In search of the source of Denisovan ancestry

bioRxiv http://dx.doi.org/10.1101/017475

Denisovan Ancestry in East Eurasian and Native American Populations.

Pengfei Qin , Mark Stoneking

Although initial studies suggested that Denisovan ancestry was found only in modern human populations from island Southeast Asia and Oceania, more recent studies have suggested that Denisovan ancestry may be more widespread. However, the geographic extent of Denisovan ancestry has not been determined, and moreover the relationship between the Denisovan ancestry in Oceania and that elsewhere has not been studied. Here we analyze genome-wide SNP data from 2493 individuals from 221 worldwide populations, and show that there is a widespread signal of a very low level of Denisovan ancestry across Eastern Eurasian and Native American (EE/NA) populations. We also verify a higher level of Denisovan ancestry in Oceania than that in EE/NA; the Denisovan ancestry in Oceania is correlated with the amount of New Guinea ancestry, but not the amount of Australian ancestry, indicating that recent gene flow from New Guinea likely accounts for signals of Denisovan ancestry across Oceania. However, Denisovan ancestry in EE/NA populations is equally correlated with their New Guinea or their Australian ancestry, suggesting a common source for the Denisovan ancestry in EE/NA and Oceanian populations. Our results suggest that Denisovan ancestry in EE/NA is derived either from common ancestry with, or gene flow from, the common ancestor of New Guineans and Australians, indicating a more complex history involving East Eurasians and Oceanians than previously suspected.

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

Gene flow between Indian populations and Australasia ~4,000 years ago

Only the press release is available so far, I will add the paper abstract when I see it on the PNAS website:

Researcher Irina Pugach and colleagues now analysed genetic variation from across the genome from aboriginal Australians, New Guineans, island Southeast Asians, and Indians. Their findings suggest substantial gene flow from India to Australia 4,230 years ago. i.e. during the Holocene and well before European contact. “Interestingly,” says Pugach, “this date also coincides with many changes in the archaeological record of Australia, which include a sudden change in plant processing and stone tool technologies, with microliths appearing for the first time, and the first appearance of the dingo in the fossil record. Since we detect inflow of genes from India into Australia at around the same time, it is likely that these changes were related to this migration.” 

Their analyses also reveal a common origin for populations from Australia, New Guinea and the Mamanwa – a Negrito group from the Philippines – and they estimated that these groups split from each other about 36,000 years ago. Mark Stoneking says: “This finding supports the view that these populations represent the descendants of an early ‘southern route’ migration out of Africa, while other populations in the region arrived later by a separate dispersal.“ This also indicates that Australians and New Guineans diverged early in the history of Sahul, and not when the lands were separated by rising sea waters around 8,000 years ago.

A relationship between Indian and Australasian populations has long been suspected on various grounds (e.g., HGDP Papuans often show membership in a "South Asian" ancestral component at low levels of resolution). It will be interesting to see the model proposed in the new paper about the admixture event leading to modern Australasians.

UPDATE: Ed Yong covers the story in Nature News:

Some aboriginal Australians can trace as much as 11% of their genomes to migrants who reached the island around 4,000 years ago from India, a study suggests. Along with their genes, the migrants brought different tool-making techniques and the ancestors of the dingo, researchers say1.

From World News Australia:

The study suggests that in addition to an earlier northern route of migration out of Africa, into Asia, and then South East Asia about 60,000 to 70,000 years ago, the second wave occurred much later, arriving during the Holocene period about 4,230 years ago.
...
“About that point in the archaeological record, there were significant changes in the use of stone tools, in hunting techniques and significantly, the introduction of the dingo,” Professor Cooper said.
...
There are other theories that may support the evidence of a more recent influx of migrants from India, including that they brought with them a disease of epidemic proportions that wiped out earlier Aboriginal populations.

UPDATE II: I added the abstract.

PNAS doi: 10.1073/pnas.1211927110

Genome-wide data substantiate Holocene gene flow from India to Australia 

Irina Pugach et al.

The Australian continent holds some of the earliest archaeological evidence for the expansion of modern humans out of Africa, with initial occupation at least 40,000 y ago. It is commonly assumed that Australia remained largely isolated following initial colonization, but the genetic history of Australians has not been explored in detail to address this issue. Here, we analyze large-scale genotyping data from aboriginal Australians, New Guineans, island Southeast Asians and Indians. We find an ancient association between Australia, New Guinea, and the Mamanwa (a Negrito group from the Philippines), with divergence times for these groups estimated at 36,000 y ago, and supporting the view that these populations represent the descendants of an early “southern route” migration out of Africa, whereas other populations in the region arrived later by a separate dispersal. We also detect a signal indicative of substantial gene flow between the Indian populations and Australia well before European contact, contrary to the prevailing view that there was no contact between Australia and the rest of the world. We estimate this gene flow to have occurred during the Holocene, 4,230 y ago. This is also approximately when changes in tool technology, food processing, and the dingo appear in the Australian archaeological record, suggesting that these may be related to the migration from India.

Link

Q2 mtDNA haplogroup in Oceania

PLoS ONE 7(12): e52022. doi:10.1371/journal.pone.0052022

The Q2 Mitochondrial Haplogroup in Oceania

Chris A. Corser et al.

Many details surrounding the origins of the peoples of Oceania remain to be resolved, and as a step towards this we report seven new complete mitochondrial genomes from the Q2a haplogroup, from Papua New Guinea, Fiji and Kiribati. This brings the total to eleven Q2 genomes now available. The Q haplogroup (that includes Q2) is an old and diverse lineage in Near Oceania, and is reasonably common; within our sample set of 430, 97 are of the Q haplogroup. However, only 8 are Q2, and we report 7 here. The tree with all complete Q genomes is proven to be minimal. The dating estimate for the origin of Q2 (around 35 Kya) reinforces the understanding that humans have been in Near Oceania for tens of thousands of years; nevertheless the Polynesian maternal haplogroups remain distinctive. A major focus now, with regard to Polynesian ancestry, is to address the differences and timing of the ‘Melanesian’ contribution to the maternal and paternal lineages as people moved further and further into Remote Oceania. Input from other fields such as anthropology, history and linguistics is required for a better understanding and interpretation of the genetic data.

Link

East Eurasian-like ancestry in Northern Europe (part 3)

(This is the third part of the series. See part 1 and part 2.)

In the first two parts of the series, I showed that northern European populations show hints of East Eurasian ancestry when compared against Sardinians. I used Dai, Han, and Karitiana as reference populations for East Eurasia. In the current post, I extend this analysis by using HGDP Papuans and the Onge (Reich et al. 2009) from the Andaman Islands.

The f4 statistics using Karitiana, Papuan, and Onge populations can be found in this spreadsheet.

Below, you can see that they are all near perfectly correlated with each other.

The visual appraisal is confirmed when we calculate the correlation coefficients:

The fact that all three populations track the same signal is strong evidence for the direction of gene flow: from Asia into northern Europe. If the signal was present in only one of the three populations, then it could conceivably be an artefact of gene flow in the opposite direction (from northern Europeans to the affected population). But, the fact that all three populations show the same pattern would require northern European-like admixture in the Andaman Islands, Papuan New Guinea and South America, which does not appear very parsimonious.

While the signals from the three populations are correlated, their intensity varies. The Z-scores provide a measure of this intensity. The mean Z-scores using a Karitiana, Papuan, and Onge reference across all populations are respectively -17.7, -8.0, and -6.0.

While I did not include the Han reference of part 1 in this analysis, inspection of the f4 statistics (which can be obtained at the bottom of that part), suggests that the Z-scores become more significant when using an Onge, Papuan, Han, and Karitiana reference in that order. For example, for the Finnish_D population, they are: -10.037, -13.2949, -23.9305, and -27.764 respectively.

It thus appears that the element contributing East Eurasian-like ancestry in northern Europeans was derived from the northern spectrum of East Eurasians; the Karitiana may live in South America today, but they trace their ancestors to northern Eurasia, having entered the Americas c. 15ka.

In my opinion, the signal has been formed by a superposition of a few factors:

1. The fact that Y-haplogroup R, the main lineage in modern northern Europeans has a common origin (Y-haplogroup P) with haplogroup Q, the main lineage in modern Amerindians, and many Siberians. We can hypothesize that the population that brought R into Europe was intermediate genetically across the Caucasoid-Mongoloid spectrum. In West Eurasia, this population admixed with the Palaeo-West Eurasians (Y-haplogroups IJ, G, and possibly LT), and contributed their DNA primarily to the northern Europeoids.
2. Other population movements of more regional impact, such as Y-haplogroup N, which affected mainly Uralic, Baltic, and East Slavic populations, as well as elements from the mixed West/East Eurasian mtDNA contact zone that ancient DNA analysis has revealed in Eastern Europe and Siberia.

The raw dumps of fourpop output for Papuan and Onge reference can be found here.

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

Austronesian spread across Indonesia

It is wonderful when different disciplines arrive at the same conclusions independently. Recent work in Austronesian languages by Gray, Drummond, and Greenhill arrived at the conclusion that Austronesian originated in Taiwan c. 5,200 years ago, and experienced a rapid expansion pulse c. 4,000 years ago that resulted in the colonization of island Southeast Asia.

This colonization event left its traces in the genomes of present-day eastern Indonesians; the pre-Austronesian inhabitants of those islands were Papuan-like, or, in terms of traditional physical anthropology Australoid, whereas the expanding Austronesian mariners were Mongoloid. If the expansion happened within the time frame in question, it can be dated by dense genotype data by looking at the relative lengths of Australoid and Mongoloid segments in extant individuals.

This is exactly what a new paper has achieved. It has determined that the "Asian" admixture signal in Eastern Indonesia dates to 4,000-3,000 years ago.

This is what the linguistic analysis by Gray et al. had to say:

It shows an Austronesian origin in Taiwan around 5200 years ago, followed bya settlement pause (pause 1) between 5200 and 4000 years ago. After this pause, a rapid expansion pulse (pulse 1) led to thesettlement of Island Southeast Asia, New Guinea and Near Oceania in less than 1000 years.

which is entirely consistent with the 4,000-3,000 year old colonization of Eastern Indonesia deduced by genetic recombination analysis.

The paper has some brilliant visualizations of information, one of which is reproduced on the left. Notice the cline of Papuan ancestry in Eastern Indonesia, east of the Wallace Line.

From the paper:

These results strongly suggest that the admixture cline in East Indonesia reflects the spread of individuals of Asian ancestry coming from the west and admixing with resident groups of  Papuan ancestry. Second, the time of admixture is highlyconsistent for the two different datasets, which were estimated bytwo different methods, and suggest that the admixture began about 4,000 y ago (Figs. 1E and 2E and Table 3). This time is in excellent agreement with estimates from archaeological and linguistic data for the arrival of Austronesian speakers in East Indonesia about 3,500–4,000 y ago (9, 21). For example, the oldest pottery found in East Indonesia, associated with the Austronesian culture, dates back to 3,500 y ago (22). Moreover , a Bayesian analysis of Austronesian languages dates the Austronesian expansion into Indonesia to about 4,000 y ago and also suggests a west to east spread across East Indonesia (9).

This is a wonderful co-validation of the (once controversial) use of Bayesian phylogenetics in linguistics, and time depth estimation via recombination in genetics, calibrated with "hard" archaeological evidence. It will be great to see the same consensus arrived for other families as well.

PNAS doi: 10.1073/pnas.1118892109

Genetic dating indicates that the Asian–Papuan admixture through Eastern Indonesia corresponds to the Austronesian expansion

Shuhua Xu et al.

Although the Austronesian expansion had a major impact on the languages of Island Southeast Asia, controversy still exists over the genetic impact of this expansion. The coexistence of both Asian and Papuan genetic ancestry in Eastern Indonesia provides a unique opportunity to address this issue. Here, we estimate recombination breakpoints in admixed genomes based on genome-wide SNP data and date the genetic admixture between populations of Asian vs. Papuan ancestry in Eastern Indonesia. Analyses of two genome-wide datasets indicate an eastward progression of the Asian admixture signal in Eastern Indonesia beginning about 4,000–3,000 y ago, which is in excellent agreement with inferences based on Austronesian languages. The average rate of spread of Asian genes in Eastern Indonesia was about 0.9 km/y. Our results indicate that the Austronesian expansion had a strong genetic as well as linguistic impact on Island Southeast Asia, and they significantly advance our understanding of the biological origins of human populations in the Asia–Pacific region.

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

The strangeness of the human genome

Here is a little experiment:

Calculate the first principal component of variation between Papuans, and Karitiana from Brazil. These are some of the populations most distant to Africa that one can find genetic data for. (One Papuan,HGDP00544, is substantially different from the rest, and is shifted towards East Asians, so he was removed, all analyses on 613,630 SNPs with all no-calls removed).

Project 18 Mbuti Pygmies+San (henceforth Palaeoafricans) and 21 Yoruba from the HGDP-CEPH onto this component.

What do we expect? According to the standard Out-of-Africa model, you expect that Palaeoafricans and Yoruba will not differ from each other along the axis in which Amerindians differ from Papuans. If you take into account the Denisovan admixture in Australo-Melanesians, you might expect Africans (who lack this admixture) to be more Amerindian-like (since Amerindians also lack that archaic component). But, you certainly don't expect in either scenario Palaeoafricans to differ from Yoruba.

What the data say. Here are the data points along PC1:

green = Papuans

magenta = Karitiana

Here is a blowup of the middle part, showing the African populations:

red = Palaeoafrican

blue = Yoruba

A t-test supports (p less than .000001) the obvious visual conclusion that Palaeoafricans differ from Yoruba in the same way that Papuans differ from Karitiana. This is quite remarkable: why would Yoruba differ from San/Pygmies in the same way that Amazonians differ from Australo-Melanesians?

The difference is not that great: the Paleoafrican/Yoruba means are -.022 and -.020 and the Papuan/Karitiana ones are -0.167 and 0.206 respectively. Hence, the difference between Palaeoafricans and Yoruba is only 0.54% or so in this projection. But it is there, and it points to events in human prehistory not covered by the "standard model".

Discussion

I have long argued that Africa should not be viewed only as a source, but also as a destination of population movemenets. If Africa was only a source, then there would be absolutely no reason for two different African groups to differ from each other in the same way that two of the most distant (from Africa) groups do. No one can reasonably argue, I think that Africans had the opportunity of any amount of gene flow with either Papuans or Amerindians.

I conjecture that the signal detected here is a legacy of a prehistoric episode of migration of Eurasians into Africa, which affected Yoruba more than it did Palaeoafricans. This population of Eurasians was slightly more similar to Karitiana than to Papuans. We will try to trace its origins next.

Using She instead of Karitiana

I repeat the previous experiment, but I use She, a far eastern ethnic group of China instead of the Karitiana.Here are the PC1 co-ordinates in this projection:

Yoruba: 0.111, Palaeoafrican: 0.108, Papuan: -0.155, She: 0.248

Hence, Yoruba are shifted by 0.74% on the Papuan-She axis relative to Palaeoafricans.

Using Tuscans instead of She

Using Tuscans the PC1 co-ordinates are:

Yoruba: 0.169, Palaeoafrican: 0.164, Papuan: -0.144, Tuscan: 0.289

Hence, Yoruba are shifted by 1.15% on the Papuan-Tuscan axis relative to Palaeoafricans.

Using Onge instead of Tuscans

Finally, I substituted Onge from the Indian Ocean for Tuscans. This analysis is based on 112,041 SNPs, so it's not directly comparable with the previous ones. Nonetheless:

Yoruba: 0.075, Palaeoafrican: 0.07, Papuan: -0.15, Onge: 0.267

Hence, Yoruba are shifted by 1.2% on the Papuan-Onge axis relative to Palaeoafricans.

Conclusion

In a previous post on McEvoy et al. (2011) I speculated about a possible West Eurasian back-migration into Africa. The results presented here are compatible with that theory, but they are also compatible with a second Out-of-Africa movement; the latter, however, if it happened, did not only affect West Eurasians, but also East Asians and even Amerindians, at least relative to Papuans who may have been more isolated than the rest.

On balance, I prefer a scenario with back-migration:

1. It is difficult to envision a second Out-of-Africa that reached Brazil in its spread but avoided Papua, moreover there are no diagnostic uniparental markers of such an event
2. It is simpler to think of a movement of Y-haplogroup DE-bearing men a short distance from "somewhere between the Indian Ocean (where the Andamanese live), and East Africa." which would introduce Eurasian-like genes into Sub-Saharan Africa.

UPDATE (May 16): See the interesting discussion on the problem of potential ascertainment bias in the comments. In short: the signal seems to persist in the She and Tuscan comparisons, but not in the Karitiana one. Perhaps this means that whatever event took place postdates the migration of Amerindians into the New World?

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

Y chromosome variation in NW New Guinea

A 2007 paper that slipped through my net at the time it appeared, but is interesting to read as it was cited in the recent study by Cox et al. (2010)

Molecular Biology and Evolution 2007 24(11):2546-2555; doi:10.1093/molbev/msm187

Patterns of Y-Chromosome Diversity Intersect with the Trans-New Guinea Hypothesis

Stefano Mona et al.

Abstract

The island of New Guinea received part of the first human expansion out of Africa (>40,000 years ago), but its human genetic history remains poorly understood. In this study, we examined Y-chromosome diversity in 162 samples from the Bird's Head region of northwest New Guinea (NWNG) and compared the results with previously obtained data from other parts of the island. NWNG harbors a high level of cultural and linguistic diversity and is inhabited by non-Austronesian (i.e., Papuan)–speaking groups as well as harboring most of West New Guinea's (WNG) Austronesian-speaking groups. However, 97.5% of its Y-chromosomes belong to 5 haplogroups that originated in Melanesia; hence, the Y-chromosome diversity of NWNG (and, according to available data, of New Guinea as a whole) essentially reflects a local history. The remaining 2.5% belong to 2 haplogroups (O-M119 and O-M122) of East Asian origin, which were brought to New Guinea by Austronesian-speaking migrants around 3,500 years ago. Thus, the Austronesian expansion had only a small impact on shaping Y-chromosome diversity in NWNG, although the linguistic impact of this expansion to this region was much higher. In contrast, the expansion of Trans-New Guinea (TNG) speakers (non-Austronesian) starting about 6,000–10,000 years ago from the central highlands of what is now Papua New Guinea, presumably in combination with the expansion of agriculture, played a more important role in determining the Y-chromosome diversity of New Guinea. In particular, we identified 2 haplogroups (M-P34 and K-M254) as suggestive markers for the TNG expansion, whereas 2 other haplogroups (C-M38 and K-M9) most likely reflect the earlier local Y-chromosome diversity. We propose that sex-biased differences in the social structure and cultural heritage of the people involved in the Austronesian and the TNG expansions played an important role (among other factors) in shaping the New Guinean Y-chromosome landscape.

Link