Very ancient ghosts in the African genome

The above figure is from a preprint (updated from last year), Recovering signals of ghost archaic introgression in African populations. But to truly get a sense of this preprint, I would highly recommend you read the supplementary material. And, to be honest, a publication from 2007, The Joint Allele-Frequency Spectrum in Closely Related Species, as the core of the method used in the preprint is developed in that paper.

Here is the abstract:

While introgression from Neanderthals and Denisovans has been well-documented in modern humans outside Africa, the contribution of archaic hominins to the genetic variation of present-day Africans remains poorly understood. Using 405 whole-genome sequences from four sub-Saharan African populations, we provide complementary lines of evidence for archaic introgression into these populations. Our analyses of site frequency spectra indicate that these populations derive 2-19% of their genetic ancestry from an archaic population that diverged prior to the split of Neanderthals and modern humans. Using a method that can identify segments of archaic ancestry without the need for reference archaic genomes, we built genome-wide maps of archaic ancestry in the Yoruba and the Mende populations that recover about 482 and 502 megabases of archaic sequence, respectively. Analyses of these maps reveal segments of archaic ancestry at high frequency in these populations that represent potential targets of adaptive introgression. Our results reveal the substantial contribution of archaic ancestry in shaping the gene pool of present-day African populations.

To get a sense of how much work went into this preprint, really do read the supplementary material. The step by step analysis convinced me pretty thoroughly that these results are not due to straightforward errors in the genotypes and classifications of the genotypes. Such things do happen, so it was nice to see them be very careful about that.

The key point is that the distribution of the conditional site frequency (CFS) spectrum in West Africans does not align with theoretical expectations. The condition here being the state in the archaic outgroup, generally the Vindijia Neanderthal. The authors ran a bunch of simulations and models and found a subset that could produce the CSF they see, the u-shaped distribution. It is represented by the graph you see at the top-right. Basically, a scenario where a diverged archaic lineage which diverged from the other human lineages before the Neanderthal-Denisovan lineage left Africa contributed to the ancestry of West Africans within the last ~100,000 years (the most likely time is ~50,000 years ago).

This is not a new finding at the highest level of generality. Jeff Wall has been beating this drum for nearly 15 years. For example, Genetic evidence for archaic admixture in Africa.

What has changed is that whole-genome sequencing, including high-quality sequences of ancient hominins, has allowed for a more robust exploration of the topic. The analysis of site frequencies was really not useful 20 years ago without genome-wide data. More data has allowed for more subtle methods.

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Reevaluating “multiple origins” for modern humans

Following up on the post below, The Deep Origins Of East African Hunter-Gatherers, as well as some discussions on Twitter, I think I want to do some clarification about where I think we are now. My thoughts shouldn’t be a surprise if you have read everything I’ve said, but I may not have put them all together in one place.

Around the turn of the century, nearly twenty years ago, the consensus had definitively turned against a “multiregional” origin of modern humans, toward one where an “out of Africa” migration ~50,000 years ago was paramount. Many people took the “paramount” part and simply asserted that we are all Africans descended from a population that flourished in the east of the continent about 50,000 years ago. There was a lot of circumstantial evidence to support this, at least spottily, from both archaeology and genetics. There were also problems and lacunae in both fields. But the data was spotty enough that the extreme position was defensible.

We now have a lot more information and need to update our model. First, most people agree that indigenous Eurasian hominins, Neanderthals and Denisovans, contributed to the ancestry of people outside of Sub-Saharan Africa. Additionally, it’s been evident for a long time now that the massive population bottleneck that is present in all non-African populations dating to ~50,000 years ago is far less evident in Sub-Saharan African genomes.

Finally, it’s pretty clear that humans with modern morphology were present within Africa for hundreds of thousands of years before the movement out of Africa.

Therefore, a new reevaluation of the old model that is converging is a possibility is that multi-regionalism was operative within Africa for hundreds of thousands of years, followed by a massive expansion on the northeast edge of Africa that resulted in most of the ancestry of other human groups outside of the continent, with some assimilation (e.g., Neanderthal). This is a far more complicated model than the older one, but sometimes the truth is more complicated than simplicity.

But I think we’ll probably need to make further modifications, and that’s because gene flow is not always unidirectional. Specifically, the Y chromosomal work, in particular, is strongly indicative of migration of lineages more typical of Eurasians expanding within Africa within the last 50,000 years. And, as a commenter on this weblog has pointed out, even the “deep lineages” within Africa, Y haplogroups A and B, show signs of massive expansion within the last 50,000 years.

This may mean that a population liminal to Africa and Southwest Asia underwent a very rapid expansion ~50,000 years ago. The replacement of indigenous lineages was far more thorough outside of Africa, with 5% or less assimilation in most places. But, it probably impacted Africa as well. Though a larger fraction of diverged modern ancestry persisted in Africans than Eurasian hominin ancestry in non-Africans. In other words, the high genetic diversity of Africans today, and particular groups like the Khoisan, is due to the mixture between an ancient migration from the same population that was the source of “out of Africa” in Eurasia and Oceania, and disparate deeply structured lineages within Africa, that date back 200-400 thousand years ago.

Additionally, I think some earlier “modern” lineages were assimilated in eastern Asia with the latest migration out of Africa. And, some of the ancestry within Africa probably predates the origin of anatomically modern humans, analogous to the case of Neanderthals and Denisovans.

Note: This is not that different of a model from Dienekes Pontikos’ ideas in the 2000s, More support for the Afrasian/Palaeoafrican hypothesis, at the high level. Basically the more evidence has come in, the less crazy his model has gotten.

Europe had a lot of demographic turnover because there were never many humans


Now things are coming into focus. Population dynamics and socio-spatial organization of the Aurignacian: Scalable quantitative demographic data for western and central Europe:

Demographic estimates are presented for the Aurignacian techno-complex (~42,000 to 33,000 y calBP) and discussed in the context of socio-spatial organization of hunter-gatherer populations. Results of the analytical approach applied estimate a mean of 1,500 persons (upper limit: 3,300; lower limit: 800) for western and central Europe. The temporal and spatial analysis indicates an increase of the population during the Aurignacian as well as marked regional differences in population size and density. Demographic increase and patterns of socio-spatial organization continue during the subsequent early Gravettian period.

If you read The genetic history of Ice Age Europe you know the very first modern humans to arrive in Europe didn’t leave a genetic footprint in future populations. And the impact of both the later Gravettian and the Magdalenian seems to have been marginal. The primary “hunter-gatherer” contribution to modern Europeans is through a group which expanded after ~15,000 BC.

In any case, there are two things that I observe in relation to the population estimates above. First, they aren’t that unreasonable for a large mammal which isn’t much of a primary consumer of plants. Second, such a small and fragmented population indicates that extinction is always a possibility. You can take a standard conservation biological view and just assume statistically that small fragmented groups are likely to extinct over enough generations. Or, you can point out that genetically such small breeding populations (remember that the genetic breeding effective population is always smaller than the census population) are likely to build up deleterious alleles, and that’s probably going to result in a decrease of long term fitness.

In other words, I think localized mutational meltdowns would be possible in this scenario.

The small populations during this period are not surprising. Many of the Neanderthal, Denisovan, and hunter-gatherer (e.g., the first WHG sample) populations had small sizes that led to homogeneity genetically and inbreeding. You see it in the homozygosity data and the runs of homozygosity. Ultimately, it was the larger population sizes due to agriculture which changed things in a fundamental sense.

This makes me wonder what was so advantageous about these marginal modern humans which allowed them to overwhelm and absorb the older Eurasian hominins?

The state origins of “modern humans” in 2018 (it’s a flux)

After reading the supplements to the new Siberian paper I have a few general thoughts that I want to layout.

First, the clines vs. clusters considerations seem to be one we need to revisit. Like the expansion of Native American peoples ~15,000 years ago, it seems that the “Out of Africa” migration pulse happened so quickly that a lot of different groups emerged at the same time. In the new paper the earliest proto-“Ancient North Eurasians” can be modeled as most similar to the West Eurasian branch of humanity (sans Basal Eurasian), but with some minor component affinity to East Eurasians. It could be that this is a function of admixture between the distinct lineages. Or, it could be that there was a fair amount of substructure within the post-Basal Eurasian “Out of Africa” meta-population.

The problem with the idea of lots of structure within this population that I see is that it might depend on the plausible effective population sizes. I’d need to know more ethnography than I do, but it seems not impossible for ~10,000 humans to be highly structured in Paleolithic social contexts, even if they were close geographically. But, this would entail a great deal of xenophobia and likely inter-group conflict.

Second, I am convinced that there were earlier “Out of Africa” migrations. Many of them. As John Hawks pointed out at ASHG the Neanderthals and Denisovans seem to be descended from a migration of African hominins that dates to somewhere after 1 million years ago. This means they replaced hominins that were present in Eurasia for ~1 million years already. Geneticists and paleontologists have both also discovered suggestive clues to likely “proto-modern” human populations that were present and admixing before the rapid expansion of Eurasians and Australasians ~40-50,000 years ago. With more ancient DNA and subtle analysis, I think we’ll find that modern human absorbed some layers between that of Denisovans and Neanderthals and the most recent expansion.

Finally, I think multi-regionalism within Africa is between plausible and likely, and that major back-to-Africa migrations that modify/challenge “Out of Africa” are possible. We are learning a lot. But that means simple elegant models are falling by the wayside.

What if everything that’s not a disease is polygenic?

In the early 2000s FOXP2 was dubbed the “language gene”. It was a sexy story. Humans exhibited accelerated adaptive evolution on this locus in relation to our relatives. Additionally, vocally oriented lineages such as birds and whales were also subject to the same process.

But over the past five years or so I’ve heard a lot of skepticism of the early claims as more genomic datasets have come online. Cell has a new paper which pretty much smashes the door down and breaks the skepticism out into the open, No Evidence for Recent Selection at FOXP2 among Diverse Human Populations:

FOXP2, initially identified for its role in human speech, contains two nonsynonymous substitutions derived in the human lineage. Evidence for a recent selective sweep in Homo sapiens, however, is at odds with the presence of these substitutions in archaic hominins. Here, we comprehensively reanalyze FOXP2 in hundreds of globally distributed genomes to test for recent selection. We do not find evidence of recent positive or balancing selection at FOXP2. Instead, the original signal appears to have been due to sample composition. Our tests do identify an intronic region that is enriched for highly conserved sites that are polymorphic among humans, compatible with a loss of function in humans. This region is lowly expressed in relevant tissue types that were tested via RNA-seq in human prefrontal cortex and RT-PCR in immortalized human brain cells. Our results represent a substantial revision to the adaptive history of FOXP2, a gene regarded as vital to human evolution.

Basically, our confidence in the inferences ran ahead of the data on hand. The reason that the story of the “language gene” spread like wildfire is that people wanted to believe. It was obvious that we were special. And we wanted to find how we were special.

In the 2000s, and even today, there was an idea that some single mutation might have allowed for the “Great Leap Forward” into behavioral modernity. I think that that model is probably wrong, and modern humanity was a more gradual and stepwise development. During the Eemian interglacial from 130 to 115 thousand years ago, agriculture did not emerge. No “lost civilizations” to our knowledge. Something happened to our species over the last 100,000 years. Probably biological, though in a way that facilitates cultural plasticity and evolution.

But genetically I bet it wasn’t that “one thing.” It was a lot of different things.

The new African “multi-regionalism” & pan-Neanderthalism

We live in times when our understanding of the origin and diversification of modern humans is undergoing great change. More concretely, our understanding of what it means to be human is transforming. The terms are overused, but perhaps it could be called a “revolution” or “paradigm shift” between the year 2000 and today.

At the end of 2010 ancient DNA made it highly likely that people outside of Sub-Saharan Africa had non-trivial Neanderthal ancestry. That is, enough ancestry that it is detectable genomically. I should also add that I think it is highly probable that the good majority of people within Sub-Saharan Africa have Neanderthal ancestry. Some of this is due to recent attenuated Eurasian back-migration (e.g., many West Africans, Nilotic people, and KhoeSan have Holocene gene-flow signals which derive from the agricultural expansions of the past 10,000 years). But, I think once deep Pleistocene genomes of African humans are sequenced we will see evidence of some Eurasian back-migration at a very ancient date (there is already some suggestive inferential evidence of this).*

Talking with a few friends this week, I realized that the famous “We are all Africans” t-shirts, which have turned into recognizable memes, should be supplemented with “We are all Neanderthals” t-shirts. So yeah, now selling them on DNA Geeks. If the Richard Dawkins Foundation can make quid on it, why not the Razib Khan et al. Foundation?

This has all been on my mind due to a review paper in Trends in Ecology and Evolution, Did Our Species Evolve in Subdivided Populations across Africa, and Why Does It Matter? (OA). If you read this blog closely you’ll see there’s not much new in it. But, it is a signpost, a marker, of the times we live in. Here’s the important bit:

Together with recent archaeological and genetic lines of evidence, these data are consistent with the view that our species originated and diversified within strongly subdivided (i.e., structured) populations, probably living across Africa, that were connected by sporadic gene flow…This concept of ‘African multiregionalism’…may also include hybridization between H. sapiens and more divergent hominins (see Glossary) living in different regions…Crucially, such population subdivisions may have been shaped and sustained by shifts in ecological boundaries…challenging the view that our species was endemic to a single region or habitat, and implying an often underacknowledged complexity to our African origins.

The first person who explicitly used the term “African multi-regionalism” that I recall was Alwyn Scally, though the general framework was shaping up years before. Frankly, I was waiting for someone to use that word. If Richard Klein’s The Dawn of Human Culture, published in 2002, was the apogee of the old model, often inchoate and more crisp in popularization than within the scientific community that we are all descended from a single East African tribe, this review paper heralds the emergence of a more complex and pluralistic framework. The emergence of modern humans within Africa then may have been a polycentric gradual and interactive process; not a singular explosion against the firmament of the antique savanna landscape.

By the late 2000s, even before the 2010 Neanderthal draft genome paper, it was starting to be evident due to genome-wide analyses of contemporary populations, that the extreme bottleneck clear in non-African populations was much more modest within Africa. That opened the possibility for the existence of deep structure within the continent that pre-dated the “Out of Africa” event. A deeper look at African hunter-gatherers indicated to many researchers that these groups diverged from other modern humans in the range of ~200,000 years before the well. Recent paleontological work has confirmed this genetic insight.

Where we are today is that some people are now arguing for the overthrow of the “Out-of-Africa” idea, whether by replacing it with an “Into-Africa” model of some sort, or resurrecting a more polycentric classical multi-regionalism (“some people” as evident in the increased frequency of emails and Twitter messages I get in this vein). I don’t think we’re there yet, not by any measure. But, it is now in the realm of very unlikely, not extremely unlikely (at least the “Into-Africa” model; it is clear that strong overwhelming demographic pulses from somewhere singular dominate the genome of most modern humans).

* I don’t think it is all that implausible that some Neanderthal back-migration into Africa occurred at some point in the last ~500,000.

The Ancient Neanderthal Mariner

More recent stuff on Neanderthals of interest, Neandertals, Stone Age people may have voyaged the Mediterranean:

A decade ago, when excavators claimed to have found stone tools on the Greek island of Crete dating back at least 130,000 years, other archaeologists were stunned—and skeptical. But since then, at that site and others, researchers have quietly built up a convincing case for Stone Age seafarers—and for the even more remarkable possibility that they were Neandertals, the extinct cousins of modern humans.

But a growing inventory of stone tools and the occasional bone scattered across Eurasia tells a radically different story. (Wooden boats and paddles don’t typically survive the ages.) Early members of the human family such as Homo erectus are now known to have crossed several kilometers of deep water more than a million years ago in Indonesia, to islands such as Flores and Sulawesi. Modern humans braved treacherous waters to reach Australia by 65,000 years ago. But in both cases, some archaeologists say early seafarers might have embarked by accident, perhaps swept out to sea by tsunamis.

The effective population size of Australian people is just too large for me to imagine that it was only a few individuals swept out on driftwood. There was some sort of sea-going craft which mediated migration to Sahul from Sundaland. Just because we have only recent evidence of sea-going craft doesn’t mean that they weren’t around for tens of thousands of years before that.

I’ve been hearing about Neanderthal tools on islands like Crete, which were never connected with the European mainland, for a while now. It seems that people are finally convinced that this is the real deal, as the stratigraphy came together to confirm dates. One thing that seems obvious from this, as well as Neanderthal “art”, is that the differences between modern humans and Neanderthals were more quantitative than qualitative. Differences of degree, not of kind.

It is hard to deny that modern human expansion between 60 and 15 thousand years ago is sui generis. Hominins didn’t make it to the New World or Sahul, what later became Oceania, until our own kind. There’s also a fair amount of evidence that our lineage pushed the northern frontier of human habitation beyond what Neanderthals ever did. But in the process of marking off our distinctiveness, it seems to me that we’ve overemphasized the differences between us and Neanderthals, and dismissed or ignored evidence of “human-like” “advanced” behaviors from them.

I’ll still go with the prediction that we’ll never find a singular gene which marks us off from other human lineages.

Arabia as Africa-across-the-sea

In antiquity ostriches and lions roamed the Syrian desert. The cheetah even still clings to a tenuous existence in the fastness of the central Iranian desert. The point being that the new finding of African modern human remains on the southeast fringe of Arabia ~85,000 years ago shouldn’t be too surprising. Old modern(ish) looking humans date to 73,000 years before the present in Southeast Asia. Modern-like ancestry can be found in eastern (Altai) Neanderthals dating to ~100,000 years ago. And the earliest humans may have arrived in Australia 65,000 years ago.

These dates are important because the genetic results indicate that much of the population divergence of modern Eurasian, Amerindian, and Oceanian peoples dates to the period between 50 to 60 thousand years ago. This was the classic epoch for the emergence of “behavioral modernity,” and the older models of “Out of Africa” which posited a rapid explosive demographic growth after a punctuated speciation even in East Africa ~60,000 years ago.

Today with remains such as Ust’-Ishim man, we can peg the admixture of Neanderthal into modern Eurasians 52,000 and 58,000 years ago. About the same period that the preponderance of the ancestry of modern Eurasians and peoples of Australia and the Americas expanded across the world, as noted above.

Most peoples in Western and Southern Eurasia also have substantial ancestry from another group which doesn’t seem to have much Neanderthal ancestry at all, the “Basal Eurasians” (BEu). This population obtained its name from the fact that it was hypothesized to have diverged from the common ancestors of northern Eurasians (the Pleistocene peoples of Europe and Siberia), eastern Eurasians, the ancestors of the Amerindians, and Oceanians, before these groups moved on and then separated (i.e., proto-Melanesians are closer to Pleistocene European hunter-gatherers than they are to BEu). These facts suggest proto-BEu was a distinct population >60,000 years ago.

The maximum range of Neanderthals

 

Because of the distribution of Neanderthal admixture across so many groups relatively evenly it probably came from a single major admixture event. Geography tells us that the most likely area of this admixture would be somewhere in the northern area of West Asia.

This implies that BEu was probably resident in the southern area of West Asia, and possibly into North Africa. We do not have any samples which are “pure BEu.” Ancient agriculturalist samples from the western Near East and the eastern Near East are high in BEu ~10,000+ years ago, but these populations are still substantially mixed with a population with affinities to Mesolithic Western European hunter-gatherers (WHG). Fu et al. 2016 use a Pleistocene transect to infer that this affinity between Near Easterners and Europeans dates to the period after ~15,000 years before the present. I presume that this late Pleistocene period was when BEu was admixed away as a pure population by an expanding hunter-gatherer culture with a nexus in Southeast Europe and into Anatolia and the trans-Caucasian region.

The recent Arabian find makes sense I think in the context of BEu and other such populations, which had diverged from the Africa metapopulation ~100,000 years ago, but had not pushed further north and east, and so mixed with Neanderthals.

But what about the older modern human remains which are showing up in eastern Eurasia? I think it is entirely likely that these populations left only a little bit of an imprint in modern groups. A paper from a few years back reported having detected such an admixture in Oceanians. The first ancient genome we have from eastern Eurasia >60,000 years ago that is from a modern human will probably yield much more satisfying results.

The big dynamic looming over the likely existence of anatomically modern human range on the edge of Africa in Arabia is that for several hundred thousand years modern humans existed within Africa as a metapopulation. The proto-Out-of-Africa population can only be understood as part of this broader metapopulation. ~100,000 years before the present humans, inclusive of Neanderthals, Denisovans, and modern humans, our species was probably defined by a set of distinct metapopulations. We know that there was gene flow between these metapopulations, but the strong evidence of purifying selection of Neanderthal and Denisovan ancestry in modern human genomes tells us that this gene flow was minimal enough that biological incompatibilities were beginning to build up and the groups were on their way to speciation as defined by the biological species concept.

There is no evidence of this between any modern populations, even the most diverged (e.g., the Khoisan, who carry Eurasian and African agriculturalist genetic material). This means that within the modern human metapopulation gene flow was sufficient to prevent incompatibilities from developing due to isolation. That being said, with the oldest (proto-)modern human skull dating to ~300,000 years, and likely discernible population structure between various African lineages going beyond 200,000 years ago, there are lots of distinct modern human groups with very long histories within Africa and on its periphery.

The earliest point that you could probably say non-African humans diverged from any African (Sub-Saharan) populations is ~100,000 years ago (and this is probably a bit too generous). A conservative estimate would suggest that modern human lineages were emerging within Africa 200,000 to 300,000 years ago. So most of modern humanity’s existence has been within Africa.

The non-African populations descend from a group which underwent a period of reduced population size vis-a-vis all the African groups. But one thing I think is important to remember is that this was probably not exceptional. We know now that over the past 5,000 years African population genetic structure has been reshaped by events such as the Bantu expansion. But there were surely small and marginal groups with low effective population sizes within Africa that either went extinct or were absorbed by other populations.

The difference in the non-African population is that it was on the edge of the modern human range, and likely occupied territory that was relatively isolated from other modern humans due to the dry nature of the Sahara during most of the Pleistocene. This prevented its absorption into more numerous groups of modern humans further south and to the west. And the strong cultural and genetic barriers with the Neanderthals probably limited gene flow as well.

But even in the inclement conditions of North Africa and West Asia for most of the past 100,000 years, modern humans may have had a larger effective population size than archaic Eurasian hominins. And with this larger effective population size, one can imagine that greater cultural creativity and genetic robustness to dynamics such as population declines gave the modern humans a long-term advantage. In this context, the existence of modern human remains in a diverse array of places across warmer areas of Eurasia before 60,000 isn’t that surprising. And, the demographic wave that swallowed Neanderthals and Denisovans probably swallowed the earlier modern humans who ventured into eastern Eurasia before 60,000 years ago!

Denisovans, Neanderthals, Yetis, oh my!

An excellent open access paper is out in Cell which explores the distribution of archaic hominin, and in particular Denisovan, ancestry, Analysis of Human Sequence Data Reveals Two Pulses of Archaic Denisovan Admixture:

Anatomically modern humans interbred with Neanderthals and with a related archaic population known as Denisovans. Genomes of several Neanderthals and one Denisovan have been sequenced, and these reference genomes have been used to detect introgressed genetic material in present-day human genomes. Segments of introgression also can be detected without use of reference genomes, and doing so can be advantageous for finding introgressed segments that are less closely related to the sequenced archaic genomes. We apply a new reference-free method for detecting archaic introgression to 5,639 whole-genome sequences from Eurasia and Oceania. We find Denisovan ancestry in populations from East and South Asia and Papuans. Denisovan ancestry comprises two components with differing similarity to the sequenced Altai Denisovan individual. This indicates that at least two distinct instances of Denisovan admixture into modern humans occurred, involving Denisovan populations that had different levels of relatedness to the sequenced Altai Denisovan.

Before you get caught up in the results, you should check out the methods. They’re pretty ingenious. Though with novel results like this people also really need to work their way through them as well (the authors present a lot of simulation results to validate the method, so I’m sure that will convince most; it certainly sways me).

The plots at the top of this post show the different distribution of Neanderthal and Denisovan admixture, by matching regions of the genome that they’ve identified as archaically introgressed. The ultimate logic is to look for variants which aren’t found in Africans, and are found in non-Africans, and scan over segments of the genome hoping that you can pick up the haplotypes that would slowly be chopped up over time through recombination that came in from Neanderthals or Denisovans.

At the top-left of the figure, you see “Northwest Europeans.” The segments tend to concentrate at the bottom-right of the panel. That means that they match the Neanderthal reference sequence to a high degree, but not the Denisovan. This makes sense since everything we know from earlier work indicates that Northwest Europeans don’t have Denisovan ancestry.

On the bottom-right you see Papuans. They’re very out of place because they are the only population in the list where Denisovan ancestry is greater than Neanderthal ancestry. This is visible in the match patterns.

South and East Asian populations exhibit a pattern with high (relative) levels of Neanderthal matches, but also a minor amount of Denisovan matching. This aligns with earlier work, which reported low levels of Denisovan admixture among populations with eastern Eurasian ancestry broadly.

The surprise is that the variation in matching to the Denisovan Altai genome exhibited a north-to-south cline. In particular, Northeast Asian populations seem to have a mix of two types of Denisovan. One, which is close to the Denisovan sequence that is normally used as a reference, and one which is diverged from it. The Papuans and South Asians seem to have Denisovan ancestry which is not so much like the Altai sample. This is not very shocking of course.

Finns barely miss the p-value cut-off (Bonferroni-corrected threshold), but they clearly have some Denisovan from East Asian gene flow, and some of it looks to be similar to the Altai Denisovan. Curiously, the Vietnamese (Kinh) don’t show any Altai Denisovan, but the Dai do. The Japanese have a lower proportion of the Altai Denisovan than the two Han Chinese samples. And very strangely the 1K Genomes samples from the New World, a substantial proportion of which have Amerindian admixture, show no Denisovan.

Pontus Skoglund immediately made a very interesting observation:

And Alexander Kim followed up:

In the thread to Skoglund’s original comment Africa Gomez notes that the authors suggest that high linkage disequilibrium in New World populations, due to recent admixture between diverged groups, may reduce the power to detect the Denisovan ancestry. So perhaps that’s that?

But for a moment, let’s set that aside. The best evidence right now is that the Denisovan admixture into Papuans, and therefore South Asians, occurred not too after the Neanderthal admixture event. That mixture is reasonably well dated because of ancient genomes which are closer to the period of admixture. But what about the second event with the Altai Denisovan? If what Skoglund says is true the date for that might be closer to the Last Glacial Maximum, and not when modern humans came to dominate the region. And I say dominate because there’s evidence that anatomically modern humans may have ventured quite far into eastern Eurasia before they finally swept aside more established lineages.

A few years back researchers found that one of the mutations that allow for Tibetan high altitude adaptation seems to have come in from a Denisovan genetic background. Spencer Wells, who knows a thing or two about Central Asia, has always half-seriously suggested that the legends of the Yeti derive from populations of archaic humans who persisted in the uplands of the heart of Eurasia.

But perhaps they weren’t pure Denisovans in any case. Work out of David Reich’s lab has suggested that Denisovans themselves, or at least the Alta Denisovan, harbors a deep ancient lineage diverged from modern humans, Neanderthals, and Denisovans, in low fractions. The “Altai Denisovan” admixture may have come into Northeast Asians via a mixed population, which arose when modern humans came to dominate eastern Eurasia, but only transmitted the Altai Denisovan ancestry later.