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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

Abstract

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.


Referenced:

  • 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

Abstract

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.


Referenced:

  • 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

Related:

  • 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.


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