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Category Archives: hybridization

More details on the Neanderthal legacy in modern humans

Is straight hair Neanderthal?

A quick note on two recent studies on the relevance of Neanderthal introgression on modern Humankind, notably the “out of Africa” branch.

Sriran Sankararaman et al., The genomic landscape of Neanderthal ancestry in present-day humans. Nature 2014. Pay per viewLINK [doi:doi:10.1038/nature12961]

Abstract


Genomic studies have shown that Neanderthals interbred with modern humans, and that non-Africans today are the products of this mixture1, 2. The antiquity of Neanderthal gene flow into modern humans means that genomic regions that derive from Neanderthals in any one human today are usually less than a hundred kilobases in size. However, Neanderthal haplotypes are also distinctive enough that several studies have been able to detect Neanderthal ancestry at specific loci1, 3, 4, 5, 6, 7, 8. We systematically infer Neanderthal haplotypes in the genomes of 1,004 present-day humans9. Regions that harbour a high frequency of Neanderthal alleles are enriched for genes affecting keratin filaments, suggesting that Neanderthal alleles may have helped modern humans to adapt to non-African environments. We identify multiple Neanderthal-derived alleles that confer risk for disease, suggesting that Neanderthal alleles continue to shape human biology. An unexpected finding is that regions with reduced Neanderthal ancestry are enriched in genes, implying selection to remove genetic material derived from Neanderthals. Genes that are more highly expressed in testes than in any other tissue are especially reduced in Neanderthal ancestry, and there is an approximately fivefold reduction of Neanderthal ancestry on the X chromosome, which is known from studies of diverse species to be especially dense in male hybrid sterility genes10, 11, 12. These results suggest that part of the explanation for genomic regions of reduced Neanderthal ancestry is Neanderthal alleles that caused decreased fertility in males when moved to a modern human genetic background.

B. Bernot & J.M. Akey, Resurrecting Surviving Neandertal Lineages from Modern Human Genomes. Science 2014. Pay per viewLINK [doi:10.1126/science.1245938]

Abstract

Anatomically modern humans overlapped and mated with Neandertals such that non-African humans inherit ~1-3% of their genomes from Neandertal ancestors. We identified Neandertal lineages that persist in the DNA of modern humans, in whole-genome sequences from 379 European and 286 East Asian individuals, recovering over 15 Gb of introgressed sequence that spans ~20% of the Neandertal genome (FDR = 5%). Analyses of surviving archaic lineages suggests that there were fitness costs to hybridization, admixture occurred both before and subsequent to divergence of non-African modern humans, and Neandertals were a source of adaptive variation for loci involved in skin phenotypes. Our results provide a new avenue for paleogenomics studies, allowing substantial amounts of population-level DNA sequence information to be obtained from extinct groups even in the absence of fossilized remains.

I don’t have access to the papers (update: I do have the second one now) but, honestly, I don’t have time either, so, even with full access, I would have to be rather shallow, given the complexity of the matter.
Nevertheless I would highlight the following:
Fitness costs
Areas of dense gene presence tend to be more depleted of Neanderthal inheritance, meaning that, at least in many cases Neanderthal genes were deleterious (harmful) in the context of the H. sapiens genome. It’s probable that they worked better in their “native” context of the Neanderthal genome but we must not understimate the risks of low genetic diversity, a problem that affected Neanderthals as well as H. heidelbergensis (species probably including Denisovans or at least their non-Neanderthal ancestry).
Partial hybrid infertility
The areas of very low Neanderthal genetic influence include those of reproductive relevance, including genes affecting the testes and the chromosome X. This is typical of the hybrid infertility phenomenon, which is part of species divergence, making more difficult or even impossible that hybrids can reproduce. This particular item emphasizes that the differential speciation of Neanderthals and H. sapiens was in a quite advance stage already some 100 Ka ago, what does not seem too consistent with the lowest estimates for the divergence of both human species (H. sapiens have been diverging for some 200 Ka and are still perfectly inter-fertile). 
Adaptive Neanderthal hair introgression
On the other hand the Neanderthal genetic legacy has been best preserved in genes that appear to affect keratin (affecting skin, nails and hair). This bit I consider of particular interest because, based on the modern distribution of hair texture phenotypes, I have often speculated that straight hair may be a Neanderthal heritage and this finding seems supportive of my speculation.
It’s possible that straight hair conferred some sort of advantage in some of the new areas colonized by H. sapiens, maybe providing better insulation against rain or cold (the ancestral Sapiens thinly curly hair phenotype is probably an adaption to tropical climate, allowing for a ventilated insulation of the head).
Some 20% of the Neanderthal genome still lives in us
Collectively, that is. The actual expressed genes are probably a quite less important proportion anyhow and the actual individual Neanderthal legacy (expressing genes and junk together) seldom is greater than 3% in any case.
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Neanderthals, Denisovans and everything else

A recent analysis of the nuclear DNA of a Neanderthal toe from Altai has caused widespread interest.
Kay Prüffer et al., The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 2013. Pay per viewLINK [doi:10.1038/nature12886]
The story of a finger and a toe
Both the Denisovan and Neanderthal DNA sequences discussed in this paper come from small bones found at the same location: Denisova cave, Altai Republic. The Denisovan sequence that revolutionized human paleogenetics a few years ago corresponds to a finger phalanx bone of some 50,000 years ago. The less notorious Neanderthal sequence discussed in this study corresponds to a toe imal phalanx, which was found in a lower layer in the same gallery of the same cave, and hence should be older.
This is very interesting to underscore because it seems to imply that Neanderthals were in Altai and specifically in Denisova cave very early, at dates similar to those we find in West Asia (Tabun excepted) and they may even be older than Denisovans in the very cave that gave them their name.
The toe sequence was found in a previous study to have Neanderthal mtDNA, closely related to the lineages of European Neanderthals of various dates and sites. Instead the finger mtDNA (Denisovan) was derived from a more ancient branch of humankind than the very point of split between Neanderthals and modern humans (H. sapiens) and has been recently shown to be related to European H. heidelbergensis from Atapuerca
Notes in red are mine.
This study focuses on the autosomal DNA of both Neanderthals and Denisovans. Unlike mtDNA, whose phylogenetic position is simple and quite straightforward, autosomal or nuclear DNA (nDNA) is extremely much more complex to understand because of its recombining nature, requiring of statistical approaches, which may get extremely complex and potentially subject to premise biases. When comparing two individuals this gets largely simplified but it is a lot more complex when doing the same with larger samples.
And that is precisely what this study does: comparing one Denisovan, several Neanderthals and also several modern humans. Therefore it is a very complex paper and the authors necessarily assume some evaluation risks, which nevertheless are discussed in depth in the supplemental material, a methodology of the Pääbo team that we can’t but greatly appreciate.
Age estimates
The study makes two age estimates, one based on a very conservative and truly unbelievable Pan-Homo split date of 6.5 Ma BP and the other based on observed per generation mutation rates, which happens to be perfectly coincident with a Pan-Homo split of 13 Ma BP, the oldest extreme of Langergraber’s estimate. This coincidence alone is of enough relevance for all molecular clock approaches, because it effectively demands the doubling of all age estimates based on the ridiculously short 6.5 Ma Pan-Homo split supposition. 
Red outlines are mine. Click to enlarge.
It also produces a semi-reasonable San-West African age estimate of c. 86-130 Ka, although I would think it a bit older in fact or at the very least at the top end. This highlights the severe difficulties of such molecular clock estimates, because a 4 Ma divergence between the alleged introgressing mystery archaic in the Denisovan genome, seems out of the question according on the archaeological and paleontological record, which only documents Homo species since c. 2 Ma ago, half that time (within the estimate but clearly very far from the top end).
Altai Neanderthal inbreeding
An important finding of this study is that the studied individual was extremely inbred, with parents in effective relationship comparable to that of grandparent and grandchild or half siblings. This inbreeding tendency, even if extreme, is not so strange in populations that have experienced founder effect bottlenecks and small population sizes. The Denisovan and the modern human Karitiana people are not so extreme but range in the lower end of double first cousins level of genetic relationship between the parents. Other Native Americans like the Mixe are close to that range, while the other compared populations, Papuans and Sardinians, show much lower levels of inbreeding.
Whatever we may think of Altai Neanderthal inbreeding, their drift parameter is still very low when compared with European Neanderthals. This is not discussed in the paper but such extreme drift also seems to imply extreme inbreeding issues in European Neanderthals, even if these may have other causes such as an extremely strong founder effect or whatever.
Bonobo-specific segments were removed, so the bonobo position is not realistic.
Inferred population history
Both populations leading to the Altai Neanderthal and Denisovans, but not modern humans, appear to have gone through a strong decline in population size since hundreds of millennia ago. The Denisovan decline seems to begin c. 800 Ka ago while the Neanderthal one may have begun c. 500 Ka ago. While this is coincident with a general expansion of the H. sapiens branch (still undifferentiated in Africa), peaking around c. 250 Ka ago before differentiation and relative decline. In their words:

All genomes analysed show evidence of a reduction in population size that occurred sometime before 1.0 million years ago. Subsequently, the population ancestral to present-day humans increased in size,whereas the Altai and Denisovan ancestral populations decreased further in size. It is thus clear that the demographic histories of both archaic populations differ substantially from that of present-day humans.

Neanderthal and Denisovan admixture in modern humans

The new tests confirm in essence the previous findings: there is significant Neanderthal introgression in modern humans descending from the migrants out of Africa and there is also significant Denisovan one among Australasian populations.

Additionally and with some caution, the authors think that much lesser Denisovan introgression (of around 0.2%) is found among East Asians and that these, as well as Native Americans, show slightly more Neanderthal admixture than West Eurasians. In my understanding this may be caused by minor African flow to West Eurasia after the admixture event (and/or residual “First Arabian” persistence) and I would think that measuring South Asians would help to clarify this issue (because African admixture is negligible in the subcontinent but they are also distinct from East Asians).

These measurements are so weak that the authors agree to all kind of cautions about them in any case.

In addition to all this, the supplemental material (section 13) also detects tiny, almost homeopathic, amounts of Neanderthal gene flow to Yorubas (~0.02%), obviously mediated by H. sapiens backflow from Asia and Europe into parts of Africa, which eventually influenced other African populations. An even more diluted amount may also be present among the Mbuti Pygmies.

Altai Neanderthal admixture in Denisovans

This issue is not really explained in the paper as such, and we have to reach out to the Supplemental Information chapter 15 in order to grasp it.

It is clear that the Altai Neanderthals are closer to Denisovans than other Neanderthals are by approx. the following fractions (directly deduced from the raw affinities listed in fig. S6a.2):

  • 2% more than Mezhmaiskaya
  • 7% more than Vindija (avg.)
  • 9% more than El Sidrón
Feldhofer appears closer instead but this sequence was not used by the authors in most tests because it has too dubious quality.

In section 15 of the supplementary material, using complex methodology and lamenting the lack of a second Denisovan sample which would be most useful, they estimate a minimal 0.5% (Altai) Neanderthal introgression in Denisovans, with strong warnings that this could well be quite higher. I don’t know why they are not even considering a more direct approach, but I would dare to guesstimate the introgression to be close to 8% from the above raw data, assuming that there are no further complexities at play, such as other Heidelbergensis introgression in European Neanderthals, etc. The drift parameter (see above) does not seem to be one such complexity because Mezhmaiskaya is almost as drifted as Vindija yet it is consistently much closer, as it seems to correspond to its specific relatedness to Altai Neanderthals in mtDNA (and possibly also in nDNA if it is admixture what causes their pseudo-tree positioning closer to the root, what would be typical).

Note in blue is mine.

Mystery archaic genetic flow into Denisovans

The authors find that some 0.5-8% of the Denisovan genome appears to come from another hominin, which split from the human trunk even earlier.

We caution that these analyses make several simplifying assumptions. Despite these limitations, we show that the Denisova genome harbors a component that derives from a population that lived before the separation of Neanderthals, Denisovans and modern humans. This component may be present due to gene flow, or to a more complex population history such as ancient population structure maintaining a larger proportion of ancestral alleles in the ancestors of Denisovans over hundreds of thousands of years.


Later in the discussion section they ponder further the implications of this finding:

The evidence suggestive of gene flow into Denisovans from an unknown hominin is interesting. The estimated age of 0.9 to 4 million years for the population split of this unknown hominin from the modern human lineage is compatible with a model where this unknown hominin contributed its mtDNA to Denisovans since the Denisovan mtDNA diverged from the mtDNA of the other hominins about 0.7–1.3 million years ago41. The estimated population split time is also compatible with the possibility that this unknown hominin was what is known from the fossil record as Homo erectus. This group started to spread out of Africa around 1.8 million years ago42, but Asian and African H. erectus populations may have become finally separated only about one million years ago43. However, further work is necessary to establish if and how this gene flow event occurred.


Going to the detail of the matter (i.e. supplemental material sections 16a and 16b), one of the key details is that present-day Africans share more derived alleles with Neanderthals than with Denisovans. This can only be explained because Denisovans have other archaic ancestry prior to their apparent divergence from Neanderthals or (what is about the same) because Denisovans diverged themselves prior to the Neanderthal-Sapiens split, what is what the mtDNA (unlike the nDNA) suggests. However the difference, even if consistent across comparisons, is too small (a few percentage points) to be attributed to the later scenario.

This means that Denisovans appear to be at nDNA level some sort of an independent branch of proto-Neanderthals with some other but minor archaic admixture. Instead at mtDNA level they appear to be unrelated to Neanderthals and related instead to H. heidelbergensis (a detail not discussed in this paper because it is a too recent independent discovery).

There are still many details to explore but, in principle, it would seem that the Denisovan branch appears to be a divergent proto-Neanderthal one (maybe related to the Hathnora hominin, which looks very much Neanderthal) with lesser other archaic (H. heidelbergensis?) admixture, which nevertheless remained prominent in their mtDNA for whatever accidental reason.

Whether the H. heidelbergensis population of Atapuerca responds to this same profile (i.e. they were Denisovans too) or belongs instead to the “other archaic” population which introgressed in the Denisovan genome remains to be solved. So far we only know the mitochondrial lineage and this one may be misleading, as seems to be the case with the Denisova hominin.

Note in red is mine

Modern human genetic evolution

Benefiting from the high quality of the archaic genomes of Altai, the authors cataloged a long list of simple mutations exclusive to our species: 31,389 single nucleotide substitutions and 4,113 short insertions and deletions (indels). Additionally they found other 105,757 substitutions and 3,900 indels shared by 90% of their modern human sample of 1094 individuals.

They suggest some lines for future research in this regard, maybe focusing on genes known to influence brain development or regions that could show signs of positive selection. These preliminary lines of research are explored in SI-20, noticing potential selection in genes that affect the ventricular zone of the brain and cell proliferation in fetal brain development.

 

Cameroonian Y-DNA lineage A00 is older than Homo sapiens

The news has been floating around in the anthropology and human population genetic circles for some time but it was not formally confirmed until now: a very ancient Y-DNA lineage appears to be so old that it can hardly be considered to be strictly Homo sapiens at its ultimate origin. The lineage is extremely rare however and has only been found so far in two men: an African-American (from the USA?) and eight Mbo individuals from Western Cameroon.

Fernando L. Méndez et al., An African American Paternal Lineage Adds an Extremely Ancient Root to the Human Y Chromosome Phylogenetic Tree. AJHG 2013. Pay per view (free 6 months after publication) → LINK [doi:10.1016/j.ajhg.2013.02.002]

Abstract

We report the discovery of an African American Y chromosome that carries the ancestral state of all SNPs that defined the basal portion of the Y chromosome phylogenetic tree. We sequenced ∼240 kb of this chromosome to identify private, derived mutations on this lineage, which we named A00. We then estimated the time to the most recent common ancestor (TMRCA) for the Y tree as 338 thousand years ago (kya) (95% confidence interval = 237–581 kya). Remarkably, this exceeds current estimates of the mtDNA TMRCA, as well as those of the age of the oldest anatomically modern human fossils. The extremely ancient age combined with the rarity of the A00 lineage, which we also find at very low frequency in central Africa, point to the importance of considering more complex models for the origin of Y chromosome diversity. These models include ancient population structure and the possibility of archaic introgression of Y chromosomes into anatomically modern humans. The A00 lineage was discovered in a large database of consumer samples of African Americans and has not been identified in traditional hunter-gatherer populations from sub-Saharan Africa. This underscores how the stochastic nature of the genealogical process can affect inference from a single locus and warrants caution during the interpretation of the geographic location of divergent branches of the Y chromosome phylogenetic tree for the elucidation of human origins.

Figure 1. Genealogy of A00, A0, and the Reference Sequence
Lineages on which mutations were identified and lineages that
were used for placing those mutations on the genealogy are
indicated with thick and thin lines, respectively. The numbers of
identified mutations on a branch are indicated in italics (four
mutations in A00 were not genotyped but are indicated as shared
by Mbo in this tree). The time estimates (and confidence intervals)
are indicated kya for three nodes: the most recent common
ancestor, the common ancestor between A0 and the reference
(ref), and the common ancestor of A00 chromosomes from an
African American individual and the Mbo. Two sets of ages are
shown: on the left are estimates (numbers in black) obtained
with the mutation rate based on recent whole-genome sequencing
results as described in the main text, and on the right
are estimates (numbers in gray) based on the higher mutation rate
used by Cruciani et al.6

It could still be a very early diverging H. sapiens lineage, as is surely the case of the more recent and slightly more common A0 (former A1b, found in Cameroonian Western Pygmies, 8.3%, and among Algerian Mozabites, 1.5% – see here) but both are in the blurry zone of the time of birth of our species (judging from archaeological and paleoanthropological data) c. 200 Ka ago. The first documented “modern human” skull, Omo 2, is dated to 190 Ka ago and it shares locality with another one, Omo 1, which is rather H. rhodesiensis, so in that “dawn of modern humankind” there was surely not a very clearly drawn line between modern humans or Homo sapiens and archaic humans or Homo rhodesiensis (or whatever). Some of those proto-Sapiens lineages still remain among us at very low levels.

Their presence may also suggest minor admixture between the first migrant H. sapiens to arrive to Cameroon and their then still close relatives from previous flows, which we don’t consider H. sapiens because we have drawn a convenient, but as we see now somewhat blurry, anthropometric or paleoanthropological line at Omo 2 and later specimens close to us in skull shape. While there is some generic comparability, the fact of admixture between such closely related populations is much less impressive than the one of admixture with Neanderthals or, probably, Homo erectus (non-Neanderthal Denisovan relatives), more distant from us in the tree of Greater Humankind. 
As for the “molecular clock” estimate I suspect that this one is correct. I would have liked to explain it today but it will have to wait because it is a complex matter and I have been all day writing for this blog, so I am quite tired now.

Update (Mar 3): Kalupitero commented in another entry that this lineage has very distinctive STR markers and that he has spotted 9 Cameroonians and one French (probably of African ancestry) with it at the Sorenson Molecular Genealogy Foundation database.

Update (Mar 5): A reader directed me to a free copy of this paper, from where I selected fig. 1 (above) and fig. 3 (below). I realized that the number of sequences detected among the Mbo was not one as I originally said but eight. They also mention that the frequency of this lineage in Africa must be very low: c. 0.19% (CI: 0.11-0.35%).

Figure 3. Median-Joining Network of A00 Haplotypes
The network is based on haplotypes (constructed with 95 Y-STRs)
of eight Mbo and an African American (AA) individual. All mutations
are assumed to be single step and were given equal weight
during the construction of the network. Marker names are indicated
without ‘‘DYS’’ at the beginning.



See also:

 

Ancient North Chinese from 40,000 years ago closely related to modern locals

Tianyuan Cave (source)
The information is sketchy as of now but the news in the press indicate that an Homo sapiens from Tianyuan Cave, near Beijing, whose fragmented remains were discovered in 2003, was closely related to modern East Asians and Native Americans. 
The paper is not yet online but the information released to the media strongly suggests that East Asians were already distinct from other populations some 40,000 years ago. This would seem to be based on the sequencing of the mitochondrial DNA and the explicit mention of Native Americans indicates that the lineage must be A, B, C or D (X, the fifth and less common matrilineage of Native Americans, is not found in East Asians, with some exceptions from Siberia, so we can exclude it safely). 

Ancient DNA from cell nuclei and maternally inherited mitochondria
indicates that this individual belonged to a population that eventually
gave rise to many present-day Asians and Native Americans, says a team
led by Qiaomei Fu and Svante Pääbo, evolutionary geneticists at the Max
Planck Institute for Evolutionary Anthropology in Leipzig, Germany. 

This would seem to discard some adventurous hypothesis floating around about tremendous demographic changes in the Paleolithic and afterwards, at least for this region. Probably not even when “mode 4” technology arrived to the region (from Altai) c. 30,000 years ago. 
In other words: the seeds of modern populations were already there c. 40,000 years ago in East Asia (and surely also in most other regions) and, even if they may have changed somewhat, they have remained the same at least to some notable degree.
Furthermore, the autosomal DNA also seems to have been sequenced to at least some degree because the researchers state that Denisovan and Neanderthal genetic inputs are at the same levels as modern North Chinese (i.e. some 0% and 2.5% respectively):

The partial skeleton, unearthed in Tianyuan Cave near Beijing in 2003,
carries roughly the same small proportions of Neandertal and Denisovan
genes as living Asians do (SN: 8/25/12, p. 22), the scientists report online January 21 in the Proceedings of the National Academy of Sciences.

Or in the words of the Max Plank Institute:

The genetic profile reveals that this early modern human was related to
the ancestors of many present-day Asians and Native Americans but had
already diverged genetically from the ancestors of present-day
Europeans. In addition, the Tianyuan individual did not carry a larger
proportion of Neanderthal or Denisovan DNA than present-day people in
the region.

This also seems to discard models implying Denisovan admixture happening in Siberia or NE Asia and would indirectly support my own hypothesis of admixture with Homo erectus (for which Denisovans, plausibly an Erectus-Neanderthal hybrid, would be just a proxy) in or near Indonesia.
Sources: Science News, Max Plank Institute.

Update (Jan 22): the paper is already online and is open access (cool!)  I don’t think I have time to discuss it today but will do tomorrow without doubt (other than the sky falls on my head, you know).

 

Propose alternative model for Neanderthal admixture in non-Africans

I must say I am totally  skeptic but just for the record:
Armando G. M. Neves & Mauricio Serva, Extremely Rare Interbreeding Events Can Explain Neanderthal DNA in Living Humans. PLoS ONE. Open Access ··> LINK [doi:10.1371/journal.pone.0047076]

Abstract

Considering the recent experimental discovery of Green et al that present-day non-Africans have 1 to of their nuclear DNA of Neanderthal origin, we propose here a model which is able to quantify the genetic interbreeding between two subpopulations with equal fitness, living in the same geographic region. The model consists of a solvable system of deterministic ordinary differential equations containing as a stochastic ingredient a realization of the neutral Wright-Fisher process. By simulating the stochastic part of the model we are able to apply it to the interbreeding ofthe African ancestors of Eurasians and Middle Eastern Neanderthal subpopulations and estimate the only parameter of the model, which is the number of individuals per generation exchanged between subpopulations. Our results indicate that the amount of Neanderthal DNA in living non-Africans can be explained with maximum probability by the exchange of a single pair of individuals between the subpopulations at each 77 generations, but larger exchange frequencies are also allowed with sizeable probability. The results are compatible with a long coexistence time of 130,000 years, a total interbreeding population of order 10⁴ individuals, and with all living humans being descendants of Africans both for mitochondrial DNA and Y chromosome.
Not only the discourse of the authors is strangely ideological (strange insistence in resuscitating the dead horse of multirregionalism and denying the rather unquestionable out-of-Africa model at least in name) but also they come to admit that:

The decision of which model correctly describes the origin of Homo sapiens is obscured by the intricacies of the statistical methods proposed for evaluating the models themselves.

And so they proceed to create their own intricate model and even more intricate interpretation.
Sincerely, their model of continuous admixture would normally cause West Eurasians (at least) to have much more Neanderthal introgression than Papuans, whose ancestors have been far away from West Eurasia (the former Neanderlands) since c. 80 Ka most probably (archaeological evidence of African-related techno-cultures in India, Petraglia 2007), while West Eurasian ancestors would have been in intense contact with Neanderthals all or most of that time until the effective Neanderthal extinction of c. 35,000 years ago. 
There’s no convoluted model nor mathematical fallacy that can circumvent that: anything but a single admixture episode or process early on in the colonization of Eurasia by Homo sapiens makes no sense.
 

Intriguing North African Neanderthal admixture paper

This new study aims to quantify Neanderthal admixture in North Africans in order to evaluate the unlikely but popular-in-some-circles hypothesis that the signature of Neanderthal admixture in non-African Homo sapiens could be caused by structure in Africa prior to the migration into Asia and beyond (“ancient African structure model” hereafter).
It does seem to add evidence against the “ancient African structure model” and, incidentally, in favor of the mainstream interpretation that North Africans have large amounts of West Eurasian ancestry (questioned without clear base in some Africanist circles). However it also arrives to some odd results regarding East Asian Neanderthal admixture which are not addressed at all in the study.
Federico Sánchez Quinto et al., North African Populations Carry the Signature of Admixture with Neandertals. PLoS ONE, 2012. Open access ··> LINK [doi:10.1371/journal.pone.0047765]

Abstract

One of the main findings derived from the analysis of the Neandertal genome was the evidence for admixture between Neandertals and non-African modern humans. An alternative scenario is that the ancestral population of non-Africans was closer to Neandertals than to Africans because of ancient population substructure. Thus, the study of North African populations is crucial for testing both hypotheses. We analyzed a total of 780,000 SNPs in 125 individuals representing seven different North African locations and searched for their ancestral/derived state in comparison to different human populations and Neandertals. We found that North African populations have a significant excess of derived alleles shared with Neandertals, when compared to sub-Saharan Africans. This excess is similar to that found in non-African humans, a fact that can be interpreted as a sign of Neandertal admixture. Furthermore, the Neandertal’s genetic signal is higher in populations with a local, pre-Neolithic North African ancestry. Therefore, the detected ancient admixture is not due to recent Near Eastern or European migrations. Sub-Saharan populations are the only ones not affected by the admixture event with Neandertals.

Europeans and Africans
First of all they take a look at the structure of European and African populations regardless of Neanderthal ancestry, which is probably of interest on its own right:
Figure 1. Results of the ADMIXTURE analysis (k = 4) with North African populations
Sadly, the Tunisian Berbers who define the North African polarity, taken from Henn 2011 and 2012, are a recognized (by Henn herself) as a highly endogamous population that behave a bit weirdly. I do not think that in this specific context they are distorting the results significantly (compare with my own exercise earlier this year) but I do think that the sample should not be used anyhow.
Otherwise we can see that:
  • There are both West Asian and European components in North Africans (the red “Tunisian Berber” component is also probably of West Eurasian ultimate origin, from my previous work, where I carefully looked at FST distances among components – however some nuances, like a probable pre-OoA* residue in North Africans are not evident in this analysis, which is too shallow).
  • There is some African (mostly North African) ancestry in Iberia (more towards the West, as we know from other studies).
  • There is some minor West Asian ancestry in Europe, consistent with a less important penetration in Neolithic (and maybe also post-Neolithic) times.
  • There is Tropical African ancestry in North Africans as well (even if the Luhyas are probably not the best proxy).
Neanderthal blood in North Africans
The main goal of the paper is however to estimate Neanderthal ancestry in North Africans, with the following results:

Table 2. Estimates of Neandertal ancestry in North African populations, along with European, Asian and Sub-Saharan African groups. [Notice that GIH is mislabeled, it actually means: Gujarati Indians from Houston].

The results for Africa and West Eurasia are more or less within expectations, what is very anomalous however is the East Asian results of c. 200% Neanderthal ancestry (relative to CEU) but let’s leave that for later.
We could well discuss however why, if North Africans are some 80% West Eurasian by ancestry their detected Neanderthal admixture is so low (c. 50-60%). It may well be a matter of diverse ancestral influences (not all West Eurasia is Europe), and would be consistent maybe with the relatively low amounts of Neanderthal admixture found in Indians (GIH, 84%). Sadly the Qatari sample was not tested for Neanderthal admixture, which would have been interesting on its own right and also in relation to North Africa
Whatever the case this is the authors’ map of estimated North African Neanderthal ancestry relative to Euro-Americans (CEU, which have c. 2.4% Neanderthal ancestry):

Figure 3. Neandertal genetic introgression in North African populations as a fraction of that found in Europeans [colored bars represent K=4 apparent ancestry as above].

Maybe the most interesting population here is MOS (Southern Moroccans) which in my December 2011 Admixture analysis of North Africans appeared to show significant amounts (14.4%) of a very distinct component that I judge as Aterian remnant (in other populations not higher than 1.5%).
While the authors think that the findings are supportive but can’t totally prove that the Neanderthal admixture appearance is real and original from Eurasia, I find the very low Neanderthal admixture signal in Southern Moroccans as very clear evidence that pre-OoA structure (which is preserved as minority component in this population apparently) that the Neanderthal admixture signal has nothing to do with any pre-OoA North African specificity. 
Otherwise South Moroccans should show a neutral signature and not this outstanding depression of Neanderthal admixture. There are surely other factors at play there (greater Tropical African admixture, lower European admixture) but this “Aterian” component should be high in Neanderthal signature if there was any pre-OoA African structure at all. 
Some people may want to cling to the proverbial burning nail, maybe arguing that the Neanderthal-like structure was in Egypt and not NW Africa. Not only that looks too much like the West Asian admixture episode that the mainstream theory argues for but it also ignores the cultural and anatomical similitudes between NW African Aterian peoples and those from Palestine in the context of the likely window for the archaeologically supported OoA: 125-90 thousand years ago. 
So, in my understanding the results of this paper are quite supportive of the mainstream (Asian admixture) model, rather dismissing the African structure counter-hypothesis, even more than the authors themselves admit to. 
European degrees of Neanderthalness?
I am sure that some readers will have noticed that there is an appearance of greater Neanderthal values among Basques (129% rel. to CEU) and Iberians (115-118%). However the differences are very small and not more marked than, for example North Tunisians (138%).
Considering the other issues that the results of this paper imply, I cannot really argue that these differences are meaningful at all. However they sparse data shown for other parts of West Eurasian would be consistent with greater Neanderthal admixture in Europe than in West Asia (and the corresponding gradation in Europe depending of Neolithic ancestry), with an apparent highest value in a population usually considered as a Paleolithic continuity genetic refuge: Basques.
But only further data and specific analysis can confirm or question this appearance. 
East Asian extremely high Neanderthal values
This is what is totally puzzling in this study and what can really bring to question all other conclusions. The authors appear to find that East Asians (CHB, CHD, JPT) have values of Neanderthal admixture that are double than those of West Eurasians. 
This clashes with all we know. In fact one of the findings of Green 2010 was that all Eurasian-derived populations have similar Neanderthal admixture values, c. 2.5%, with lesser population or individual variations only. This has only been confirmed once and again in successive studies, for example John Hawks earlier this year, who actually claimed that Europeans held slightly more Neanderthal admixture than East Asians.
Then why do the Sánchez Quinto team find such brutal East Asian Neanderthal admixture values? No idea. They don’t even mention the matter in all the paper. And that is a big flaw, which can only cause readers to doubt the whole paper or even the methodology altogether. 
Any ideas?
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*OoA: Out of Africa, it refers to the human migration episode and related founder effect (bottleneck) which populated Asia and its peripheral minor continents (Australasia, Europe, America) with our species, Homo sapiens. It is a critical episode in human prehistory and probably the time when most if not all Neanderthal admixture happened. But, in principle, already in Asia.
 

East Asians now claimed to be "more Neanderthal" than Europeans

Unlike what John Hawks had apparently found a few months ago but similar to what I thought apparent from the original Green et al. data back in 2010. 
Mathias Meyer et al., A High-Coverage Genome Sequence from an Archaic Denisovan Individual. Science 2012. Pay per view ··> LINK [doi: 10.1126/science.1224344]
Denisovan ancestry is claimed now to be only found among Aboriginal Australasians (Papuans) but then again the data in the supplementary material (freely accessible) seems, to my untrained eyes, to allow for a thin Denisovan genetic influence in all Eurasia. 
I withhold my judgment because there seems to be a lot of sensibility to methodology in this hair-splitting excercise. John Hawks however has written a lengthy article trying to explain why both results appear contradictory regarding which levels of Neanderthal admixture. I would not bet much for his explanation however: I’d rather suspect that the methodology is not sound enough to estimate very thin admixture, so they are getting contradictory results in the uncertainty zone, what is just logical – even if a Schrödingerian kind of logic, of course.
Another finding is that Denisovans were apparently quite endogamous had very low diversity for modern standards, specially in the short bloc zone (ancient bottleneck) but also in the long bloc one (recent endogamy)*.

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*Red text was updated, slashed out text was removed after first publication.