Archive for the ‘Anthropology’ Category

The Mesolithic Blind Spot

January 26, 2013 4 comments

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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


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

Expanding Hybrids And The Rise Of Our Genetic Common Denominator

September 29, 2012 10 comments

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

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

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

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

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

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

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

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

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

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

Science DOI: 10.1126/science.1224344

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


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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Both species even shared the same cave:

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

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

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

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

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

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

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

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


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

The Demise of Oriental Neolithic Admixture

September 9, 2012 Leave a comment

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

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

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

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

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

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

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

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

The article:

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

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


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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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


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


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

Evolutionary Tales Behind Ötzi’s Mesocephalic Skull

September 6, 2012 6 comments

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.

3-D reconstruction of Ötzi’s skull

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.

‘Dinaric’ Bell Beaker skull, 2200 BC, found in Molenaarsgraaf, Holland. Notice the flat occiput, an entirely new development in Europe.

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)

According to one theory, the beginning of artificial cranial deformation was linked to the first appearance of brachycephaly, because people were not happy with this evolutionary change.

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)

Recent evolution includes the shape and a profound structural reorganization of the brain, and an increased cerebellum.

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.


  • Ash & Robinson – The Emergence of Humans, 2011, link
  • Arensburg et al. – Cranial deformation and trephination in the Middle East, 1988, link
  • Arsuaga et al. – The Sima de los Huesos crania (Sierra de Atapuerca, Spain). A comparative study, 1996, link
  • Anthony – The Horse, The Wheel, And Language, 2009, link
  • Bartels – A Test of Non-metrical Analysis as Applied to the ‘Beaker Problem’, 1998, link
  • Bernhard – Anthropological Studies on the Mummy from the Ötztal Alps, 1994, link
  • Bischof – Total Dream Loss: A Distinct Neuropsychological Dysfunction after Bilateral PCA Stroke, 2004, link
  • Brace et al. – The questionable contribution of the Neolithic and the Bronze Age to European craniofacial form, 2005, link
  • Brace – Cro-Magnon and Qafzeh — vive la Difference, 1996, link
  • Brown – Recent human evolution in East Asia and Australasia, 1992, link
  • Charles – Back into the north: the radiocarbon evidence for the human re-colonisation of the north-western Ardennes after the Last Glacial Maximum, 1996, link
  • Charles – Late Magdalenian chronology and faunal exploitation in the North-Western Ardennes”, Ruth Charles, 1998, link
  • Chambon & Salanova – Chronologie des sépultures du IIIe millénaire dans le bassin de la Seine, 1996, link
  • Crawford – Sumer and the Sumerians (second edition), 2004, link
  • De Smet et al. – The Cerebellum and Language: The Story So Far, 2007, link
  • Fana et al. – Sexual dimorphism and asymmetry in human cerebellum: An MRI-based morphometric study, 2010, link
  • Fawcett & Nicolson – Dyslexia: the role of the cerebellum, 2008, link
  • Guy et al. – Deux Cranes trépanés de la sépulture collective mégalithique de la Chaussée-Tirancourt (Somme), 1989, link
  • Hawks – Selection for smaller brains in Holocene human evolution, 2011, link
  • Kutschera – Radiocarbon dating of the Iceman Ötzi with accelerator mass spectrometry, 2001, link
  • Lee et al. – Emerging genetic patterns of the european neolithic: Perspectives from a late neolithic bell beaker burial site in Germany, 2012, link
  • Leonard et al. – Effects of Brain Evolution on Human Nutrition and Metabolism, 2007, link
  • Lichardus et al. – La protohistoire de l’Europe, 1987
  • Morelli et al. – A Comparison of Y-Chromosome Variation in Sardinia and Anatolia Is More Consistent with Cultural Rather than Demic Diffusion of Agriculture, 2010, link
  • Munro – Prehistoric Scotland and its place in European civilization; being a general introduction to the “County histories of Scotland, 1899, link
  • Nafplioti – Late Minoan IB destructions and cultural upheaval on Crete:
    A bioarchaeological perspective, 2012, link
  • Panagiaris – A Physico-Anthropological Study of Skeletal Material from Neolithic Age to Hellenistic Times in Central Greece and Surrounding Region (dissertation), 1993, link, review by Dienekes Anthropology Blog – A physico-anthropological study of skeletal material from Neolithic age to Hellenistic times in Central Greece and surrounding region, July 22, 2012, link
  • Pinter et al. – Neuroanatomy of Down’s Syndrome: A High-Resolution MRI Study, 2001, link
  • Ponce de León et al. – Neanderthal brain size at birth provides insights into the evolution of human life history, 2008, link
  • Rightmire – Homo in the Middle Pleistocene: Hypodigms, Variation, and Species Recognition, 2008, link
  • 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