Tuesday, 4 December 2012

Disentangling the histories of mtDNA haplogroups M1 and U6

mtDNA haplogroups M1 and U6 are often mentioned in terms of Eurasian back-migration in Africa. The former is the only clade of the Asian haplogroup M which occurs in Africa at all; the latter is the only clade of the West Eurasian haplogroup U that does the same. These haplogroups also tend to co-exist in North and East Africa, although they are largely absent in sub-Saharan Africa. Different ideas have been offered for their occurrence, including a "Paleolithic" spread or a more recent one associated with the spread of Afroasiatic languages.

The new paper offers useful new data on this debate. The most important conclusion is that despite their oft-mentioned association, these two haplogroups appear to have distinct histories. One argument for this is their separate geographic distribution:

M1 (on panel A) is much more common in Northeast Africa and the Near East (including the Caucasus), whereas U6 (panel B) is more confined in Africa, and has its stronger peak in NW Africa, being rare in NE Africa.

An interesting aside, is that all the mysterious M1 from the Caucasus belongs to subclade M1a, while the smaller M1b clade tends to co-occur with M1a in other parts of Africa and the Near East. This indicates a founder effect for the origin of Caucasian M1a, but leaves open the issue of the immediate origins of M1. Hopefully it will become possible to place this haplogroup within the broader M phylogeny in the future.

The Bayesian skyline plots also contrast M1 and U6 in terms of their demographic histories:

The authors argue that these histories are inconsistent with either a very early dispersal history with the Dabban industry, as well as a more recent spread with Afroasiatic. From the paper:
The transition from the Middle Palaeolithic to Upper Palaeolithic in North Africa is characterised by the appearance of the “Dabban”, an industry that is restricted to Cyrenaica in northeast Libya and represented at the caves of Hagfet ed Dabba and Haua Fteah [19]. Whilst a techno-typological shift occurred within the Dabban ~33 KYA [19], starker changes in the archaeological record occurred throughout North Africa and Southwest Asia ~23-20 KYA, represented by the widespread appearance of backed bladelet technologies. The appearance of these backed bladelet industries more or less coincides with the timing of the Last Glacial Maximum (LGM) (~23-18 KYA), including: ~21 KYA in Upper Egypt [20]; ~20 KYA at Haua Fteah with the Oranian [21]; the Iberomaurusian expansion in the Jebel Gharbi ~20 KYA [22]; and the first Iberomaurusian at Tamar Hat in Algeria ~20 KYA [23]. The earliest Iberomaurusian sites in Morocco appear to be only slightly younger ~18 KYA [24].
A disassociation of these haplogroups from the UP in North Africa might be consistent with my idea that the UP was in part a cultural revolution that spread not only with people, but often with ideas across a species that already had the "biological machinery" for behavioral modernity and was already established in both Africa and the Near East.

As for the connection to Afroasiatic, the authors detect a linguistic correlation with M1a, which, however, appears too old to have been involved directly in the spread of this language family:
Concerning haplogroup M1 individually, a significant correlation with languages was observed. Furthermore, within M1, it appears that the correlation is mostly due to M1a. However, given the small sample size of M1b, any potential signal correlating with language might not be detectable. Interestingly, M1a has a likely East African origin, but its coalescent age of ~21 KYA still largely predates that of the proto-AA. Maybe a sub-clade of M1a would still give a similar correlation, but there are not sufficient samples to allow splitting M1a into its various sub-clades, and to test for a correlation. Although we found a correlation, limited sample sizes do not allow drawing unambiguous connection between genes and languages. Furthermore, it is also possible that this putative sub-clade of M1 does not testify for the expansion of AA speaking people, but was already present among the people who inhabited the area before the spread of the AA languages.
Personally, I am in favor of an East African origin of Afroasiatic, as this makes sense of various lines of evidence, one of which is the African shift of the "Southwest_Asian" component that is modal in Semitic populations. I envision that M1 was geographically circumscribed in a NE African population after its much earlier arrival from Asia and piggy-backed onto the expansion of Afroasiatic speakers, thus explaining the observed correlation. A good analogy would be with the expansion of, say, haplogroup H in the Americas which piggybacked on the European colonization, even though the coalescence age of H predates the arrival of Europeans in the New World by many millennia.

BMC Evolutionary Biology 2012, 12:234 doi:10.1186/1471-2148-12-234

Divorcing the Late Upper Palaeolithic demographic histories of mtDNA haplogroups M1 and U6 in Africa

Erwan Pennarun et al.

Abstract (provisional)
A Southwest Asian origin and dispersal to North Africa in the Early Upper Palaeolithic era has been inferred in previous studies for mtDNA haplogroups M1 and U6. Both haplogroups have been proposed to show similar geographic patterns and shared demographic histories.

We report here 24 M1 and 33 U6 new complete mtDNA sequences that allow us to refine the existing phylogeny of these haplogroups. The resulting phylogenetic information was used to genotype a further 131 M1 and 91 U6 samples to determine the geographic spread of their sub-clades. No southwest Asian specific clades for M1 or U6 were discovered. U6 and M1 frequencies in North Africa, the Middle East and Europe do not follow similar patterns, and their sub-clade divisions do not appear to be compatible with their shared history reaching back to the Early Upper Palaeolithic. The Bayesian Skyline Plots testify to non-overlapping phases of expansion, and the haplogroups' phylogenies suggest that there are U6 sub-clades that expanded earlier than those in M1. Some M1 and U6 sub-clades could be linked with certain events. For example, U6a1 and M1b, with their coalescent ages of ~20,000-22,000 years ago and earliest inferred expansion in northwest Africa, could coincide with the flourishing of the Iberomaurusian industry, whilst U6b and M1b1 appeared at the time of the Capsian culture.

Our high-resolution phylogenetic dissection of both haplogroups and coalescent time assessments suggest that the extant main branching pattern of both haplogroups arose and diversified in the mid-later Upper Palaeolithic, with some sub-clades concomitantly with the expansion of the Iberomaurusian industry. Carriers of these maternal lineages have been later absorbed into and diversified further during the spread of Afro-Asiatic languages in North and East Africa.


Thursday, 16 August 2012

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.


Friday, 20 July 2012

Redating of the Early Upper Paleolithic site of Riparo Mochi (Italy)

There are two possibilities on how the early Aurignacian entered Europe. According to one hypothesis, its bearers followed the Danube, which formed a natural corridor into the heartland of the continent which was, at the time, thickly forested. A different hypothesis is that the early Aurignacian entered Europe via the Mediterranean. Distinguishing between the two hypotheses depends on obtaining reliable chronological estimates for the Mediterranean and Central European Aurignacian

A recent dating of a site in the Swabian Jura suggested that the Aurignacian was earlier attested in Central Europe. But, another paper in the Journal of Human Evolution examines meticulously the sequence in the Moch rockshelter and finds that it is just as early.
Comparisons with dates for other Upper Palaeolithic contexts outside Italy suggest that the date of the Protoaurignacian of Mochi compares closely. In Fig. 9a the start boundaries for the earliest Aurignacian evidence at the sites of Geissenklösterle (Germany), Abri Pataud and Isturitz (France) are compared to the start boundary for unit G in Mochi. The first two sites were dated recently in Oxford with reliable methodologies (Higham et al., 2011; Higham et al., in press) while for Isturitz only a small number of dates exist for the earliest Upper Palaeolithic (Szmidt et al., 2010). This comparison reveals that the lowermost Aurignacian levels at Geissenklosterle (AHIII) and Isturitz (C4d) date to the same period as Mochi G, at around 42.7-41.5 ka cal BP (68.2%). The earliest Aurignacian of Abri Pataud dates slightly later to around 41e40 ka cal BP (68.2%), but the assemblage there has always been considered more evolved, so this is not surprising. No Mousterian dates are included in any of these calculations, therefore the start boundaries in the Bayesian models are not well constrained at their earliest end. What is interesting is that there appears to be a close similarity between the dates for the Protoaurignacian and Early Aurignacian sites in Germany on the Danube and on the Mediterranean coast. This might suggest a rapid dispersal of both variants of the Aurignacian across Europe at c. 44-42 ka cal BP.
It does appear that the Aurignacian was a continent-wide punctuational event in Europe which occurred in the middle to late 40 thousands ka cal BP.

Either there were two streams into Europe (Danubian and Mediterranean), or one stream that quickly inundated much of the continent. Given that the argument for the Danubian Corridor is partly related to the ease of access it provided, it is difficult to imagine how the people who followed it would quickly stray far from it all the way to Italy. Overall, it does appear that there were multiple streams into Europe, and perhaps new research in the Balkans, Eastern Europe, and West Asia, may help us trace the earlier predecssor of these streams before they followed their separate ways into Europe.

Journal of Human Evolution DOI:10.1016/j.jhevol.2011.11.009

A new chronostratigraphic framework for the Upper Palaeolithic of Riparo Mochi (Italy)

Katerina Douka et al.

The rockshelter of Mochi, on the Ligurian coast of Italy, is often used as a reference point in the formation of hypotheses concerning the arrival of the Aurigancian in Mediterranean Europe. Yet, the site is poorly known. Here, we describe the stratigraphic sequence based on new field observations and present 15 radiocarbon determinations from the Middle Palaeolithic (late Mousterian) and Early Upper Palaeolithic (Aurignacian and Gravettian) levels. The majority of dates were produced on humanly modified material, specifically marine shell beads, which comprise some of the oldest directly-dated personal ornaments in Europe. The radiocarbon results are incorporated into a Bayesian statistical model to build a new chronological framework for this key Palaeolithic site. A tentative correlation of the stratigraphy to palaeoclimatic records is also attempted.


Thursday, 21 June 2012

Ethiopian origins (Pagani et al. 2012)

The study attempts to answer four questions:
Our current study is motivated by four questions. First, where do the Ethiopians stand in the African genetic landscape? Second, what is the extent of recent gene flow from outside Africa into Ethiopia, when did it occur, and is there evidence of selection effects? Third, do genomic data support a route for out-of-Africa migration of modern humans across the mouth of the Red Sea? Fourth, assuming temporal stability of current populations, what are the estimated ages of Ethiopian populations relative to other African groups?
Link to press release. Link the supplemental data.

The authors reiterate that modern humans left Africa 50-70kya, a hypothesis that seems to me pretty much dead in the light of recent archaeological evidence.

The lack of antiquity in the Ethiopian population, even in only the African component thereof argues against that population being ancestral to modern humans. Note that if the Out-of-East Africa hypothesis is correct, then skulls like Omo I represent ancestral modern humans and they are followed much later by modern humans anywhere else. So, while anatomical modernity may have emerged in East Africa --or maybe not; let's not forget that we have early modern skulls from the region in part because of the excellent preservation conditions and excess of scholarly interest-- there is no evidence that they spread from there.

I have little doubt that my own theory about substantial back-migration of Eurasians into Africa will eventually win the day. Of course, I am not referring to the recent (in the last 3,000 years) admixture with West Eurasians that the Ethiopian population has undergone, but rather to the more ancient migration that was probably associated with Y-haplogroup DE-YAP.

The fact that the African component of diverse African populations is more closely related to West than to East Eurasians is one piece of evidence among many for that scenario. Hopefully, it can be tested soon using whole genome data which may have enough density to detect much older admixture events.

UPDATE I: Since the dates in the paper are based on ROLLOFF, a piece of software that is not publicly available more than a year after its announcement, and which contradicts other software released by the same authors, I will take the Queen of Sheba stories circulated in the media with a huge grain of salt.

The American Journal of Human Genetics, 21 June 2012 doi:10.1016/j.ajhg.2012.05.015

Ethiopian Genetic Diversity Reveals Linguistic Stratification and Complex Influences on the Ethiopian Gene Pool

Luca Pagani et al.

Humans and their ancestors have traversed the Ethiopian landscape for millions of years, and present-day Ethiopians show great cultural, linguistic, and historical diversity, which makes them essential for understanding African variability and human origins. We genotyped 235 individuals from ten Ethiopian and two neighboring (South Sudanese and Somali) populations on an Illumina Omni 1M chip. Genotypes were compared with published data from several African and non-African populations. Principal-component and STRUCTURE-like analyses confirmed substantial genetic diversity both within and between populations, and revealed a match between genetic data and linguistic affiliation. Using comparisons with African and non-African reference samples in 40-SNP genomic windows, we identified “African” and “non-African” haplotypic components for each Ethiopian individual. The non-African component, which includes the SLC24A5 allele associated with light skin pigmentation in Europeans, may represent gene flow into Africa, which we estimate to have occurred ∼3 thousand years ago (kya). The African component was found to be more similar to populations inhabiting the Levant rather than the Arabian Peninsula, but the principal route for the expansion out of Africa ∼60 kya remains unresolved. Linkage-disequilibrium decay with genomic distance was less rapid in both the whole genome and the African component than in southern African samples, suggesting a less ancient history for Ethiopian populations.


Saturday, 26 May 2012

43,000-year old Aurignacian in Swabian Jura

A new paper continues the re-assessment of the radiocarbon dating record in Europe. It pushes the Aurignacian of Central Europe back in time, but not as far back as the appearance of modern humans in Europe. The implication is that the advanced music and art of the Aurignacian did not accompany modern humans as they made their first steps into Europe, but rather developed there.

The authors distinguish between a "strong" version of their model (which would posit a monocentric origin of music/art around the Geissenkoesterle site), and a "weak" one in which these innovations were contributed in parallel by different regions. A better understanding of the origin of different innovations and their assignment to specific groups of modern humans may help us better understand what was the "common core" of behavioral and technological modernity that facilitated the success of our species.

From the paper:

The majority of scholars conclude that the Aurignacian is the earliest signature of the first modern humans in Europe. Recent research suggests that this is not likely to be the case. Benazzi et al. (2011) have shown that the Uluzzian of Italy and Greece is likely to be a modern human industry based on the reanalysis of infant teeth in the archaeological site of Cavallo, and also demonstrated that it dates to 45,000-43,000 cal BP. Other dated examples from other Uluzzian sites (e.g., Higham et al., 2009) fall into the same period, and the Uluzzian is always stratigraphically below the Proto- Aurignacian in Italian sites where both co-occur. This adds an additional level of complexity to the emerging picture of early human dispersals and suggests that the Aurignacian does not represent the earliest evidence of our species in Europe. 
Taken together, these results suggest that modern humans arrived in Europe as early as ~45,000 cal BP and spread rapidly across Europe to as far as southern England between 43,000 and41,000 cal BP. The dates for the lower Aurignacian at Geissenklosterle fall in the same period and appear to pre-date the ages for the Proto- Aurignacian and Early Aurignacian in other regions (Fig. 6). The new results suggest that the caves of the Swabian Jura document the earliest phase of the Aurignacian, and the region can be viewed as one of the key areas in which a variety of cultural innovations, including figurative art, mythical images, and musical instruments, are first documented. These dates are consistent with the Danube Valley serving as an important corridor for the movement of people and ideas (Conard, 2002; Conard and Bolus, 2003). 
The new radiocarbon dates from Geissenklosterle document the presence of the Aurignacian in the Swabian Jura prior to the Heinrich 4 cold phase, with the Early Aurignacian beginning around 42,500 cal BP. In the coming years, excavations in the Swabian Jura will continue and new radiometric dates should contribute to an improved understanding of the spatial-temporal development of the Aurignacian and its innovative material culture.
From the press release:
Researchers from Oxford and Tübingen have published new radiocarbon dates from the from Geißenklösterle Cave in Swabian Jura of Southwestern Germany in the Journal of Human Evolution. The new dates use improved methods to remove contamination and produced ages between began between 42,000 – 43,000 years ago for start of the Aurignacian, the first culture to produce a wide range of figurative art, music and other key innovations as postulated in the Kulturpumpe Hypothesis. The full spectrum of these innovations were established in the region no later than 40 000 years ago.
Journal of Human Evolution doi:10.1016/j.jhevol.2012.03.003

Τesting models for the beginnings of the Aurignacian and the advent of figurative art and music: The radiocarbon chronology of Geißenklösterle

Thomas Higham et al.

The German site of Geißenklösterle is crucial to debates concerning the European Middle to Upper Palaeolithic transition and the origins of the Aurignacian in Europe. Previous dates from the site are central to an important hypothesis, the Kulturpumpe model, which posits that the Swabian Jura was an area where crucial behavioural developments took place and then spread to other parts of Europe. The previous chronology (critical to the model), is based mainly on radiocarbon dating, but remains poorly constrained due to the dating resolution and the variability of dates. The cause of these problems is disputed, but two principal explanations have been proposed: a) larger than expected variations in the production of atmospheric radiocarbon, and b) taphonomic influences in the site mixing the bones that were dated into different parts of the site. We reinvestigate the chronology using a new series of radiocarbon determinations obtained from the Mousterian, Aurignacian and Gravettian levels. The results strongly imply that the previous dates were affected by insufficient decontamination of the bone collagen prior to dating. Using an ultrafiltration protocol the chronometric picture becomes much clearer. Comparison of the results against other recently dated sites in other parts of Europe suggests the Early Aurignacian levels are earlier than other sites in the south of France and Italy, but not as early as recently dated sites which suggest a pre-Aurignacian dispersal of modern humans to Italy by ∼45000 cal BP. They are consistent with the importance of the Danube Corridor as a key route for the movement of people and ideas. The new dates fail to refute the Kulturpumpe model and suggest that Swabian Jura is a region that contributed significantly to the evolution of symbolic behaviour as indicated by early evidence for figurative art, music and mythical imagery.


Friday, 20 January 2012

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.