denisovan-like populations that – as for now – potentially inhabited the large geographic stretch between their attested remains in the Altai mountains and their attested genetic contributions in Melanesia. Mendez et al. (2012) suggested ‘that the archaic ancestor contributing the deep lineage to Melanesians and the specimen from Denisova were members of genetically differentiated populations’, what indeed should make us wonder about the Asian location, or nature, of such unsampled hominine groups we are still missing from the record of potential archaic admixtures. Even locally admixted homo erectus have already been proposed.
Now, Hu’s fixed non-Neanderthal-non-Denisovan remainder and the ambiguous 4% apparently shared component between both sampled hominines, suggest ~40-50% ancestral overlap between Neanderthals and Denisovans for the admixtures attributed to Denisovans, against only ~4-5% ancestral overlap for Neanderthal-like admixtures. The unambiguous Denisovan component left may be considered fully Asian in origin, even though Meyer et al report an opposite effect on the current availability of Denisovan alleles all over the world:

Interestingly, we find that Denisovans share more alleles with the three populations from eastern Asia and South America (Dai, Han, and Karitiana) than with the two European populations (French and Sardinian) (Z = 5.3). However, this does not appear to be due to Denisovan gene flow into the ancestors of present-day Asians, since the excess archaic material is more closely related to Neandertals than to Denisovans (Meyer et al., 2012)

Indeed, the contribution from Denisovans is found ‘almost’ exclusively in island Southeast Asia and Oceania. Hence, Meyer’s assumption this effect is directly related to a higher proportion of archaic Neanderthal alleles in Asia justifies a ‘worse case’ scenario, where the ‘true’ Asian share could probably increase to 18-19%, against up to 81% rare archaic haplotypes that could now be tentatively attributed to essentially Eurasian Neanderthal admixtures. For now we are only interested in the counts of Neanderthal-like admixtures, so we could propose a conversion of Hochreiter’s rare haplotype counts results, that reduces the non-African count of rare haplotypes to ~5,224 Neanderthal non-African haplotypes, and that reduces the ‘non-exclusive Asian’ haplotypes to ~5,581 Neanderthal non-exclusive Asian haplotypes, while the same maximum of Hochreiter’s 9,554 haplotypes could still be assumed to be both ‘Neanderthal’ and ‘non-exclusive European’.
For sure, such an increased proportion for Neanderthal-like admixtures in Europe doesn’t make Meyer’s results more intuitive. All the contrary, Meyer’s 24% lower European contribution should make us wonder where the differences went to. Apparently, a changed proportion of non-African Neanderthal-like admixtures in Europe compared to Asia needs proportional compensation elsewhere. Unfortunately, this effect has not been illustrated in any of the studies that aim to quantify Neanderthal admixtures one way or the other.

Different scenarios based on Hochreiter’s rare haplotypes, Hu’s proportions of archaic contribution, and the following viable assumptions: Zero Eurasian and Afro-Asian components for scenario #1; Zero Eurasian and Afro-Eurasian components for scenario #2; Zero European and Afro-Eurasian components for scenario #7. The Meyer-scenarios assume a 24% lower non-African European component than Asian, while #1 and #2 were also calculated for equal shares. Lower Neanderthal-like proportions for Europe in comparison with Asian apparently imply a higher count for shared Afro-European haplotypes. The invariable high Afro-European component and less relevant Eurasian, Afro-Asian and Afro-European components are in support of an underpinning Eurasian substructure for the Neanderthal admixed population; and a massive expansion of already admixed European populations into Africa.

For a better comprehension I elaborated several possible solutions, combining the information of Hochreiter, Meyer and Hu. Hochreiter supplied values for three linear equations that involve six variables, representing the rare haplotype counts characterized as ‘exclusive European’, ‘exclusive Asian’, ‘Eurasian’, ‘Afro-Asian’, ‘Afro-European’ and ‘Afro-Eurasian’ . Meyer’s published proportion between European and Asian haplotypes introduces a fourth equation, that for comparison could be alternated with a more intuitive scenario that has non-African European and Asian rare haplotypes evenly distributed. However, a set of linear equations may only be solved (but not necessarily) if the number of equations is the same as the number of variables. Thus two variables remain undefined, what means that an array of solutions is still possible. I worked out a number of different scenarios, each based on two additional assumptions that are necessary to solve the equations. Thus, for scenario #1 I choose zero values for the Eurasian and Afro-Asian components; for scenario #2 I choose zero values for the Eurasian and Afro-Eurasian components; for scenario #3 I kept the Eurasian and Afro-European components on zero; for scenario #4 the same for the Afro-Asian and Afro-Eurasian components; for scenario #5 the Afro-European and Afro-Eurasian components were kept zero; for scenario #6 the same for the Afro-European and Afro-Asian components; and for scenario #7 zero values were assumed for the Afro-Eurasian and European component, the latter being valid only for the Meyer variant of the equations.
Scenarios #3-5 can’t be solved for natural values and scenario #6 is ambiguous. The remaining scenarios #1, #2 and #7 all show the predominance of shared Afro-European rare haplotypes, while Afro-Asian, Eurasian and Afro-Eurasian components are lower and not always required for a valid result. The effect of Meyer’s result can be illustrated for scenarios #1 and #2, where lower Neanderthal-like proportions for Europe in comparison with Asian apparently imply a higher count for shared Afro-European haplotypes and lower counts for Afro-Asian and Afro-Eurasian haplotypes.
These scenarios reveal the Afro-Asian component as fairly irrelevant, and the Afro-Eurasian component emerges as moderately weak. Only the Afro-European component remains definitely prominent in all scenarios. Remarkably, simulations that increase the Eurasian shared component are directly proportional to increases of the Afro-European component, while both are inversely proportional to the Afro-Eurasian component. This behavior supports the hypotheses that the Afro-Eurasian shared component is only moderately present; that at least the Asian Neanderthal admixtures don’t share any African origin or association in particular; and that Neanderthal haplotypes rather seem to have expanded proportionally into Africa and Asia alike from a European center. Especially the increased Afro-European component is remarkable, since an ancestral origin results problematic for rare haplogroups that feature a structural deficit in Asia.
At this stage it is impossible altogether to distinguish between haplotypes that introgressed through Neanderthal admixtures and those that may be ‘safely’ regarded ancestral to both Neanderthal and modern humans – so we should refrain from doing so beforehand. How ancestral the shared African haplotypes could possibly be? African substructure is no longer viable as a major explanation of Neanderthal admixtures in Eurasia. Actually, African substructure was already contradictory with the earlier Out-of-Africa bottleneck-and-homogeneity paradigms, and an additional west-to-east substructure to explain essentially different admixture patterns for Europe and Asia, is even less conceivable. Instead, ‘recent admixture with Neanderthals accounts for the greater similarity of Neanderthals to non-Africans than Africans’ (Yang et al., 2012). Less exclusive scenarios, that allow for early admixture events in the ancient Near Eastern contact zone, aren’t any less problematic for the discrepancy and leave the much lower Afro-Asian component without explanation. The most progressive and intuitive Out-of-Africa scenario, that considers the predominantly European distribution of Neanderthal haplotypes and predicts an increased admixture rate in Europe, now results falsified by this closer examination of Meyer’s 24% lower European rate. Apparently, the current distribution of admixtures only appeared to be in favor of any overall Out-of-Africa framework. The apparent lack of shared Afro-Asian haplotypes doesn’t indicate an African route for Asian admixtures, nor does the low count of shared Afro-Eurasian haplotypes advocate the importance of an ancestral component. Instead, an underpinning West-East dichotomy or Eurasian substructure already in place for the Neanderthal population before the attested admixture has already been proposed as a valid explanation:

Europeans and Asians could show distinct components of Neanderthal admixture if they had admixed with European and central Asian Neanderthals, respectively (Alves et al., 201)

The Afro-European shared haplotypes can’t be older than the long term genetic differentiation of Eurasian Neanderthals, what adds up to the already expounded rejection of African substructure in a recent Out-of-Africa scenario. A better explanation may be found in a massive expansion (or ‘backmigration’) of European populations into Africa, and a corresponding submersal of almost their full share of Neanderthal admixtures inside Africa subsequent to some late-Neanderthal admixture event.
Now the falsification of an important shared ancestral compenent in the African count of rare haplotypes becomes evident, Hochreiter’s data, reporting that ‘haplotypes matching the Denisova or the Neandertal genome are also found, in some cases exclusively, in Africans’, may be viewed in an entirely new perspective. If introgression of Denisovan admixtures was part of a rather ancient gene flow, albeit considerably younger than the Eurasian Neanderthal differentiation still noticeable in the strongly regionalized Neanderthal admixtures, some Denisovan alleles could have reached Africa contemporaneously with the ‘other’ archaic admixtures that arrived there through the European route, as displayed by the calculated haplotypes pattern above. Especially the world-wide distribution of shared Neanderthal-Denisova alleles raises some questions into this direction.
More detailed analysis on the immune gene OAS1, involved in ‘Denisovan’ introgression, revealed this gene was embedded in a very divergent string of DNA, referred at as the ‘deep lineage’ haplotype. Its divergence from all the other extant OAS1-related haplotypes was strong enough to exhibit the signature of archaic introgression, what means the haplotype ‘may have introgressed into the common ancestor of Denisova and Melanesians via admixture with an unsampled hominin group, such as Homo erectus’ (Mendez et al., 2012). The haplotype resembles the Denisovan haplotype ‘with the exception of one site (position 30504), at which the extant human carries the derived C and the Denisova specimen carries the ancestral T’, but even more striking is the current homogeneity of the deep lineage:

Broadly distributed throughout Melanesia, the deep lineage exhibits very low intraallelic diversity […], with an estimated TMRCA of ~25 kya (Mendez et al, 2012)

The attested Denisovan fossils in the Altai mountains had a slightly more ‘ancestral’ version of the gene, thus being different from the extant ‘deep lineage’. Actually, this unique signature boils down to a single hybridization event for this haplotype that involved one ancestral parent not unlike, but slightly different from the sampled specimen of Denisova Cave. Also Meyer’s observation that ‘Papuans share more alleles with the Denisovan genome on the autosomes than on the X chromosome’ and that eg. on chromosome 11 Denisovan ancestry is estimated to be lower in Papuans than in East Eurasians, corroborate to this hypothesis:

[…] there is significant variability in Denisovan ancestry proportion compared with the genome-wide average not just on chromosome X, but also on individual autosomes that have estimates that are also lower (or higher) than the genomewide average. (Meyer et al., 2012 sup)

Unfortunately, despite the negative evidence accumulated by Meyer et al. in their supplement against their own sex-biased modern population-history pet theories, their main article stopped short of dwelling on far more interesting factors such as hybrid chromosome repatterning that include ‘natural selection against hybrid incompatibility alleles, which are known to be concentrated on chromosome X’ and a marked uneven distribution of Denisovan ancestry also in the autosomes.

With hybrids, crossover events tend to compromise lineage specific regulatory regions on the chromosomes. Only favorable repatterning of the hybrid chromosomes results in viable offspring.

The disproportionate absence of Denisovan admixtures on the X chromosome virtually excludes a sex-biased demographic history in Oceania as an explanation and indeed, in their supplement Meyer et al. elaborated a potential rejection on logical grounds: also migrating males bring in their share of X chromosomes, so this way it can’t just disappear. A removal of Denisovan chromosome X by natural selection after the gene flow can be excluded as well: selection acting on genomic functional elements can be detected by its indirect effects on population diversity at linked neutral sites (McVickers et al., 2009), but Meyer’s team was right that they couldn’t establish that archaic ancestry was affected by the proximity to genes. However, natural selection against hybrid incompatibility alleles is still a poorly understood process – and especially if considered applicable just to the protein coding genes that constitute only about 3 percent of the human genome. This year the ENCODE Project Consortium confirmed actually over 80% of the genome to be involved in biochemical functions, in particular outside of the protein-coding regions. Genetic viability is most of all determined by the proper regulation of gene expression. Hence, much of the genome is considered constrained by biological constraints against evolutionary change. Of interest are the ‘large number of elements without mammalian constraint, between 17% and 90% for transcription-factor-binding regions as well as DHSs and FAIRE regions’ (Dunham et al., 2012), referring to regions linked to regulatory functions. But even here, the autors hold that depressed derived allele frequencies indicate ‘an appreciable proportion of the unconstrained elements are lineage-specific elements required for organismal function, consistent with long-standing views of recent evolution’.
It should be obvious that nature can’t expect much viable offspring from a fusion of gametes that brings together lineage specific regulatory regions in a random fashion. The deleterious effects of random hybrid recombination appear to be inversely proportional to chromosome crossover events during meiosis, that normally happens once for each generation. First generation hybrid offspring typically has enough directly inherited consistency of their regulatory regions on their genome left for being viable. But next generation chromosome crossover may already affect the regulatory processes of the haploid gametes being produced by meiosis. Initially, this seriously affects fertility and only the sheer scale of gamete production may compensate for the high probability of next-generation hybrid malfunction. This close relation between hybrid viability and a limited array of favorable crossover events, that shouldn’t compromise the regulatory functionality of the hybrid genome, apparently resulted also in a marked variability of ancestry proportions for each chromosome across the genome of Denisovan admixed populations.
For hybrids, selective processes are more efficient when directed at regulatory viability just before and during conception. Post-natal fitness, on the other hand, is most of all based on the ‘proven technology’ of coding genes whose selective advantage and usefulness were already attested in the parent species. Natural selection based on the success of coding genes thus may have been of less importance in recent hominine evolution than could be expected for the profound genetic change modern humans apparently went through. This detail can indeed be confirmed in the modern genome by the above mentioned lack of genetic sweep, despite important repatterning and recent genetic innovation due exactly to the occurrence of abundant hybridization in recent human evolution.
For the moment this issue should be considered isolated from the origin of the shared Neanderthal-Denisovan haplotypes, especially since this portion was already in place for the sampled Neanderthal and Denisovan specimen. Tentatively, this shared portion could be attributed to an earlier ‘bi-directional’ gene flow, leaving the specific Denisovan admixtures in Melanesia apparently to a subsequent hybridization event that only seems to have affected modern populations. The proposal above of a single hybridization event virtually excludes a scenario where the hybrid population could be considered firmly rooted in a local archaic population. Naturally, this runs counter to an array of earlier proposals that rather link Denisovan admixture events with a wide geographic range of Denisovan hominine presence between the Altai mountains and SE Asia (Reich); with different places during the migration of modern humans (Rasmussen); with distinct Denisovan admixture events in Oceanians and East Asians (Skoglund and Jakobsson); or with a process of continuous admixture where migration routes overlap with archaic hominine ranges (Currat and Excoffier).
However, a single late-Denisovan hybridization event doesn’t suffice as an exclusive scenario in the light of new evidence that posits Denisova Cave as a hotbed of Neanderthal contact. Abundant remains of Neanderthal were found nearby the cave:

The Chagyrskaya 6 mandible […] allows us now to link this material morphologically as well to the Neanderthals in Western Eurasia. Several questions remain: the timing and extent of Neanderthal expansion into the Altai, and especially the potential coexistence and interaction between Neanderthals and Denisovans. Based on availabe dates, the Neanderthals in Okladnikov cave and the possibly slightly earlier Chagyrskaya remains overlap with the wide range of dates for Layer 11 of Denisova cave. (Viola et al., 2012)

Both species even shared the same cave:

we have determined a high-quality nuclear genome from a pedal phalanx found in Denisova Cave in 2010. We show that the pedal phalanx derived from a Neandertal and thus that Neandertals as well as Denisovans have been present in the cave. (Sawyer et al., 2012)

Extensive contacts should at least have initiated a kind of fusion between the Neanderthal and Denisovan parent species into a single population where in time, due to multiple hybridization events, the variability of introgressed DNA would have been restored and integrated, into the Neanderthal genetic heritage and vice-versa. Hybrid repattering of admixed chromosomes probably wouldn’t have raised Denisovan heterozygosity beyond the elevated levels observed in modern populations, and less given the outstanding native homozygosity of the sampled Denisovans as a starting point. Indeed, the Denisovan sample has a reduced heterozygosity compared to any of the present-day humans analyzed by Meyer et al, though they reported the relative ratios of heterozygosity as fairly constant, what could be considered problematic for the assumption of archaic Neanderthal admixture already present in the shared DNA with Denisovans. However, 29 coding CCDS genes could be identified with more than one fixed non-synonymous SNC where ‘Denisova’ carries the ancestral allele, while in eight of these (OR2H1, MUC17, TNFRSF10D, MUC6, MUC5B, OR4A16, OR9G1, ERCC5), the Denisovan individual appeared heterozygous for all SNCs present in the gene. In table S44 it can be verified that 37% of this heterozygosity can be found in chromosome 11, 13% in chromosomes 6 and 7, and 11% in chromosome 8, while eleven chromosomes are homozygous for all investigated genes. Though Meyer’s team proposes this to be the result of duplications or repetitive regions, this heteromorph signature basically leaves the possibility of hybridization more than open. Since this results focus on the fixed non-synonymous SNC where Denisova carries the ancestral allele and modern humans the derived allele, the documented non-ancestral polymorphisms of Denisova even resemble modern-like admixtures.
According to Dienekes, within the group of polymorphic Eurasian SNPs there are less Denisovan than Neanderthal SNPs that are also monomorphic in the African Mbuti Pygmys. Because, actually the relation between Denisovans and Pygmy is ancestral and they share ancestral SNPs. This might reflect a lower penetration into Africa of the shared Denisovan-Neanderthal portion of archaic admixtures. If so, this could be partly due to a Denisovan origin of this shared portion, though some degree of Eurasian Neanderthal substructure may be involved as well. Interestingly, this also implies the tentative modern-like part of potentially admixtured (ie. polymorphic) SNPs in the Denisovan genome is actually less ‘African’ than the Out-of-Africa hypothesis should be happy with. If anything, despite some modern-like features, those admixtures should be assumed of eastern Neanderthal origin.

Proposed hybrid flows for various archaic components, superimposed on Denisovan related HLA-A gene distribution. Blue arrows carry Neanderthal admixtures; red-blue arrows carry mixed Neanderthal-Denisovan admixtures; the green arrow represents East African input; and brown arrows represent Asian admixture and reflux. Question marks represent unknown archaic hominines that may have contributed locally and possibly also to the common genetic denominator of modern humans.

Another modern-like feature of the potential Denisovan-Neanderthal hybridization is the above mentioned outstanding heterozygosity of chromosome 11, that almost screams for continuity with the hybrid signature of the same chromosome in Papuans, where Denisovan ancestry is strikingly low. I really wonder what could have been the impact of these hybrid changes for the now widespread Denisovan-like mtDNA segment inserted into this same chromosome 11 of modern human populations all over the world, as described in a previous post; and what could have been the link with the survival of insert-like mtDNA in the aboriginal DNA found in the Lake Mungo 3 remains (LM3) dated 40kya. But even a much lesser extend of any gradual continuation with respect to Denisova-related selective processes against hybrid incompatibility alleles would only make sense if modern populations are themselves the continuation of these same ancient hybridization processes. Apart from what this might imply for the very nature of the modern genome in general, we could at least incorporate this signature of a continuous hybridization process, that tentatively links the Altai Mountains with Oceania, in what we know about the current distribution of Denisovan admixtures. A northern route around the SE Asiatic habitat of probably very different archaic hominine populations, some of them possibly more erectus-like or even more habilis-like, such as Homo floresiensis (Argue et al., 2012), seems at present more likely than a straightforward direct southern route:

However, in contrast to a recent study proposing more allele sharing between Denisova and populations from southern China, such as the Dai, than with populations from northern China, such as the Han, we find less Denisovan allele sharing with the Dai than with the Han (Meyer et al., 2012)

Current evidence even seems to favor a specific Korean route before turning south along the Chinese coasts down to Oceania:

The enrichment of Neandertal haplotypes in Koreans (odds ratio 10.6 of Fisher’s exact test) is not as high as for Han Chinese from Beijing, Han Chinese from South, and Japanese (odds ratios 23.9, 19.1, 22.7 of Fisher’s exact test) – see also Figure 7. In contrast to these results, the enrichment of Denisova haplotypes in Koreans (odds ratio 36.7 of Fisher’s exact test) is is higher than for Han Chinese from Beijing, Han Chinese from South, and Japanese (odds ratios 7.6, 6.9, 7.0 of Fisher’s exact test) (hochreiter et al., 2012)

It has been suggested that ancient HLA-A genes of the primate immune system only survived on human chromosome 6 by balanced selection in the Denisovan lineage. Hence, the current geographical distribution of this genes is often taken as indicative for the wherabouts of Denisovan admixed descendents. As you can see on the attached map, the hybrid Denisovan trail described above corresponds fairly well with this view, except for Yunnan and Tibet where possible Denisovan-like admixtures are largely below detection level and certainly not derived from Melanesian arrivals. It can’t be excluded that here we may find the root origin of the archaic population whose remains were so far attested only in Denisova Cave. Interestingly, this hypothetized ultimate origin of the archaic Denisovan population is adjacent to Indo-China, where hominine evolution may have been as old and divergent as in Africa.
Thus, it becomes ever more difficult to identify with, or deny descendance of a particular hominine branch. Recent human evolution is like a snowball rolling down the hill. What we are is just everything what came down from the hill, and what didn’t stop rolling. We may question our ability to really take a turn since for all we know the ball just gathers more snow and increases momentum. We can’t even say our trail downhill was human all the way, or where it started, or define what sets the participants apart from everything else around it. But here we are, something completely new on the face of the earth. And most of it, we have in common.


  • Adcock et al. – Mitochondrial DNA sequences in ancient Australians: Implications for modern human origins, 2001, link
  • Alves et al. – Genomic Data Reveal a Complex Making of Humans, 2012, link
  • Argue et al. – An hypothesis for the phylogenetic position of Homo floresiensis, European Society for the study of Human Evolution 2012 meeting, link
  • Dienekes – A surprising link between Africans and Denisovans, Blog September 27, 2012, link
  • Dunham et al. – An integrated encyclopedia of DNA elements in the human genome, 2012, The ENCODE Project Consortium, link; Online review Universität Heidelberg: Allegedly Useless Parts of the Human Genome Fulfil Regulatory Tasks, 6 September 2012, link
  • Cox et al. – Testing for Archaic Hominin Admixture on the X Chromosome: Model Likelihoods for the Modern Human RRM2P4 Region From Summaries of Genealogical Topology Under the Structured Coalescent, 2008, link
  • Curnoe et al. – Human Remains from the Pleistocene-Holocene Transition of Southwest China Suggest a Complex Evolutionary History for East Asians, 2012, link
  • Hawks – Denisova at high coverage, Blog 2012-08-30, link
  • Hawks – Which population in the 1000 Genomes Project samples has the most Neandertal similarity?, Blog 2012-02-08, link
  • Hawks – Modern humans in with a whimper, Blog 2012-07-20, link
  • Hochreiter et al. – Rare Haplotypes in the Korean Population, at ASHG 2012, link
  • Hu et al. – Analysis of contributions of archaic genome and their functions in modern non-Africans, at ASHG 2012
  • McVicker et al. – Widespread Genomic Signatures of Natural Selection in Hominid Evolution, 2009, link
  • Mendez et al. – Global genetic variation at OAS1 provides evidence of archaic admixture in Melanesian populations, 2012, link, or try here
  • Meyer et al. – A High-Coverage Genome Sequence from an Archaic Denisovan Individual, 2012, link, supplement
  • Sankararaman et al. – A genomewide map of Neandertal ancestry in modern humans, at ASHG 2012
  • Sawyer et al. – Neandertal and Denisovan Genomes from the Altai, European Society for the study of Human Evolution 2012 meeting, link
  • Scally et al. – Revising the human mutation rate: implications for understanding human evolution, 2012, link
  • Viola et al. – A Neanderthal mandible fragment from Chagyrskaya Cave (Altai Mountains, Russian Federation), European Society for the study of Human Evolution 2012 meeting, link
  • Yang et al. – Ancient Structure in Africa Unlikely to Explain Neanderthal and Non-African Genetic Similarity, 2012, link
  • Yotova et al. – An X-linked haplotype of Neandertal origin is present among all non-African populations, 2011, link

The Demise of Oriental Neolithic Admixture

September 9, 2012 Leave a comment

The old idea that Europe is a result of Neolithic immigration from the Near East is ever harder to sustain. Certainly, a variety of grains jumped over from Southwest Asia to the virgin Neolithic world outside “as is”, but much of Neolithic culture discovered in Europe can’t be derived as easily and unequivocally from the same eastern source. Not even pottery, that developed pretty late and almost simultaneously on both sides of the Bosporus from what now increasingly emerges as a quite ‘backward’ PPNB-level of Neolithic civilization.
Until recently, the idea of a Neolithic ‘wave of advance’ could still count on the overwhelming support of geneticists, that interpreted the undeniable NW-SE cline in the distribution of several genetic markers as evidence of Neolithic expansion at the cost of Europes native population. Paleogenetic investigation already attested the low impact of Neolithic mtDNA, the Neolithic contribution of Y-DNA on current populations is ever more contested, and the autosomal DNA of Ötzi the Iceman rather suggests important post-Neolithic genetic shifts, that moreover appears to have been predominantly towards the north. The attested lack of an eastern component in Ötzi’s genome could be readily identified in comparison to modern populations, and raises sceptical questions about his purported “eastern” identity. The simple observation that Ötzi’s utter absence of any genetic Asia-shift necessarily implies that Ötzi does not represent the genetic heritage of Asiatic agriculturists is sound enough, notwithstanding the continuous stream of worthless articles that still demand otherwise. The same could be stated about his Y chromosome marked by haplogroup G2a. As I already explained elsewhere on this blog his DNA may have been different from Mesolithic ethnicities of northern origin, but closely related to the native population south of the Alps. Thus also the very proposition that Europe’s main Neolithic proponents, to be found in LBK and Cardium cultures, are genetically “eastern” at all is increasingly at odds with their sharing of their most common Y-DNA with Ötzi’s.

The Venus and the Sorcerer, an Aurignacian (30,000–32,000 years BP) rock ornament found in Chauvet cave, Ardeche, has an extinct steppe bison crouching over a great black female pubic triangle in a sexual pose. This by far oldest attested mythological theme of humanity was still important when the Frankish Quinotaur allegedly fathered the semi-legendary founder of the Merovingian dynasty, thus being a remarkable example of geographic continuity.

Now the study of Arenas et al. (2012) reveals that true Western Asian range expansions into European could only be considered reminiscent within the current pattern of genetic traces, if their age would be predominantly older than Neolithic. Europe has a clear SE-NW cline of genetic variation and right from the start this was always attributed to Neolithic expansion from the Near East. This interpretation, however, simply can’t stand up to careful scrutiny. Human genes are not like barley, emmer, lents and all other Neolithic crops being attributed an ultimate origin in the Near East, that all can be easily handed over between Neolithic societies and blurred from north to south and back again. Indeed, population geneticists rarely seem to realize that a range expansion is a two-dimensional process, of a population on an expansion wave that are fanning out slowly over a wider area rather than moving on a straight line. A population that expands from location A to equidistant locations B, C and D thus accumulate genetic distances AB, AC and AD that will be exceeded by lateral genetic distances BC, CD and DB. For the Principal Component Analysis (PCA) this should normally cause the first PC axis to be orthogonal to the expansion axis.

Orientation of PC1 gradients in different scenarios for (A) Pure paleolithic range expansions SE-NW; (B) Expansion-range contraction-reexpansion of the Paleolithic populations, with a refuge area covering all southern Europe and active migrations to the South during the range expansion. (C) same as B, but with a refuge area restricted to the Iberian refugium. The green line is the median, the still much steeper red line is the PC gradient orientation inferred from previous investigation (Piazza et al., 1995)

In a previous post I discussed the possible impact on genetic variance, that for this reason is most likely to increase within the circular ripples of the expansion wave (and hence the discussed increase of R1b-U106 variance towards the east, while the oldest and most varied haplotypes can be found in the west).
The authors realize that ‘PCA gradients can occur even when there is no expansion’, but only explore the possible impact of genetic differentiation over time and discard the scenario:

[…] Our simulations thus show that […] admixture between Neolithic and Paleolithic humans have drastic effects on PC1 gradients, and suggest that very large levels of Paleolithic ancestry are necessary to produce SE-NW PC1 gradients (Arenas et al., 2012)

Their model of paleolithic ancestry doesn’t take into account recent evidence on the continuity of archaic human genes, that might have strengthened the SE-NW gradient. Neither do the authors consider extremely quick range expansions without any orthogonal axis, that indeed weren’t feasible by Neolithic transport methods, but could have been a factor in Greek and Roman times up to nowadays. Instead, the autors chose to expand on an alternative range expansion from the hypothetized Iberian LGM (Last Glacial Maximum) refugium that was perpendicular to previous and subsequent range expansions from western Asia. Interestingly, the opposite effects on range expansion gradients didn’t simply phase out the Neolithic contribution, it was obliterated:

[…] our simulation results show that a PC1 SE-NW cline is not compatible with a major contribution of Neolithic populations into the gene pool of current Europeans, but with a major LGM refuge area for Paleolithic populations in the Iberian peninsula (Arenas et al., 2012)

The article:

Mol Biol Evol (2012) doi: 10.1093/molbev/mss203

Arenas et al. – Influence of admixture and Paleolithic range contractions on current European diversity gradients, 2012, link


Cavalli-Sforza and colleagues (1963) initiated the representation of genetic relationships among human populations with principal component analysis (PCA).Their study revealed the presence of a southeast–northwest (SE-NW) gradient of genetic variation in current European populations, which was interpreted as the result of the demic diffusion of early Neolithic farmers during their expansion from the Near East. However, this interpretation has been questioned, as PCA gradients can occur even when there is no expansion, and because the first PC axis is often orthogonal to the expansion axis. Here, we revisit PCA patterns obtained under realistic scenarios of the settlement of Europe, focusing on the effects of various levels of admixture between Paleolithic and Neolithic populations, and of range contractions during the Last Glacial Maximum (LGM). Using extensive simulations, we find that the first PC (PC1) gradients are orthogonal to the expansion axis, but only when the expansion is recent (Neolithic). More ancient (Paleolithic) expansions alter the orientation of the PC1 gradient due to a spatial homogenization of genetic diversity over time, and to the exact location of LGM refugia from which re-expansions proceeded. Overall we find that PC1 gradients consistently follow a SE-NW orientation if there is a large Paleolithic contribution to the current European gene pool, and if the main refuge area during the last ice age was in the Iberian Peninsula. Our study suggests that a SE-NW PC1 gradient is compatible with little genetic impact of Neolithic populations on the current European gene pool, and that range contractions have affected observed genetic patterns.

Inmediately south of the glaciers were Steppe Tundras, where temperate latitudes allowed high levels of bioproductivity.

This study departs from the necessity of Last Glacial Maximum Refugiums, places where people survived during the last glacial period in the northern hemisphere. Nearly all ice sheets were at their Last Glacial Maximum (LGM) positions from 26.5 ka to 19 to 20 ka (Clark et al., 2009). According to the theory people disappeared – naturally – from the lands covered by glaciers, but also – and this is questionable – from a broad belt of steppe-tundra borderland in northern, central and eastern Europe down south to southwestern France, the Ligurian coast and the Adriatic Sea. A pattern of forest steppes emerged in southern Europe considered (more?) ‘benign’ to human habitation. Favorable places must have been Italy, by then connected through Tuscany by a land bridge with Elba, Corsica and Sardinia respectively, the Iberian peninsula and the southern Balkan, the latter being directly connected to Anatolia and the Middle East. Somehow ‘LGM refugionists’ considered LGM humanity trapped inside the southern forest steppes, effectively isolated by the southern limits of the extended steppe-tundras. Still, at Europe’s temperate latitudes intense sunlight and loess soils permitted a high level of bioproductivity; mosses, lichens, grasses, and low shrubs that fed mammoths, horses, bison, giant deer, aurochs and reindeer. It is hard to conceive why LGM Europeans would have left this northern paradise behind and contracted to southern refugia – and choose Iberia while during LGM the western Mediterranean basin was much stronger affected by climate change than the Balkan peninsula. Still the preferred LGM refugium, at least to scientific proponents and their mathematics, remained Iberia. This peninsula has a considerable overlap with the Franco-Cantabric region, that includes the southern half of France and the coastal area of northern Spain. In the prehistorical record this region was culturally homogeneous and possibly it was the most densely populated region of Europe in the Late Paleolithic. Highlights of artistic expression before and after LGM demostrate cultural continuity remained virtually unaffected even by the supposed upheavels during LGM. Well known highlights are the rock paintings of wild mammals and human hands in the cave of Altamira, Cantabria (~18,500 years ago, Upper Solutrean, and between ~16,500 and ~14,000 years ago, Lower Magdalenean); the famous Magdalenean paintings of Lascaux, Dordogne, estimated at 17,300 years ago; and the Chauvet Cave (Chauvet-Pont-d’Arc) in Ardèche, whose paintings were confirmed to be much older, between 30,000–32,000 years BP (Aurignacian).
The sudden appearence of real art of such high quality, defies all concepts of gradual evolution in artistic style and human mental capacities. However, the ultimate source of this art may be less visible, like the ancient cave paintings in Nerja, Andalusia (Spain), that emerged this year as possibly the oldest yet found. Organic remains at the spot indicated an even more incredible age than Chauvet Cave: being at least 42,000 years old, these must have been almost for sure the work of Neanderthals. Actually, there is not any reason to presume that knowledge of painting wasn’t native to the wider region. At least the use of paint, for whatever purpose, was already widely known among hominins about a quarter of a million years ago, from the Rhine to southern Africa:

Identification of the Maastricht-Belvédère finds as hematite pushes the use of red ochre by (early) Neandertals back in time significantly, to minimally 200–250 kya (i.e., to the same time range as the early ochre use in the African record) (Roebroeks et al., 2012)

Over this timedepth it would be more than amazing, even bizarre, that the most beautiful horses of Chauvet Cave have so much in common with the horses of the “nave” of Lascaux around the great black cow, almost 15,000 years younger! Indeed, on the basis of stylistic comparison, the Chauvet cave rock ornamentations were initially estimated as being Solutrean (22–17 ka BP) and Magdalenian (17–10 ka BP). This apparent attestation of cultural continuity over thousands of years, however, has a slight geographic component that I conceive as contradictory to the LGM concept. An Iberian LGM refugium would require the people of the Chauvet Cave cultural complex in Ardeche to have migrated to and fro Iberia before arriving in Lascaux, Dordogne. Since Altamira is located well inside the boundaries of the Iberian LGM refugium and dated only slightly after LGM, we might presume that according to the Iberian Refugium concept Altamira rock ornaments are transitionary between Chauvet and Lascaux. They are not. The Altamira hands are not sufficiently unique since painted hands are an ornament in rock art all over the world and the Altamira horses are of a different style. Even the Altamira crouching steppe bison does not have anything to do with Chauvet’s ‘The Venus and the Sorcerer’ having an extinct steppe bison crouching over a great black female pubic triangle in a sexual pose. If the crouching element in Altamira, devoid of all sexual implication, would nevertheless represent the survival of a technical style, preserved by travelling artists, it should be explained why this sexual implication was lost in Altamira while unique European mythological interpretations of the Sorcerer may be readily recognized in historic fertility gods like Crete’s Minotaur, the Frankish Quinotaur (Rhine) and the Celtic Cernunnos as depicted on the “Pillar of the Boatmen” (Seine). Another representation of the paleolithic myth may have survived even in the Sumerian god of creation Enki, sometimes depicted as a bull. Apparently, the Altamira representation attests a different tradition, with an equally problematic transition towards the art of Lascaux. Apparently, the argument in favor of a considerable detour of Paleolithic people quite north of the Pyrenees through-Spain-before-arriving-back-north in Lascaux, is not yet supported by compelling evidence and rather remains the product of grand speculation.

The LGM refugium boundaries of southern Europe, even the very concept of any LGM refugium at all from 26.5 ka to 19 to 20 ka, would be severely compromised if some kind of Franco-Cantabrian local continuity indeed persisted between the art of Chauvet and Lascaux. All scenarios investigated by Arenas et al. showed better results for simulations that ran with low Neolithic admixture. A best fit was warranted by a disproportionate role for the genetic component of a westernmost LGM refugium:

When southern Europe is considered as a single large refugium, PC1 maps show E-W gradients (Figures 2B and S3B), but when the LGM refugium is restricted to the Iberian Peninsula, PC1 maps show steeper NW-SE gradients (Figures 2C and S3C). (Arenas et al., 2012)

The scenarios described by Arenas et al. also investigated the option of mere (Upper) Paleolithic range expansions from oriental origin without subsequent LGM contraction, and indeed the results were very similar to the simulations of a refuge area restricted to the Iberian Peninsula with a history of expansion-range contraction-reexpansion for Paleolithic populations. However, a simple paleolithic range expansion may be insufficient for a true approximation of the NW-SE gradient if a longer history of genetic differentiation could compensate for the drift imposed by LGM refuge scenarios. Unwittingly Arenas et al. depart from the complete replacement of previous populations at the start of the Upper Paleolithic by modern man, and unfortunately this grand mistake already rendered the study obsolete before publication:

The onset of the initial settlement of Europe by Paleolithic populations was set to 1,600 generations ago, corresponding to 40,000 years ago (Mellars 2006) assuming a 25y generation time. In this initial range expansion, we assume that Paleolithic populations completely replaced archaic populations without any interbreeding. (Arenas et al., 2012)

Archaic admixture is a hot item nowadays and already shattered the once popular extinction scenarios attributed to the onset of the Upper Paleolithic. An older age of local genes would make the whole LGM refuge issue virtually irrelevant for understanding current genetic configurations, so I would call this a draw. The main difference of models without LGM refuges is they require continuous habitation everywhere south of the LGM glaciers for a much longer time – and actually there isn’t any reason why they didn’t. Humans just had to follow the game, and wasn’t deterred by the cold to follow their routes up to the food and water at the frontiers of iceage glaciers. Upper Paleolithic people were able enough to do so throughout LGM, and their inmediate predecessors had the advantage of a better climate: the last Ice Age in Europe (Weichselian) was nothing compared with the previous one (Saalien), that ended 130,000 years ago. Of course, simulations of Middle Paleolithic range expansions would account for a more pronounced genetic dichotomy on the European NW-SE axis and thus give better results than Upper Paleolithic range expansions, thus eliminating the need for incorporating LGM refugium related population contractions behind the Pyrenees in the model.

Maximum extention to the south of the Ice Age glaciers that are relevant to human habitation. Red line: Weichselien 11.5 kya – 116 kya; Yellow line: Saalien 128 kya – 238 kya; Blue line: Elsterien 418 kya – 465 kya.

Having said the necessary on LGM refugia, I value the Arenas et al. study for debunking stale assumptions on the Asiatic character of Neolithic influence and the wrongfully implied impact on Europe’s NW-SE genetic gradient. However, the absence of strong mtDNA and autosomal DNA signals for Paleolithic SE-NW range expansions doesn’t necessarily imply consistency with a pre-Neolithic scenario – and indeed probably it doesn’t for Y-DNA. The source of inspiration for this study was mtDNA evidence (Pereira et al., 2005), whose European dichotomy and timeline is now mirrored by the geographic clines of autosomal DNA. Now, the Y-chromosome evidence features some intriguing dichotomies all by itself: ‘western’ R1b against ‘eastern’ R1a; R1b that features an internal dichotomy on SNP S127; and, more recently, R1a that apparently features another west-east dichotomy internally on SNP Z645. The latter dichotomy is continued further east by subclades of Z645, ie. European R1a SNP Z283 against Asiatic R1a SNP Z93. Hence it has all appearance the accumulation of various West/Central European Y-DNA haplogrouos are related and, despite a strong West to East gradient, are thus incompatible with results that previously suggested an important role of a Neolithic expansion:

[…] that R1b1b2 was carried as a rapidly expanding lineage from the Near East via Anatolia to the western fringe of Europe during the Neolithic. (Balaresque et al., 2010)

Naturally, this introduces a new inconsistency in the genetic evidence between Y-chromosome dating on one hand, and mtDNA and autosomal dating on the other hand. Klopfstein (2006) discussed Allele Frequency Clines (AFCs) were ‘mutations having arisen during Paleolithic range expansions should show larger absolute frequency differences than those having occurred during a pure Neolithic expansion’. Genetic differentiation perpendicular to the main direction of range expansions was not his concern for the very massive nature of his AFC-driven model, and still his model shared the preference for pre-Neolithic range expansions:

As expected from our previous results, the average final frequency of the mutation is found much higher after the Paleolithic expansion than after the Neolithic expansion (44% and 2% in the colonized area, respectively) – Klopfstein et al., 2006

Nor, indeed, was the Klopfstein study specifically meant to include Y chromosome genetics in his model. Still, only Y-chromosome substructure appears to be compatible with slow SE-NW range expansions (Balasques et al., 2010). The accepted YDNA dates for the European SE-NW gradiënt, however, are generally considered inconsistent with a pre-Neolithic or Paleolithic scenario. Between haplogroup dating of especially Y-chromosomes is based on obsolete assumptions on extremely large proportions of poorly understood ‘junk DNA’. Like already predicted in a previous post (Evolving Chimps are Messing Up Y-DNA Dating), the actual proportion of functional DNA is already accepted to be much higher, implying a more compromised viability at conception time of deleterious mutations, what in turn translates to actually lower mutation rates. It should be noted the Iberian refugium hypothesis isn’t compatible with Iberian Y-DNA, though maybe a pre-Neolithic development of some R1a and R1b in a wider European context is – especially now the accepted mutation rate keeps dropping.
At this moment it has all appearance that Neolithic DNA south of the Alps was rather much more ‘Sardinian’ and ‘Ötzi-like’ than anything else, ie. virtually devoid of any significant genetic shift to the east. Ethnical continuity of this type may have extended much further east than genetic analyses on current populations would allow us to consider without the evidence currently available in paleogenetic samples – even of an eastern location within Europe as remote as Bulgaria: ‘Strikingly, an analysis including novel ancient DNA data from an early Iron Age individual from Bulgaria also shows the strongest affinity of this individual with modern-day Sardinians’ (Sikora et al., 2012). Time will tell the publication of this find will deal the final blow to current scientific beliefs that concern important Neolithic immigration of Asiatic agriculturists. Much easier would it be to assume the remaining mtDNA and autosomal DNA gradients are simply the exaggerated, sex-biased result of quick range expansions from the east, that blurred all preceding slower range expansions beyond recognition – except for the Y-chromosome gradiënt mentioned above.****) After all, the lengthy debates and elaborate calculations about the origin of a considerable genetic east-shift, and the genetic SE-NW cline in Europe, may simply reduce to the ‘quick range expansion’ that was due to a previously unsuspected popularity in the Classic world of girls from across the Bosporus, as marriage partners.

****) The European clines for YDNA R1b and R1a are nowadays (2014) recognized as fairly recent (late-Neolithic) star-like expansions:
The Larmuseau et al. – Recent Radiation within Y-chromosomal Haplogroup R-M269 Resulted in High Y-STR Haplotype Resemblance (2014) study ‘reveals a strong Y-STR haplotype resemblance among West-European males belonging to haplogroup R-M269, which is most likely the result ofrapid population expansion. This expansion event should have been accompanied by an accumulation of allelic variance, such that the action of mutation and genetic drift had no chance to generate distinctive, subhaplogroup-specific haplotypes.’
Likewise, the Underhill et al. – The phylogenetic and geographic structure of Y-chromosome haplogroup R1a (2014) study admits that the ‘[w]hole Y-chromosome sequence analysis of eight R1a and five R1b individuals suggests a divergence time of ~25,000 (95% CI: 21,300–29,000) years ago and a coalescence time within R1a-M417 of ~5800 (95% CI: 4800–6800) years’.
In this light, it has become most unlikely any of these West-East clines of the YDNA R have anything to do with the Neolithic advance.
More Mesolithic origin of these clines have already been treated in The Mesolithic Blind Spot.


  • Arenas et al. – Influence of admixture and Paleolithic range contractions on current European diversity gradients, 2012, link
  • Balaresque et al. – A Predominantly Neolithic Origin for European Paternal Lineages, 2010, link
  • Clark et al. – The Last Glacial Maximum, 2009, link
  • Kuhlemann et al. – Last glaciation of the Šara Range (Balkan peninsula): Increasing dryness from the LGM to the Holocene, 2009, link
  • Morelli et al. – A Comparison of Y-Chromosome Variation in Sardinia and Anatolia Is More Consistent with Cultural Rather than Demic Diffusion of Agriculture, 2010, link
  • Pereira et al. – Highresolution mtDNA evidence for the late-glacial resettlement of Europe from an Iberian refugium, 2005, link
  • Roebroeks et al. – Use of red ochre by early Neandertals, 2012, link, On the news
  • Sadier et al. – Further constraints on the Chauvet cave artwork elaboration, 2012, link
  • Sikora et al. – On the Sardinian ancestry of the Tyrolean Iceman. To be presented at the annual meeting of ASHG, 2012, link
  • Züchner – Grotte Chauvet Archaeologically Dated, 2000, link


  • The Paris Review Daily. The Spring Issue: Werner Herzog and Jan Simek on Caves
    December 30, 2011 | by John Jeremiah Sullivan, link
  • El Mundo – ¿La obra de arte más antigua de la Humanidad? 07/02/2012, link
  • Mail online, 7th February 2012: ‘The oldest work of art ever’: 42,000-year-old paintings of seals found in Spanish cave, link