Any migratory link of short headedness or ‘brachycephaly’ with the Neolithic advance can be excluded. The lack of any eastern – or northern – shift in the DNA of Ötzi, as observed in my previous post on the subject, should be enough to falsify all assertions accumulated in scientific history about an eastern origin of the ‘modern’ tendency towards shorter brains. This certainly doesn’t support any link either with a theorized ‘extended expansion’ of kurganized populations in the Bronze Age. Ötzi’s DNA was absolutely ‘western’, even more so than current European populations whose genetic gravity seems to have shifted predominantly towards a more northern signature nowadays – especially in Central Europe, where Ötzi is from.
Peculiar, therefore, was Ötzi’s moderately short, ‘mesocephalic’ skull shape, still rare in his time. Intermediate between the traditional ‘long-headed’ shapes, and innovative ‘short-’, or ’round-headed’ shapes, these skulls start to pop up in the European record – indeed! – about the time of Ötzi. Bernhard (1994) described his skull thus:
[The length-breadth-index] of the mummy’s skull is mesocranic, i.e. of medium length in relation to the breadth of skull. The skull is relatively high (akrocranic) compared to its breadth (Bernhard, 1994)
According to the anthropological criteria of the Frankfurt Agreement (1882), the Cranial Index (CI) of Ötzi (CI = 75.9) was still far from being brachcephalic (short headed, CI over 80) and just slightly too short for being dolichocephalic (long-headed, CI up to 74.9). In the French system his skull classifies as ‘Subdolichocephalic’, indicating his departure from the pre-Neolithic dolichocephalic past indeed meant only slightly shorter, in agreement with the proposition that Ötzi represents the first onset towards the short modern brain.
Indeed, an eastern origin of brachycephaly is problematic in many ways. It can’t be simply deduced from current nor past populations anywhere. Neolithic populations were hardly any less dolichocephalous than Mesolithic aboriginals, even in the supposed Neolithic homelands in the Middle East. The European appearance about 3000 BC of ‘alpine’ round-headedness, often accompanied by a flat ‘dinaric’ occiput, was sudden and contrasted with an older mediterranean-nordic phenotype. So far, no reliable relationship between culture and phenotype could be established, even though in Western Europe this cranial modification was often linked with the introduction of Bell Beaker culture. The Iberian pensinsula, another candidate for the hypothetized homeland of Bell Beaker, was certainly not the origin of dinaric or alpine types: shorter skulls could only be confirmed in a few Portuguese burials, Mallorca and a few dubious cases in the Meseta and the levante (Lichardus), while their presence in Catalonian megaliths rather preceded immigrant maritime and regional Beaker styles.
Another line of thought makes the association with Bronze Age mountaineers that descended to the lowlands to sell their ores, probably based on a purported – though unsupported – theory that brachycephaly was a new adaptation against colder climates in mountainous regions. In Greece such a mountainous origin may indeed fit the evidence: according to Dienekes, Panagiaris’ study (1993) on the Ancient Greek population “from a physical anthropological perspective (413 male and 354 female crania, using 65 biometric characters as well odontological traits)”, concluded that “the greater period of discontinuity in the material is observed during the Helladic period (=Bronze Age in Greek archaeology), where broad-headed incoming groups appear, side by side with the older Mediterranean population” (Dienekes, July 22, 2012). Actually, the period mentioned in the text for this change to be already noticeable was Protohelladic, about 3000 BC, ie. only a few centuries later than Ötzi (3370-3100 cal.BC – Kutschera, 2001):
From the Neolithic to Hellenistic times, in the Helladic space, we find as dominant element the mediterranean genetic substratum
The greatest migration of population which took place in ancient times seems to have happened during the Bronze Age, and it is characterized by a genetic flow from mountainous populations of Pindos towards the southern main part of Greece. The culmination in the intensity of these processes took place during the Early Bronze Age (Protohelladic) and the first half of the Middle Bronze Age (Mesohelladic). (Panagiaris, 1993)
No tendencies to this extend can be detected in the pre-Neolithic human fossil record, not even during the Ice-Age. Almost contemporaneously also non-European phenotypes passed through this quite radical change, towards an world-wide emergence of brachycephaly. Non-dolichocephalic types were quite new, despite Ötzi even to the Alps, while in the Carpatian Basin, even though broad-headedness is nowadays considered native in these regions, their introduction had to wait for the arrival of the Western European Bell-Beaker culture.
Interestingly, amidst a predominantly long-headed population, intrusive brachycephalic elements already reached the northern Italian Remedello and Rinaldone cultures shortly before the advance of Bell Beaker. Ötzi’s mesocephaly could thus as well have been due to hybridization with southern neighbors and indeed, Ötzi’s measurements groups best with these northern Italians (Bernhard 1994). Next in line are representatives of the contemporaneous Horgen culture in eastern Switzerland, that is often linked with the Seine-Oise-Marne (or SOM) culture. Surprisingly, this was one of those regions that allegedly constituted a strong brachycephalous bearing at an early stage. Some Neolithic-period continuity of a brachycephalous element is suggested for the region between Rhine and Seine.
Post-war clashes of grand ideologies that defined the past, during the most insane century of humanity ever, still have their effect on 21st century science. Taboos on phenotype evidence caused much once carefully collected information to be now ignored, avoided or simply lost. However, brachycephalic remains at Furfooz, Belgic Ardennes, originally claimed to be Magdalenian by Dupont (1872), are nowadays rather considered Neolithic (Charles, 1996), thus contradicting previous statements that Furfooz – and brachycephaly – constitued another Upper Paleolithic element in Europe next to the long-headed Cro Magnon and the prognathic Grimaldi types. Coexistence in the European landscape of profoundly different phenotypes over a longer period remains unattested until the Neolithic, and if so the close-range genetic differentiation and isolation implied would have been a remarkable feat in human evolution. More reliable Neolithic results were first found in Grenelle, west of Paris. Munro (1899) mentioned the ‘highly brachycephalic’ type of two skulls found in the cavern of Tertre-Guerin (Seine-et-Marne), and sixteen brachycephalic skulls out of thirty-three from a series of sepulchral caverns at Hastiere in Belgium. The former belonged to an advanced neolithic culture that practised trepanning, and produced polished stone celts, with and without horn-casings. Their culture is arbitrarily dated between 3300-2700 BC, mainly to comply with the more secure dates of the related Horgen culture in Switzerland. Though culturally important, so far this closely related complex located in more mountainous territory couldn’t be credited with the origin of brachycephaly either.
Any association with an immigrant racial component, new in (West and Central) Europe and potentially accompanied by new dominant genetic markers, is highly hypothetical. Bell Beaker culture was often linked with Y-chromosomes marked by haplogroup R1b, that in a recent investigation on ancient DNA could already be confirmed in some very old samples recovered from a site in Kromsdorf, northeast of Weimar in Thuringia (Lee et al., 2012). The ultimate origin of this marker is hypothetized to have been somewhere else, though at least the current European distribution is most likely the result of a long term process rather than impelling migrational events that could be readily identified in the archeological record. Grand conclusions on a distant origin can’t be established for a very common European marker whose distribution rather reveals the remnants of an older European dichotomy in R1b (Morelli et al., 2010). Even the physical type of Bell Beaker folks results unlikely to indicate anything more than rather weak exogenetic admixtures.
Actually, the origin of brachycephaly is elusive and all points to a quite modern, homoplastic innovation. This skull type represents the clearest departure from Cro Magnon’s occipital bun, allegedly inherited from Neanderthal. Indeed, Lohring Brace claims that the Upper Paleolithic and subsequent Mesolithic of northwest Europe simply developed there in situ out of Neanderthal precursors. However, subsequent changes of the skull were dramatic. The origin of those changes are impossible to localize, but apparently accelerated in regions where increased levels of gene flow could be expected. Some places were hit harder by the change than others:
The craniofacial form of Cro-Magnon allies with the living populations of northwestern Europe, specifically with the fringes in Scandinavia and England, but not with the European continent.
Everything from the details of mastoid process form and nuchal muscle attachments to fully “bun-shaped” occiputs demonstrates a continuity from Neanderthal morphology to what visible in the inhabitants of the fringes of western Europe today in Norway, the Faeroe Islands, and England [...] Given those aspects of occipital morphology in living northwest Europeans, one would have to predict fossil ancestors with a similar configuration. Fossil predecessors exist with the right occipital characteristics [...], and they are called Neanderthals. (Brace, 1996)
The demise of the bun is remarkable, since the occipito-temporal region counts as ‘one of the most derived anatomical areas in the evolution of the Neanderthal lineage’ (Rosas et al., 2008). Migrationists typically pulled their own migrational rabbit out of the hat for their explanations, but all they could offer was some faint notion of an Asiatic source – for having a strong presence of brachycephaly nowadays. Noteworthy is that early Asiatic specimens typically miss any tendency towards brachycephaly, and featured dolichocephalic as anywhere else. Back in time the development of Asiatic skulls parallels Europe even in the occipital bun, a feature of the lost Peking man fossils, still reminiscent in the ~20-30 kya Liujiang hominin (Ash & Robinson, 2011) – despite Liujiang’s already much more rounded occiput having an angularity of 122º, ie. well within the diagnostic range of modern humans (above 114º). If such reduced angularity of the occiput preluded the emergence of shorter skulls at all it should be noted this tendency was observed already in some early sapiens near Israel’s Qafzeh cave, dated to 96-115,000 B.P. Interpreted as ‘modern’ rather than ‘racial’, the remarkable variation of the feature was attributed to sexual dimorphism in the occiput rather than the involvement of a round headed hominin in what could have been a racial hybridization event: a flexed occipital that carries a torus-like bulge centrally (Skhul IX) was interpreted as ‘male’ while an evenly rounded occiput with no development of a transverse torus (eg. Qafzeh 9) was interpreted as ‘female’. This kind of sexual dimorphism is unknown among modern humans and neither does this derive from preceding hominins, as illustrated by the pre-Sapiens paleodemes found in Spain at the Sima de los Huesos, Sierra de Atapuerca. Though considered part of the paleospecies ‘Homo Heidelbergensis’ that forked into the Neanderthal and African Sapiens lineages (‘A conservative minimum estimate for the age of the fossils is now said to be 530 Ka’ – Rightmare 2008), their sexual dimorphism is rather diagnosed by size differences comparable to recent populations. The ‘purity’ of early sapiens in the Near East was never sufficiently questioned, while actually they roamed the frontier between Neanderthal and African hominins, each having cranial characteristics of their own. Still, none of these early differences may seriously be associated with modern brachycephaly, or reveal its origin. Angled occipitals and dolichocephaly were still common among the victims of the Tell Brak killing field, early Neolithic Syria. Senyurek (1951d, pp. 614-15) concluded that “the majority of the Chalcolithic and Copper Age inhabitants of Anatolia were dolichocephals of mainly Eurafrican and Mediterranean types, and that the brachycephals, probably representing the invaders, were rare in these periods. This study has further supported the conclusion that the earliest inhabitants of Anatolia were longheaded, and that the brachycephals came in subsequently.” The alleged introduction of brachycephaly in Mesopotamia during the subsequent Sumerian period, as represented in art, was never confirmed by actual finds:
[...] in iconography the Sumerians were represented with short heads, while the skulls found at Ur and all other sites were long (Soltysiak, 2004)
This ‘Sumerian problem’ of a Mesopotamian population devoid of attested brachycephaly, while originally being characterised by dolichocephaly, appears to be part of an international ‘Brachycephaly problem’. Hittite planocciputs in Anatolian art dates from much later, is equally unsupported by corresponding skulls and postdates the ‘Bell Beaker problem’ of brachycephaly in the west. Only this year a similar tendency was described for Bronze Age Crete, essentially unrelated to marked historical events:
Therefore these results suggest a gradual rounding of the cranial shape for the Central Cretan population in the course of the Bronze Age, resulting from the increase of the cranial breadth in relation to cranial length. They further provide negative evidence for a disruption of the biological history of the Knossos population following the LMIB destructions due to an increase in the biodistance between the samples dating immediately prior and following the destructions.
The gradual rounding of the cranial shape of the Central Cretan population over the course of the Bronze Age and the very similar shape of the Gypsades, Sellopoulo and Mavrospelio crania can be more clearly appreciated by plotting the Cranial Index (100*maximum cranial breadth/glabello – occipital length) data. The Cranial Index describes the cranial shape and higher cranial indices reflect a more rounded cranium. [...]
The gradual increase in Cranial Index over the Bronze Age most probably reflects gene-flow from populations biologically different from the Early Bronze Age Cretan population and from inter-population biological interactions (admixture) in the succeeding periods. (Nafplioti, 2012)
Assumed Neolithic intrusions from outside, of populations very different from the European native populations, have been a pitfall for genetic investigators before. Genetic investigation on Neolithic skeletons failed to support the traditional view of Neolithic migrants leaving a dominant imprint on the current European population. Even though assumed essentially non-European, their Neolithic genetic contribution must have suffocated amidst apparent Mesolithic influences in a process already explained as Mesolithization elsewhere on this blog. Moreover, at least the cultural package of LBK, the main “intrusive” Neolithic complex in northern Europe, seems to have developed in Hungary before it spread on the North European plain. The initial advent of the Neolithic LBK groups was swift and influential, but within four centuries there was a decline. The Rossen, Bischheim and Michelsberg cultures developed from LBK stock and apparently their material culture was much appreciated over a wider area, but this success eventually petered out when territorial expansion turned into stagnation. In general there was a noticeable environmental adaptation that inherited from a more Mesolithic way of life. In turn, the acceptance of Neolithic elements within the communities of their Mesolithic neighbors can’t be attributed to anything else but induced inspiration. Many elements of the TRB, a more natively-inspired Neolithic culture, seem to originate in Mesolithic contexts, even though the proximity of the LBK heritage must have been decisive for their appearance. Notwithstanding adaptive processes and the emergence of a completely new physical type, the demise of the Neolithic component seems closely connected with Mesolithization and hence, the resilience of pre-Neolithic populations that in traditional archeology was lost out of sight.
Speculation on an eastern origin of the planocciput remains without evidence, though the despair for finding a geographic origin in the east still rings through contemporary publications:
A. Wierciñski, contrary to the earlier authors, found a far more complicated anthropological structure in the Mesopotamian population, which made the previous search for [a brachycephalic] “Sumerian race” pointless. In his opinion the area of Tibet (or generally Central Asia) may be considered as the Sumerians’ place of origin. (Soltysiak, 2004)
Planoccipital (‘flat’) skulls definitely postdate ancestral AMH areas and remain absent in pre-Neolithic contexts as far as Eastern Asia. Everywhere the deviation from dolichocephaly seems to be a fairly recent development.
Indeed, for all we know, brachycephaly only started to increase in the Late Neolithic and apparently still continues to do so. Whatever the origin, only the success of Bell Beaker apparently turned brachycephaly into an important ethnic marker. Hooton (1947) described Bell Beaker as ‘a Nordic-Alpine cross grown taller and more rugged than either parental races through hybrid vigour’. Coon pointed out the formative blend didn’t occur in Britain since there the brachycephalous Alpine element, an essential ingredient, was still lacking. The nasal convexity and occasionally flattened occiput of the Bell Beaker type was perhaps qualified more correctly by Coon as Dinaric, though this doesn’t resolve the Bell Beaker origin either. Some Dinaric-like characteristics may indeed be reminiscent to admixtures dragged into the west during the Neolithic, though their ultimate origin remains unresolved.
Even in the Carpatian Basin, where Dinaric traits still prevail nowadays, this physical type has a rather recent history:
[...] the appearance of the characteristic planoccipital Taurid type, unknown until then from the Carpathian Basin, in the populations of some later cultures (e.g. Kisapostag and Gáta-Wieselburg cultures) suggests a mixture [of Bell Beaker people] with the local population (Zoffmann, 2000)
The Dinaric type was no less the result of dinarization in the wider region of the Carpatian Basin as anywhere else. Evolution may be involved, possibly triggered by a Neolithic tipping point to be associated with cultural developments that vastly surpassed geographic and ethnic boundaries. The cultural link may be illustratied by late-holocene tendencies towards a new custom of cranial deformation, to the result of occipital flattening and (hyper)brachycephaly. Possibly there is a reverse relationship:
A suggestion was that the beginning of artificial cranial deformation was linked to the first appearance of brachycephaly during the Upper Palaeolithic period and a desire of prehistoric men to continue with a preceding “longhead tradition” (Zivanovic, 1982) – Arensburg et al., 1988
Examples of this fashion pop up first in a wide range of Neolithic societies. Remarkably, the alleged cultural isolation of the Americas, already contradicted by contemporaneous Neolithic culture, is turned on its head by the practice of cranial deformation that once flourished with an incidence of 90% of the total population in some regions. The possible relation to real brachycephaly is eg. corroborated by the reported association of the practice of cranial deformation with Armenians and Pueblo Indians. Brachycephaly is represented today in the midwest and among many of the northwestern tribes, especially, though not exclusively, associated with Na-Dené languages. This group allegedly belongs to the much broader Dené–Caucasian superfamily, which also contains the North Caucasian languages, Sino-Tibetan languages, and Yeniseian languages, thus establishing the only major linguistic connection of populations on both sides of the Bering Sea. Large linguistic families are commonly associated with more advanced cultural groupings and at least the Na-Dené grouping on the Eurasian side are remarkable for their often ancient link with the Neolithic way of life. A chain of cultures thus appears to have participated in both cranial deformation and the holocene transition towards brachycephaly and Neolithic culture. Cranial deformation was fashionable in the Yeniseaian contact zone of Dené–Caucasian and the Afanasevo culture, often considered ancestral to the Tocharian branch of Indo-European populations. The custom also penetrated into the largely contemporaneous North-West Caspian steppe area in Russia, populated by the allegedly Indo-European Catacomb culture more to the west. Dating issues of human bones previously attributed an excessive age to both cultures, due to lower 14C values on their attested ‘fluvial’ menu compared to terrestal samples. Only nowadays such an enigmatic eastern origin can be dismissed in favor of a quick eastward expansion of Indo-European cultures, reaching Afanasevo territory not before 2500 BC – thus indeed being slightly younger than Catacomb culture.
Most 14C dates of human bones of the Early Catacomb and East Manych Catacomb culture are older than expected. [...] The consumption of river food is the basis of the reservoir effect in the collagen of human bone.
Using these corrections, we conclude that the historical time interval for the Early Catacomb culture is 2600–2350 cal BC, instead of 3300/2900–2450 cal BC, and for the East Manych Catacomb culture is 2500–2000 cal BC, instead of 2900/2800–2300 cal BC. (Shishlina et al., 2007)
Indo European culture and populations travelled west to east in Asia, making it even more remarkable that cranial deformation apparently travelled in opposite direction. Or maybe the fashion was older along the Atlantic rim and part of the transition of Mediterranean and Atlantic megalithic cultures to Bell Beaker culture? In Malta this cultural change was indeed accompanied by the first western attestation of cranial deformation.
Whatever happened, at the end the once well-established Cro-Magnon type simply disappeared:
Basques and Canary Islanders are clearly associated with modern Europeans. When canonical variates are plotted, neither sample ties in with Cro-Magnon as was once suggested. (Brace, 2005)
Next to cranial deformation, a truly ‘evolutionary’ origin of brachycephalic skulls may have been obscured by another environmental, ie. epigenetic element. Plasticity can be demonstrated by historic fluctuations of the cranial index (a ratio of skull length to width):
[...] factors such as climate, as well as cultural change (such as increased tool development and use) might have led to changes in skull morphology in late Neolithic/early Bronze Age Britain (Brodie 1994:80)
Brodie and other researchers found that: Cranial Index does seem to correlate positively with temperature and negatively with humidity
Brodie speculated that Neolithic cranial morphology was influenced by these cold, damp conditions. In contrast, during the early Bronze Age (2480 cal BC- 1450 cal BC), the climate was apparently drier. Brodie argues that as a result, the gradual increase in the Cranial Index which occurred in northwestern Europe during the Neolithic and early Bronze Age could have been in response to climatic improvement (Bartels, 1998)
These climatological fluctuations can’t explain wider tendencies towards simultaneous cranial changes in disparate locations, as has been expressed in the investigation on the changes in Crete already mentioned above:
An alternative interpretation implicating the thermoregulatory model of Beals et al. (1984) and adaptation to colder climatic conditions carries less weight. (Nafplioti, 2012)
Whatever the cultural and possibly climatologic causes, accelerated cranial evolution must have been involved. Initially, since Neanderthal, those changes seem to concentrate on enlargements of the frontal lobe, but a profound structural reorganization seems to occur only much later, including the overall brain shape, an increased cerebellum and – remarkably! – a decreased brain mass since 10k years ago. Using new technology, researchers have produced a replica of a 28,000-year-old early modern human, ‘Cro Magnon 1′, that provided further evidence for the theory that the human brain has been shrinking: the brain was found to be about 15-20% larger than our brains.
Mean cerebellum volume in Neandertals (106.35 ~12.32 cm3) is both absolutely and relatively smaller than the mean for recent humans (139.76 ~2.54 cm3). Additionally, a plot of NetBrain against CBLM (Fig. 5) clarifies that CQ in Neandertals is low also because the rest of the brain [...] is large, compared with the recent human sample [...]. Cro-Magnon 1 [...] embodies the archaic pattern of a relatively large NetBrain and a relatively small cerebellum. (Weaver et al., 2005)
The reduction of endocranial capacity of modern humans, except for the cerebellum, is significant and runs counter to the common perception of an evolutionary tendency towards ‘bigger brains’:
[...]within the past 10,000 years the average endocranial volume in European females reduced from a mean of 1502 ml to a recent value of 1241 ml. This decrease of approximately 240 ml in 10,000 years is nearly 36 times the rate of increase during the previous 800,000 years. (Hawks, 2011)
The volume of Ötzi’s brain fits this picture, since despite his short stature (~159 cm) his brain size was still well above the modern average:
With 1535 cm3, it lies markedly above today’s male average of approximately 1450 cm3. (Bernhard, 1994)
Brain size relates mathematically to body size, though this doesn’t diminish the value of a bigger brains. True, studies have found a very small relationship between brain size and intelligence, and many other factors affect brain intelligence. Indeed, some take the reduction as an indication of evolutionary progress of one kind or another:
The evolution of smaller brains in many recent human populations must have resulted from selection upon brain size itself or on other features more highly correlated with brain size than are gross body dimensions (Hawks, 2011)
At least, all seems to indicate that in general brain reduction does not affect mental capacities, with one important exception: the cerebellum:
In the australopithecines and early members of the genus Homo, the cerebral hemispheres were large in proportion to the cerebellum, compared with other hominoids. This trend continued in Middle and Late Pleistocene humans, including Neandertals and Cro-Magnon 1, who have the largest cerebral hemispheres relative to cerebellum volume of any primates, including earlier and Holocene humans. (Weaver, 2005)
Did investigators overlook the possibility that overall brain shrinkage and an increased cerebellum may be interrelated?
The high energy cost of the human brain is generally considered an important evolutionary constraint to brain development:
The energy demands (kcal/g/min) of brain and other neural tissues are extremely high—approximately 16 times that of skeletal muscle. Consequently, the evolution of large brain size in the human lineage came at a very high metabolic cost
Brain metabolism accounts for ~20% to 25% of resting metabolic rate (RMR) in an adult human body. This is far more than the 8% to 10% observed in other primate species and still more than the 3% to 5% allocated to the brain by other (nonprimate) mammals (Leonard et al., 2007)
The extremely high neuron ratio of the cerebellum thus implies an even higher energy cost to humans than the grey matter of the cerebral cortex. For this reason an increased cerebellum would require overall brain reduction to allow humans to remain at the same level of metabolic cost. Genetic correlation of brain size with body mass or stature does not rely on evolutionary changes, so a selective process must have enforced a new energetic trade-off due to the increased cerebellum.
Apparently, some parts of the brain are more easily “compressed” than others. The remarkable increase of the cerebellum in modern humans is incompatable with the traditional view on its function, that merely involved motor control. An evolutionary increase of the cerebellum is nowadays deemed necessary for modern humans, allegedly being congruent to an increase of human skills. It has already been established the cerebellum has a much larger contribution, including linguistic functions:
The precise nature of the cerebellar involvement in linguistic processing is not yet clear.
[...] results led to the clinical awareness of a modulating role of the cerebellum in various language processes.(De Smet et al., 2007)
Other cognitive processes important to modern life may be involved as well, and actually there is nothing ‘inferior’ about the cerebellum to contradict this suspicion:
The cerebellum is a very densely packed and deeply folded subcortical brain structure situated at the back of the brain [...] In humans, it accounts for 10-15% of brain weight, 40% of brain surface area, and 50% of the brain’s neurons. (Fawcett & Nicolson, 2008)
We have to be aware, though, that brain reduction may also be part of a simple ‘domestication process’. Down’s syndrome (DS) inborn pathology also features brain reduction averaging ~17% according to Pinter et al., 2001, using a set of apparently low-average comparison subjects. However, DS brain reduction reaches a 33% peak for the cerebellum. Indeed, a flattened occiput symptomatic for Down’s syndrome (DS) can’t even be attributed to a disproportionate reduction of the occipital lobes. Remarkably, DS overall brain reduction compares to that of modern man since Neanderthal and early AMH, and is only truly regressive for the reduced cerebellum.
An increased role of the cerebellum also implies an improved interconnectivity with the cerebral cortex, and related changes to optimize the brain structure towards shorter ‘communication lines’ all the way to the frontal parts implicated in planning complex cognitive behavior, personality expression, decision making and moderating social behavior:
Neuroanatomical studies showed neuronal pathways linking the cerebellum with autonomic, limbic and associative regions of the supratentorial cortex. More specifically, cortical areas send information to the cerebellum via the basilar pons, and deep cerebellar nuclei send information back to prefrontal areas through dentatothalamic pathways (De Smet et al., 2007)
Could this be the secret behind Ötzi’s slightly mesocephalic skull, and the general post-neolithic tendency towards brachycephaly and a flatter occiput? The sudden appearance of cranial deformation is a testimony of the reluctance by which this physical change was received by contemporanous populations. But the costs of an improved brain may have been heavier than beauty. If current differences defined by the Down syndrome may be any indication, collateral ‘damage’ of a shrunken brain could have been in the realm of behavior, such as an individual loss in the capacity of self-determination, or an increased sense of social dependence? – what for sure would be a comfortable advantage to some in a more advanced society that takes care of most of their needs. The contemporaneous reduction of the strong posterior projection in the ‘bun’ of earlier sapiens and Neanderthal may also suggest that overall cerebral reduction may have affected the occipital lobes more than other parts. Since this location is associated with REM sleep and dreaming, it might be tempting to link this specific reduction to the emotionally less complicated rationality necessary to cope with the rapid changes of a Neolithic world. More specifically, would decreased occipital lobes have reduced the importance of dreamed reality in daily life?
So far it is hard to relate cerebellar volume to mental functions or capabilities. Current populations apparently have very similar abilities to “manage complexity,” and studies on the between-group variability of cerebellar volume for living people are rare and incomplete. Tang et al. (2010) reported clearly visible ethnic differences between the Chinese and Caucasian populations, where the former has a relatively shorter but wider brain atlas compared to the widely-used ICBM152 template, based on Caucasian brains. This picture corresponds to more brachycephaly measured in east Asiatic populations. Comparative information on cerebellum volume would be more than welcome to evaluate modern variation.
The apparent inverse relationship between reduced brain mass and increased cerebellum is just one of the many changes in the human physique that seems to have initiated during the Neolithic. Evidence of genetic sweep tends to suggest genetic change was more important after the introduction of agriculture than during the previous Upper Paleolithic transition towards anatomically modern humans. Indeed, the genome of Ötzi already supplied essential insights on the accelerated evolutionary change that hit humanity since the (Late) Neolithic. Likewise, Ötzi’s mesocephaly occurred in this critical period of neuroanatomical change. Hopefully, a thorough investigation on the tissues of Ötzi’s brain will shed more light on the evolutionary mechanisms behind this issue in the near future.
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- Rightmire – Middle and later Pleistocene hominins in Africa and Southwest Asia, 2009, link
- Rosas et al. – Endocranial Occipito-temporal Anatomy of SD-1219 From the Neandertal El Sidron Site (Asturias, Spain), 2008, link
- Shishlina et al. – The Catacomb Cultures of the North-West Caspian Steppe: 14C Chronology, Reservoir Effect, and Paleodiet, 2007, link
- Soltysiak – Physical anthropology and the “Sumerian problem”, 2004, link
- Tang et al. – The construction of a Chinese MRI brain atlas: a morphometric comparison study between Chinese and Caucasian cohorts, 2010, link
- Weaver – Reciprocal evolution of the cerebellum and neocortex in fossil humans, 2005, link
- Zoffmann – Anthropological sketch of the prehistoric population of the Carpathian Basin, 2000, link
The acceptance of hybridization processes in the origin of species already came much closer with fossil DNA analyses and more detailed comparisons with extant organisms. For humans the strong suggestion of genetic ‘admixtures’, already claimed in various genetic studies dealing with Neanderthal and Denisova hominines, is reinforced by new investigations that now even start to penetrate the holiest of Out of Africa strongholds, that is Africa. This is no longer about a select set of single genes whose implications for origin and whereabouts could be happily reduced, but about entire sequences of diverging genome ‘regions with unusual patterns of genetic variation’: new results reveal the survival in African genes of ‘an archaic population that split from the ancestors of anatomically modern humans ~700 kya.’ (Hammer et al., 2011). Being much more than a mere warning against obsolete paradigms, this should already give us a valuable insight in what happened within the human species at a supra-regional level.
In Africa the introgression event of ‘archaic’ humans was claimed to have happened about 35kya, recent enough for not spoiling the Recent Out of Africa theory altogether. So now we are required to believe that homo sapiens interbred first in Eurasia (and the north of Africa) and only afterwards with their closest African neighbors? A patched “Recent Out of Africa” scenario would now ‘predicate’ that Homo Sapiens quickly replaced much older hominines anywhere but in Sub-Saharan Africa. However, mere reluctance to believe otherwise may eventually prove futile:
I bet that a few years from now, we will look with amazement at the naivete of the passing Out of Africa orthodoxy that bundled all Africans into an amorphous category of “our ancestors in Africa”. It is also becoming clearer that increased African genetic variation is, at least in part, due to the continent being home to multiple deeply divergent populations that persisted, in various admixtures down to the present. (Dienekes’ blog, 2011-9-16)
The amount of new scientific publications able to shed more light on the issue is already dazzling and for sure preludes an inevitable change of paradigm:
We are only now beginning to harness the power of full human genomes for evolutionary inferences, but it is inevitable that a new theory of human origins will appear that will reconcile the different and conflicting lines of evidence. That theory must take into account latent admixture as a cause of African genetic diversity, and it must also harmonize with the paleoanthropological record. (Dienekes’ blog, 2011-9-19)
Scientists already speak out openly on how the ‘vast amount of recombination information in the human genome has long been ignored or deliberately avoided in studies on human population genetic relationships’ (Xu et al., 2011). The latter now introduced a method of ‘chromosome-wide haplotype sharing’ (CHS) to reconstruct reliable phylogenies of human populations and state that instead of variation being an unbiased measure of population age, ‘the majority of the variation in CHS matrix can be attributed to recombination.’
Unfortunately, time and origin of the admixtures remain hard to quantify. Sampled fossil hominines so far didn’t correspond to much closer modern matches in the wider geographic region. Denisova admixtures have top levels in SE Asia and Australia while traces are virtually absent in South Siberia, where of both Denisova fossils were found. Likewise, Neanderthal admixtures have top levels in East Asia and the Americas, far removed from the known European habitats of Neanderthal, where 1000 Genome Project results are at most comparable, and sowehat lower in northern Europe. In his blog John Hawks suggests population history and natural selection may have caused this distorted picture, while much of the purported evidence for local continuity of Denisova genes may be of a quite different magnitude. Certain HLA genes, part of the modern human immune system also found in the genomes of Denisova and Neanderthal hominines, would have been straightforward evidence for introgression and local continuity – if only those genes didn’t derive from much older primate genes. Balanced natural selection could have been an alternative to account for the survival of ancient genes, supplying false positives for the survival of a select set of Denisova genes. Still, the current geographical distribution of the HLA-A*11 variety found in Denisova, by Parham, concurred remarkably with that of other derived Denisova alleles, published afterwards:
[...] we found that East Asian populations, particularly Southeast Asian populations, had, on average, a greater frequency of the derived Denisova allele compared with other populations (except for Oceanians) [...]. (Skoglund & Jakobsson, 2011)
Since this particular HLA-A*11 variety is mostly found in Asians and never in Africans this indeed suggests introgression by interbreeding outside of Africa. True, such alleles existed already at the same position in the genomes of apes, but now with supporting evidence this detail should supply an entirely new dimension to the issue: introgression of DNA previously conserved merely on evolutionary sidelines should imply temporal extinction of the gene on the main hominine lineage!
At least, extinction is exactly what happened at a much larger scale with primate ABO blood group genes: chimpanzees so far attested for blood type A and some O, but not for B, and gorillas attested for blood type B and some O, but not for A. The ABO blood type is controlled by a single ‘ABO’ gene, for humans on the long arm of the ninth chromosome (9q34).
In the case of human ABO blood group genes, three alleles (i.e., A, B, and O alleles) have been observed, but it is known that chimpanzees have two alleles (i.e., A and O alleles). (Kitano et al., 2000)
Blood groups are inherited from both parents, that may be homozygous for one or heterozygous for two classes. This means that despite being ancient, any of the groups could become extinct once an epidemic demands a strong response that involves unbalanced selection of another allele. Eg., blood group O was observed to have an advantage against malaria, leading to the hypothesis that ‘selective pressure imposed by malaria may contribute to the variable global distribution of ABO blood groups in the human population.’ (Rowe et al., 2007). Since malaria is strongly related to warm wetland habitats, this may be an example of an ancient immune system whose usefulness and survival may be a matter of habitat. If so, then speciation – that implies a formative stage of isolation within a new habitat – also implies an increased risk. Among the great apes only orangutan attested all three types, suggesting that extinction of immune system-related alleles may indeed have happened more often. Reintroduction of ancient genes that became lost may be an almost impossible affair without subsequent introgression by hybridization. Nowadays such potential hybridization partners may be hard to find for chimps or gorillas, probably characterizing the evolutionary costs of their speciation. However, for the human lineage hybridization remained a possibility with species or subspecies that co-evolved within a wide range of different habitats, where different survival patterns and demands had their unique effect on local adaptations, ie. including the immune system! In summary, balancing selection may play a trick on us here, but the evidence is highly suggestive of the deep time depths involved for the genetic divergence achieved before introgression.
Equally remarkable was the absence of Denisova genes being confirmed for Central and South Asia, closer to the fossil origin. The route of Denisova genes to SE Asia must have led through East Asia, but the replacement in Central Asia by other rare varieties of HLA raises even more questions. Such as the origin of the Central Asiatic allele HLA-B*73, not attested in Denisovans, but in modern humans always associated with the ‘Denisovan’ HLA-C*15 antigen, thus suggesting either an hitherto unknown presence in other Denisovans, or a hybrid neighbor.
A recently deciphered genome “from a 100-year-old lock of hair donated by an Aboriginal man” confirmed that despite long time isolation, their proportion of Neanderthal segments match that observed in European and Asian sequences. This Neanderthal component may have been available when the ‘aboriginal Australians split from the ancestral Eurasian population 62,000 to 75,000 years B.P.’ (Rasmussen et al., 2011). However, even though according to the latest insights East Asians are considered significantly closer to Denisova relative to Neandertal, the morphology of aboriginals is rather related to archaic populations and fossils in the wider region of South and South East Asia:
This study has shown that Southeast Asia was settled by modern humans in multiple waves: One wave contributed the ancestors of present-day Onge [Andaman Islands], Jehai [Malaysia], Mamanwa [Philippines], New Guineans, and Australians (some of whom admixed with Denisovans)
we considered the possibility that the secondary gene-flow event into the ancestors of Australians and New Guineans came from relatives of Chinese (CHB) rather than western Negritos such as the Onge. (Reich et al., 2011)
Indeed the Denisova admixtures follow a rather geographic pattern, being present in eastern Indonesia and among the Mamanwa ‘Negritos’, but virtually absent in the ‘Negritos’ of Malaysia and the Andaman Islands. Most probably the aboriginals, where tests revealed ‘slightly less allele sharing than observed for Papuans’ – got the component from their closest geographic neighbors, thus flouting the Out of Africa model and increasing the mystery of the timing and origin of Denisova intrusion.
[...] it is becoming increasingly difficult to imagine a structure model that can fully explain the complex pattern of archaic ancestry in non-Africans without invoking any restricted admixture events with archaic humans. Instead, we suggest that direct gene flow from archaic populations is the most likely explanation for the shared genetic ancestry between East Asian populations and the Denisova genome (Skoglund & Jakobsson, 2011)
Likewise, somewhat lower averages of the Neanderthal component in their previous (esp. north-) European heartlands and unpublished reports of unrelated archaic admixtures both in Europe and South Asia should make us weary about the significance of current geography for the origin question at all. If dislocation of genetic affinity with fossil samples defines a tendency, we can’t even be sure the African archaic admixtures mentioned above indeed derive from an African core region. However, Wall et al. (HGV2011) reported that part of the genetic regions on the human genome ‘were found in the genomes of both sub-Saharan African and non-African populations’. At least some of the archaic admixture became international, not unlike we already known of the V and M haplotypes of gene ASAH1, coalescent-time depth 2.4 million years ago, that ended up evenly dispersed around the world. The mere age of the African archaic introgressive DNA currently under investigation vastly exceeds the age of Neanderthal and Denisova, even that of their (and our) common ancestor Homo heidelbergensis, an extinct species of the genus Homo that lived between 600 and 400 thousand years ago. This seems to be ever less in agreement with the traditional biological species concept (BSC) that tends to relate speciation with highly effective reproductive isolation, and questions the very nature of the human speciation process over time.
Actually, current biology textbooks don’t hesitate anymore to supply ‘prohibitive’ answers, that simply urge to be applied to the human species:
Typically, gene flow occurs between the different populations of a species. This ongoing exchange of alleles tend to hold the population together genetically. (Campbell Biology, ninth edition, 2011)
Speciation still occurs by the evolution of reproductive isolation, but ‘there are many pairs of species that are morphologically and ecologically distinct, and yet gene flow occurs between them.’ An example is the grizzly bear and the polar bear, that despite occasional natural hybridization remain distinct. ‘This observation has led some researchers to argue that the biological species concept overemphasizes gene flow and downplays the role of natural selection.’ (Campbell Biology, 2011). Some other species appear to be actually fully hybrid, like the Tiger Swallowtail Butterfly (appalachiensis): ‘Inter-specific hybridization is widespread in nature and may have important consequences in evolution, from the transfer of adaptive alleles between species to the formation of hybrid species’ (Kunte et al., 2011). According to the investigators the ‘evolution and persistence of appalachiensis in contact with its parental species suggests that hybridization among animals may result in selectively favored hybrid species that contribute to biodiversity.’ Hence, this example exposes a ‘potential role for natural selection in the origin and maintenance of hybrid species.’
Indeed, ‘hybridization is not always a dead end, as the BSC might suggest, but a potential source of new array of hybrids (hybrid swarms) that may establish themselves, eventually in new ecotone habitats, and evolve as new species. One common feature of the process that accompanies hybridization is the rapidity of genome repatterning which is hardly explained by the conventional mutation and recombination rates. Rather, transposition bursts ensuing hybridization suggest their involvement in these rapid genome reorganizations.’ (Fontdevila, 2005)
The risk of speciation may be genetic isolation and inbreeding, the risk of illimited hybridization of subspecies is the potential loss of local environmental adaptations, like the white color of polar bears following the example above. Over time, reproductive barriers may be either reinforced or weakened. In the latter case, hybridization may eventually lead to ‘the fusion of the parent species’ gene pool and a loss of species.’ (Campbell Biology, ninth edition, 2011)
As such, there is no specific reason why mere biology wouldn’t supply answers for the apparently torturous evolution of the human species, or for the sudden appearance of African apes:
In a punctuated pattern, new species change most as they branch from a parent species and then change little for the rest of their existence. (Campbell Biology, 2011)
Both patterns of how species evolve have been observed for the radiation of the mammals over the last 165-million-year. The majority of mammal species, including even the most speciose orders (Rodentia and Chiroptera), experienced an explosive 10-52 fold increase in the rate of evolution only during their initial formation up to the common ancestor. Stable rates of evolution of species, however diverse, were recorded almost everywhere else.
These results necessarily decouple morphological diversification from speciation and suggest that the processes that give rise to the morphological diversity of a class of animals are far more free to vary than previously considered. Niches do not seem to fill up, and diversity seems to arise whenever, wherever and at whatever rate it is advantageous. (Venditti et al., 2011)
The sudden appearance of chimps and also gorilla in the fossil record may indicate their speciation occurred relatively rapidly, when they occupied and then filled their ecological niches. Over the wider humanoid lineage things may be different:
For species whose fossils changed more gradually [...] it is likely that speciation in such groups occurred relatively slowly, perhaps taking millions of years. (Campbell Biology, 2011)
How literally we could take these ‘millions of years’ for the lineage leading to great apes and modern man? Decades of behavioral studies resulted in the insight that apes are far more hominized than was once believed. According to Krützen et al. (2011) this already applies to the cultural plasticity of orangutan. Since this tendency to share particular behaviors in a group was also demonstrated in wild populations of chimpanzees this suggests evolutionary roots in the ancestors that all great apes share with humans. How realistic this would be for the biological species concept, assuming orangutan diverged from our common ancestor 15 mya, or more? Many hominizing tendencies, like the slowing down of juvenile growth, could develop for all humanoid lineages well after such divergence dates. Or would hominized behavior invoke exactly the opposite of BSC with the first onset of organizing a beneficial habitat to the temporarily impaired, like hybrids? Hominized groups could offer better opportunities to overcome some hybrid-related barriers such as lower fitness and fertility. Better survival opportunities would enhance the possibility that hybrid-related genome repatterning could stabilize recombination by endogenous purifying selection over a longer period, maybe several generations, to the effect that both fitness and fertility could be restored over time by the natural resilience of genetic processes. Indeed, if hybridization may explain parallel developments among humans and great apes, we could postulate genetic exchange between diverging ape lineages spanning millions of years.
The laboratory or Reich in Boston has a record in the study of hybrid-driven evolution, and substantiated hybridization already in 2006 for the hominine lineage. What the team called a ‘realistic upper bound of < 17 Mya for human-orangutan genome divergence' resulted in a common ancestor with chimpanzee less than 5.4 mya, including a considerable period of mutual hybridization:
Most strikingly, chromosome X shows an extremely young genetic divergence time, close to the genome minimum along nearly its entire length. These unexpected features would be explained if the human and chimpanzee lineages initially diverged, then later exchanged genes before separating permanently. (Patterson et al., 2006)
The study concluded that introgression of chimp-like DNA in the human lineage, or the other way round, happened after about 1,2 million years of divergence. This year’s ICHG meeting a team of accredited scientists led by J. X. Sun presented a tight refinement of previous date estimates:
Human-chimpanzee speciation is estimated to be 3.92-5.91 Mya, challenging views of the Toumaï fossil [Sahelanthropus] as dating to >6.8 Mya and being on the hominin lineage since the final separation of humans and chimpanzees. (Sun et al., 2011)
Indeed, despite initial efforts to link this transitional period of hybridization with older hominines, the time span of Ardipithecus would make a much better match, and more so due to the immediate succession of Australopithecus: this hominine ancestor complied even less to the more chimpanzee-like anatomy commonly expected with the genetic similarity of humans and chimps:
In an assessment of fossils from Kanapoi (3.9-4.2 Myr ago), the anagenetic series Ar. ramidus, Au. anamensis and Au. afarensis has been hypothesized. The evidence reported here from the Afar Rift constitutes a strong test from a single stratigraphic succession that fails to falsify this hypothesis (White et al., 2006)
The cited evidence of introgression revolted against traditional phylogeny, but the proposal adhered to the established view: one single lineage up to a common ancestor of humans and chimps. Supportive molecular evidence and dating is commonly cited, but the devil is in the details:
Although chimpanzees are our closest relatives, there are many loci at which humans and gorillas (or chimpanzees and gorillas) are the most closely related; we estimate that this is the case over about 18–29% of the genome (Patterson et all, 2006 Supp.)
Likewise, ‘data based on morphological analyses and with the data based on mitochondrial ribosomal genes [...] suggest a closer relationship between gorilla and chimpanzee’ (Rasheed et al., 1991).
A much longer history of shared ‘hominizing’ evolution that encompass all great apes may be implied, and more so by additional inconsistencies in the order African apes are supposed to have diverged from the lineage leading to modern humans:
The late-divergence hypothesis [...] specifically focuses on the divergence between humans and the ape, emphasizing that there were two different divergence points in the evolution of recent hominoids. (Wolpoff, 1982)
Thin enamel, knuckle walking and specialized feet for grasping are just a few shared features of African apes that are difficult to reconcile with two separate speciation events from an otherwise more hominine fossil record. For instance, despite Begun’s certainty on the knuckle-walking habits of our earliest common hominid ancestors, this remains utterly hypothetical – and utterly unsuported by more complete and recent fossils like A. sediba, and even Ardipithecus had not evolved the hands and wrists of a knuckle-walker. Homoplasty among different African apes that feature knuckle-walking is equally unsupported:
[This study] does not support the hypothesis of a knuckle-walking complex, nor does it support the contention that knuckle-walking could have been easily evolved independently in chimpanzees and gorillas. (Williams, 2010)
Instead, Grehan and Schwartz (2010) make a case for grouping ‘the monophyly of hominids and various Miocene–Pliocene fossil apes and orangutans into a ‘dental-hominoid clade’, with the African apes as a sister clade along with the putative [hominines] Ardipithecus and Sahelanthropus.’ In this view only the early hominine Orrorin could link the ‘dental-hominoid-clade’ to humans, thus suggesting a smooth transition along this lineage to hominids, but leaving the close family relationship with African apes unresolved.
Orrorin is [...] already quite distinct morphologically from the African Great Apes (Gorillidae). This indicates a divergence between Hominidae and Gorillidae that dates back to a substantial period prior to 6 Ma, and we estimate about 8-7 Ma for this event. If so, then the discovery of Orrorin refutes all hypotheses in which humans diverged from apes later than 7 Ma, including most of the recent estimates by molecular biologists who tend to think of the divergence as having taken place later than 5 Ma, and even as recently as 2.5 Ma. (Martin Pickford, 2001)
Molecular evidence favors a close relation with African apes, but a much tighter morphological affiliation of the human lineage with orangutan can be observed:
[...] in addition to the development of low-cusped cheek teeth and thick molar enamel, humans shared a significant number of derived features uniquely with the orangutan (e.g. in reproductive physiology (gestation length, estriol levels, absence of estrus), degree of cerebral asymmetries, fetal adrenal zone size, lack of keratinized ischial callosities, mammary gland separation, hair length, incisive foramen number] (Schultz, 2004)
Indeed, the duration of the menstrual cycle varies with species; about 29 days in orangutans, about 30 days in gorillas and about 37 days in chimpanzees. Only the genus Hoolock (previously Bunopithecus), probably the most basal member of the lesser apes (gibbons), match human females ‘precisely’ – except for a considerable variability – in having an average menstrual cycle of 28 days (Geissmann et al., 2009). Cytogenetic evidence pleads for a shared development that considerably exceeds a basal relationship with great apes but unfortunately, so far gibbons are generally dismissed as even more distant from humans than orangutan.
Grehan (2006) expanded on this paradox by noting that ‘the orangutan relationship is supported by about 28 well-supported characters, and it is also corroborated by the presence of orangutan-related features in early hominids’ such as a thickened posterior palate and anterior zygomatic roots. We could add characteristics of their close fossil relatives such as dental structure, thick enamel, shoulder blade structure, thick posterior palate, single incisive foramen.
Comparative morphology supports a unique common ancestry for humans and orangutans as the only phylogenetic theory with substantial corroborated evidence. Even supporters of a unique common ancestry for humans and chimpanzees collectively support more (26) orangutan-related human characters than they do for chimpanzee-related human characters (Grehan, 2006)
Despite the impressive list of unique correlations shared between the human lineage and orangutans, the vast overall genetic distance between the species is often cited as evidence to a deep and rather straightforward phylogenetic affiliation. Genetic isolation of the orangutan lineage – according to molecular evidence between 14-17 mya (million years ago)- doesn’t help in understanding the last recorded interspecies hybridization event between ancestral humans and chimps from the ‘dental-hominoid’ point of view. In the words of Schwartz such an extended period of geneflow between widely divergent ape lineages certainly “pushes the limits of credulity” regarding the hybridization hypothesis.
For the moment I could suffice to notice that morphological and molecular evidence, that challenges the joint divergence of hominines and chimp ancestors from the ancestors of gorilla, may be explained by introgression: as in the example of hybrid polar bears, hybridization doesn’t necessarily imply the fusion of divergent evolutionary adaptive lineages. But hybridization could have complicated the hominid phylogeny beyond limits over a very long time, and even more so as the common source of adaptive radiation events towards speciation was rooted in a common ancestry that started long ago as a balanced process between evolving species.
Actually, human curiosity supplied comparable results for other species, suggesting relative time depths that correspond to what could be expected for the hybridization of diverging ape lineages:
Recent interspecific hybridizations have been well documented for the Bos and Bison species [...] : zebu and ox in several tropical regions; zebu and banteng in Indonesia; taurine cattle and yak in China, Mongolia and Siberia, etc. Ox-zebu hybrids are completely fertile, while male progeny of other hybridizations are sterile. Earlier introgression events may be indicated by the anomalies in the mitochondrial phylogeny [...] that are incongruent with trees of nuclear genes, AFLP fingerprints (these studies) and Y chromosomal sequence variation
Since exchange of genetic material depends on the geographical overlap of the regions inhabited by the species and their ancestors, this is consistent with the hypothesis that reticulation influenced the phylogeny of the Bovini. (Buntjer et al., 2001)
Cross-breeding of ox (genus Bos) and bison yielded fertile females and (mostly) infertile males. The same was implied by Reich, Pattison and colleges for hominine interbreeding with chimps. The fossil record already distinguishes bison in the range late Pliocene-Early Pleistocene up to 2 million years ago, while the origin of Bos (ie. cows) is contested. Their divergence is unlikely to be less than 2 million years, and possibly considerably longer:
The oldest clear evidence of Bos is the skull fragment ASB-198-1 from the middle Pleistocene (~ 0.6 – 0.8 Ma) site of Asbole (Lower Awash Valley, Ethiopia).
Although the origin of Bos has traditionally been connected with Leptobos and Bison [...] we propose here a different origin, connecting the middle Pleistocene Eurasian forms of B. primigenius with the African Late Pliocene and early Pleistocene large size member of the tribe Bovini Pelorovis sensu stricto.
The Bison lineage [...], based on skull anatomy, can be interpreted as resulting from anagenetic evolution of the Late Pliocene forms of Leptobos across the Plio-Pleistocene transition (~2.0 – 1.7 Ma)
The cranial anatomy of Bos, however, is highly derived as to be considered the result of a direct anagenetic evolution from any form of Leptobos. Martinez-Navarro et al., 2007)
Bison cows ordinarily conceive for the first time at 2 years of age while chimps reach their reproductive age only at 13.5 years, almost 7 times later. Accordingly, this translates to the feasibility of an extended period of geneflow for the ape lineage that may even exceed the lapse of 10 million years to bridge all genetic divergence between the common ancestor of all great apes and the reported chimp-hominine hybridization event.
As a caveat it should be noticed that fertile first generation (F-1) half-bison bulls are also registered (Wyoming Thunder being one example). This possibility increases when the bull parent already had some cattle blood, though in some cases this could not be confirmed. This observation typifies hybrid infertility as an essentially temporal evolutionary problem.
A strict phylogenetic model appears to be insufficient to reconcile genetic evidence with the origin of the human lineage from any ape clade in particular. Common biological insights on speciation suggest we should get rid of the thought that divergence, even irreversible speciation is the most natural thing to happen over time. Adaptive radiation may not be synonymous with isolation, especially in the initial period when the new phenotypes are still evolving. A re-evaluation of the entire fossil evidence would be necessary before we could even try to clarify the most controversial issues in human evolution today.
New paleontological evidence and analysis can often be relied on for correcting the phylogeny, even if molecular and morphological data turn out to be contradictory or are giving false positives. This was true respectively for whales, whose fossil ancestors confirmed their genetic affiliation with even-toed ungulates, and the Laotian rock-rat Laonastes whose genetic missing link status for New World Caviomorpha and ‘African’ Hystricognathi didn’t survive renewed scrutiny due to new fossils that revealed it as a Lazarus species of the extinct -essentially Asiatic- diatomyid taxon. Instead, so far paleontological data didn’t resolve contradictory evidence for hominids. There is an ever stronger tendency among scientists to reject the reliability of fossil evidence, and to recur to the possibilities of ‘extraordinary plasticity’.
True, mosaic evolution is considered rampant among primates, from the earliest prosimians up to modern humans, and the list of abortive evolutionary lineages towards modern primates and humans is getting ever more awesome. The ancestors of hominines must have been generalists that had still much in common with the very first anthropoids, or apes maybe as early as late Oligocene, irrespective of the evolutionary changes that were attested in the fossil record of Eurasiatic apes commonly identified as members of two clades, Dryopithecus and Sivapithecus. Unlimited plasticidity of species would open up the possibility of a thorough rejection of all current fossil evidence. Any primitive African ape could have remained in stasis for millions of years, in the middle of countless abortive lineages each well on its way to evolve into the same direction, until one ancestral species followed in their footsteps and plunged itself into an accelerated evolution towards the surviving modern African apes and hominines? and assumes African apes and humans developed from another common ancestor. In a Popperian sense this scenario can´t be falsified, since no fossils are required to meet this standard, what renders this scenario remarkably unscientific. But, could it be?
Only recently molecular evidence forced scientists to the abandon their reliance on morphological and anatomic arguments for equids, whose fossil record was once considered a textbook example of gradual, straight-line evolution. The North American evolutionary sequence from ‘Eohippus’ (Hyracotherium) to ‘Equus’, that eventually became an immigrant to the Old World, was exploited as an argument by Thomas Huxley in his defense of Darwins evolution theory. For a long time this remained one of the most widely-known examples of simple evolutionary progression, notwithstanding the few decades we already knew this ‘straight line’ was rather a bush, where even gradual transformation didn’t always apply. Regarding the once flourishing bush of species, modern equines – like humans! – were still considered a single twig. However, the scientific community was utterly unprepared for the blow this concept would receive of molecular evidence extracted from fossils. Nowadays we have compelling evidence that at least once this twig became intertwined with another.
Cladistic analysis of dental, cranial, and postcranial characters separate Hippidion and Equus into two different clades, which share the North American late Miocene Pliohippus as a common ancestor around 10 MA (Prado and Alberdi 1996).
Alternatively, MacFadden (1997) has suggested that Equus is derived from Dinohippus, and Hippidion from Pliohippus sensu lato (including Astrohippus), implying that the divergence between Dinohippus and Pliohippus occurred prior to 10 MA.
(Orlando et al., 2007)
Molecular evidence proved that the Hippidion, an extinct south american horse with some Pliohippus characteristics, was most similar with moders equids.
Hippidion is considered to be a descendant of the pliohippines, a primitive group of Miocene horses that diverged from the ancestral lineage of equines (a category including all living and extinct members of the genus Equus, such as caballine horses, hemiones, asses, and zebras) prior to 10 Ma ago [...]. A recent study presented genetic data from three southern Patagonian specimens morphologically identified as Hippidion. Unexpectedly, the sequences clustered inside the genus Equus (Weinstock et al., 2005)
Hippidion differed less from caballine equids than all extant non-caballine equids (including donkeys, zebras etc.). This result inspired the team to question the deep morphological split:
The close phylogenetic relationship between Hippidion and caballine horses is in direct contrast to current paleontological models of hippidiform origins. Nevertheless, we are confident that these sequences are those of Hippidion rather than the South American caballine form E. (Amerhippus), which dispersed into South America about 1 to 1.5 Ma later than Hippidion. (Weinstock et al., 2005)
On morphological grounds, the phylogenetic separation between the lineages of Pliohippus/Hippidion and Dinohippus/Equus (modern equines) was previously estimated at 10 mya, and tentatively associated with the merychippine radiation of 15 mya. but the close genetic relationship now attested for Hippidion and caballine equids shatters such deep divergence. Equine evolution now faces the same dilemma as the human origin question, where morphology and molecular evidence are equally at odds. History repeated itself and like what happened before in paleoanthropology in the face of molecular evidence, scientific consensus rather conformed to the biological species concept and concluded that morphology was deceiving:
These data suggest that temporal and regional variation in body size and morphological and anatomic features should be considered a sign of extraordinary plasticity within each of these lineages. Such environment-driven adaptative changes would explain why the taxonomic diversity of equids has been overestimated on morphoanatomical grounds. (Orlando et al., 2007)
Another phylogeny isn’t hard to make, but even the divergence date of extant equines becomes questionable now the DNA of all three extinct American horse species was revealed to cluster specifically with cabelline horses. Genetically, the most recent common ancestor of all modern equids should have lived ‘merely’ ~5.6 mya, and still this appears inconsistent with proposals towards a single Out of America exodus event through Beringia during the glacials, at most 3 mya. Perhaps the easiest way to deal with evolutionary inconsistencies is to just forget about the need of a strict phylogenetic tree at all. For being a viable alternative to morphological continuity, hybridization processes must have been an important element in equine evolution for millions of years. Naturally, divergence dates would easily be overestimated with a last common hybrid ancestor, and easily underestimated for the species – or subspecies – that were the constituent components of the hybridization. For sure this would urge for another evolutionary model, and perhaps the identification of very different genetic signals.
It is suggested that among mammals, equines exhibit the highest rate of chromosomal evolution. Commonly considered Old World immigrants from North America, they feature a progressive ‘decrease’ of their chromosome count moving further away from Beringia: Prezewalski still has 66 chromosomes, 2 more than the domestic horse that is commonly believed to belong to the same species. Of their closest neighbors, the Asian asses, the count ‘drops’ to 56, while the African ass could preserve 62 chromosomes. Extant zebras count 46 chromosomes for the northern Grévy-zebra, 44 chromosomes for the common plains zebra and 32 for the southernmost mountain zebra. Before, maybe inspired by equivocal ideas concerning equine evolution, scientists were inclined to assume the primacy of chromosome fusion in karyotypic evolution, but:
Recent advances in cell-cycle regulation, chromosome behavior, fossil record, and phylogenetic inferences dispute that the primary direction of karyotypic evolution by sequential fusion of chromosomes is toward an arbitrary reduction in diploid number. (Kolnicki et al., 2000)
Lower chromosome counts of equids the further away from the American origin of Equus may now be attributed to conservatism, and the higher counts to ongoing change and evolution.
A key postulate of Todd’s karyotypic fission theory is the idea that in a postfissioned karyotype with a high number of acrocentric chromosomes, a trend for acrocentrics to revert to smaller mediocentrics by pericentric inversion (or centric fusion) repotentiates the karyotype for further fissions correlated with episodes of adaptive radiation directly inferable in the fossil record (Fontdevila, 2005)
For instance, the reduction-argument has been ‘turned on its phylogenetic head’ with investigations on cycads – often mistaken for palms or ferns, but only distantly related to either. The cycad fossil record dates to the early Permian, 280 mya.
Zamia is unique among cycads in that both inter- and intraspecific chromosome numbers range from 16 to 28, excluding 20 [...], with varied karyotype composition
The large size of chromosomes in all cycad taxa excluding Zamiaceae [...] indicates that chromosomal fission has been rare or absent in these taxa.
Molecular analysis has generated limited evidence for any chromosomal rearrangements, including chromosomal fission and pericentric inversion, as the main mechanism driving karyotypic evolution in Zamia.
(Olspon et al., 2011)
In chromosomal fission the total number of chromosome arms remains the same, ‘whereas pericentric inversion and/or hybridization of different karyotypes may either add or subtract from the total arm count’:
Pericentric inversions of the different combinations of telocentric chromosomes and/or hybridization were almost certainly involved in generating the chromosome arm numbers observed, a conclusion based on the size and number of chromosomes. Chromosome arm counts for all [Zamia] taxa in this study [...] suggest that chromosomal fission, pericentric inversion, hybridization of different karyotypes and a combination of these mechanisms occurred in the evolutionary history of this genus (Olspon et al., 2011)
All corroborate to the notion that – under certain circumstances – adaptive radiation and speciation are symptomatic to chromosomal change.
The significance is obvious: ‘Chromosomal fission decreases genetic hitchhiking by severing transcentromeric linkages, allowing for direct selection on newly unlinked genes’ (Olspon). However, there must also be a drawback since in the course of evolution the number of chromosomes didn’t increase without limit. As for cycads in general, and most zamia in particular, the preferred count seems to stabilize at a low number chromosomes: ‘most early diverging cycad taxa have 2n= 16 or 18, with mostly metacentric and submetacentric chromosomes’.
Despite the exceptional features of some members of the clade, chromosomal stability and equilibrium is suggested for most cycad species. A straightforward correlation with morphological variability and stressful or widely variable habitats, that would require high levels of genetic adaptation, is falsified by the stable habitat, primitive morphology and high chromosome number found at the species Z. roezlii that inhabits the Colombian rainforest. The high age of the clade may be important evidence that fission may also be reminiscent of adaptive radiation events in the past. Over time this may be compensated by a corresponding reversal of the chromosome count by fusion. At least this is indicated in basal vertebrates, where ‘some ancestral segments were fused prior to the divergence of salamanders and anurans’ (Voss et al, 2011).
A pattern of chromosomal equilibrium may be observed in cichlid fishes:
Perciformes represents the largest order of vertebrates with approximately 9.300 species. It includes more than 3.000 species of the family Cichlidae [1,2] that is one of the most species-rich families of vertebrates
Phylogenetic reconstructions are consistent with cichlid origins prior to Gondwanan landmass fragmentation 121-165 MYA
The karyotype formula 2n = 48 st/a [subtelo/acrocentric] elements is characteristic of Perciformes
Although there is extensive variation in the karyotypes of cichlid fishes (from 2n = 32 to 2n = 60 chromosomes), the modal chromosome number for South American species was 2n = 48 and the modal number for the African ones was 2n = 44.
Pericentric inversions are thought to be the main mechanism contributing to changes in the basal chromosome arm size of Perciformes. Other mechanisms of
chromosomal rearrangement and translocation probably have contributed to the karyotypic diversification of South American cichlids. The chromosome number variation observed in some species suggests that events of chromosomal translocation followed by chromosome fission and fusion were also involved.
(Poletto et al., 2010)
Like already observed with horses, increased chromosome counts rather represent an evolutionary stage of change rather than a new equilibrium. Kolnicki’s karyotypic fission theory that ‘ posits that all mediocentric chromosomes simultaneously fission’ is just a variation of the theme:
That chromosomal diversity of such distinct taxa is explicable by fission implies this mode of animal evolution is important.
Increases up to nearly doubling of smaller derivative chromosomes throughout the Cenozoic underlie adaptive radiations, at least in artiodactyls, carnivores, lemurs, Old World monkeys, and apes. (Kolnicki, 2000)
This is not the place to discuss the general applicability of Kolnicki-type processes, except that Müller’s hypothesized ancestor of the lesser apes (Hylobatidae or gibbons) may now be attributed too lightly to an amazing diploid chromosome number of 2n = 64. For clarity I simply discard any existing intention to derive great ape chromosomes from a similar hypothetic ancestor, confident that in the same effort nobody would try seriously to derive monkeys from great apes. All gibbons share the same three chromosomal fission events with other apes that compare with macaque chromosome numbers 2, 7 and 13 and the corresponding fissioned pairs: for humans chromosomes 7 and 21, 14 and 15, 20 and 22 respectively. This detail strongly pleads for an ultimate derivation of gibbon chromosomes from the same macaque-like ancestor having a reduced set of chromosomes (2n = 42), as well as from the same ancestral ape having 2n = 48 chromosomes like great apes. Then subsequent changes should have reduced the count for Hoolock genus to 2n = 38, an even lower diploid chromosome number than macaques, while for other gibbon genera the number is higher: 44 (Hylobates), 50 (Symphalangus) and 52 (Nomascus), respectively. This implies that all additional ape-related fusion events on chromosomal level, as observed for humans and gibbons, were preceded by these three fission events that are shared by all apes.
Fission is one way to trigger accelerated recombination, and to increase plasticity. Hybrid-driven recombination is another, whether or not in combination with the mechanism of fission. Reversely, biological justification of chromosome fusion may rather be found among the advantages of synteny, ie. the physical co-localization of genetic loci on the same chromosome. It is suggested that genetic change by hybridization is not an overnight process, and may create instability on chromosome level for at least a few generations. Hybridization of chromosomes and homogenization processes, per definition occurring after considerable divergence, opens up a whole new array of possible combinations, but also new risks of meiotic nondisposition. Natural selection could become a cumbersome, even impossible strain to reproduction if also the whole array of possible deleterious combinations would eventually result in low-fitness birth. Reproductive consequence would be less for miscarriages, or just lower rates of viable gametes. Still, even the fecundity of plants would be harmed by the possibility of unlimited recombination, not in the least for the reproductory investments of cycads that also have the record for the world’s largest sperm. Encapsulation of heterozygous content in fused chromosomes could reduce this risk to future generations. It goes without saying that fusion of chromosomes also offers a better protection against cytogenetic instability of hybrids. As such, fusion of chromosomes emerges as a potential strategy towards endogenous purifying selection and increased fitness of the hybrid lineage.
An example of chromosomal instability is trisomy, that typically results in miscarriage, or low-fitness offspring. Human low-fitness births related to trisomy are the Patau syndrome (trisomy 13), that affects somewhere between 1 in 10,000 and 1 in 21,700 live births, the Edwards syndrome (trisomy 18) that occurs in approximately 1 in 3,000 conceptions and half this rate for live births, with a median lifespan of 5–15 days, and the Down syndrome, whose incidence is due to trisomy 21 for 95% of the cases, and estimated at one per 800 – 1000 births.
Trisomies of all chromosomes with the exception of chromosome 1 have been reported in spontaneous abortions in humans; however, the only numerical autosomal anomalies surviving to birth are trisomies 13, 18, and 21. There are only six reported cases of autosomal trisomies in live horses ([...] 23, 26, 27, 28, 30, and 31) [...]. Similar to that observed in humans, trisomies in horses predominantly involve small chromosomes. (Brito et al., 2008)
Human trisomy indeed involves chromosomes that are either small (18, 21), or with low gene density (13), apparently important preconditions against a spontaneous abortion. Despite the deleterious nature of the three trisomy-ridden human chromosomes mentioned above, these already existed before the lesser apes split off from great ape ancestors. Chromosomes 13 and 18 must have been present even in the common ancestor of apes and macaques. Only different gibbon genera managed to neutralize these potential dangers by fusion: in Hylobates the equivalents of human chromosomes 13, 18 and 21 are all fused (respectively with chromosomes equivalent to 3, fissioned remnants of 1 and 15).
Even though Hominoidea chromosomes 13, 14, 15, 18, 20, 21, and 22 constitute a single, uninterrupted chromosomal block in the lar gibbon, most of them are part of larger chromosomes and/or show internal rearrangements. (Misceo et al., 2008)
Such evidence may indicate that chromosome fusion is neither coincidental nor imperative per definition. This is especially interesting for the unique fusion of two ancestral great ape chromosomes into human chromosome 2.
This fusion was evidenced by similarities in chromosome banding patterns as well as homologies in DNA sequences, where chimps make the best match. Normally, the extreme ends of chromosomes (telomeres) form a dynamic buffer against loss of internal sequences and prevent chromosomes from fusing, but apparently here telomeric DNA was involved in the fusion, to the extend that some telomeric DNA was preserved at location 2q13 near the new centromere.
Comparative cytogenetic studies in mammalian species indicate that Robertsonian changes have played a major role in karyotype evolution [..]. This study demonstrates that telomere-telomere fusion, rather than translocation after chromosome breakage, is responsible for the evolution of human chromosome 2 from ancestral ape chromosomes. (IJdo et al., 1991)
Somehow this event set us apart from great apes. As the assigned number indicates, chromosome 2 is our second largest chromosome. Commonly described as important for cognitive capacities, this particular fusion implies the importance of synteny for imposing genetic stability on cytogenetic level, that exceeds protection against semi-viable trisomy.
Evolving species may be expected to rely on an evolutionary boost to give them an edge. Since non-deleterious point mutations are rare, much depends on a quick and adequate mechanism to experiment with new complex DNA combinations. Species having low effective population sizes may have a problem if biological divergence is insufficient for regular recombination to produce successful genetic results. At major adaptive radiation events a species could recur to fission as a strategy to compensate for an initially low biological divergence. Next, increased divergence by the process of adaptive radiation may be expected to eventually reduce the need for fission – unless effective population sizes remain too low for harboring major biological variety. Lesser apes may have continued on the strategy of fission where great apes didn’t, implying their divergence probably occurred right here. Instead the lineage of great apes, including hominines, could take advantage of hybridization to incorporate successful mutations in the genome, no matter where these originated. This mechanism must have been a possibility within a certain time window, somewhere between population divergence and irreversible speciation. An extended continuation of this process may have relied on sub-species cross-breeding and hybridization – ie. contrasting with recurrent vicariance events as cited in the case of the gibbon genera, where low effective population sizes urged for continuous cytogenetic change in order to cope with the needs of environmental adaptation. Either way such periods of adaptive radiation should have left traces in the human chromosomes, not in the least if true hybridization was involved:
Contrary to the view that hybrids are lineages devoid of evolutionary value, a number of case studies are given that show how hybrids are responsible for reticulate evolution that may lead to the origin of new species. Hybrid evolution is mediated by extensive genome repatterning followed by rapid stabilization and fixation of highly adapted genotypes. Some well-documented cases demonstrate that bursts of transposition follow hybridization and may contribute to the genetic instability observed after hybridization. The mechanism that triggers transposition in hybrids is largely unknown. (Fontdevila, 2005)
Geneflow within the genetic continuum of a species happens all along, but let’s ‘[...] define hybridization as gene flow between two populations after an isolation barrier has formed between them.’ (Patterson et al., 2006 Supp.). The latter is most likely a major element in evolution, still waiting for recognition. And a potential cul de sac since, contrary to equids, zamia and gibbons, chromosomal changes in great apes and humans are far from impressive. No chromosomal fission event postdated the divergence from lesser apes, not even in hominin-specific evolution. Genetic recombination was significant enough for rapid change and plasticity, but apparently without the need for massive reorganization on chromosomal level, or even significant mutational activity on genetic level. Segmental duplications make a remarkable exception:
Although [the genomes of] terminal hominid lineages show an excess of [segmental] duplications, the most significant burst of activity (4–10-fold [...]) occurs in the common ancestor of human/chimpanzee and gorilla and after divergence of gorilla from the human–chimpanzee lineage [...] We note that this burst of duplication activity corresponds to a time when other mutational processes, such as point substitutions and retrotransposon activity, were slowing along the hominoid lineage. (Marques-Bonet et al., 2009)
Duplication indeed contributes to diversity, though indicative of actual genetic activity rather than anything else:
Gene models associated with signal transduction, neuronal activities (for example, neurotransmitter release, synaptic transmission) and muscle contraction are significantly enriched in human, chimpanzee and orang-utan lineage-specific duplications [...]. Human and great-ape shared duplications or those shared with macaque are, in contrast, enriched for biological processes associated with amino acid metabolism [...] or oncogenesis (Marques-Bonet et al., 2009)
Some sort of genomic destabilization is implied ‘at a period before and perhaps during hominid speciation’. But why and how this process could have been so different for humans, compared with an evolutionary strategy towards increased chromosomal change for lesser apes?
Exchange of alelles between hominine subspecies is nowadays sufficiently attested in modern genome research, but cross-breeding of diverging subspecies – or species! – should suggest chromosomal change of a higher order. Indeed, at least something has happened on chromosome level since the human divergence from apes, most notably the reduction of the chromosome count from 48 to 46, or the unique X-transposed region of the human Y-chromosome, dated right after chimp divergence and a virtually unprecedented event all by itself.
A third sequence class in the human MSY euchromatin — the X-transposed sequences — has no counterpart in the chimpanzee MSY. The presence of these sequences in the human MSY is the result of an X-to-Y transposition that occurred in the human lineage after its divergence from the chimpanzee lineage (Hughes et al., 2011)
Also chromosomal changes in chromosome 7, one of the new ape chromosomes that originated by fission, could be mentioned: the chromosome was subject to a pericentric inversion (including the centromere) after the divergence of orangutan, followed by a paracentric inversion after the divergence of gorilla. Another translocation of genetic information from chromosome 15 to chromosome 4 has been documented only for African apes: gorilla suffered deletions that preclude proper interpretation, but all derived basepairs of the 4q copy in chimps indicate this to be the result of hybrid recombination that happened before the divergence of gorilla:
If the duplication was followed by speciation and independent accrual of mutations, we would expect to find the human 15q and chimpanzee 15q copies to show higher identity to each other than either does to the copy found on chimpanzee 4q. Instead, the two chimpanzee copies are the most closely related pair of this trio.
By comparing ~19.1 kb of hand-curated, well-aligned block-5 sequences, we find that the chimpanzee 4q and 15q copies are only 1.43% diverged (Jukes-Cantor adjusted). They also share 43 derived mutations, including a 4-bp deletion that disrupts the ORF of gene H, not seen in the macaque or human 15q copies.
In contrast, the human 15q and chimpanzee 15q copies are 1.65% diverged and share 22 derived mutations not seen in chimpanzee 4q; and the human 15q and chimpanzee 4q copies are 1.64% diverged and share 13 derived mutations not seen in chimpanzee 15q.
(Rudd et al., 2008)
Such macro genetic events may be of an entirely different category than the published evidence that involve autosomal admixture of genetic regions from different hominine subspecies (Neanderthal, Denisova), or even of genetic harmonizing on the X-chromosome, already quoted as valid evidence for true cross-species genetic exchange with chimpanzee ancestors. Still, they are only in modest agreement with the prospected results of radical hybridization.
Notwithstanding an extended period of great ape evolution, lasting millions of years since the divergence of lesser apes, it has all appearance that over time hybridization remained a gradual process and rarely exceeded the level of subspecies crossbreeding.
Ever since this last major hybridization event(s) between chimp and human ancestors the hominine lineage apparently entered an extended period of rapid development. A full discussion is not the context of this article, but we can be sure nature did its utmost to exploit all available intra-species diversity to experiment with genetic recombination. There is an increasing awareness of natural interbreeding and admixture on subspecies level, whose impact on human evolution genetic science only started to disentangle. Another challenge still awaits us in the preposition that hominines could be essentially more related to orangutan than chimpanzees. Genetically this doesn’t seem right, but a successful hybrid is also a collation of DNA and morphology that rather define a new composition than an average of parental features. Current evidence corroborates to the implication that the genetic result of hybridization isn’t even random:
[...] endogenous selection is acting against intermediate hybrid individuals, that is, those that contain the highest number of alien genetic elements (Arnold, 1997). In a similar way, Rieseberg et al. (1996), working with H. anomalus, found that similar linkage groups of genes exist in several artificial hybrid lines with high fertility. (Fontdevila et al., 2005)
All we could propose is a complicated pattern of cross-breeding events to close the evolutionary gap of up to 16 million years since common Griphopiths precursors of great apes started to diverge.
Griphopithecins are the first cosmopolitan hominoid taxon, probably as a result of their powerful jaws and teeth that allowed them to exploit a wide variety of resources.
I see the entire region from Germany and Turkey in the north to Kenya in the south as a potential core area in which early hominids could have evolved. But there are major gaps in the record. For example, one species of Kenyapithecus is known from 16–16.5 Ma in Turkey and another from Kenya at about 13.5 Ma [...]. It was probably present elsewhere in the intervening interval of time but we have not yet found the fossils. From this core area these stem hominids (not specifically related to either living group of hominids, pongines, or hominines) eventually split, with one segment of the distribution of species dispersing to the north and east and another to the north and west. The causes of this dispersal are unknown, but griphopithecins are the most primitive hominids we know. The later-occurring sivapithecins of Asia and dryopithecins of Europe are more modern, and strong cases can be made that they are related to living orangutans and African apes and humans, respectively. (Begun, 2010)
If both components indeed represent sister lineages of apes rooted in the Miocene, it would be taunting to bolster this almost impossible preposition with genetic evidence.
I suggest the fuss about our purported lack of relatedness with the apparently quite basal gibbon genera might give us an important clue. If both great ape genera acquired their humanizing features by an extended period of hybridization, their common ancestor may indeed remind us to primitive small apes:
[...] Griphopithecus and its relatives retain primitive postcrania. They are more monkey-like than ape-like [...] without any indications of the suspensory capabilities of all later fossil and living great apes (Begun, 2010)
Cytogenetic evidence cited above reveals that chromosomes of small apes share the basic pattern that set great apes apart from macaques and thus may derive from an ancestor having eg. orangutan-like chromosomes. From this point onwards small apes can be defined as monophyletic, what may be confirmed by genetic evidence:
Among hominoid primates, gibbons alone contained Alu elements in their EIF1AY gene of the Y chromosome. (Kyung-Won Hong et al., 2007)
There have been different interpretations of the hylobatid evolutionary history regarding the four different gibbon genera, but: ‘Maximum likelihood and Bayesian analyses support Hoolock as the most basal, and both molecular and karyological studies have supported this alternative’ (Israfil et al., 2010).
Much of the uncertainty was caused by the implied ‘radiation of the main genera over an interval of less than 1 Ma’, what according to Israfil’s calculations happened between 6.4-8 mya. However, if this radiation event happened completely isolated from other apes then humans and two species of chimps should have an equal genetic distance to all gibbon genera. All the contrary, when distances between taxa were estimated by two measures of sequence divergence, using DNA sequence of the complete mitochondrial control region and adjacent phenylalanine-tRNA, the Hoolock stood out as the gibbon species being closest to all outgroups – especially humans. One way to interpret this results is to consider a much closer relationship between gibbons and great apes than vanity allows us to do, and a radiation event that was less monophylitic than commonly assumed. Instead, genetic evidence would indicate the various gibbon originated by a two-stage isolation from a common source of Miocene apes that were still interconnected by geneflow. The slightly greater distances with chimps in comparison with humans would then be explicable by proceeding geneflow within the clade of great apes, and – notwithstanding an extensive and quite recent history of chimp-human hybridization – a higher degree of (spatial?) isolation for the genetic component of chimps in comparison with humans. Humanizing processes didn’t advance within the gibbon genera as much as within great apes, including orangutan, what should remind us to the primitive stage of development the griphopith ancestors of great apes really had:
[Griphopiths] are more monkey-like than ape-like, as is Proconsul, in having fore and hind limbs of roughly equal length, without any indications of the suspensory capabilities of all later fossil and living great apes (Begun, 2010)
The divergence of the lineage leading to small apes must have happened long before at least two parallel lineages of great apes ‘humanized’ together with hominines. In the fossil record brachiating of great apes seems to develop first within the Dryopith clade, and at this stage one might wonder what could be the involvement here of a gibbon-type introgression event. Contrary to our Griphopith ancestors, modern humans and great apes retain many physical characteristics that suggest a brachiator ancestor, including flexible shoulder joints and fingers well-suited for grasping.
Dryopithecus [...] is known from postcranial remains, which are dramatically different from those of the griphopithecins and Proconsul. They show unambiguous indications of the importance of highly mobile limbs and suspensory positional behavior
I interpret this change to be extremely important in the evolution of the African and human clade. It allowed Dryopithecus to remain relatively large and yet retain the capacity to exploit terminal branch resources, by spreading its weight among the branches and by hanging below them to conserve energy [...]. It also represents the evolutionary origins of human mobile and highly dexterous upper limbs.
In addition to being relatively primitive compared to later species, the teeth of Dryopithecus differ from those of the griphopithecins in having a thin layer of enamel and less rounded cusps. They more closely resemble the teeth of chimpanzees and have been interpreted as adaptations to a soft fruit diet, as in modern chimpanzees [...]. The later occurring dryopithecins Hispanopithecus, Rudapithecus, and Ouranopithecus share even more postcranial derived characters with living great apes (Begun, 2010)
However, again the molecular dates remain difficult to reconcile with the fossil record:
The appearance of Dryopithecus at about 12 Ma parallels the first appearance of Sivapithecus at nearly the same time, suggesting that they diverged from a common ancestor possibly 13 to 16 Ma. (Begun, 2010)
The great ape-gibbon split simply doesn’t concur with the gibbon radiation dates:
Based on a consensus estimate of 15 Ma for the great ape-gibbon split, Chatterjee (2006) undertook molecular clock analyses using cytochrome b gene data and suggests the gibbon radiation dates to approximately 10.5 Ma. (Chatterjee, 2009)
This is still considerably less than the Raaum et al. (2005) estimate of a ‘divergence date of 15.0–18.5 Ma based on the entire mitochondrial genome’ (Chatterjee, 2009), thus apparently contradicting the possible hybridization signal mentioned above.
Molecular clock analysis is often used to estimate the date of speciation events in evolutionary history, but what can be said about its reliability? It didn’t come as a big surprise that paleoanthropologists were reluctant to abandon all the views they still cherished immediately for the sake of biochemistry:
[Wolpoff] admits [...] that ramapithecines are also a stem group for the African apes, whose tooth enamel is very thin. This would be a full reverse evolution towards a dentition very similar to that of Dryopythecus. Is this a parsimonious hypothesis? (Bonis, review on Wolpoff, 1982)
Schwartz criticized newly adapted scenarios ‘defending presumed phylogenetic hypotheses rather than rigorous presentations of such hypotheses’, that essentially left the purported ‘reversal’ in dental characteristics of chimps and gorilla back to the primitive conditions of Dryopithecines, unanswered.
I am not swayed by blanket statements of how similar Pan and [hominines] are because most of the similarities appear to be primitive retentions, and I am so far unpersuaded by karyological and biochemical studies for similar reasons as well as others.(Schwartz, review on Wolpoff, 1982)
Even Wolpoff, trying very hard to conciliate paleoanthropology with molecular evidence, couldn’t help to incite Sarich by stating:
Probably the best way to summarize the very disparate points raised is that the “clock” simply should not work [...] Consequently, although biochemical evidence seems to support a late Homo-Pan divergence, I believe this is a red herring, and that the molecular “clock”does not support any divergence time (Wolpoff, 1982)
One main issue that remains to be answered is how selective processes may have biased the genetic distances between species, and their biochemistry that, as a matter of fact, directly reflects evolutionary changes of their DNA.
Indeed, the molecular “clock” turned out unreliable because of variation ’caused, in part, by uncertainty or assumptions in key parameters, such as divergence times between species, generation times and ancestral population sizes’ (Conrad et al., 2011). But new results on the very mutation rates themselves indicate that apparently there is more internal logic to mutations on chromosome level than mathematicians were able to assume or deal with. Mutation rate differences exist and already turned out to be essentially individual:
[...] future studies promise to revolutionize our understanding of mutation processes and how they vary between individuals and between families as a result of age, genetic background and environmental exposures (Conrad et al., 2011).
This insight came too late for the immediate resurrection of our theorized ‘dental-hominoid’ ancestor, though in some act of posthumous generosity variable mutation processes should certainly provide for more nuance. How some basal species – humans, chimps and … hoolocks? – could remain genetically more ‘related’ on a molecular level than warranted by their morphological distance? Molecular constraints dictated that African apes and the hominine lineage should share a recent common ancestor, but the underpinning assumptions are still full of inconsistencies. ‘Single recent origin’ may be an interesting null-hypothesis to geneticists, but to paleoanthropology this increasingly reverts into the same unmanageable preposition as before. Molecular evidence is still a pretext to challenge common sense where it may oblige human minds to search for answers about themselves within a limited time window, that in turn implies a limited scope of geography. Adding here the constraints of emotional inquisition and lurking nationalism inherent to any limited region of choice, we could conclude ironically that paleoanthropology still finds itself right in the middle of all the fuss where Darwin’s theory of evolution once started.
- Milfred Wolpoff – Ramapithecus and Hominid Origins, 1982, link
- Reece et al. -
Campbell Biology, ninth edition, 2011, ISBN 9780321558237
- Grehan – Mona Lisa smile: the morphological enigma of human and great ape evolution, 2006, link
- Jeffrey H.Schwartz – Barking up the Wrong Ape–Australopiths and the Quest for Chimpanzee Characters in Hominid Fossils, 2004, link, or try here
- Feng-Chi Chen and Wen-Hsiung Li – Genomic Divergences between Humans and Other Hominoids and the Effective Population Size of the Common Ancestor of Humans and Chimpanzees, 2001, link
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- Beynon et al. – On thick and thin enamel in hominoids, 2005, link
- Hughes et al. – Conservation of Y-linked genes during human evolution revealed by comparative sequencing in chimpanzee, 2005, link
- Begun – Sivapithecus is east and Dryopithecus is west, and never the twain shall meet, 2004, link
- Begun – Miocene Hominids and the Origins of the African Apes and Humans, 2010, link
- Begun – Dryopithecins, Darwin, de Bonis, and the European origin of the African apes and human clade, 2009, link
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- Lebatard et al. – Cosmogenic nuclide dating of Sahelanthropus tchadensis and Australopithecus bahrelghazali: Mio-Pliocene hominids from Chad, 2008, link
- Fast Breaking Comments, 2001, By Martin Pickford
- Martin Pickford & Brigitte Senut – Hominoid teeth with chimpanzee- and gorilla-like features from the Miocene of Kenya: implications for the chronology of ape-human divergence and biogeography of Miocene hominoids, 2005, link
- Kordos & Begun – A new cranium of Dryopithecus from Rudabánya, Hungary, 2001, link
- Senut et al. – First hominid from the Miocene (Lukeino Formation, Kenya), 2001, link
- Wolpoff – Sahelanthropus or ‘Sahelpithecus’?, 2002, link
- Brunet et al. – A new hominid from the Upper Miocene of Chad, Central Africa, 2002, link
- Brunet et al. – New material of the earliest hominid from the Upper Miocene of Chad, 2005, link
- Michael Ashburner – The Genomes of Diptera, in Evolutionary Biology of Flies, edited by David K.Yeates and Brian M.Wiegmann, 2005, ISBN 0-231-12700-6, link
- Berger et al. – Australopithecus sediba: A New Species of Homo-Like Australopith from South Africa, 2010, link
- Bernhard Zipfel et al. – The Foot and Ankle of Australopithecus sediba, 2011, link
- Mijares et al. – New evidence for a 67,000-year-old human presence at Callao Cave, Luzon, Philippines, 2010, link or read review John Hawks: a foot short
- Plagnol & Wall – Possible ancestral structure in human populations, 2006, link
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Evolution is a slow process, not a magic stick that turns one species into another one. Could our species be the exception? This is worth a thought, now new genetic results reveal each and everyone of us descends from Neanderthal as well as other hominins.There is nothing gradual about the change of Neandertal into “us” and moreover, there is a growing awareness that other hominins besides early Anatomically Modern Humans (AMH) contributed their genetic share to the current human genepool. Maybe this traditional concept of evolution, that evolved from Darwins observations of the animal world, explains why Green et al. in their 2010 article “A Draft Sequence of the Neandertal Genome” rather picture the genome of modern humans conform the traditional view, ie. as the end point of a single human lineage “out of Africa”, that now according to new results amalgamated along the way at random with some stray genes from other hominins. However, what those allegedly exogenetic contributions to the modern genepool have in common are their sheer incompatibility with this hypothetised single human lineage, and the emergence of rapid genetic changes.
Green et al. investigated the differences between Africans and non-Africans in relation with the (draft) Neanderthal genome and revealed 1-4% of the modern human genepool could be accounted for by Neanderthal only. Green et al., 2010:
“Under the assumption that there was no gene flow from Neandertals to the ancestors of modern Africans, the proportion of Neandertal ancestry of non-Africans, f, can be estimated by…”
“Assuming that gene flow from Neandertals occurred between 50,000 and 80,000 years ago, this method estimates f to be between 1 and 4%“
“We note that a previous study found a pattern of genetic variation in present-day humans that was hypothesized to be due to gene flow from Neandertals or other archaic hominins into modern humans (81). The authors of this study estimated the fraction of non-African genomes affected by “archaic” gene flow to be 14%, almost an order of magnitude greater than our estimates, suggesting that their observations may not be entirely explained by gene flow from Neandertals.”
“We expect that further analyses of the Neandertal genome as well as the genomes of other archaic hominins will generate additional hypotheses and provide further insights into the origins and early history of present-day humans.”
But let us define “gene flow”: the study explicitly excluded shared ancestral genes and gene flow from Neanderthals to the ancestors of modern Africans. This 1-4% only reflects the measurable genetic differences between African and non-African haplotypes explained by Neanderthal, and thus is just a minimum amount. What we miss is an assessment of the maximum amount, that would instead reveal the percentage of early African genes that exclude any Neanderthal input in the genome of non-African modern humans. This could prove to be a much more cumbersome excercise, not in the least because we don’t know yet how to tell apart all truly African from other non-Neanderthal hominin genes.
Only the genetic deviations in modern humans with respect to the Neanderthal genome were investigated. None were found or mentioned in genes that nowadays harbour truly cross-hominin haplotypes. Previously the “European” H2 haplotype of the gene MAPT and the “Eurasian” haplotype D of the Microcephalin-1 gene were recognized as definitely different from the haplotypes associated to Homo Sapiens, and consequently dubbed (prematurely) “Neanderthal” by some. The sheer differences between the various haplotypes of such genes already suggested cross-breeding of hominins that share a common origin with modern humans that coalescence to dates that vastly exceed the AMH-Neanderthal split under investigation. Indeed, neither haplotype was found on Neanderthal and by default the Neanderthal version of MAPT and Microcephalin-1 must be considered compatible with the haplotypes commonly associated with modern humans. Green et al., 2010:
This analysis shows that some old haplotypes most likely owe their presence in present-day non-Africans to gene flow from Neandertals. However, not all old haplotypes in non-Africans may have such an origin. For example, it has been suggested that the H2 haplotype on chromosome 17 and the D haplotype of the microcephalin gene were contributed by Neandertals to present-day non-Africans (12,79, 80). This is not supported by the current data because the Neandertals analyzed do not carry these haplotypes.
Likewise, the study doesn’t resolve the precise origin of the other newly identified non-Neanderthal genes. Was the AMH gene pool already amalgamated with a wide variety of exogenetic hominin contributions at the moment African AMH and Neanderthal met? Such contacts should have increased the genetic differences between early African AMH and Neanderthal about the time of ingression. On the other hand, as far they could verify with modern genes, Green et al. were pretty determined that their Neanderthal samples did not feature ingression:
Thus, all or almost all of the gene flow detected was from Neandertals into modern humans.
This emerging picture of the AMH genome being like a sponge to exogenetic influences against isolated Neanderthal communities that preserved their genetic purity until extinction is amazing. Admixtures being confined to quite recent developments confirm the effects of culture in human evolution, that thus must have included increased contact and communicaton between hominin groups. To a certain degree admixtures may have involved even African AMH’s own African neighbours. Green et al.:
[...]old population substructure in Africa has been suggested based on genetic as well as paleontological data.
However, in the article this substructure suggested by Green et al. only concerned a possible African’s AMH or sub-saharan special relationship to Neanderthal up north:
If after the divergence of Neandertals there was incomplete genetic homogenization between what were to become the ancestors of non-Africans and Africans, present-day non-Africans would be more closely related to Neandertals than are Africans.
For sure, recent cross-hominin gene flow of the H2/MAPT or D/Microcephalin-1 type would require an African substructure much deeper than the one implied by this study. Older cross-hominin events may include “African” V and M haplotypes of gene ASAH1, where a coalescent-time depth of 2.4 million years ago tend to marginalize the differences with Neanderthal. The Green paper did not give a clue about the Neanderthal haplotype and thus does not resolve the question of potential post-split date hybridization in Africa. Based on dates and global currency, haplotype M could have been of heidelbergensis and haplotype V a successful African cross-hominin addition. Kim et al. 2007:
it should be noted that the pattern of genetic diversity of ASAH1 and other loci is compatible with the proposal that the human population was once geographically structured and genetically differentiated in Africa
The predominance of the V lineage is observed in both Africans and non-Africans
[...] Furthermore,the number of haplotypes in the V lineage is only 6, yet it is 11 in the M lineage. These hold true in both African and non-African samples
The most parsimonious explanation for the sharing of this pattern across all four [worldwide reference] populations is that the sweep occurred prior to the radiation of modern humans out of Africa.
the TMRCA of the V lineage is estimated as 200 +/-50KY from Genetree analysis [...] and 340 +/- 80 KY on the basis of the average nucleotide diversity [...] On the other hand, the TMRCA of the M lineage is 320 +/- 70KY from the Genetree analysis and 680 +/- 180 KY from the nucleotide diversity. Compared with the M lineage, the relatively recent origin of the predominant V lineage implies that it has been rapidly increasing in frequency.
Haplotype M/ASAH1 would not be surprising for Neanderthal, but haplotype V/ASAH1 would raise questions about the extend of early human hybridization events, and where it all started. Such and other potentially recent African cross-hominin evidence should put the impact of the Neanderthal lineage on modern humans in a completely different perspective. Unfortunately the Green paper didn’t intend to resolve the interbreeding questions already raised in previous publications on the subject. Moreover, single genes are hardly significant to the degree of admixture and the significance of African non-AHM contributions are still a matter of debate. Wall et al. (2009) insist on at least a considerable West African non-AMH hominin component:
We find evidence for this ancient admixture in European, East Asian, and West African samples, suggesting that admixture between diverged hominin groups may be a general feature of recent human evolution.
Instead, the announced results of a New Mexico investigation “didn’t find evidence of interbreeding in the genomes of the modern African people included in the study” (Nature News,20 April 2010). Conventional wisdow still has it that hominin admixture was a recent AMH feature, primarily linked to Out of Africa expansions and post-dating the AMH-Neanderthal split, but at least an African origin of haplotypes H2/MAPT and D/Microcephalin-1 would apply for special pleading. A specifically eastern Asian RRM2P4 haplotype even computes a coalescent-time of 2.3 million years ago and a quite short LD sequence virtually rules out a recent adquisition of this gene – that moreover must have been confined to the people of eastern Asia!
Let us return to the 1-4% measurable admixture. Like John Hawks already put it, this estimate “is so high that this is not just a few genes introgressing in from Neandertals — it is a big fraction of the neutral, non-coding part of the genome.” This portion was deduced from the signal of gene flow retrieved from the segments with the lowest divergence to Neanderthal: [Non-African] “segments, with few differences from the Neandertals, tend to have many differences from other present-day humans, whereas African segments do not“. However, I don’t agree it is just this “visible” part of the Neanderthal genome that survived. This must be just the low-mutation-rate part of Neanderthal that pops up from the graphs, where strongly homogenizing selective forces in Africa about 200 kya must have reduced variability among AMH. Subsequent strong selective forces during AMH expansion kept variablity lower at non-African high mutation rate segments.
The premise of this certainty of dealing with Neandertal admixtures is that other causes of a low divergence to Neanderthal, such as low mutation rates, “would produce monotonic behaviors” on the above diagram. Here it shows that African and non-African segments that most closely resemble the Neanderthal genome may diverge considerably from the reference genome of mister Craig Venter, thus confirming high variability, and 94% of these diverging, high variability genes are of confirmed European ancestry. Moreover, the results of “identified regions in which there is considerably more diversity outside Africa” (Green et al.) show 80% tag SNPs (133 out of 166) and 83% of the regions (10 out of 12) pointing to a specific Neanderthal origin. Note the potential contribution of other hominins to this unexpected variability seems to be rather low, and we can only assume the remaining non-Neanderthal tag SNPs and regions could be African – if this weren’t so contradictory to Out of African type bottleneck scenarios. All these results seem to be in sheer contrast to concurrent genetic and phenotype results that rather indicated a “smooth loss of genetic diversity with increasing distance from Africa” (Manica et al., 2007). The contradictory clines involved inhibit a simple extrapolation of the diagram to the Neanderthal survival of the remaining 96% of their genome, ie. somewhere hidden on the part where diagram behavior is “monotonic” (ie. a straight line). Basically, in line with the comments made by Relethford, 2008, the current data doesn’t exclude this possibility at all:
[...] the observation of higher African diversity supports the other genetic (and fossil) evidence for an African origin for modern humans, but does not distinguish between an African origin with replacement and an African origin with admixture outside of Africa except to say that if there was any admixture it was not of sufficient magnitude to erase the genetic signature of an African origin.
High non-African variability on certain regions is remarkable, but so is the implied low African variability at these same locations. Let us reverse the assessment and consider the potential backmigration or diffusion from a hybrid source in Eurasia into Africa, conform the one already implied by the purported cross-hominin D haplotype of the microcephalin-1 gene found in only 30% of subs-saharan Africans. The Green paper is not conclusive about the origin of African counterparts of the mentioned non-African high variability genetic regions, but for sure the ingression back into Africa of a reduced set of “bottlenecked” non-African haplotypes would have a similar result on the diagram if regions of higher Neanderthal divergence were caused by higher mutation rates of these regions, and thus bottlenecked were to remain within the bandwith of African variability. However, the low world-wide frequency of this off-modal variability would also imply the reduction of high mutation speed variability among non-African populations, possibly due to some kind of post-Neanderthal event. This scenario would be in agreement with a more recent ingression of new genes and the heavy selective pressures implied during this process.
It should be investigated if much of the higher African variability indeed involve segments having a higher mutation rate, since strong natural selection at an early stage, contrary to the Neanderthal situation, could have obliterated much of the deeper African substructure. If this would be the case, there wouldn’t be any argument left against extrapolating the survival of virtually the whole genome of Neanderthal among non-Africans – i.e. except for the few genes and sweep areas associated to AMH related evolutionary changes elsewhere. This result would be irrespective of the African substructure proposed by Green et al. or sheer Neanderthal relatedness of early AMH, and in agreement with the announced New Mexican results, that Africa remained largely exempt of reminiscent cross-hominin interbreeding variability. African hybridization, if any, thus would have been concurrent with strong selective processes.
Long time, bidirectional genetic diffusion should be taken in consideration, and we still don’t know to what extend the advance of AMH into Neanderthal territory also involved hybridization with other hominins. However, having this assumption of 1-4% of the modern human genome just being the detectable part of the surviving Neanderthal genome in mind, it will be much easier to estimate Neanderthal survival. Green et al. (2010) estimate the frequency of candidate Neanderthal regions among non-Africans averaging “13%, and all less than 30%“. Now even the Mesolithic survival of Europeans as a result of the Neolithic wave of advance is still a matter of scientific dispute, this possible 13% Paleolithic result of potential Neanderthal survival may shed more light on this issue.
The real Neanderthal differences were found in regions where “the Neanderthal carries fewer derived alleles than expected relative to the human allelic states. A unique feature of this method is that it has more power to detect older selective sweeps”, ie. neighbouring DNA of a mutation in a region that defines a haplotype where reduced variation is an indication of few chromosome cross-overs, and thus of recent and strong positive natural selection. Such haplotypes are often referred to as a region of LD (linkage desequilibrium) for being characterized by DNA patterns that are overrepresented in the population, thus being not as random as it should be after a certain count of cross-overs. The Green et al. investigation yielded a limited set of such AMH related genetic regions that are low or depleted of Neanderthal derived alleles, and that thus could prove useful in the search for the genome or genomes of African hominins.
We identified a total of 212 regions containing putative selective sweeps [...] We ranked the 212 regions with respect to their genetic width [...] because the size of a region affected by a selective sweep will be larger the fewer generations it took for the sweep to reach fixation [...] Thus, the more intense the selection that drove a putative sweep, the larger the affected region is expected to be. [...] The widest region is located on chromosome 2 and contains the gene THADA,where a region of 336 kb is depleted of derived alleles in Neandertals. [...] Changes in THADA may thus have affected aspects of energy metabolism in early modern humans. (Green et al., 2010)
Mutations in several genes on the 20 widest regions have been associated with diseases affecting cognitive capacities. One single AMH gene at such a location (RUNX2) was suggested to be related to the most striking morphological changes associated with the Neanderthal “extinction”.
The Green paper is not very clear about the reasons why these sweep areas are lower in derived Neanderthal DNA compared to other regions, except for saying that the method to identify regions where the Neandertal carries fewer derived alleles than expected relative to the human allelic states [...] has more power to detect older selective sweeps. This by itself has the potency to even put the truly ‘Sapiens’ origin of this cherrypicked sweep areas in doubt, if the difference with Neanderthal would turn out to be too much. Note it is useless to play down the Neanderthal component based on unrelated selective sweep areas, while even larger sweep areas from a different hominin origin exist that are not even as closely related to AMH as Neanderthal. E.g. Hardy et al. (2005) about the (non-Neanderthal) H2/MAPT haplotype:
Interestingly, a recent assessment of LD (linkage disequilibrium) across the genome in different populations suggested that the MAPT locus was the longest region of LD in Europeans.
A close relationship between AMH and Neanderthal only solves part of the problem of knowing what DNA haplotypes originated where. Indeed, it complicates matters considerably knowing that especially the larger sweep areas of the AMH genome segments found exceptionally low in derived Neanderthal DNA, qualify most for being admixtures from hominins unrelated to AMH. Successful genes are most likely to reach saturation and to become fixed into the whole human population, and also are most likely to reduce overall variability. A deep African substructure as a source for new genes that are low in derived Neanderthal DNA would only make sense if evolution accelerated also among groups whose genes were less related to AMH’s proposed Neanderthal-like kin in the neighbourhood. However, the African origin of AMH is currently sought in the north of sub-saharan Africa, not south. Those AMH thought to have ultimately passed the selective sweep out of Africa thus should have received at least some genetic improvements from further south, what is remarkable considering the attested focus of AMH development around Ethiopia. If the alternative could be sought rather in local hybridization then one might wonder about the fate of southern African hominins. Where did the evidence of interbreeding go in the genomes of the modern African people? Indeed, the team of the University of New Mexico that conducted this analysis, due for publication in the near future, claims no such evidence exists. The gradual increase of variability towards the south is no argument in favour of interbreeding, nor acceptable as evidence of a southern African origin of AMH. It is evidence of continuity.
At the annual meeting of the American Association of Physical Anthropologists in Albuquerque, New Mexico, on 17 April, this team asserted that extinct species interbred with the ancestors of modern humans twice, allegedly first at about 60,000 years ago in the eastern Mediterranean. Nature News: “The researchers suggest that the population from the first interbreeding went on to migrate to Europe, Asia and North America. Then the second interbreeding with an archaic population in eastern Asia further altered the genetic makeup of people in Oceania.” The precise details are still unpublished, but especially the genetic interbreeding model of the second event “at about 45,000 years ago in eastern Asia” raises questions “about the range of species, like H. heidelbergensis”, since “Human skeletons found at Lake Mungo in New South Wales, Australia, have robust features, which may represent the result of interbreeding“.
Homo heidelbergensis is often considered the last direct ancestor of both Neanderthal and modern humans, though others rather consider Homo antecessor in this role. The remains of this hominins center in Spain and are dated between 1.2 million and 800,000 years ago. About 600 kya the first heidelbergenses in Europe already appear to be on the the evolutionary line to Neanderthal. Ever more robust forms of purported heidelbergensis derivation arrived on the scene, but not only in future Neanderthal territory. Robust phenotypes appeared almost everywhere, including southern Africa where apparently closely related forms (Rhodesia Man) became prominent between 600 – 250 kya. However, not even the mtDNA split date between Neanderthal and modern humans exactly indicate Homo antecessor as the most recent common ancestor (MRCA):
mean = 465,700 years ago; 321,200–618,000 years ago, 95% HPD (Krause et al., 2010)
The specimen of Rhodesian Man found at Broken Hill, Zambia, also referred to as Kabwe skull, put the mark of a general development towards maximum robustness before this African lineage gave away to a geographically rather scattered development towards gracile AMH. Unfortunately there is a dating problem here. Rhodesian Man shared many morphological features with rapidly modernizing precursors of AMH in northeast Africa that could have been contemporaneous. Like European Neanderthal, it doesn’t look like Rhodesian Man was much in a hurry to evolve into the “right” direction. Human modernization probably reached southern Africa from the north. It is striking that geographic isolation probably wasn’t a precondition to the development of African AMH, since an Ethiopian origin is rather somewhere in the middle between Neanderthal and Broken Hill. Indeed, rather quite close to the eastern Mediterranean, where according to the New Mexico team, in a Recent Out of Africa (ROA) scenario about 60,000 years ago, the first Neanderthal hybridization event should have taken place.
The current substructure and global distribution of mtDNA is unlikely to resolve the origin, for being too young. The mitochondrial “Eve”, the female MRCA that was the ancestral mother of all modern humans, was born only 200,000 years ago, making it impossible to even define an older African origin. In the vein of recent insights this discrepancy could be interpreted as a strong signal of natural selection involving mitochondria, even within Africa. In his blog article on the new paper of Green et al. John Hawks reproaches everyone that still don’t know, and that take their misconception as an argument in favour of extinction scenarios:
I’ve been saying it for years. I’ve published it. Will you learn to listen to me, already?
The mtDNA of Neandertals is gone because it conferred some disadvantage. There are many reasons to suspect this — the Neandertal variation is itself apparently recently derived; the human variation is clearly in disequilibrium, especially outside Africa; the mtDNA genes affect functions that differ greatly in Neandertal and recent populations, including energetics, longevity, and brain; there are clear signs of mtDNA selection in many recent human populations.
But where did the pre-sapiens mtDNA in Africa go in view of a heidelbergenis takeover, and did current mtDNA really originate in Africa? Neanderthal mtDNA isn’t so very different to take this for granted anymore. The overwhelming success of apparent heidelbergensis mtDNA and the absence of a significant signal of African hybridization may imply the death blow to older African lineages before heidelbergensis. Current African variability can’t even beat the overall post-heidelbergensis variability deduced from a draft of the Neanderthal genome. Extinction scenarios like those that traditionally accompany Out of Africa hypotheses may not be utterly useless after all.
Mitochondrial extinction was not just an issue of Neanderthal: the age of mtDNA recovered from LM6, the early modern human of Lake Mungo, Australia, even exceeds the age of modern mtDNA. Similar DNA at chromosome 11 of especially Eurasian modern humans indicate an inclusion event of a type of mtDNA that may have been common outside Africa once, and that may point to an eastern expansion of heidelbergenses dating back up to even 300,000 years ago. This mtDNA coalescent-time depth suggests that eastern Asia and Oceania may have been overrun by the heidelbergenses that were geographically closer to East Africa. In between, in the Middle East, the type of mtDNA might have changed with the fortunes of Neanderthal, or otherwise early Asiatic Neanderthal may have been the carriers of this type of mtDNA, in which case there should have been a reversed link to eastern Africa. The findings of Xinzhi Wu are in agreement to the latter:
There is a morphological mosaic between H. s. erectus and H. s. sapiens in China. The existence of common features and the morphological mosaic suggest continuity of human evolution in China. That there are a few features which are more commonly seen in the Neanderthal lineage, occurring in a few Chinese fossil skulls, probably suggests gene flow between China and the West. (Xinzhi WU, 2004)
Based on the evidence of continuity and gene flow, a new hypothesis, Continuity with Hybridization, was proposed in 1998 for characterizing human evolution in China. (Xinzhi WU, 2004)
At least across the eastern fringes of generally accepted Heidelbergensis/Neanderthal territory, hybridization was noticed in the fossile record, suggesting this process started indeed long before the purported exodus of AMH out of Africa.
“It is also suggested the Homo heidelbergensis is represented in Asia by the Dali skull and the Jinnishuan skeleton, both from China, and dated at between 200,000 and 300,000 years old. Precise dating of these fossils is important, because they might be contemporaneous with the last Homo erectus fossils in China” (de Arsuaga & Martinez, 1998)
According to the New Mexico announcement, hybridization in East Asia has been confirmed on the genetic level. A possible origin in a hypothetized African substructure in a Recent Out of Africa scenario is no issue here, though the investigators are careful to link a possible pre-Sapiens reminiscence in the East Asiatic (and Oceanic) genes to more or less related heidelbergensis rather than local hominins in the region that derive directly from much older forms. Nature News:
Theodore Schurr, a molecular anthropologist at the University of Pennsylvania in Philadelphia, said the genetic model showing interbreeding raises questions about the range of species, like H. heidelbergensis.
The exotic genetic results of the Denisova hominin, for that matter, proves that we can’t think too light about the close genetic distance of eastern Asian people to the rest of the world. The genetic differences of hominins that developed in isolation for such a long time should have left a mark impossible to miss. The few haplotypes of genes that indeed attest an extremely high age, just don’t add up to appreciable levels of admixture that, like now attested with Neanderthal, represent a certain percentage. Thus all along the bulk of exogenetic influences appears drowned amidst very much related heidelbergensis genes, whose differences to modern genes can be assumed to be more moderate. The coalescent-time depth of heidelbergensis is much less than a million years while the genus Homo might be three times that age.
The early arrival of heidelbergensis as a new hominin quickly replacing older hominins, also created an opportunity to differentiate into geographical phenotypes. Naturally, the degree of differentiation would increase closer to the place of the heidelbergensis origin. The proximity of Europe and West Africa to Iberia, home to the above mentioned ancestral Homo antecessor, would locate potential hotspots of heidelbergensis variability in those same places, thus making heidelbergensis hybridization feasible. Contact zones could be assumed at the fringe of heidelbergensis dispersal, but also close to more archaic forms that may now be assumed in Neanderthal Europe and West Africa. Prospected contact zones for hybridization can thus be hypothetized to include geographic regions where diverged branches of a wider heidelbergensis family (also Neanderthal, early sapiens etc) probably met:
- Middle East, the most likely contact zone between African sapiens and Neanderthal
- West Africa, probably not so far from the oldest heidelbergenses and deepest heidelbergensis substructure in case of an important role of nearby Homo antecessor as an inmediate precursor
- China, the likely scene of prolonged contact that most probably involved much earlier local hominins as well
Without exception, these prospected zones of genetic interaction and the earliest hotspots of modern features in the fossile record turn out to be close together. Indeed, the earliest attestations of AMH also include Morocco at the western side of Africa:
… an early Homo sapiens juvenile from Morocco dated at 160,000 years before present displays an equivalent degree of tooth development to modern European children at the same age. (Smith et al., 2007)
These include China, where “existence of common features and the morphological mosaic suggest continuity of human evolution” (Xinzhi WU, 2004) from about 200 kya, when hominins like Dali start to appear.
Attestations, of course, also include NE Africa, at the perifery of the Middle East, where the first emergence of AMH (Omo I and II) appears to be especially typified by variety, rather than being evidence of a single, isolated lineage. McDougall et al., 2004:
Here we confirm that the Omo I and Omo II hominid fossils are from similar stratigraphic levels in Member I of the Kibish Formation, despite the view that Omo I is more modern in appearance than Omo II
Our preferred estimate of the age of the Kibish hominids is 195 5 kyr, making them the earliest well-dated anatomically modern humans yet described.
Hominin variety has been noticed and studied before, but rarely to this degree at a single site. The evolutionary trend towards the modern features of AMH is not unlikely to have been preluded by inter-hominin contact, cq. starting about 200kya, rather than that inter-hominin contact was the unequivocal result of quite recent AMH expansions “out of Africa”. Like Garrigan et al. already put it in 2005:
Alternatively, the AMH phenotype may be the by-product of such admixture events.
What new clue would this observation give us about the evolution of AMH?
Cosmopolitan behavior and universal physial acceptance might have been of prime importance to those early humans that were located at the inter-hominin contact zones, and whose survival depended on their ability to cope with human differences, both physical and behavioural. The underlying assumption is that communication and language can be properly understood by taking into account their relation with other important behavioural, social, and cognitive processes – and the corresponding genetic modifications to ascertain a selective advantage. About 200 kya the level of human development must have reached a critical point, when the most economic response to first contact with other groups had changed. The nature of selective forces changed as well, thus accelerating cognitive improvements that boosted the evolution of e.g. that select set of genes mentioned by Green et al., 2010. Indeed, this must have happened right in the middle of contact zones.
Note accelerated evolution in contact zones doesn’t strictly imply hybridization, since it basically involves an adaptive response to increased environmental stress due to the demands of frequent “cosmopolitic” contacts.
Physical acceptability might have been another factor. Wearing clothes could have been one strategy to conceal the differences and this custom seems to originate from about the same time. Science News, 8th of May 2010:
Using DNA to trace the evolutionary split between head and body lice, researchers conclude that body lice first came on the scene approximately 190,000 years ago. And that shift, the scientists propose, followed soon after people first began wearing clothing.
Cloths as a social invention would overcome the practical arguments against a correlation with decreasing body hair in hot climates.
The human response to the physical appearance of others might also have accelerated the development of typical “modern” features that accompanied the rise of AMH. A positive response that commonly derives from typical “child-like” features associated with AMH might have invoked another strategy involving physical change. The investigation of Green et al., 2010, teaches us that much of these modernizing changes are possibly regulated (suppressed?) by a single new gene, considered exempt from a Neanderthal origin:
One gene of interest may be RUNX2(CBFA1). It is the only gene in the genome known to cause cleidocranial dysplasia, which is characterized by delayed closure of cranial sutures, hypoplastic or aplastic clavicles, a bell-shaped rib cage, and dental abnormalities (70). Some of these features affect morphological traits for which modern humans differ from Neandertals as well as other earlier hominins. For example, the cranial malformations seen in cleidocranial dysplasia include frontal bossing, i.e., a protruding frontal bone. A more prominent frontal bone is a feature that differs between modern humans and Neandertals as well as other archaic hominins. The clavicle, which is affected in cleidocranial dysplasia, differs in morphology between modern humans and Neandertals (71) and is associated with a different architecture of the shoulder joint. Finally, a bell-shaped rib cage is typical of Neandertals and other archaic hominins. A reasonable hypothesis is thus that an evolutionary change in RUNX2 was of importance in the origin of modern humans and that this change affected aspects of the morphology of the upper body and cranium.
A natural selection-driven advance of a small set of modernizing genes would do the rest of the trick. Neanderthal did not evolve slowly to AMH, but neither did Neanderthal disappear. Neanderthal survived, because they tricked human evolution by swaying the magic stick. The Neanderthal phenotype disappeared as rapidly as it took for a small set of AMH genes to gain prevalence. Cultural changes were the precondition for the success of these new genes, including RUNX2. The physical change could have been a matter of a couple of generations.
Or does all of this mean that Neanderthal disappeared anyway, because Neanderthal hybridization already happened long before AMH entered Europe and the rest of the world? Very unlikely, since on their natural selection-driven way through European Neanderthal territory, the new AMH genes were brought by those that also carried the exclusive haplogroup H2/MAPT gene. The Neanderthal genes may have been the same east and west, so instead we have to focus on the way how AMH genes entered. Now understanding hybridization better as the trigger for AMH related change, we should recognize this cross-hominin genetic MAPT admixture as the genetic marker to be associated with the “modernization” of European Neanderthal. This is the ultimate indication that AMH related hybridization didn’t stop in the Middle East. The magic stick even touched some unknown, unrelated hominin that exclusively roamed European Neanderthal borderland on the eve of modern ingression, but none could override the Neanderthal genes already there.
- Green et al. – A Draft Sequence of the Neandertal Genome, 2010, link
- Xinzhi Wu – On the origin of modern humans in China, 2004, link
- Xinzhi Wu – Fossil Humankind and Other Anthropoid Primates of China, 2004, link
- Garrigan et al. – Evidence for Archaic Asian Ancestry on the Human X Chromosome, 2005, link
- Burbano et al. – Targeted Investigation of the Neandertal Genome by Array-Based Sequence Capture, 2010, link
- John Hawks Weblog – Neanderthals Live! 2010, link
- John Hawks Weblog – Multiregional evolution lives! 2010, link
- Hardy et al. – Evidence suggesting that Homo neanderthalensis contributed the H2 MAPT haplotype to Homo Sapiens, 2005, link
- Neanderthals may have interbred with humans – Nature News 20 April 2010, link
- Wall et al. – Detecting Ancient Admixture and Estimating Demographic Parameters in Multiple Human Populations, 2009, link
- Manica et al. – The effect of ancient population bottlenecks on human phenotypic variation, 2007, link
- The Human Lineage – Matt Cartmill,Fred H. Smith,Kaye B. Brown, 2009, link
- Juan Luis de Arsuaga and Ignacio Martínez – The chosen species: the long march of human evolution, 1998, English translation 2006, link
- Smith et al. – Earliest evidence of modern human life history in North African early Homo sapiens, 2007, link
- McDougall et al. – Stratigraphic placement and age of modern humans from Kibish, Ethiopia, 2004, link
- Science News – Lice hang ancient date on first clothes, May 8th, 2010, link
- Garrigan et al. – Deep haplotype divergence and long-range linkage disequilibrium at xp21.1 provide evidence that humans descend from a structured ancestral population, 2005, link
- Hie Lim Kim and Yoko Satta – Population Genetic Analysis of the N-Acylsphingosine Amidohydrolase Gene Associated With Mental Activity in Humans, 2008, link
- Relethford – Genetic evidence and the modern human origins debate, 2008,link
Nobody expected a great surprise. Genetic testing of the little finger of an early hominin child found in the Siberian Denisova Cave, Kostenki, in the middle of archeological remains pertaining to Upper Paleolithic culture, would almost for sure confirm DNA similar to ours. There was a slim change that the pinky belonged to a Neanderthal from the neighborhood that got lost, but everything pointed at a an unequivocal member of the advanced group of hominins responsible for introducing symbolic art all over the world, the so-called anatomically modern humans (AMH).
The collection of personal adornments and artifacts suggestive of symbolic behavior from the Early Upper Paleolithic deposits of Denisova Cave, Altai, is one of the earliest and the most representative of the Upper Paleolithic assemblages from Northern and Central Asia. Especially important is a fragment of a bracelet of dark-green chloritolite, found near the entrance to the eastern gallery of the cave in the upper part of stratum 11. The estimated age of the associated deposits is ca 30 thousand years. According to use-wear and technological analysis, techniques applied for manufacturing the specimen included grinding on various abrasives, polishing with skin, and technologies that are unique for the Paleolithic – high-speed drilling and rasping. The high technological level evidences developed manual skills and advanced practices of the Upper Paleolithic cave dwellers. (Derevianko et al., 2008)
Neanderthal were readily dismissed as potential authors of local Upper Paleolithic art, due to what boils down to a deep distrust against anything that would deem them capable of such a feat, and they were the only other early hominins around that we knew of – at least culturally speaking, since we don’t have much more than a little pinky after all. And indeed, the first genetic results showed the world was right about one thing: the little finger did not belong to a Neanderthal child. But nobody could have guessed how wrong the usual lot of junk scientists were about almost anything else. This was not the child from the same flesh and blood of modern humans, but a member of a previously unknown ancestral human subgroup.
Dr. Johannes Krause, of the Max Planck Institute in Germany, sequenced the entire mitochondrial DNA (mtDNA) genome and showed almost two times as many differences to modern human mtDNA as does Neanderthal mtDNA. You can find the genome at GenBank or EMBL using record ID FN673705 and check it out by yourself: Even Neanderthal was a close relative to modern humans compared to this hominin!
A phylogenetic analysis similarly shows that the Denisova hominin mtDNA lineage branches off well before the modern human and Neanderthal lineages (Fig. 3). Assuming an average divergence of human and chimpanzee mtDNAs of 6 million years ago, the date of the most recent common mtDNA ancestor shared by the Denisova hominin, Neanderthals and modern humans is approximately one million years ago (mean = 1,040,900 years ago; 779,300–1,313,500 years ago, 95% highest posterior density (HPD)), or twice as deep as the most recent common mtDNA ancestor of modern humans and Neanderthals (Krause, 2010)
Established paleo-anthropology is now faced with the challenge to rewrite the book of human evolution. And of course first things first, the dates were adjusted to make a better fit with pre-AMH cultures:
We note that the stratigraphy and indirect dates indicate that this individual lived between 30,000 and 50,000 years ago. At a similar time individuals carrying Neanderthal mtDNA were present less than 100 km away from Denisova Cave in the Altai Mountains, whereas the presence of an Upper Palaeolithic industry at some sites, such as Kara-Bom and Denisova, has been taken as evidence for the appearance of anatomically modern humans in the Altai before 40,000 years ago. (Krause et al., 2010)
Nobody has ever heard of pre-AMH bracelets, so let’s conveniently forget for a while about that fragment of a polished bracelet with a drilled hole, that was found earlier in the same layer that yielded the bone. Is it possible that here we have evidence that points to a third species, next to Neanderthal and AMH? A species, that might have been as civilized as a AMH, or a beast our ancestors didn’t breed with, or anything else that didn’t involve “us” so we can understand? The publication of Krause carefully omitted this pressing question and the word went out that for sure Krause had already access to autosomal data that could explain why. That Denisova child might have been anything but a Yeti.
Sure, mtDNA doesn’t make a species, no matter how different it may be from modern humans. There was no need for Krause to mention this. But divergence of mtDNA lineages has been taken as an indication of divergent hominin developments before. Explicitly with respect to Neanderthal, whose attested and validated mtDNA lineage was deemed sufficiently homogeneous and different from ours to provoke a definite ordeal. However, now we have the Denisova mtDNA sample to teach us modesty. After all, there are lots of things about mtDNA that need better understanding before we can even attempt to solve the question of how the modern forms spread, and how they evolved.
All conspires against the notion that paleogenetic mtDNA of Neanderthal, and now even more so the mtDNA from Denisova Cave, might be the precursor of modern mtDNA. It couldn’t have evolved so rapidly to modern mtDNA. A study on 44,000-year-old remains of Adelie penguins in Antarctica even confirmed the potential overestimation of the mutational change that is used for dating mtDNA of paleogenetic samples. This stems from a bias that is caused by nonsynonymous mutations, involving notable coding changes that are potentially deleterious and most likely won’t persist very long due to natural selection. Accordingly, only a portion of the mutational changes can be observed over a longer period of time:
Rates of evolution of the mitochondrial genome are two to six times greater than those estimated from phylogenetic comparisons. Subramanian et al., 2009)
The investigation showed that only the effect of synonymous mutations (“silent mutations”) in the mtDNA genome, that involve coding synonyms for the same proteins, remain stable. To retrieve the phylogenetic dates only these “silent mutations” should be measured, ie. changes on coding genes that produce coding synonyms that won’t affect the function of the gene. Mutations that effectively change the functionality of a gene and thus are most likely to be (slightly) harmful, get lost over time, since such mutations would finally bring about the extinction of a lineage and thus shouldn’t count for calculating the age of surviving lineages. The mtDNA “molecular clock” thus should only involve properly identified “silent mutations”.
This results were also important for interpreting the paleogenetic mtDNA samples of hominins.
Mildly deleterious mutations initially contribute to the diversity of a population, but later they are selected against at high frequency and are eliminated eventually. Using over 1,500 complete human mitochondrial genomes along with those of Neanderthal and Chimpanzee, I provide empirical evidence for this prediction by tracing the footprints of natural selection over time. The results show a highly significant inverse relationship between the ratio of nonsynonymous-to-synonymous divergence (dN/dS) and the age of human haplogroups. Furthermore, this study suggests that slightly deleterious mutations constitute up to 80% of the mitochondrial amino acid replacement mutations detected in human populations and that over the last 500,000 years these mutations have been gradually removed. (Subramanian, 2009)
Interestingly, this dN/dS ratio among Neanderthal was initially reported strikingly high.
These results suggest that slightly deleterious amino acid variants segregate within populations, and that differences in the intensity of purifying selection may affect mtDNA dN/dS ratios. Previous estimates based on mean pairwise differences (MPD) within the mtDNA HVRI suggested that Neandertals (MPD = 5.5) had an effective population size similar to that of modern Europeans (MPD = 4.0) or Asians (MPD = 6.3), but lower than that of modern Africans (MPD = 8.1) (Krause et al., 2007b). Recent population genetic analyses have revealed a higher mtDNA amino acid substitution rate (Elson et al., 2004) and relatively more deleterious autosomal nuclear variants (Lohmueller et al., 2008) in Europeans than in Africans, presumably due to the smaller effective population size of Europeans. Thus, it seems plausible that Neandertals had a long-term effective population size smaller than that of modern humans. (Green et al., 2008)
However, the new information supplied by the Denisova hominin reveals this assumed feature of Neanderthal mtDNA was actually a mistake:
The 12 proteins encoded by the Denisova hominin mtDNA (excluding ND6, Supplementary Information) show low per-site rates of amino acid replacements (dN) when compared to the per-site rates of silent substitutions (dS), consistent with strong purifying selection influencing the evolution of the mitochondrial proteins (dN/dS=0.056). Notably, when the evolution of mitochondrial protein-coding genes in modern humans, Neanderthals, chimpanzees and bonobos is gauged in conjunction with the Denisova hominin mtDNA, a previously described reduction of silent substitutions causing an increased dN/dS in Neanderthals is not observed. This is probably due to a more accurate reconstruction of substitutional events when the long evolutionary lineage leading to modern humans and Neanderthals is subdivided by the Denisova hominin mtDNA (see Supplementary Information) (Krause et al., 2010)
The immediate result of this new finds is that an earlier proposed reduction in length of the Neanderthal mtDNA lineage “about three times as large as would be expected if it was entirely due to the age of the fossil” (Green, 2008), resulting in an earlier common ancestor to modern humans, is wrong. The shrunken phylogenetic tree was accordingly corrected for by Krause: the mean age of the most recent mtDNA ancestor of modern humans and Neanderthal went down from 660.000 t0 465,700 years ago.
(mean = 465,700 years ago; 321,200–618,000 years ago, 95% HPD) (Krause et al., 2010)
The feature that contemporary dN/dS values of modern humans are high, especially among Europeans, also corresponds to current assumptions that concern a younger age or (in the case of Europeans) of a smaller effective population size. May this be another lousy interpretation of results that are barely understood? This could be another example of a solution that supplies an easy way out of a complex issue.
There might be more. COX2 is a coding gene located on mtDNA. According to Green et al.(2008):
COX2 has experienced four amino acid substitutions on the human mtDNA lineage after its divergence from the Neandertal lineage [...]
Fixed mutations indeed tend to define both human lineages as mono-phyletic blocks. But the paper only mentions COX2 as a potential indication of divergent evolution, and due to the new information revealed by the Denisova hominin nothing remains of Green’s assertions that Neanderthal coding mtDNA is strikingly different from modern human mtDNA. The main argument why this would be irreconcilable with a continuous development can now be rejected:
The observation of four nonsynonymous substitutions on the modern human lineage, and no amino acid changes on the Neandertal lineage, stands in contrast to the overall trend of more nonsynonymous evolution in Neandertal protein-coding genes (Table 1), and deserves consideration. (Green, 2008)
There is NO overall trend among Neanderthal towards a more nonsynonymous evolution, hence the four new proteins that correspond to four nonsynonymous substitutions on the modern human lineage do not indicate a striking new tendency, since this kind of mutations happened all the time, also among Neanderthal.
The age calculations gain in reliability once the synonymous mutations involved are better identified and harbored on the phylogenetic tree, by comparing more hominins and branches. Quite considerable purifying selection has now been identified as applicable to both Denisova and Neanderthal mtDNA. However, the mtDNA of an old skeleton in Australia already showed us that neither of this leads us closer to the mtDNA of modern humans.
Whatever the nuance of details, that scream variety and continuity in human evolutionary development, we can’t deny a striking, almost exclusive unity of AMH mtDNA compared to the different forms that have been recovered from Neanderthal and – even more – Denisova:
The genealogies of mtDNA sequences in most human populations, including Aboriginal Australians, characteristically have very little hierarchical branching structure. This pattern of sequence variation is consistent with a population expansion following a population bottleneck and is generally taken as supporting the recent out of Africa model. Under this model, all contemporary sequences spread globally with an expanding population that replaced all other people and all other lineages. Africa has been postulated as the source of the expansion because some populations in Africa have more sequence diversity than populations anywhere else. (Adcock et al., 2001)
Almost, since the discovery of ancestral mtDNA of the gracile early human, found at Lake Mungo, Australia (code named LM3, age 62 kya), that is unmistakably an AMH, also attests the extinction of quite distinct outliers. There must have been a huge and progressive selective thrust towards modern mtDNA. The mtDNA of LM3 was kind of “modern” alright, but definitely the genetic distance fell outside the range of modern humans. The investigators observed this find poses a serious challenge to the “interpretation of contemporary human mtDNA variation as supporting the recent out of Africa model” (Adcock et al., 2001), effectively reducing Africa as a refuge for outgroups that have accumulated change and drifted apart rather than being a true indication of the source of all AMH related mtDNA. But even more so, the find strongly indicates that the current lack of hierarchical branching structure among humans can’t be understood as the direct result of a succession of AMH migrational waves alone. Some waves phased out and lost their origin from the record. Could it be possible that something about mtDNA triggered the worldwide substitution of extremely divergent older forms by the reduced array of current forms? Then how did this happen?
Let us regard the issue in a wider genetic perspective and forget about cheap scenarios of cannibal hominins exterminating each other, a view that conveniently ignores autosomal evidence of inter-hominin gene flow. One little segment of non-coding mtDNA can be found on the Displacement (D-) loop or control region, that is involved in repair activities. It has an analogy in the telomers of nuclear DNA, that are highly prone to insertion and deletion processes. This little region may be subject to the random change and stochastic speed-density that are necessary to infer a neutral “molecular clock”, but the location of this region on the mitochondria introduces a substantial bias in the basic assumption of overall neutrality. I will return at this issue.
Several studies have demonstrated the ongoing transfer and integration of mitochondrial DNA sequences into nuclear chromosomes. The evolutionary inclination of mtDNA genes to move from the D-loop control zone to the nuclear autosomal part of the DNA could be studied in more detail on the paleogenetic sample of an AMH fossil found near Lake Mungo, Australia, dated 40kya (Bowler et al.,2003):
“His mtDNA belonged to a lineage that only survives as a segment inserted into chromosome 11 of the nuclear genome, which is now widespread among human populations.” (Adcock et al., 2001)
This particular strand of early human (AMH) mtDNA vanished from the mitochondrial record ever since, all over the world, but the insertion in chromosome 11 flourished, especially outside Africa:
Overall, 39% of chromosomes tested carried the insertion. In four African populations, the frequency of chromosomes carrying the insertion ranges between 10 and 25%, whereas it varies between 38% and 78% in populations tested in Europe, Asia, Oceania, and South America.(Zischler et al., 1995)
Assuming a lower evolutionary rate in nuclear DNA, “these mitochondrial integrations might preserve the ancestral state of the mitochondrial sequence that existed at the time of transposition and could therefore be regarded as ‘‘molecular fossils.’’” (Zischler et al., 1998). Previous investigation on a similar, albeit much older Insert on chromosome 9 that “took place on the lineage leading to Hominoidea (gibbon, orangutan, gorilla, chimpanzee, and human) after the Old World monkey–Hominoidea split” (Zischler et al., 1998), that happened in the range of 17–30 MYA in a common ancestor of all hominoids, already established the value of nuclear insertions for reconstructing ancestral mitochondrial sequences of the Most Recent Common Ancestor (MRCA):
Thus, the MRCA sequence deduced from homologous integrations in different species will represent the ancestral mtDNA sequence more reliably and with less sequence ambiguities than an ancestral sequence deduced from the fast-evolving mtDNA sequences. (Zischler et al., 1998)
The Insert on chromosome 11 definitely suggests fossil information of some early AMH individual, or at least of a hominin that interbred with early AMH. The closest match to the mtDNA of this particular individual was indeed an AMH, the gracile LM3 dated 40kya (Bowler et al., 2003) found in Australia at Lake Mungo. However, a simple comparison of the Insert to the current genome of modern human mtDNA reveals that this individual can’t possibly be the direct ancestor of modern human mtDNA. No close mtDNA matches of LM3 nor the Insert survived and the mtDNA of LM3 doesn’t indicate direct matrilinear inheritance of the original mtDNA source of this autosomal Insert either.
The LM3 Sequence Belongs to an Early Diverging mtDNA Lineage. The divergence of the LM3 sequence before the MRCA of contemporary human sequences is indicated by its grouping with the Insert sequence, which other reports have suggested diverged before the MRCA of sequences in living humans.
Although this analysis did not reliably establish an early divergence of the LM3/Insert lineage, it demonstrated that the lineage is unusually long. (Adcock et al., 2001)
This presentation of the Insert as a member of a single branch together with LM3 may be an oversimplification. The location of the Insert at the mtDNA phylogenetic tree of humans suggest an even more pronounced outlier:
Upon comparing 243 bp of a human-specific integration (Zischler et al. 1995) that corresponds to the conserved part of the mitochondrial D-loop of all available hominoid (n=14) and human (n=261) mtDNA sequences, only two insert-specific substitutions were traced, with both the ape mtDNA sequences and all human mtDNA sequences being identical at these positions. (Zischler et al. 1998)
Salient detail is that the two Insert specific substitutions (A on 16259 and C on 16288) are now covered by the mtDNA of the Denisova hominin. Even though the other differences with Denisova are big enough to exclude a close affiliation, this remarkable detail invites to the tentative proposal that the divergence of the Insert sequence could have happened long before the MRCA of human sequences that also include LM3.
This rare scope on a deep Eurasian affiliation, combined with extant aboriginal polymorphisms that echo the survival of Insert and LM3 features in the haplogroup N and M branches of modern mtDNA, suggest a much more complicated phylogenetic tree than the one currently in use. Aboriginal mtDNA polymorphisms drawn in the figure of Adcock et al., 2001 (above) are part of a mixture of the closely related haplogroups N (~P?) and M (Q?) that up to now define the earliest Out of Africa scenario. Together they could be closer to an extinct group of Eurasian outliers than African branches separately. Also typical East Asian loci of mtDNA show a remarkable similarity, making the case of African branches being ancestral to haplogroups N and M less straightforward. The establishment of any “reversed tree”, however, is hampered by the apparent extinction or extreme “pruning” of what might have been an enormous Eurasian mtDNA variability. Any scenario that reverses the tree should account for this low extant Eurasian variability in comparison with Africa.
Let’s return to the assumed “neutrality” of mitochondrial DNA inheritance. High variability of the control region might suggest otherwise. One of the prerequisites of fast evolution is a fast mechanism underneath genetic change, and the purpose of fast mtDNA mutations could be just that, to put the precondition of rapid evolutionary change. Anyhow, a similar observation was made concerning the massive STR of chimps on the Y-chromosome, that seem to be secondary to the incredible evolutionary changes on the Y-chromosome as observed in the recent study of Hughes et al. (2010) I already wrote about here.
A set of interesting differences of mtDNA between humans is located on the Hypervariable Region (HVR). Most strikingly, HVR is not highly variable per definition. For instance, investigations on the Ayu fish (Takeshima et al., 2005) revealed the Hypervariable region may also turn into a Hypovariable region, what suggests a special functionality of the property defining HVR (or general D-loop) variability. And a substantial susceptibility to damage.
The mitochondria continuously reproduce themselves at intervals averaging about 2 weeks, like bacteria by a process of binary fission. They generate most of the cell’s (chemical) energy supply and because mitochondria use oxygen as an electron acceptor, they produce harmful free radicals that may cause genetic damage, often deletion mutations. This free radical damage to mtDNA cannot be repaired, basically because the regular repair mechanisms of the cells can’t access the mitochondria and the mitochondrion has no repair mechanism of its own. Therefore, mitochondria accumulate damage at each mitochondrial generation, what gradually leads to malfunction and ultimately affects the health of the organism as a whole.
However, this dreary scenario must have some constraints, or else all life on earth would already have ended millions of years ago. Somehow the reproductory system must have been exempted from this process, or at certain circumstances, and also it seems the genetic damage to mitochondria can be slowed down by exercise, both physical and mental, but especially by consuming antioxidants like vitamin C or omega-3 fatty acids. These are abundant in fresh fruit, raw meat and fish, indispensable supplements to the species that lost the functionality of the L-gulonolactone oxidase (GULO) gene – amongst whom one of the two major primate suborders, the Anthropoidea (Haplorrhini), that happens to include human beings, together with tarsiers, monkeys and apes. Originally meant as a genetic “improvement” for getting rid of the old and weak when food shortages occurred, ie. those most badly in need of antioxidants to remain healthy, the loss of this gene also effectively confined this suborder of primates to subsistence in the tropics. Only humans succeeded in finding new habitats in colder climates. They left the hot places where fruits were available all year round and traditionally made up an important addition to the menu, because they could. Only humans evolved into great hunters, and developed the necessary skills to catch fish, in order to compensate for the irregular availability of fresh fruits. Notwithstanding unfavorable climates, they managed to keep their necessary supply of antioxidants at a save level. And they did, for hundreds of thousands of years. Until everything changed at the eve of Upper Paleolithic – when human cultural advance reached a critical level.
What went amiss when humans reached their first cultural highlights? Their success triggered important improvements in their living standards, that moved their prime focus away from the concerns of harsh survival, and towards the community around the fire. They spend more time preparing their meals, started to cook their meat and fish and thus destroyed their main antioxidant food supplies. Degenerative diseases made their introduction and invoked new selective pressures, that caused a steady gene flow from the south to rejuvenate the slowly degenerating mitochondrial lineages in the north. In the mean while females ceased to worry about the survival of the fittest and developed a preference for “feminine looking men over their more rugged counterparts” (DeBruine et al., 2010), triggering the most notorious changes in the human anatomy that resulted in Anatomically Modern Humans as a progressive tendency all over the world.
However, this does not fully explain the current low overall variability of mtDNA even in fruit-rich tropical territories in comparison to the attested mtDNA of early AMH such as Lake Mungo 3. Still, cultural level related natural selection might be a good trail to follow.
Booming AMH culture most probably also entailed a closer contact between different groups within a wider economical areas. For sure this new behavioral patterns would have initiated a catastrophic increase of contagious diseases as soon viruses and bacteria could circulate freely among newly interconnected communities. However, this also implies a strong relation between resistance against (new) infections and mtDNA, that vastly exceed the benign effects of Vitamin C. The relation between mtDNA, antioxidants and the development of new “genetic” cures may reach a lot further. At this point it is tempting to regress to the behaviour of mtDNA and its facility to travel to nuclear DNA, and evaluate the genetic potential of mtDNA as a genetic laboratory against new diseases. Indeed, the immune system is where human DNA might have evolved most and is where most human variability occur.
Despite the high homology between chimpanzee and human genes at the level of amino acid sequences, human genome contains 1418 genes that do not have direct orthologues in chimpanzee, many of which are related to immune defence.
A number of genome-wide scans for positive selection have recently been performed (Wagner, 2007). They confirm that many immune genes and their regulatory sequences have been the subjects of positive selection in humans.
Population genomics is still in its infancy and the specific predictions may vary among studies but this is where future discoveries are anticipated. (Danilova, 2008)
Then, survival of just one little branch of early human mtDNA must point directly to the main focus of Upper Paleolithic development. Of the early mtDNA strands only those that accumulated in Africa were safeguarded against the effects of progressive damage, due to the continuous availability antioxidants. But in the center of change the preconditions for rapid change were set, including the extinction of mtDNA that did not meet the new standards of natural selection against the inevitable pandemics of cultural cohabitation and coexistence. Relatively low population density prevented the accumulation of high haplotype diversity, and the surviving mtDNA haplogroups in Eurasia obliterated all traces of a long, rich and diverse hominin history. To the effect that the false positives of mtDNA lured the public opinion into thinking that a long list of pre-AMH hominins, that include famous names like Neanderthal, Peking Man, Rhodesian Man, Denisova hominin etc., became extinct.
We can’t solve the origin question with a narrow scope, since the only truth is that we still don’t know. However, the Denisova hominin shows us one important clue: the more we know, the more complicated the solution. And most probably, the more hominins involved.
- Krause et al. – The complete mitochondrial DNA genome of an unknown hominin from southern Siberia, 2010, link (paysite): try here
- Krause et al. – A complete mtDNA genome of an early modern human from Kostenki, Russia; 2010, link
- Derevianko et al. – A Paleolithic Bracelet from Denisova Cave, 2008, link
- Howell et al. – Molecular clock debate: Time dependency of molecular rate estimates for mtDNA: this is not the time for wishful thinking, 2008, link
- Adcock et al. – Mitochondrial DNA sequences in ancient Australians: Implications for modern human origins, 2001, link
- Ovchinnikov et al. – Molecular analysis of Neanderthal DNA from the northern Caucasus, 2000, link
- Orlando et al. – Revisiting Neandertal diversity with a 100,000 year old mtDNA sequence, 2006, link
- Green et al. – A Complete Neandertal Mitochondrial Genome Sequence Determined by High-Throughput Sequencing, 2008, link (paysite): try here
- Takeshima et al. – Unexpected Ceiling of Genetic Differentiation in the Control Region of the Mitochondrial DNA between Different Subspecies of the Ayu Plecoglossus altivelis, 2005, link
- Sankar Subramanian – Temporal Trails of Natural Selection in Human Mitogenomes, 2009, link
- Subramanian et al. – High mitogenomic evolutionary rates and time dependency, 2009, link
- Zischler et al. – A nuclear ‘fossil’ of the mitochondrial D-loop and the origin of modern humans, 1995, link
- Zischler et al. – A Hominoid-Specific Nuclear Insertion of the Mitochondrial D-Loop: Implications for Reconstructing Ancestral Mitochondrial Sequences, 1998, link
- DeBruine et al. – The health of a nation predicts their mate preferences: cross-cultural variation in women’s preferences
for masculinized male faces, 2010, link
- Nadia Danilova – Evolution of the Human Immune System Evolution of the Human Immune System, 2008, link
- Allard et al. – Control region sequences for East Asian individuals in the Scientific Working Group on DNA Analysis Methods forensic mtDNA data set, 2004, link (paysite), try here
- Bowler et al. – New ages for human occupation and climatic change at Lake Mungo, Australia, 2003, link
- PhyloTree.org – Global human mtDNA phylogenetic tree, 2010, main
- Kris’s Archaeology Blog – Possible New Hominid Species Identified
- John Hawks Weblog – Hobbit version 2.0: the undiscovered hominin
- John Hawks Weblog – An earlier initial Upper Paleolithic at Kostenki
- Science News – Ancient Penguin DNA Raises Doubts About Accuracy of Genetic Dating Techniques
- The Scientist – Surprising mtDNA diversity
- Hendrickson et al. – Mitochondrial DNA Haplogroups influence AIDS Progression, 2009, link (declining Mesolithic mtDNA U5 may be a possible clue towards repeated extinction of northern mtDNA haplogroups).