Denisovan ancestry in Oceanians (and some in South Asians)

Current Biology DOI: http://dx.doi.org/10.1016/j.cub.2016.03.037

The Combined Landscape of Denisovan and Neanderthal Ancestry in Present-Day Humans

Sriram Sankararaman et al.

Some present-day humans derive up to ∼5% [ 1 ] of their ancestry from archaic Denisovans, an even larger proportion than the ∼2% from Neanderthals [ 2 ]. We developed methods that can disambiguate the locations of segments of Denisovan and Neanderthal ancestry in present-day humans and applied them to 257 high-coverage genomes from 120 diverse populations, among which were 20 individual Oceanians with high Denisovan ancestry [ 3 ]. In Oceanians, the average size of Denisovan fragments is larger than Neanderthal fragments, implying a more recent average date of Denisovan admixture in the history of these populations (p = 0.00004). We document more Denisovan ancestry in South Asia than is expected based on existing models of history, reflecting a previously undocumented mixture related to archaic humans (p = 0.0013). Denisovan ancestry, just like Neanderthal ancestry, has been deleterious on a modern human genetic background, as reflected by its depletion near genes. Finally, the reduction of both archaic ancestries is especially pronounced on chromosome X and near genes more highly expressed in testes than other tissues (p = 1.2 × 10−7 to 3.2 × 10−7 for Denisovan and 2.2 × 10−3 to 2.9 × 10−3 for Neanderthal ancestry even after controlling for differences in level of selective constraint across gene classes). This suggests that reduced male fertility may be a general feature of mixtures of human populations diverged by >500,000 years.

Link

Neandertal and Denisovan DNA from Melanesians

Admixture models are out of control these days, with 4 inferred archaic introgressions into three groups of Eurasians (Europeans, East Asians, Melanesians). The model on the left has to be a simplification/incomplete/wrong in some way (Melanesians are not an outgroup to Europeans and East Asians; Europeans have "Basal Eurasian" ancestry via Early European Farmers; Denisovans have some kind of weird archaic ancestry that Neandertals don't, and according to a recent study, the Altai Neandertal also has some kind of weird Proto-Modern Human lineage). In any case, this may not matter much for the problem at hand which is excavating archaic DNA from Melanesian genomes.

But, if you combined all the admixtures inferred in the literature, you'd probably need something like 8 admixtures to  model 5 populations. Time and data will show which of them are real, and reveal news ones (e.g., in Africans, who remain blissfully simple in the absence of archaic African genomes).

Science DOI: 10.1126/science.aad9416

Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals

Benjamin Vernot et al.

Although Neandertal sequences that persist in the genomes of modern humans have been identified in Eurasians, comparable studies in people whose ancestors hybridized with both Neandertals and Denisovans are lacking. We developed an approach to identify DNA inherited from multiple archaic hominin ancestors and applied it to whole-genome sequences from 1523 geographically diverse individuals, including 35 new Island Melanesian genomes. In aggregate, we recovered 1.34 Gb and 303 Mb of the Neandertal and Denisovan genome, respectively. We leverage these maps of archaic sequence to show that Neandertal admixture occurred multiple times in different non-African populations, characterize genomic regions that are significantly depleted of archaic sequence, and identify signatures of adaptive introgression.

Link

mtDNA history of Oceania (Duggan et al. 2014)

AJHG doi:10.1016/j.ajhg.2014.03.014

Maternal History of Oceania from Complete mtDNA Genomes: Contrasting Ancient Diversity with Recent Homogenization Due to the Austronesian Expansion

Ana T. Duggan et al.

Archaeology, linguistics, and existing genetic studies indicate that Oceania was settled by two major waves of migration. The first migration took place approximately 40 thousand years ago and these migrants, Papuans, colonized much of Near Oceania. Approximately 3.5 thousand years ago, a second expansion of Austronesian-speakers arrived in Near Oceania and the descendants of these people spread to the far corners of the Pacific, colonizing Remote Oceania. To assess the female contribution of these two human expansions to modern populations and to investigate the potential impact of other migrations, we obtained 1,331 whole mitochondrial genome sequences from 34 populations spanning both Near and Remote Oceania. Our results quantify the magnitude of the Austronesian expansion and demonstrate the homogenizing effect of this expansion on almost all studied populations. With regards to Papuan influence, autochthonous haplogroups support the hypothesis of a long history in Near Oceania, with some lineages suggesting a time depth of 60 thousand years, and offer insight into historical interpopulation dynamics. Santa Cruz, a population located in Remote Oceania, is an anomaly with extreme frequencies of autochthonous haplogroups of Near Oceanian origin; simulations to investigate whether this might reflect a pre-Austronesian versus Austronesian settlement of the island failed to provide unequivocal support for either scenario.

Link

Neandertal STAT2 haplotype in Eurasians

Two recent papers have argued that African population structure or late Middle Paleolithic/Upper Paleolithic Neandertal admixture have contributed to the finding that Non-Africans appear to be a few percent more similar to Neandertals than Africans are across the genome. I would add that modern human admixture in the Vindija individual remains a distinct possibility.

What percentage of the ~3% Eurasian excess can be accounted by each of these three processes? The jury is out, and we won't find out until someone decides to tackle the problem comprehensively and/or new ancient DNA samples become available to inform the discussion. African population structure cannot be discounted, and intriguing new evidence may appear thanks to ancient DNA analysis.

But, there is a different approach to detecting Neandertal admixture that zeroes in on specific genomic locations and dissects them in great detail. This single-region approach provides evidence for admixture, without necessarily arguing about how extensive it was.

The single-region dissection was previously used in the Hammer lab to identify the first very convincing evidence for archaic admixture in Africans and Melanesians. In a new paper, Mendez et al. identify a small region in chromosome 12 that shows evidence for archaic introgression from Neandertals, or a species closely related to them.

But, it is worthwhile to begin with a list of other Neandertal introgression candidates from the literature:

Thus far, only a handful of loci have been hypothesized to have entered the human gene pool through archaic admixture and positive selection, including MAPT (MIM 157140),5 MCPH1 (MIM 607117),3 and particular alleles at the HLA locus (MIM 142800, 142830, 142840).6 However, analysis of the Neanderthal genome failed to provide evidence of introgressive alleles at the former two loci.1 Because of its role in fighting pathogens, HLA presents an instance where it is relatively easy to conceive of an a priori reason that acquisition of an archaic Eurasian HLA allele would benefit human ancestors, especially as they expanded into new habitats.7 However, the fact that HLA haplotypes are known to exhibit transspecific polymorphism and show evidence of strong balancing selection 8,9 increases the probability that similarities between modern and archaic haplotypes are due to ancestral shared polymorphism (i.e., as opposed to archaic admixture). In addition, the SNPs tagging the main HLA haplotype that was said to have introgressed were not observed in the Denisova or Neanderthal draft genomes. 

So, what lines of evidence support the notion that the new STAT2 haplotype is the "real deal"?

First, N matches the Neanderthal sequence at all 18 sites that fall within the resequenced 8.6 kb STAT2 region and have Neanderthal sequence coverage (Table 1). Second, N lineages are broadly distributed at relatively low frequencies in Eurasian populations (Figure 3) and are not observed in sub-Saharan African populations (Table S6). Third, the N haplotype extends for ~130 kb in West Eurasians and up to ~260 kb in some East Asians and Melanesians, producing much stronger LD than that observed in sub-Saharan Africans.

...

Given that the N lineage and the reference sequence diverged ~600 kya, these results suggest that population structure has influenced the recent evolution of this locus. Balancing selection alone is not expected to maintain this extent of LD and consequently is not sufficient to explain these patterns. Moreover, although a strong bottleneck could generate extended LD similar to the levels we observe near STAT2 in non-Africans, it would not explain why the N lineage went extinct in Africa (i.e., why the SNPs associated with the N lineage in non- Africans were not observed in sub-Saharan Africans that are part of our WGS or public SNP panels).

...

We point out that although a recent common ancestry between a human lineage and Neanderthal sequences might indicate gene flow between Neanderthals and modern humans, this information alone does not inform us about the direction of gene flow. With the additional evidence of the observed extent of LD in modern human sequences, it is possible to infer that the N lineage introgressed into modern humans (either from Neanderthals or another archaic source that contributed to both Neanderthals and AMH).

Actually, the N haplotype is observed in North Africa, but this might be due to relatively recent back-migration. One might also argue that a recent bottleneck in a Eurasian population generated the high degree of LD, and the N haplotype was lost in a back-to-Africa migration, or North-to-Sub-Saharan Africa migration. But, that would not seem to explain how the deeply divergent lineage persisted in the North African population of proto-modern humans for such a long time; the evidence for recent common ancestry of N with the Neandertal haplotype would argue against incomplete lineage sorting (=inheritance of related forms of the haplotype from before the modern-Neandertal divergence).

All in all, this probably represents the best evidence for Neandertal-to-modern introgression to date. As full genomes of different human groups become available, it will be possible to automate this analysis and pick off other such strong signals. This may not indicate the level of admixture, but it might provide strong evidence against the idea of reproductive isolation between modern humans and Neandertals.

It is also noteworthy that this is barely consistent with the coastal migration theory with respect to the origin of Australo-Melanesians, because humans trekking along the coast would not have the opportunity to admix with Neandertals who are completely unattested there in either their physical, or archaeological (Mousterian) form.

But, it is consistent with my Out-of-Arabia theory. Australo-Melanesian Y chromosomes belong to the CF clade of the phylogeny. I have speculated that the post-70ka climate crisis in Arabia spurred some human groups to escape north (CF), and others to remain south (DE). The latter eventually gave rise to the major African lineage, heading west (E), as well as a relic Asian lineage heading east (D) that was later inundated by the descendants of CF. If Australo-Melanesians are descended from the CF folk who went north out of Arabia, then they too would have had the opportunity to admix with Neandertals in the Near East.

The American Journal of Human Genetics, Volume 91, Issue 2, 265-274, 10 August 2012

A Haplotype at STAT2 Introgressed from Neanderthals and Serves as a Candidate of Positive Selection in Papua New Guinea

Fernando L. Mendez, Joseph C. Watkins and Michael F. Hammer

Signals of archaic admixture have been identified through comparisons of the draft Neanderthal and Denisova genomes with those of living humans. Studies of individual loci contributing to these genome-wide average signals are required for characterization of the introgression process and investigation of whether archaic variants conferred an adaptive advantage to the ancestors of contemporary human populations. However, no definitive case of adaptive introgression has yet been described. Here we provide a DNA sequence analysis of the innate immune gene STAT2 and show that a haplotype carried by many Eurasians (but not sub-Saharan Africans) has a sequence that closely matches that of the Neanderthal STAT2. This haplotype, referred to as N, was discovered through a resequencing survey of the entire coding region of STAT2 in a global sample of 90 individuals. Analyses of publicly available complete genome sequence data show that haplotype N shares a recent common ancestor with the Neanderthal sequence (∼80 thousand years ago) and is found throughout Eurasia at an average frequency of ∼5%. Interestingly, N is found in Melanesian populations at ∼10-fold higher frequency (∼54%) than in Eurasian populations. A neutrality test that controls for demography rejects the hypothesis that a variant of N rose to high frequency in Melanesia by genetic drift alone. Although we are not able to pinpoint the precise target of positive selection, we identify nonsynonymous mutations in ERBB3, ESYT1, and STAT2—all of which are part of the same 250 kb introgressive haplotype—as good candidates.

Link

Introgression of archaic haplotype at OAS1 in Melanesians (Mendez et al. 2012)

It seems that Michael Hammer was good on his promise that in 2012 "This year, we should be able to confirm what we found and go way beyond that."  In a new paper, conclusive evidence is presented about introgression of an archaic sequence into Melanesian populations. The argument is as follows:

• Melanesians are more diverse in that region than Africans.
• The common ancestor of the "archaic" and "African" haplotypes lived >3 million years ago.
• The "archaic" haplotype matches the ancient DNA from the Denisova hominin.
• Balancing selection (which can sometimes maintain extremely old polymorphism) is not reasonable in this case, because it would need to maintain both "archaic" and "African" haplotypes for a long time, but then (inexplicably) would continue to operate in Melanesia and cease to operate everywhere else.

Notice that once again, this is based on resequencing a small region of the genome. This is why I am all the more confident in my prediction that the advent of full genome sequencing will uncover more archaic admixture in humans. It may not always be able to use all the above listed criteria to confirm this admixture (since we do not and cannot have ancient DNA from all the archaic hominins that once roamed the planet), but all the remaining ones will suffice to make a very good case for introgression.

What I find particularly interesting, is that Mendez et al. re-iterate a few times that genomewide averages admit to different explanations:

Full genome comparisons of the Neandertal and Denisova draft genomes with modern human sequences have revealed different amounts of shared ancestry between each of these archaic forms and anatomically modern human (AMH) populations from different geographic regions. For example, a higher proportion of SNPs was shared between non-African and Neandertal, and between Melanesian and the Denisova genomes, than between either Neandertal or Denisova and extant African genomes (Green et al. 2010; Reich et al. 2010). An intriguing possibility is that these patterns result from introgression of archaic genes into AMH populations in Eurasia. However, this SNP sharing pattern could also be explained by ancestral population structure in Africa (i.e., without the need to posit introgression). For example, if non-Africans and the ancestors of Neandertals descend from the same deme in a subdivided African population, and this structure persisted with low levels of gene flow among African residents until the ancestors of non-Africans migrated into Eurasia, then we would expect more SNP sharing between non-Africans and Neandertals (Durand et al. 2011). 

... 

While genome-wide comparisons detect more sequence agreement between non-African and Neandertal genomes, and between Melanesian and Denisova genomes, the specific loci exhibiting these signals have not yet been identified. Furthermore, current analyses do not elucidate the relative roles of recent introgression versus long-term population structure in Africa in explaining these patterns.

The current paper does a good job at showing how in one particular region archaic introgression into Melanesians is indeed the best explanation for the evidence. But, the fact that the authors seem to re-iterate the possibility of African population structure and repeatedly caution against using patterns of genomewide sharing between modern and archaic humans is a strong hint that there are more things to come on the topic.

We should remember that the widely-circulated estimates of Neandertal->Eurasian introgression are based on genomewide averages. It is true that Reich et al. (2010) identified 13 regions of potential Neandertal introgression, which together make up a very small portion of the human genome. So, the jury is out on whether African population structure or Neandertal introgression is responsible for most of the genomewide pattern.

What you can be sure of is that many scientists are busy lining up full genomes from different human populations as we speak, and finding plenty of regions where haplotypes of extremely old divergence times co-exist in our species. We will probably learn more about such efforts during 2012.



Mol Biol Evol (2012)doi: 10.1093/molbev/msr301

Global genetic variation at OAS1 provides evidence of archaic admixture in Melanesian populations

Fernando L. Mendez, Joseph C. Watkins and Michael F. Hammer

Recent analysis of DNA extracted from two Eurasian forms of archaic human show that more genetic variants are shared with humans currently living in Eurasia than with anatomically modern humans in sub-Saharan Africa. While these genome-wide average measures of genetic similarity are consistent with the hypothesis of archaic admixture in Eurasia, analyses of individual loci exhibiting the signal of archaic introgression are needed to test alternative hypotheses and investigate the admixture process. Here, we provide a detailed sequence analysis of the innate immune gene, OAS1, a locus with a divergent Melanesian haplotype that is very similar to the Denisova sequence from the Altai region of Siberia. We re-sequenced a 7 kb region encompassing the OAS1 gene in 88 individuals from 6 Old World populations (San, Biaka, Mandenka, French Basque, Han Chinese, and Papua New Guineans) and discovered previously unknown and ancient genetic variation. The 5' region of this gene has unusual patterns of diversity, including 1) higher levels of nucleotide diversity in Papuans than in sub-Saharan Africans, 2) very deep ancestry with an estimated time to the most recent common ancestor of >3 million years, and 3) a basal branching pattern with Papuan individuals on either side of the rooted network. A global geographic survey of >1500 individuals showed that the divergent Papuan haplotype is nearly restricted to populations from eastern Indonesia and Melanesia. Polymorphic sites within this haplotype are shared with the draft Denisova genome over a span of ∼90 kb and are associated with an extended block of linkage disequilibrium, supporting the hypothesis that this haplotype introgressed from an archaic source that likely lived in Eurasia.

Link

mtDNA of Oceanians (Ballantyne et al. 2011)

Forensic Sci Int Genet. 2011 Sep 20. [Epub ahead of print]

MtDNA SNP multiplexes for efficient inference of matrilineal genetic ancestry within Oceania.

Ballantyne KN, van Oven M, Ralf A, Stoneking M, Mitchell RJ, van Oorschot RA, Kayser M.

Abstract

Human mitochondrial DNA (mtDNA) is a convenient marker for tracing matrilineal bio-geographic ancestry and is widely applied in forensic, genealogical and anthropological studies. In forensic applications, DNA-based ancestry inference can be useful for finding unknown suspects by concentrating police investigations in cases where autosomal STR profiling was unable to provide a match, or can help provide clues in missing person identification. Although multiplexed mtDNA single nucleotide polymorphism (SNP) assays to infer matrilineal ancestry at a (near) continental level are already available, such tools are lacking for the Oceania region. Here, we have developed a hierarchical system of three SNaPshot multiplexes for genotyping 26 SNPs defining all major mtDNA haplogroups for Oceania (including Australia, Near Oceania and Remote Oceania). With this system, it was possible to conclusively assign 74% of Oceanian individuals to their Oceanian matrilineal ancestry in an established literature database (after correcting for obvious external admixture). Furthermore, in a set of 161 genotyped individuals collected in Australia, Papua New Guinea and Fiji, 87.6% were conclusively assigned an Oceanian matrilineal origin. For the remaining 12.4% of the genotyped samples either a Eurasian origin was detected indicating likely European admixture (1.9%), the identified haplogroups are shared between Oceania and S/SE-Asia (5%), or the SNPs applied did not allow a geographic inference to be assigned (5.6%). Sub-regional assignment within Oceania was possible for 32.9% of the individuals genotyped: 49.5% of Australians were assigned an Australian origin and 13.7% of the Papua New Guineans were assigned a Near Oceanian origin, although none of the Fijians could be assigned a specific Remote Oceanian origin. The low assignment rates of Near and Remote Oceania are explained by recent migrations from Asia via Near Oceania into Remote Oceania. Combining the mtDNA multiplexes for Oceania introduced here with those we developed earlier for all other continental regions, global matrilineal bio-geographic ancestry assignment from DNA is now achievable in a highly efficient way that is also suitable for applications with limited material such as forensic case work.

Link

Widespread Denisovan admixture (Reich et al. 2011)

Table S2 from the paper (pdf) gives the Denisova admixture as a fraction of the Papuan New Guinea highlander Denisova admixture. It seemed almost certain to me that Australian aboriginals would register such admixture, as they have often been described, on physical anthropological grounds, as closer to Papuans than to any other human population. But, it is nice to see the evidence (or lack thereof) for Denisova admixture quantified in various groups described as "Negrito" or "Australoid" by traditional physical anthropology.

The inference, by the authors, that Denisova admixture took place in Southeast Asia itself makes sense to me. This admixture may have been variable to begin with, but it was reduced in Southeast Asia itself as the number of modern humans in it grew, absorbing the Denisova-admixed early inhabitants, with the latest episode taking the form of the arrival of East Eurasian populations (traditional Mongoloids) that seem to lack this admixture altogether.

The interesting question now seems to be: with Denisovans spread from the Altai to Southeast Asia, how did the ancestors of East Asians avoid having any?

UPDATE: Figure 1 from the paper shows Denisovan admixture as a fraction of that in New Guineans:

One of the most interesting findings of the paper is that the extent of Denisova admixture is strongly correlated with the extent of Near Oceanian (Australian-Papuan) admixture.

An interesting question is to what extent does Denisova admixture contribute to the differentiation between Australasians and other modern humans? The following admixture graph gives an idea:

You can see that 7% Denisova introgression into the ancestors of Australians/New Guineans is inferred to have been "diluted" by roughly 50-50 admixture with Denisova-deficient modern humans, leading to the ~4% figure of Denisova admixture in extant Australians/New Guineans. This was further diluted in populations like Mamanwa, by admixture with East Asians.

It seems likely that inter-population differentiation within the species H. sapiens may be driven, at least in part, by admixture with archaic humans, and is not only the result of isolation post-Out of Africa. If Franz Weidenreich were alive, he would probably be smiling.

UPDATE II: A possible reason why East Asians lack Denisovan admixture is given by Mark Stoneking, as quoted in Nature:

Stoneking says that this pattern hints at at least two waves of human migration into Asia: an early trek that included the ancestors of contemporary Aboriginal Australians, New Guineans and some other Oceanians, followed by a second wave that gave rise to the present residents of mainland Asia. Some members of the first wave (though not all of them) interbred with Denisovans. However, the Denisovans may have vanished by the time the second Asian migrants arrived. This also suggests that the Denisovan's range, so far linked only to a cave in southern Siberia, once extended to Southeast Asia and perhaps Oceania.

Given that the Denisova hominin is about 41ka old, that would imply that East Asian ancestors moved through their territory after that date, when the Denisovans were already extinct, partially absorbed by first-wave "Australasian-like" people.

We must also consider the possibility that the Denisovans themselves may have been intrusive to Siberia; could the Altai Denisovans be remnants of a Southeast Asian population that fled out of the way of the modern humans that migrated to Australasia? If that is the case, then East Asian ancestors may lack Denisovan admixture because they had already reached the far east when Denisovans started moving north.

I, for one, can't wait until we start getting ancient DNA from Upper Paleolithic H. sapiens, who knows what new surprises are in store for us?

The American Journal of Human Genetics, 22 September 2011
doi:10.1016/j.ajhg.2011.09.005

Denisova Admixture and the First Modern Human Dispersals into Southeast Asia and Oceania

David Reich et al.

It has recently been shown that ancestors of New Guineans and Bougainville Islanders have inherited a proportion of their ancestry from Denisovans, an archaic hominin group from Siberia. However, only a sparse sampling of populations from Southeast Asia and Oceania were analyzed. Here, we quantify Denisova admixture in 33 additional populations from Asia and Oceania. Aboriginal Australians, Near Oceanians, Polynesians, Fijians, east Indonesians, and Mamanwa (a “Negrito” group from the Philippines) have all inherited genetic material from Denisovans, but mainland East Asians, western Indonesians, Jehai (a Negrito group from Malaysia), and Onge (a Negrito group from the Andaman Islands) have not. These results indicate that Denisova gene flow occurred into the common ancestors of New Guineans, Australians, and Mamanwa but not into the ancestors of the Jehai and Onge and suggest that relatives of present-day East Asians were not in Southeast Asia when the Denisova gene flow occurred. Our finding that descendants of the earliest inhabitants of Southeast Asia do not all harbor Denisova admixture is inconsistent with a history in which the Denisova interbreeding occurred in mainland Asia and then spread over Southeast Asia, leading to all its earliest modern human inhabitants. Instead, the data can be most parsimoniously explained if the Denisova gene flow occurred in Southeast Asia itself. Thus, archaic Denisovans must have lived over an extraordinarily broad geographic and ecological range, from Siberia to tropical Asia.

Link

The spread of Austronesian farmers across the Pacific

This is the first of three interesting papers that appear ahead of print in Current Anthropology. Peter Bellwood reviews the spread of farming across the Pacific from its two sources (China including Taiwan, and the New Guinea highlands).

Related:

• Major East-West divide in Indonesian Y chromosomes
• More on geographical divide between Asian and Melanesian types in Indonesia (Cox et al. 2010)
• Demographic history of Oceania (Wollstein et al. 2010)

Current Anthropology http://www.jstor.org/stable/full/10.1086/658181

Holocene Population History in the Pacific Region as a Model for Worldwide Food Producer Dispersals

Peter Bellwood

Pacific prehistory (excluding Australia) since 3000 BC reflects the impacts of two source regions for food production: China from the Yangzi southward (including Taiwan) and the western Pacific (especially the New Guinea Highlands). The linguistic (Austronesian, Trans–New Guinea), bioanthropological/human genetic, and Neolithic archaeological records each carry signals of expansion from these two source regions. A combined consideration of the multiregional results within all three disciplines (archaeology, linguistics, and biology) offers a historical perspective that will never be obtained from one discipline or one region alone. The fundamental process of human behavior involved in such expansion—population dispersal linked to increases in human population size—is significant for explaining the early spreads of food production and language families in many parts of the world. This article is concerned mainly with the archaeological record for the expansion of early food producers, Austronesian languages, and Neolithic technologies through Taiwan into the northern Philippines as an early stage in what was to become the greatest dispersal of an ethnolinguistic population in world history before AD 1500.

Link

Archaic Denisovans contributed to modern Melanesians

I love articles like this, because they force us to re-evaluate everything we thought we knew. I'll probably have much more to say on this paper once I read it, but for the moment I can't help but notice that the finding that the Denisova specimen belonged to a population that contributed DNA to modern Melanesians puts the description of various early Homo sapiens skulls as "Australoid" by various researchers in the past into a whole new perspective.

Indeed, I myself have used MCLUST to classify Upper Paleolithic skulls, and a number of them such as Markina Gora get the label of "Australoid". This is usually explained as an consequence of their greater robusticity, which links them to modern Australo-Melanesians, but the finding that a pre-modern population that lived in Eurasia did contribute genes to Melanesians, certainly raises all sorts of questions.

UPDATE I

This is not a simple paper to read, if we also add the extensive supplementary material, so I will probably give my impressions and thoughts on it in piecemeal fashion.

The first interesting part comes from Table 1 in the paper. This contains values of the authors' D statistic D(H1,H2,archaic,chimpanzee) which shows how more frequently population H1 matches an archaic group than H2 does. A positive value suggests that H1 is more "archaic"-like.

The authors consider Neandertals (in the form of Vindija and Mezmaiskaya), as well as Denisova as the "archaic" groups of interest.

D values are consistently positive for H1=Papuans/Melanesians and H2 either African or Eurasian. This suggests indeed that Australo-Melanesians have archaic admixture from a population related to Denisova.

UPDATE II

It is interesting that the authors are back-pedalling on the idea that specifically Neandertal admixture is responsible for the "archaic" genes found in Eurasians in the previous paper.

I think there are two reasons behind this: first of all, all Eurasians are closer to Denisova than Africans are. Melanesians are even more closer. But, Eurasians are closer to Neandertals than they are to Denisovans.

What this means is that Eurasians did not admix with Neandertals themselves but with a population that was closer to Neandertals than to Denisovans.

The second reason why I think that the idea of specifically Neandertal admixture is rejected is the fact that it makes no sense: the D statistic is 7.5 for Cambodians and 3.3 for Sardinian with standard errors of 1.2 and 1.5.

This means that Cambodians have more "Neandertal" admixture than Sardinians do, which makes absolutely no sense if specifically Neandertal admixture was the reason, as Neandertals were a West Eurasian-distributed species.

So, while not all is well for the Neandertal admixture theory, they also argue (in the supplementary material) that the alternative theory (which I've argued for, of archaic structure) is weakened by the new evidence. I'll think about their argument in a future update.

UPDATE III

The authors did not consider the possibility of modern human to Denisova gene flow. Here is their reason (from the supplement):

Gene flow from modern humans into the ancestors of Denisovans is not only unsupported by the D-statistics, but is also historically implausible. The Denisova phalanx is more than 30,000 years old, and in our opinion is likely to be more that 50,000 years old (SI 12). The more ancient age estimate is older, and the more recent age estimate is only slightly younger than the age of the oldest confirmed modern human remains outside of Africa and the Levant. It is difficult to envision a plausible scenario in which the Denisovan population could have ancestry from a modern human group that experienced mixture in an area near where Melanesians live now, and then migrated to Siberia in just a few thousand years.

And, yet, we have evidence now of much older modern humans in South China, in the form of the Zhirendong mandible, which dates from ~100ky.

UPDATE IV

Looking at supplementary table S8.2 is quite interesting, because it gives the D statistics for intra-African "Neandertal" gene sharing.

The highest one is with H1=Yoruba and H2=Mbuti at 2%. What this means is, in essence, that Yoruba are more Neandertal-like than Mbuti are. How is this possible if a positive D value is reflective of admixture between Eurasians and Neandertals? There are no Neandertals in Nigeria to Neandertalize Yoruba with respect to Mbuti Pygmies.

This either means that Neandertal admixture is not the cause of the positive D statistics, or alternatively, that Yorubans are not pure Africans but have experienced back-migration of Neandertal-admixed Eurasians that Mbuti Pygmies did not experience to the same extent.

How interesting that Mbuti Pygmies (the least "Neandertal") and Papuans (the most "Denisovan") are the two most divergent living humans with an Fst of 0.377. Is it the case the different patterns of archaic admixture are contributing to this?

UPDATE V

It is unfortunate that the authors did not sample East Africans yet again. The authors do not consider Z-scores below 3 (in absolute value) significant, so, the Yoruba/Mbuti score (for Neandertals) of 2.4 does not achieve significance, but it is almost there.

If the authors' theory is correct, then we expect to see no variation (or only variation attributed to noise) within native African populations with respect to their inferred "Neandertal admixture", as Neandertals were a Eurasian species.

It is perplexing why yet again East Africans were not sampled: if you are claiming Eurasian-African differences in archaic admixture, sampling East Africans who live in-between Eurasians and Africans is the natural thing to do!

Nature 468, 1053–1060 (23 December 2010) doi:10.1038/nature09710

Genetic history of an archaic hominin group from Denisova Cave in Siberia

David Reich et al.

Using DNA extracted from a finger bone found in Denisova Cave in southern Siberia, we have sequenced the genome of an archaic hominin to about 1.9-fold coverage. This individual is from a group that shares a common origin with Neanderthals. This population was not involved in the putative gene flow from Neanderthals into Eurasians; however, the data suggest that it contributed 4–6% of its genetic material to the genomes of present-day Melanesians. We designate this hominin population ‘Denisovans’ and suggest that it may have been widespread in Asia during the Late Pleistocene epoch. A tooth found in Denisova Cave carries a mitochondrial genome highly similar to that of the finger bone. This tooth shares no derived morphological features with Neanderthals or modern humans, further indicating that Denisovans have an evolutionary history distinct from Neanderthals and modern humans.

Link

A rare genomic look at Aboriginal Australians

How strange that modern genetics is supposed to have invalidated the concept of race, yet, at every turn, it confirms most of the basic racial taxonomic observations of people working only with their eyes and, much later, their calipers.

On the left is the frappe analysis from the supplementary material, the Oceanian populations are seen on the far right.

The Australasid cluster emerges as an entity at K=5, showing Caucasoid admixture (AUR), Mongoloid admixture (MEL), and no apparent admixture (PAP).

At K=8 it is evident that the Caucasoid admixture in Aboriginal Australians is specifically European in origin, certainly the result of colonization in very recent times.

What can account for the Mongoloid admixture in Melanesians? It is probably the recent spread of Austronesian languages, arguably the most epic maritime language spread before Columbus, which affected a good deal of the southern hemisphere from Madagascar through Indonesia, Micronesia, Melanesia, and all the way to Polynesia on the far end.

As for the unadmixed Papuans, the indigenous inhabitants of New Guinea, their results are not surprising: there is a lack of admixture of East Asian Y chromosomes on the island, even in its most affected NW corner (Bird's head) where this admixture runs only to about 2.5%.

The American Journal of Human Genetics, doi:10.1016/j.ajhg.2010.07.008

Whole-Genome Genetic Diversity in a Sample of Australians with Deep Aboriginal Ancestry

Brian P. McEvoy et al.

Australia was probably settled soon after modern humans left Africa, but details of this ancient migration are not well understood. Debate centers on whether the Pleistocene Sahul continent (composed of New Guinea, Australia, and Tasmania) was first settled by a single wave followed by regional divergence into Aboriginal Australian and New Guinean populations (common origin) or whether different parts of the continent were initially populated independently. Australia has been the subject of relatively few DNA studies even though understanding regional variation in genomic structure and diversity will be important if disease-association mapping methods are to be successfully evaluated and applied across populations. We report on a genome-wide investigation of Australian Aboriginal SNP diversity in a sample of participants from the Riverine region. The phylogenetic relationship of these Aboriginal Australians to a range of other global populations demonstrates a deep common origin with Papuan New Guineans and Melanesians, with little evidence of substantial later migration until the very recent arrival of European colonists. The study provides valuable and robust insights into an early and important phase of human colonization of the globe. A broader survey of Australia, including diverse geographic sample populations, will be required to fully appreciate the continent's unique population history and consequent genetic heritage, as well as the importance of both to the understanding of health issues.

Link

More on geographical divide between Asian and Melanesian types in Indonesia (Cox et al. 2010)

I had previously posted about a paper showing a sharp divide in Indonesia between "Asian" and "Melanesian" Y chromosomes. A reader alerts me to another paper from this year, which discovers this divide using autosomal and X chromosome polymorphisms.

From the paper:

this transition is shifted eastward relative to Wallace’s line—a boundary that separates the biogeographic regions of Asia and Wallacea. At its southern limit, Wallace’s line falls between the islands of Bali and Lombok (figure 1), which are separated by a deep-water sea channel that marks the southern edge of the Sunda
Shelf. During ice-age glacial advances, the Sunda land mass included Borneo, Bali, Java and Sumatra, together with mainland Southeast Asia. However, even in periods
of low sea level, deep water in Wallacea separated the Sunda shelf from the eastern landmass of Sahul (connecting New Guinea and Australia). While the distribution of
many flora and fauna conforms to Wallace’s line, the seafaring capabilities of human settlers to this region undoubtedly overcame this barrier to dispersal. Indeed, Asian ancestry exceeds 50 per cent as far east as the island of Alor, which is well within Wallacea and approximately 1000 km east of Bali, as well as on the island of Sulawesi, which is located east of Wallace’s line in the north (figure 1). Curiously, Wallace himself noted this difference, positing a second line in eastern Indonesia corresponding to changes in human phenotype (Wallace 1869; Cox 2008). Wallace’s second ‘phenotypic’ line broadly parallels the rapid decline in Asian admixture identified here. It is refreshing to see (for once) a paper which acknowledges that modern genetics did not discover the wheel but has to a large extent confirmed what previous generations of scientists, working with their eyes (and later their calipers) could plainly see.

A visually interesting figure from the paper illustrates what a "cline" actually is.

We can see how west of 120 degrees longitude there is a uniform area of Asian ancestry, then a sharp transition zone and then a fairly uniform area of Melanesian ancestry.

The above figure illustrates one of the arguments of those (like me) who assert that racial variation in humans is real: the fact that it geographically punctuated (no smooth cline). The smooth areas of uniformity east/west of 120deg deserve to be recognized as real entities.

For visual illustration, three examples from Deniker's The races of man: a New Caledonian woman representing an "eastern" Melanesian type, a group of people from Flores (where, according to the current paper Asian admixture runs at 62%), and finally a Javan man representing a "western" Indonesian Mongoloid type.

Proc. R. Soc. B (2010) 277, 1589–1596

doi:10.1098/rspb.2009.2041

Autosomal and X-linked single nucleotide polymorphisms reveal a steep Asian–Melanesian ancestry cline in eastern Indonesia and a sex bias in admixture rates

Murray P. Cox

Abstract

The geographical region between mainland Asia and New Guinea is characterized by numerous small islands with isolated human populations. Phenotypically, groups in the west are similar to their neighbours in mainland Southeast Asia, eastern groups near New Guinea are similar to Melanesians, and intervening populations are intermediate in appearance. A long-standing question is whether this pattern primarily reflects mixing between groups with distinct origins or whether natural selection has shaped this range of variation by acting differentially on populations across the region. To address this question, we genotyped a set of 37 single nucleotide polymorphisms that are evolutionarily independent, putatively neutral and highly informative for Asian–Melanesian ancestry in 1430 individuals from 60 populations spanning mainland Asia to Melanesia. Admixture analysis reveals a sharp transition from Asian to Melanesian genetic variants over a narrow geographical region in eastern Indonesia. Interestingly, this admixture cline roughly corresponds to the human phenotypic boundary noted by Alfred Russell Wallace in 1869. We conclude that this phenotypic gradient probably reflects mixing of two long-separated ancestral source populations—one descended from the initial Melanesian-like inhabitants of the region, and the other related to Asian groups that immigrated during the Paleolithic and/or with the spread of agriculture. A higher frequency of Asian X-linked markers relative to autosomal markers throughout the transition zone suggests that the admixture process was sex-biased, either favouring a westward expansion of patrilocal Melanesian groups or an eastward expansion of matrilocal Asian immigrants. The matrilocal marriage practices that dominated early Austronesian societies may be one factor contributing to this observed sex bias in admixture rates.

Link

Major East-West divide in Indonesian Y chromosomes

As usual I have my reservations about the time estimates in this paper, but it is very useful as a guide to genetic variation in Indonesia, an island nation of composite origins where the indigenous population forms part of the S/SE Asia/Oceania zone of "Australoids", probably reflecting early out-of-Africa humans taking the southern route, while this population has been influenced by movements from the north: Caucasoids into India, and Mongoloids or Mongoloid-influenced people into Indonesia.

Getting back to the ever-present time issue; the inferences on this paper are, of course, based on assumption about Y-STR diversity accumulation that I have criticized elsewhere and I will not repeat.

But, isn't it strange that the authors claim a Paleolithic gene pool, while, at the same time, discovering a sharp divide? Common sense dictates that genetic distinctions across a long time span would be blurred, and there would be no sharp divide.

Sharp divides are created by recent population movements and are maintained by insurmountable geographical barriers (e.g., the Sahara or the Pacific) that persist for a long-time.

Molecular Biology and Evolution, doi:10.1093/molbev/msq063

Major East-West Division Underlies Y Chromosome Stratification Across Indonesia

Tatiana M. Karafet et al.

Abstract

The early history of Island Southeast Asia is often characterized as the story of two major population dispersals: the initial Paleolithic colonization of Sahul 45 thousand years ago and the much later Neolithic expansion of Austronesian-speaking farmers 4,000 years ago. Here, in the largest survey of Indonesian Y chromosomes to date, we present evidence for multiple genetic strata that likely arose through a series of distinct migratory processes. We genotype an extensive battery of Y chromosome markers, including 85 SNPs/indels and 12 Y-STRs, in a sample of 1,917 men from 32 communities located across Indonesia. We find that the paternal gene pool is sharply subdivided between western and eastern locations, with a boundary running between the islands of Bali and Flores. Analysis of molecular variance reveals one of the highest levels of between-group variance yet reported for human Y chromosome data (e.g., ?ST = 0.47). Eastern Y chromosome haplogroups are closely related to Melanesian lineages (i.e., within the C, M and S subclades) and likely reflect the initial wave of colonization of the region, while the majority of western Y chromosomes (i.e., O-M119*, O-P203, and O-M95*) are related to haplogroups that may have entered Indonesia during the Paleolithic from mainland Asia. In addition, two novel markers (P201, P203) provide significantly enhanced phylogenetic resolution of two key haplogroups (O-M122, O-M119) that are often associated with the Austronesian expansion. This more refined picture leads us to put forward a four-phase colonization model in which Paleolithic migrations of hunter-gatherers shape the primary structure of current Indonesian Y chromosome diversity, and Neolithic incursions make only a minor impact on the paternal gene pool, despite the large cultural impact of the Austronesian expansion.

Link

Bronze Age origin of Semitic languages

Bayesian phylogenetic methods, originally developed for biology, have been increasingly -and successfully- applied to linguistic data in recent years (e.g., for Indo-Europeans, Melanesians, and Austronesian speakers from the Pacific).

The current paper proposes a Bronze Age origin for Semitic languages, ~3 thousand years after the split of European from Anatolian Indo-European speakers. I don't find this particularly surprising, as Semitic has been, until relatively recently, much more geographically constrained than Indo-European, and -due to the early literacy of the populations of the Near East, its post-Neolithic arrival can be observed in the archaeological record itself.

It also explains a facet of Y-chromosome distribution, that I have commented on before, namely the fact that the common Near Eastern haplogroup J2 extends from Europe to South Asia in a "horizontal zone" accompanied with little of its sister clade J1, but in the Near East itself, there is a "vertical zone" from the Black and Caspian seas to Arabia of high J1 frequency. As I have explained recently, the mixed J2/J1 frequency in the central Near East is due to an enrichment with J1 lineages of a population that had (in pre-Semitic times) a high J2/J1 ratio like those of Europe, Asia Minor, and Iran. J1 should not be seen as exclusively Semitic, but it can't be denied that the major factor affecting its current spread has been the arrival of Semites from the South, the latest episode of which involved the spread of Arab Muslims.

The current study also demonstrates that linguistic Bayesian phylogenetics (LBP) has no inherent bias to produce older dates for language dispersals; while the origin of the Indo-European (IE) language family has been dated to the early European Neolithic, and now Semitic to ~6,000 years, the spread of Melanesian languages to Pleistocene times, and of the Austronesian settlement of the Pacific to ~5,000 years. The congruence between LBP and traditional archaeology in all these cases should force IE exceptionalists who cling to the old theory of "steppe horse riders" to explain why, only in the dispersal of IE, it should LBP should have failed.

The paper also has free supplementary data, including a multistate phylogeny (pdf) of Semitic languages (reproduced top left of this post).

(More details to follow after I thoroughly read the paper)

UPDATE (Aug 27):

From the paper:

Furthermore, Eblaite (no Eblaite wordlists were available for our study), the closest relative of Akkadian and the only other member of East Semitic, was spoken in the Levant (specifically the northeast Levant or present-day Syria; Gordon 1997), which is also where some of the oldest West Semitic languages were spoken (Ugaritic, Aramaic and ancient Hebrew). The presence of ancient members of the two oldest Semitic groups (East andWest Semitic) in the same region of the Levant, combined with a possible long interval (100–3000 years) between the origin of Semitic and the appearance of Akkadian in Sumer, suggests a Semitic origin in the northeast Levant and a later movement of Akkadian eastward into Mesopotamia and Sumer (see figure 1 for a map of our proposed Semitic dispersals).

An origin of Semitic in northeast Levant (Syria) would be consistent with the observed east-west cline of decreasing J1 frequency in the Levant; the authors do, however, mention that the possibility for unknown extinct languages of the Semitic language may shift both the age of the language and its place of origin.

Lacking closely related non-Semitic languages to serve as out-groups in our phylogeny, we cannot estimate when or where the ancestor of all Semitic languages diverged from Afroasiatic. Furthermore, it is likely that some early Semitic languages became extinct and left no record of their existence. This is especially probable if early Semitic societies were pastoralist in nature (Blench 2006), as pastoralists are less likely to leave epigraphic and archaeological evidence of their languages.

A pastoralist association of Semitic languages is also consistent with the observed correlation of haplogroup J1 with herders and J2 with settled farmers in the Near East.


Proc. R. Soc. B 7 August 2009 vol. 276 no. 1668 2703-2710

Bayesian phylogenetic analysis of Semitic languages identifies an Early Bronze Age origin of Semitic in the Near East

Andrew Kitchen et al.

Abstract

The evolution of languages provides a unique opportunity to study human population history. The origin of Semitic and the nature of dispersals by Semitic-speaking populations are of great importance to our understanding of the ancient history of the Middle East and Horn of Africa. Semitic populations are associated with the oldest written languages and urban civilizations in the region, which gave rise to some of the world's first major religious and literary traditions. In this study, we employ Bayesian computational phylogenetic techniques recently developed in evolutionary biology to analyse Semitic lexical data by modelling language evolution and explicitly testing alternative hypotheses of Semitic history. We implement a relaxed linguistic clock to date language divergences and use epigraphic evidence for the sampling dates of extinct Semitic languages to calibrate the rate of language evolution. Our statistical tests of alternative Semitic histories support an initial divergence of Akkadian from ancestral Semitic over competing hypotheses (e.g. an African origin of Semitic). We estimate an Early Bronze Age origin for Semitic approximately 5750 years ago in the Levant, and further propose that contemporary Ethiosemitic languages of Africa reflect a single introduction of early Ethiosemitic from southern Arabia approximately 2800 years ago.

Link

Demographic history of African farmers and hunters (Cox et al. 2009)

From the paper:

Median times since the onset of population growth are 1,863 (513–6,625), 1,027 (97–6,656), and 901 (38–6,497) generations ago, for the San, Biaka and Mandenka, respectively. Given a generation interval of 28 years [21], these values correspond to chronological dates of 52, 29 and 25 thousand years ago (or 37, 21 and 18 kya if we assume a 20-year generation interval). We obtain similar results with our larger Yoruban dataset. We infer a growth rate of 1.7×10⁻⁴ per generation (4.3×10⁻⁶–6.6×10⁻²), and a time of onset of growth at 1,280 (28–6,780) generations ago (or 36 kya), and 5-fold growth from ancestral size (Table 2)

...

The data from the three surveyed non-African populations (French Basque, Chinese Han, and Melanesians) are inconsistent with the simple growth model, presumably because they reflect more complex demographic histories. In contrast, data from all four sub-Saharan African populations fit the two-phase growth model, and a range of onset times and growth rates is inferred for each population. Interestingly, both hunter-gatherers (San and Biaka) and food-producers (Mandenka and Yorubans) best fit models with population growth beginning in the Late Pleistocene.

I am very doubtful of low-level exponential growth sustained over hundreds of generations, very doubtful that modern-day human gene pools contain a strong enough signal of past demographic history, and very doubtful that the demography of Eurasians is more complex than that of Africans. The paper could probably be improved by taking into account admixture processes in Africa itself, i.e., the fact that both African farmers and hunter-gatherers are the result of fairly recent admixture events, with introgressing of "farmer" genes in both San and Pygmies being particularly important.

The observed difference in inferred demography for Eurasians and Africans certaintly means something, but it's hard to evaluate how strong the case is for the scenario proposed in this paper.

UPDATE: The authors consider a simple 2-way admixture model for either recent cryptic admixture, or the Bantu expansion (3kya):

In the presence of gene flow or admixture (or a combination of both), our inference methods would tend to overestimate the effects of population growth, thus leading us to infer slightly older and stronger growth than actually occurred.

But, what about more ancient admixture? The recent Tishkoff et al. paper suggests substantial structure and admixture in African populations that goes well beyond a simple Bantu+Hunter-gatherer model. Even clusters that appear to be homogeneous in that study may reflect stabilized blends of earlier admixture events. If Europeans came into contact with Africans after Pygmies and San had disappeared (as seems likely to happen eventually), we would not even know that such peoples ever existed. How many more small hunter groups were absorbed by expanding African populations (pre-Neolithic or Neolithic), leaving no trace today?

Unlike the authors, I think Eurasian demography is fairly simple in comparison to the African one. There is nothing metaphysical about this guess: Africa, being the cradle of Homo sapiens, is likely to have had the largest human populations, for the longest time. These populations did not sit idly for so long, waiting to be discovered by outsiders, but experienced growth, admixture, competition leading to extinction or absorption, etc.

PLoS ONE 4(7): e6366. doi:10.1371/journal.pone.0006366

Autosomal Resequence Data Reveal Late Stone Age Signals of Population Expansion in Sub-Saharan African Foraging and Farming Populations


Murray P. Cox et al.

Abstract

Background

A major unanswered question in the evolution of Homo sapiens is when anatomically modern human populations began to expand: was demographic growth associated with the invention of particular technologies or behavioral innovations by hunter-gatherers in the Late Pleistocene, or with the acquisition of farming in the Neolithic?

Methodology/Principal Findings

We investigate the timing of human population expansion by performing a multilocus analysis of≥20 unlinked autosomal noncoding regions, each consisting of ~6 kilobases, resequenced in ~184 individuals from 7 human populations. We test the hypothesis that the autosomal polymorphism data fit a simple two-phase growth model, and when the hypothesis is not rejected, we fit parameters of this model to our data using approximate Bayesian computation.

Conclusions/Significance

The data from the three surveyed non-African populations (French Basque, Chinese Han, and Melanesians) are inconsistent with the simple growth model, presumably because they reflect more complex demographic histories. In contrast, data from all four sub-Saharan African populations fit the two-phase growth model, and a range of onset times and growth rates is inferred for each population. Interestingly, both hunter-gatherers (San and Biaka) and food-producers (Mandenka and Yorubans) best fit models with population growth beginning in the Late Pleistocene. Moreover, our hunter-gatherer populations show a tendency towards slightly older and stronger growth (~41 thousand years ago, ~13-fold) than our food-producing populations (~31 thousand years ago, ~7-fold). These dates are concurrent with the appearance of the Late Stone Age in Africa, supporting the hypothesis that population growth played a significant role in the evolution of Late Pleistocene human cultures.

Link

Ancient mtDNA and craniometric evolution of Amerindians

This paper shows that while the mtDNA gene pool of Amerindians did not undergo substantial change since the Holocene (haplogroups B, C, D were detected in the ancient samples, all of them common today), their cranial morphology changed from a more generalized to a more Mongoloid pattern.

In my opinion, the fact that Amerindians evolved in a Mongoloid direction may suggest one of three things:

1. proto-Mongoloid traits were present as tendencies in the founding population, and they evolved in parallel in the Americas and in East Asia
2. proto-Mongoloid traits were absent in the founding population, and they evolved independently in the Americas
3. proto-Mongoloid traits were absent in the founding population, but they were added by limited gene flow from Asia

Even in Asia itself, except for isolated finds in Siberia, the first full-blown Mongoloids emerge in the Holocene. The Mongoloid type even spread to the south of the continent, which was formerly occupied by populations more similar to Australo-Melanesians.

Why the type became so successful remains to be seen; adaptive explanations for a rounder skull, flatter face, and heavy eyelids have been proposed as responses to extreme arctic cold, but why would similar phenotypes be selected for in regions of less extreme climate?

Sexual selection might play a role, although it would be difficult to establish over such a large area.

My guess is that various aspects of the Mongoloid pattern existed in low frequency or as isolated tendencies across East Eurasia and America. As populations grew during the Holocene, these traits spread in a wider range. Naturally, in the periphery, their blending was incomplete, with different quasi-Mongoloid types emerging there, e.g., prominent-nosed, round-headed Amerindians vs. flat-nosed, long-headed Proto-Uralics.

Thus, ancestral Amerindians either already had, or later received -by limited gene flow- a set of Mongoloid traits from Asia, which were selected for the same reasons as they did in Asia, but the "bottleneck" of the Bering did not allow them to receive the full package of traits.

PLoS ONE doi:10.1371/journal.pone.0005746

Discrepancy between Cranial and DNA Data of Early Americans: Implications for American Peopling

S. Ivan Perez et al.

Abstract

Currently, one of the major debates about the American peopling focuses on the number of populations that originated the biological diversity found in the continent during the Holocene. The studies of craniometric variation in American human remains dating from that period have shown morphological differences between the earliest settlers of the continent and some of the later Amerindian populations. This led some investigators to suggest that these groups—known as Paleomericans and Amerindians respectively—may have arisen from two biologically different populations. On the other hand, most DNA studies performed over extant and ancient populations suggest a single migration of a population from Northeast Asia. Comparing craniometric and mtDNA data of diachronic samples from East Central Argentina dated from 8,000 to 400 years BP, we show here that even when the oldest individuals display traits attributable to Paleoamerican crania, they present the same mtDNA haplogroups as later populations with Amerindian morphology. A possible explanation for these results could be that the craniofacial differentiation was a local phenomenon resulting from random (i.e. genetic drift) and non-random factors (e.g. selection and plasticity). Local processes of morphological differentiation in America are a probable scenario if we take into consideration the rapid peopling and the great ecological diversity of this continent; nevertheless we will discuss alternative explanations as well.

Link

Genetic admixture in eastern Indonesia

From the paper:

Although less pronounced in EI compared to other regions, we observed a higher eastern Asian component with mtDNA than with NRY-DNA, and conversely a higher Melanesian component with NRY-DNA than with mtDNA in EI, similar to what has been described for Island Melanesia (Kayser et al. 2008) and Polynesia (Kayser et al. 2006). As described elsewhere, a history of sex-biased admixture between Austronesians and non- Austronesians might explain this result, confirming previous surveys in Near and Remote Oceania on the modality of the Austronesian migration (Hage and Marck 2003; Kayser et al. 2006; Kayser et al. 2008; Kayser, Lao, and Stoneking 2008).

Molecular Biology and Evolution, doi:10.1093/molbev/msp097

Genetic admixture history of eastern Indonesia as revealed by Y-chromosome and mitochondrial DNA analysis

Stefano Mona et al.

Abstract

Eastern Indonesia possesses more linguistic diversity than any other region in Southeast Asia, with both Austronesian (AN) languages that are of East Asian origin, as well as non-Austronesian (NAN) languages of likely Melanesian origin. Here, we investigated the genetic history of human populations from seven eastern Indonesian islands, including AN- and NAN-speakers, as well as the relationship between languages and genes, by means of non-recombining Y-chromosomal (NRY) and mitochondrial DNA (mtDNA) analysis. We found that the eastern Indonesian gene pool consists of East Asian as well as Melanesian components, as might be expected based on linguistic evidence, but also harbours putative indigenous eastern Indonesian signatures that perhaps reflect the initial occupation of the Wallacea by aboriginal hunter-gatherers already in Palaeolithic times. Furthermore, both NRY and mtDNA data showed a complete lack of correlation between linguistic and genetic relationships, most likely reflecting genetic admixture and/or language shift. In addition, we noted a small fraction of the NRY and mtDNA data shared between eastern Indonesians and Australian Aborigines likely reflecting an ancient link between Asia and Australia. Our data thus provide insights into the complex genetic ancestry history of eastern Indonesian islanders characterized by several admixture episodes, and demonstrate a clear example of the lack of the often-assumed correlation between the genes and languages of human populations.

Link

Bacteria and the human peopling of the Pacific

A new paper in Science looks at the peopling of the Pacific from the perspective of genetic diversity of the bacterium H. pylori which is found in people's stomachs.

Related to: Bayesian phylogenetics of languages and the timing of Austronesian settlement of the Pacific from Taiwan

Science doi:10.1126/science.1166083

The Peopling of the Pacific from a Bacterial Perspective

Yoshan Moodley et al.

Abstract

Two prehistoric migrations peopled the Pacific. One reached New Guinea and Australia, and a second, more recent, migration extended through Melanesia and from there to the Polynesian islands. These migrations were accompanied by two distinct populations of the specific human pathogen Helicobacter pylori, called hpSahul and hspMaori, respectively. hpSahul split from Asian populations of H. pylori 31,000 to 37,000 years ago, in concordance with archaeological history. The hpSahul populations in New Guinea and Australia have diverged sufficiently to indicate that they have remained isolated for the past 23,000 to 32,000 years. The second human expansion from Taiwan 5000 years ago dispersed one of several subgroups of the Austronesian language family along with one of several hspMaori clades into Melanesia and Polynesia, where both language and parasite have continued to diverge.

Link

Cranial robusticity in Australians

From the paper:

Instead, cranial robusticity among the Australians and other modern humans can reasonably be explained on the basis of current knowledge of cranial development-function, as well as a phylogenetic scenario consistent with genetic studies of the population history of Aboriginal Australians (e.g. Hudjashov et al., 2006). Thus, the earliest Australians might be thought of as having evolved from the earliest modern humans who migrated from Africa into East/Southeast Asia around 60-70 kyr. The Australian Pleistocene/Early Holocene human record indicates the presence of marked variability in cranial form. However, it is not possible with present genetic data to determine whether the continent was colonised during a single migration by a population with a highly variable cranial form or in two major events by people with different cranial morphologies.

From Hudjashov et al. (2007) mentioned in the text:

The analysis reveals no evidence for any archaic maternal or paternal lineages in Australians, despite some suggestively robust features in the Australian fossil record, thus weakening the argument for continuity with any earlier Homo erectus populations in Southeast Asia. (ii) The tree of complete mtDNA sequences shows that Aboriginal Australians are most closely related to the autochthonous populations of New Guinea/Melanesia, indicating that prehistoric Australia and New Guinea were occupied initially by one and the same Palaeolithic colonization event approximately 50,000 years ago, in agreement with current archaeological evidence. (iii) The deep mtDNA and Y chromosomal branching patterns between Australia and most other populations around the Indian Ocean point to a considerable isolation after the initial arrival. (iv) We detect only minor secondary gene flow into Australia, and this could have taken place before the land bridge between Australia and New Guinea was submerged approximately 8,000 years ago, thus calling into question that certain significant developments in later Australian prehistory (the emergence of a backed-blade lithic industry, and the linguistic dichotomy) were externally motivated.

Journal of Archaeological Science doi:10.1016/j.jas.2008.11.021

Possible Causes and Significance of Cranial Robusticity Among Pleistocene-Early Holocene Australians

Darren Cunroe

Abstract

An analysis of possible developmental-functional causes of cranial form suggests that the unusual morphology of ‘robust’ Pleistocene/Early Holocene Australians such as Willandra Lakes Human 50 might best be explained by four underlying factors: possession of a 1) large neurocranium, 2) narrow cranial base, 3) viscerocranium with considerable midfacial projection, and 4) large dentition, especially the cheek teeth, with their associated large jaws and high volume masticatory muscles. Some of these features are likely to be highly heritable, while others are caused/exaggerated by influences from ageing processes, diet, and a hunter-gatherer lifestyle in an arid environment. These underlying ‘causes’ are either apomorphies of H. sapiens (1 & 2) and thus absent from pre-modern specimens such as from Ngandong, or represent plesiomorphic features of latter Homo (3 & 4). It is concluded that combining current knowledge of cranial development-function with genetic studies of the population history of Aboriginal Australians provides the most parsimonious solution to understanding their evolutionary origins.

Link

500K SNP study of Oceanian populations

Related: Genetic structure of Pacific Islanders

Molecular Biology and Evolution, doi:10.1093/molbev/msn128

Gene Flow and Natural Selection in Oceanic Human Populations, Inferred from Genome-wide SNP Typing

Ryosuke Kimura et al.

It is suggested that the major prehistoric human colonizations of Oceania occurred twice, namely, about 50,000 and 4,000 years ago. The first settlers are considered as ancestors of indigenous people in New Guinea and Australia. The second settlers are Austronesian-speaking people who dispersed by voyaging in the Pacific Ocean. In this study, we performed genome-wide SNP typing on an indigenous Melanesian (Papuan) population, Gidra, and a Polynesian population, Tongans, by using the Affymetrix 500K assay. The SNP data were analyzed together with the data of the HapMap samples provided by Affymetrix. In agreement with previous studies, our phylogenetic analysis indicated that indigenous Melanesians are genetically closer to Asians than to Africans and European Americans. Population structure analyses revealed that the Tongan population is genetically originated from Asians at 70% and indigenous Melanesians at 30%, which thus supports the so-called "Slow train" model. We also applied the SNP data to genome-wide scans for positive selection by examining haplotypic variation, and identified many candidates of locally selected genes. Providing a clue to understand human adaptation to environments, our approach based on evolutionary genetics must contribute to revealing unknown gene functions as well as functional differences between alleles. Conversely, this approach can also shed some light onto the invisible phenotypic differences between populations.

Link

Austronesian expansion in Admiralty Islands of Melanesia

Molecular Biology and Evolution, doi:10.1093/molbev/msn078

The impact of the Austronesian expansion: evidence from mtDNA and Y-chromosome diversity in the Admiralty Islands of Melanesia

Manfred Kayser et al.

The genetic ancestry of Polynesians can be traced to both Asia and Melanesia, which presumably reflects admixture occurring between incoming Austronesians and resident non-Austronesians in Melanesia before the subsequent occupation of the greater Pacific; however, the genetic impact of the Austronesian expansion to Melanesia remains largely unknown. We therefore studied the diversity of non-recombining Y-chromosomal (NRY) and mitochondrial (mt) DNA in the Admiralty Islands, located north of mainland Papua New Guinea, and updated our previous data from Asia, Melanesia and Polynesia with new NRY markers. The Admiralties are occupied today solely by Austronesian-speaking groups, but their human settlement history goes back 20,000 years prior to the arrival of Austronesians about 3,400 years ago. On the Admiralties we found substantial mtDNA and NRY variation of both Austronesian and non-Austronesian origin, with higher frequencies of Asian mtDNA and Melanesian NRY haplogroups, similar to previous findings in Polynesia, and perhaps as consequence of Austronesian matrilocality. Thus, the Austronesian language replacement on the Admiralties (and elsewhere in Island Melanesia and coastal New Guinea) was accompanied by an incomplete genetic replacement that is more associated with mtDNA than with NRY diversity. These results provide further support for the "Slow Boat" model of Polynesian origins, according to which Polynesian ancestors originated from East Asia but genetically mixed with Melanesians before colonizing the Pacific. We also observed that non-Austronesian groups of coastal New Guinea and Island Melanesia had significantly higher frequencies of Asian mtDNA haplogroups than of Asian NRY haplogroups, suggesting sex-biased admixture perhaps as a consequence of non-Austronesian patrilocality. We additionally found that the predominant NRY haplogroup of Asian origin in the Admiralties (O-M110) likely originated in Taiwan, thus providing the first direct Y-chromosome evidence for a Taiwanese origin of the Austronesian expansion. Furthermore, we identified a NRY haplogroup (K-P79, also found on the Admiralties) in Polynesians that most likely arose in the Bismarck Archipelago, providing the first direct link between northern Island Melanesia and Polynesia. These results significantly advance our understanding of the impact of the Austronesian expansion and of human history in the Pacific region.

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