Since 2010 the combination of improvements in genomic technology and ancient DNA have totally revolutionized our understanding of the human past through genetic techniques. In the 2000s there was a “live debate” about archaic introgression into modern human genomes, in large part because the techniques were not powerful enough to answer the questions that were being asked (nevertheless, many thought they really knew the answer already!).
With the sequencing of the Neanderthal in 2010 we saw that non-Africans seemed to carry more Neanderthal alleles than Africans, which was suggestive evidence of archaic admixture. Before the end of the year, the Denisovans were discovered, and it was clear that their impact was significant in the Papuans (and to some extent Oceanians generally). These discoveries were a shock already, but over the years more and more subtle discoveries have occurred. To some:
– Researchers believe that the Neanderthals have some ancestry from a basal modern population (a group that diverged a long time ago)
– Lots of debate about whether greater estimated Neanderthal fraction in East Asians was due to a second admixture or dilution of the original admixture by later mixing in West Eurasians, or, differential natural selection in different populations (I lean toward the middle position)
– It is clear that there is some Denisovan ancestry in East and South Asians, as well as in peoples of the New World. And, it seems quite clear that these admixtures were from different branches of the Denisovan group of humans
– It seems quite likely that Papuans may have multiple admixture events from Denisovan populations or from people related to the Denisovans
– There is lots of circumstantial evidence that Neanderthals and Denivosons may harbor ancestry from earlier human lineages that were present in Eurasia when their ancestors pushed out of Africa ~750,000 years ago
– Lots of evidence for deep ancestry admixture within Africa
– Basal Eurasians. What are they? We still don’t know!
…humans outside of Africa trace about 2% of their genomes to admixture from Neanderthals, which occurred 50–60 thousand years ago1. Here we examine the effect of this event using 14.4 million putative archaic chromosome fragments that were detected in fully phased whole-genome sequences from 27,566 Icelanders, corresponding to a range of 56,388–112,709 unique archaic fragments that cover 38.0–48.2% of the callable genome. On the basis of the similarity with known archaic genomes, we assign 84.5% of fragments to an Altai or Vindija Neanderthal origin and 3.3% to Denisovan origin; 12.2% of fragments are of unknown origin. We find that Icelanders have more Denisovan-like fragments than expected through incomplete lineage sorting. This is best explained by Denisovan gene flow, either into ancestors of the introgressing Neanderthals or directly into humans…
The power of the Icelandic dataset is that they got really high coverage genomes, 30x, and phased them together to generate a lot of confident haplotypes. 3.3% Denisovan out of the 2-3% that’s archaic is really small. But if you have enough data you can find it.
They had to do simulations and run some HHMs to get here. I’m not sure I believe it. But I also think it’s plausible. The two models they present are:
– Denisovans mix into Neanderthals who mix into humans
– A Denisovan related population mixes into early non-African humans just before they mixed with Neanderthals
As time goes by I suspect we’ll find many small details of past interaction.
The phylogenetic relationships between hominins of the Early Pleistocene epoch in Eurasia, such as Homo antecessor, and hominins that appear later in the fossil record during the Middle Pleistocene epoch, such as Homo sapiens, are highly debated…Here we present the dental enamel proteomes of H. antecessor from Atapuerca (Spain)…Homo erectus from Dmanisi (Georgia)…two key fossil assemblages that have a central role in models of Pleistocene hominin morphology, dispersal and divergence. We provide evidence that H. antecessor is a close sister lineage to subsequent Middle and Late Pleistocene hominins, including modern humans, Neanderthals and Denisovans. This placement implies that the modern-like face of H. antecessor—that is, similar to that of modern humans—may have a considerably deep ancestry in the genus Homo, and that the cranial morphology of Neanderthals represents a derived form. By recovering AMELY-specific peptide sequences, we also conclude that the H. antecessor molar fragment from Atapuerca that we analysed belonged to a male individual. Finally, these H. antecessor and H. erectus fossils preserve evidence of enamel proteome phosphorylation and proteolytic digestion that occurred in vivo during tooth formation…
This is an 800,000 year old sample from Spain. Proteins are more robust than DNA, so they last longer, but they tend to give less information. But at the scale of species-wide differences there is enough variation to establish some tentative relationships.
Previously some researchers argued H. antecessor was ancestral to modern humans. This seems to suggest this is unlikely. Or at least that antecessor is not the dominant direct ancestor.
The recent big paper on ancient DNA from East Asia has opened up a bit of a semantic can of worms. If you read all these ancient DNA papers with their stylized models you start to develop a sense of the big overall framework, but even in a big sprawling preprint with copious supplements, it is hard to make sense of things if you haven’t read what’s come before. With that in mind, I did a twitter thread where I outlined my own view and interpretation of how non-Africa was populated by modern humans in the last ~50,000 years with a focus on eastern Eurasia.
But I shouldn’t just leave it at Twitter. So I here I stand.
click to enlarge
Above is a simple map, and to the right a stylized phylogram, that shows you the general gist of my thinking and what I’ve gleaned from the papers. First, we know that around 50,000 years ago there was a massive expansion from Africa or its margins all across Eurasia, and, that it reached Oceania really early.
Before that expansion it seems one group, we now call them “Basal Eurasians,” split off before the lineage that led to the peoples of Europe, Siberia, East Asia, South Asia, and Oceania. I set that at 60,000 years ago. Then around 50,000 years ago a group of populations that give rise to the peoples of Pleistocene East and South Asia, and Oceania, split off from groups that became the early Siberians (“Ancient North Eurasians”) and Pleistocene European hunter-gatherers.
I said Pleistocene because there has been massive population change across eastern Eurasia during the Holocene.
In South Asia about half the ancestry derives from populations with affinities or origins in western Eurasia, whether that be West Asia (Iranian-related farmers who occupied the northwestern fringe of the subcontinent expanding south and east), or further north in Central Eurasia and Eastern Europe (Sintashta-Andronovo). The balance is often termed “AASI”, or “Ancient Ancestral South Indian.” The mitochondrial evidence (lots of basal M) suggests deep and diversified lineages in South Asia, so I am willing to agree that this group descends from the first of the recent Out-of-Africa or Out-of-Africa-liminal* pulse of migrants 50,000 years or so ago. But, I do think it is not implausible that some of the ancestry of AASI derives from back-migration from Southeast Asia, which would be prime human habit during the dry and cold Pleistocene.
Further east, you have groups in Southeast Asia proper. If you listen to The Insight podcast you know that Pleistocene Southeast Asia was a much larger landmass due to lower sea levels. Not only was there more territory, but much of it was open wooded savannah, which often supports higher human populations than a tropical rainforest. In any case, most of the human population that lives in this region today descend mostly from farmers who occupied what is today the Yangzi river valley in China. There are exceptions. The Negritos of Malaysia and the Andamanese seem to be reflections of the peoples who were dominant in the region in the Pleistocene and most of the Holocene. Further east, there are Negritos in the Phillippines, who are distantly related to those further west but seem somewhat more connected to the Oceanians, even further eastward.
We know that the humans were in Australia by 40-45,000 years ago, at the latest. This establishes a timeline for the point of divergence of all these lineages. Though Andamanese are used as proxies for AASIs in population genetic analyses, it turns out they are very distantly related to them. All of these dark-skinned people across southern Eurasia and into Oceania are more related to each other than they are to East Asians, but only very distantly and marginally.
Speaking of which, the 40,000-year-old sample from Tianyuan near Beijing is the oldest representative of the human groups which we now term East and Southeast Asian. We know from this sample, and how it relates to other people in eastern Eurasia, that there was already significant differentiation across the region. I assume this had to have happened around 45-50,000 years ago. The time is less important then to note that the split between East Eurasians and West Eurasians, and within East Eurasians and West Eurasians, occurred in very rapid succession. This is the hallmark of an expanding species which occupies “empty” landscapes and fills all the possible niches very fast, and then stabilizes.
An easy dichotomy would be to label the Tianyuan people the northern clade, and what is often termed “Australasian” the southern clade. But it’s not that simple. The most recent paper, aligning with earlier results, argues that the Jomon people of ancient Japan (related to or ancestors of the Ainu) are about a 50:50 mix between the “northern” (Siberian?) and “southern” lineages. But Japan is in northern East Asia! Additionally, they also find that the oldest modern layer in Tibetans is also more closely related to the “southern” lineage. Finally, we know some populations in Amazonia are more closely related to the “southern” lineage than they “should” be, indicating that some “southern” ancestry came over Beringia.
To me, it makes it clear that the two lineages had a very different geographical distribution during the Pleistocene.
The Jomon culture dates to ~16,000 years ago, right after the Last Glacial Maximum. We don’t know when the two distinct populations mixed, but I wouldn’t be surprised if it was quite early, as Siberian populations moved toward the coast. I assume that haplogroup D, found in both Tibet and Japan, has some origin among the “southern” people. Physical anthropologists have long noted some broad similarities in morphology between some “Australoid” people in India, Australian Aboriginals, and the Ainu of Japan. As the divergence between these groups is 45,000 years ago, the similarities may still be coincidences, but perhaps they are share ancestral characters?
We also need to think about Native American peoples. It looks like this group is a mixture of “northern” East Asians, related to the Devil’s Gate population, and ANE populations. This situates some of the post-Tianyuan groups in Siberia, but recall some Amazonians have “Australasian” affinities. The reality is that I think “southern” lineage population was long present along the Pacific fringe. The Jomon heritage is clear evidence of that. It is not implausible that there was structure in ancient Beringia, and some coastal populations with “southern” ancestry moved on earlier than the inland groups, and were mostly replaced except in the deep Amazon.
Finally, we can mention the strange Paleo-Tibetan “southern” ancestry. Again, there are peculiarities in Tibetan morphology which don’t make them in the same class as East Asians, but that can be attributed to high altitude adaptation. If the Paleo-Tibetans were the earliest population, they probably may have mixed with the Denisovans to obtain EPAS1. But, the majority of Tibetan ancestry seems to date to successive waves of “northern” populations that moved onto the plateau from the north and east. So who were the Paleo-Tibetans most closely related to? If I had to guess, I would say AASI. They may have moved onto the plateau from the south.
This is obviously exceedingly simple. There are many likely details I got wrong, as well as details I left out (I think that “southern” lineages were very common in the southern half of China deep into the Holocene, spanning the region between Tibetan and Jomon Japan). But, it gets across the gist of the broader framework in East Asia.
Here is the one-sentence version: rapid expansion, diversification, stabilization, then much more recent mixture between all the lineages.
* I believe that “modern” African humans were present in southern Eurasia in some form and numbers between 50 and 100 thousand years ago. But, I think they left a very light genetic imprint on modern populations. I accept that modern humans were in Sumatra 65,000 years ago, but I think almost all the ancestry is from groups which expanded 50,000 years ago, from the west.
After a few years of presentations and preprints, the new high-quality whole-genome analysis of the HGDP dataset is finally published in Science, Insights into human genetic variation and population history from 929 diverse genomes. The HGDP dates back 30 years, so this is the culmination of a long line of research. The authors in this paper looked at nearly 1,000 HGDP individuals at high coverage sequencing, meaning that they had extremely good confidence in their calls of the state of a base across all 3 billion pairs.
This is in contrast to the ~600,000 markers in the original HGDP analyses from the 2000s, which came from results of a “SNP-array.” A SNP-array of this form focuses on the variation by looking at polymorphic sites (sites which vary in the population). How did they originally determine what was polymorphic? Unfortunately, they had to rely on European populations, so the original analyses were using a quite skewed measuring stick. Whole-genome analyses bypass these problems because you get the totality of sequence information, and, the high-coverage means you can confidently call very rare variations in some of these individuals (they’re not false positives).
The HGDP was assembled by L. L. Cavalli-Sforza and curated from ethnographically interesting populations. Therefore, it is useful to compare it to the 1000 Genomes, which tends to focus on more conventional populations. The 1000 Genomes has 2,500 individuals, sequenced at somewhat lower coverage on average. While this project yielded 70 million polymorphisms, the 1000 Genomes Project had 85 million. Most of these are rare. The power to detect rare polymorphisms is useful in elucidating population structure because rare polymorphisms tend to be evolutionary new, and so reflect more recent differentiation.
For example, they compared Yoruba, Mbuti, and non-Africans. Looking at common polymorphisms the Yoruba are closer to non-Africans while looking at rare ones they are closer to Mbuti. Why? The rarer polymorphisms reflect recent differentiation, and there has been recent gene flow between Mbuti and Yoruba.
On the whole, they recapitulated earlier findings but using more sophisticated methods that leveraged their whole-genome data they added some wrinkles. For example, some populations diverged in a very sharp and distinct fashion, such as Han and Yakuts, or Druze and Sardinians. But for the populations that diverged between 150,000 and 50,000 years ago, mostly within Africa, the separations were more gradual and probably characterized by repeated gene flow between the descendent groups (e.g., Non-Africans, Yoruba, Mbuti, San, etc.).
This reiterates that there isn’t a one-size-fits-all narrative we can use to talk about the emergence of modern populations and the way those populations are patterned. There are debates about whether we are a “clinal” species or not. I don’t think that’s a good question, because as implied in this paper a great deal of the past diversity has been collapsed through recent admixture events. The authors also detect deep and complex structure and differentiation. They’re clearly just scratching the surface.
Finally, there is more reiteration of the nature of Neanderthal and Denisovan admixture. The Neanderthals who mixed into early humans were quite homogeneous, or, there were not many of them. The haplotypes are not too numerous, and, they don’t exhibit the patterns you’d expect from different admixtures and source populations. The diversity is too great to be a single individual, but it could have been a small number. The main caution I would suggest here is that Neanderthals seem to often be quite homogeneous on the local scale.
The Denisovans are a different story. They detect the difference between Oceanian and non-Oceanian Denisovan ancestry (the Oceanian source Denisovans were quite distinct from the Altai Denisovans). But they also detect a different Denisovan contribution to the genomes of the Cambodians. The indigenous people of the Phillippines also harbor different Denisovan ancestry (not in this paper). The “Denisovans” seem to have been a cluster of different lineages that persisted in parallel for a long time.
Where is there to go next with the HGDP. At some point, better technologies will allow for a more thorough exploration of structural variation. I’ve emphasized this is an analysis of the sequence because that’s what it is. There is more information in non-sequence variation that they’ll get to one day (there was some structural analysis in this paper, but I believe that we are currently technology limited).
A new preprint reports on the peculiar Y chromosomal patterns that one finds in Neanderthals, Denisovans, and modern humans. Spencer Wells has told me that Y and mtDNA are actually much more informative now that we have an ancient DNA autosomal scaffold. I think that’s right. The strange result from Neanderthals is both their Y and mtDNA lineages seem to form a clade with modern humans, while Denisovans the outgroup, though the whole genomes cluster Denisovans with Neanderthals. This reminds us that we put way too much weight on mtDNA during the molecular ecology heyday of the 2000s.
…Here we present sequences of the first Denisovan Y chromosomes (Denisova 4 and Denisova 8), as well as the Y chromosomes of three late Neandertals (Spy 94a, Mezmaiskaya 2 and El Sidrón 1253). We find that the Denisovan Y chromosomes split around 700 thousand years ago (kya) from a lineage shared by Neandertal and modern human Y chromosomes, which diverged from each other around 370 kya. The phylogenetic relationships of archaic and modern human Y chromosomes therefore differ from population relationships inferred from their autosomal genomes, and mirror the relationships observed on the level of mitochondrial DNA. This provides strong evidence that gene flow from an early lineage related to modern humans resulted in the replacement of both the mitochondrial and Y chromosomal gene pools in late Neandertals. Although unlikely under neutrality, we show that this replacement is plausible if the low effective population size of Neandertals resulted in an increased genetic load in their Y chromosomes and mitochondrial DNA relative to modern humans.
First, the first author gives due credit to the bench scientists who managed to get usable Y chromosomal sequences out of ancient DNA. That’s not a trivial task. Second, confirming both earlier autosomal and mtDNA work, it does seem that the Neanderthal lineage experienced Y and mtDNA turnover during the last 400,000 years, with the donor population being an outgroup to most modern humans, albeit closer to that lineage than the Denisovan clade (the Y evidence suggests it’s an outgroup to all modern humans, but the autosomal work is more difficult to pin down in terms of dating of divergence). Third, the replacement of the Y and mtDNA aren’t random, but a function of fitness differences due to the accumulated burden of deleterious alleles. Using simulations they show that very small differences can give notable selective advantages and result in likely replacement of mutation burdened lineages. Finally, we see a different dynamic with Denisovans.
In fact, the Denisovan Y divergence is suspiciously concordant with the autosomal divergence dates in some models.
Many years ago John Hawks pointed out to me that some of the patterns in human evolution may simply be a consequence of large population sizes for Homo in Africa. When it comes to Neanderthals this seems to be a reasonable way to think about it. The genetic and non-genetic evidence points to huge fluctuations in population size of Neanderthals, so the accumulation of deleterious mutations is plausible, and, impact by more numerous southern Homo lineages seems likely. But what about “Denisovans”? I think this work will be part of a tradition that shows Denisovans exhibit fundamentally different population dynamics as compared to Neanderthals.
While Neanderthals seem to have been a coherent population from the Altai to Europe, undergoing repeated bottlenecks, I think Denisovans were a diverse array of populations that exhibited a wide range in population sizes (this is genetically supported by recent work which shows diverse Denisovan contributions to East, South, and Southeast Asians). Additionally, the region of the Old World that seems to be second to Africa in being suitable ape habitat is Southeast Asia.
Finally, due to the reality that colder climates present better opportunities for DNA preservation, we may obtain some of our best understanding of the genomics of paleo-modern humans outside of Africa from Neanderthals as more and more data accumulates. The non-African populations today seem to be almost exclusively descended from an African or Africa-adjacent expansion that dates to ~50,000 years ago. But archaeology and suggestive genetic clues indicate that there were other African lineages which ventured out 100 to 200 thousand years ago. These did not leave a major impact on today’s populations, but with enough Neanderthal genomes, one might be able to reconstruct these people.
As a follow-up to the post below, I thought I would make certain expectations and assumptions more explicit on my part. The new methods to infer our species’ population history are quite complicated and require a lot of analytical and computational firepower. They’re predicated on big datasets (e.g., whole genomes, and lots of them) and high-powered computational methods (not just in inference and analysis, but also simulation). All models are wrong, but some give more insight than others. From talking to people who work on this field, no one even working on these models assumes that they’re extremely high fidelity to the past. Rather, they’re pulling out insightful fragments of the truth. We’ll need to bring together both genetics and paleoanthropology to really get what’s going on.
In any case, there is a simpler and more old-fashioned framework that I always keep in mind to which I think is important. The past few million years of hominin evolution are strongly shaped by biogeographic parameters. There are two areas of the world where I see that researchers are digging up a fair amount of complexity for the origins of modern humans. One of them is Africa. But the other is Southeast Asia. For example, last year’s Multiple Deeply Divergent Denisovan Ancestries in Papuans (this paper is an illustration, if you keep track of this field you know it’s not an outlier for this region). Why is this?
I think the answer is simple, and it has to do with geography and climate. During the Pleistocene Africa and Southeast Asia had the greatest area of tropical woodland in the Old World. This is optimal hominin habit in many ways, though clearly hominins can occupy other habits (e.g., the Dminasi hominins). Though Eurasian hominins such as Neanderthals and Denisovans were quite successful as measured by persistence for long periods of time, the extant genomic evidence indicates that at northern latitudes hominins tended to be able to maintain themselves only at low population densities (at least before agriculture). The genetic data from Mesolithic European hunter-gatherers tend to support this proposition as well; they were characterized by low diversity. Similarly, Amerindian populations seem to have gone through a striking bottleneck during their high latitude sojourn.
For various reasons, a lot of genetics, genomics, and ancient DNA, has focused on high latitude hominins. Modern genetics is skewed toward Europeans, while ancient DNA began in the north due to better preservation. But I think high and mid-latitude hominins give a skewed and simple view of the human past due to small effective population sizes and high levels of regional turnover. In contrast, both Africa and Southeast Asia have been characterized by high population sizes of hominins and high speciosity. As we dig deeper into the genomics of these regions for our lineage, we’ll stumble upon “mysteries” which reflect the reality that these regions were home to many different and large numbers of hominins, and we can detect these imprints in the genomes…
Broadly, the results are getting at something which plenty of people have been noticing for many years: when it comes to Sub-Saharan Africans, there is something deeply diverged in West Africans vis-a-vis non-West Africans. These results seem to suggest that the divergence between this outgroup lineage and our own is a bit earlier than the modern-Neanderthal/Denisovan split. There are many abstruse statistical inferences and simulations, and it looks like the reviewers made them do a lot of analyses. But the general result is something other groups have seen as well, so I believe it. Additionally, the admixture of this lineage into West Africans seems to have occurred about 50,000 years ago, suspiciously close to the general expansion of modern humans out of Africa (or the most recent expansion).
From the discussion:
The signals of introgression in the West African populations that we have analyzed raise questions regarding the identity of the archaic hominin and its interactions with the modern human populations in Africa. Analysis of the CSFS in the Luhya from Webuye, Kenya (LWK) also reveals signals of archaic introgression, although our interpretation is complicated by recent admixture in the LWK that involves populations related to western Africans and eastern African hunter-gatherers (section S8) (20). Non-African populations (Han Chinese in Beijing and Utah residents with northern and western European ancestry) also show analogous patterns in the CSFS, suggesting that a component of archaic ancestry was shared before the split of African and non-African populations. A detailed understanding of archaic introgression and its role in adapting to diverse environmental conditions will require analysis of genomes from extant and ancient genomes across the geographic range of Africa.
A new (open access) paper in Cell, Identifying and Interpreting Apparent Neanderthal Ancestry in African Individuals, is making a big splash in the media. Whether you believe this paper on its own is conditional on how deeply you can grok the methods. Honestly I don’t know if I trust myself to render any judgment until I’ve replicated the whole analysis pipeline. Intuition doesn’t come from a priori.
That being said, in light of other factors and our general understanding of hominin gene flow this is a highly plausible result. They conclude that “A model that combines both of these events, elevated back migration and human-to-Neanderthal gene flow, matches the empirical data best across all features.” Gene flow from neo-African modern humans into Neanderthals seems very likely. Similarly, it is quite possible that there was widespread Eurasian back migration into Africa. But, that back migration was West Eurasian.
The “problem” with the older models is that it simply assumed that groups such as the Yoruba had no Neanderthal ancestry, presupposing a particular model of paleoanthropological gene flow where Africa is purely a source, rather than also a sink. Assume nothing!
A few days ago Spencer and I recorded a “predictions for 2020s” episode for The Insight, before we go back to “regularly scheduled programs.” One of the topics (of ten) we discussed is that the old “Out of Africa” model is going to be marginalized/complicated.
What did we mean by this? Some of the hints are already present in David Reich’s Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past. If you look at and analyze genome-wide data, especially ancient data, there are just too many strange results to be accounted for by our current consensus understandings. There are new things we’ll learn. And some of the old things will be wrong. We just don’t know what.
In the 1980s and 1990s, and into the 2000s, the “Out of Africa” narrative was one that the “community” of paleoanthropology went hard into (and to a lesser extent human geneticists). Perhaps too hard. Not only is there “archaic” admixture outside of Africa, but there is “deep structure” within Africa. At some point, there are too many epicycles, and there needs to be a major model revision.
Over ten years ago Dienekes Pontikos presented what I thought at the time was a “crazy” paradigm of back-to-Africa migration. Though I’m still not sure of that particular model, I think there is a high likelihood of reciprocal gene-flow between Africa, and Eurasia, especially Western Eurasia, within the last few hundred thousand years. The debates around Y haplogroup E, which is modal within Africa, but also present with deep lineages in Eurasia, shed light I think on some of the complexity.
Instead of a single “Out of Africa” movement 50-60,000 years ago, there seems to have been a sequence of events 50-100,000 years ago which resulted in the population genetic patterning that we see around us. Some of it is the classic wave expansion from a small founder group for non-Africans, but within Africa it seems there were also expansions and admixtures, albeit more complicated, continuous, and long-standing. Some of the deepest branches within African population history go back hundreds of thousands of years, but much of it dates to expansions with closer affinities to non-Africans 50-100,000 years ago.
Sometimes it can be exciting to say that the question is the answer….
The Insightis back with a 2-hour episode. If you unsubscribed due to a lack of new content, please resubscribe. Spencer and I devoted this episode to a “decade wrap-up,” so we had a lot to talk about (OK, ten general things to talk about, as we did a countdown), but there are already episodes in the queue on demographic transition, Levantine and Papuan genomics, and natural selection in the Americas, that will be dropping in early 2020.
Due to the constraint of time, we couldn’t really explore in full depth something that has been on our minds for a while: the likely seminal role of Southeast Asia, and Sundaland in particular, in the (re)settlement of Eurasia. Spencer has been telling me for years that Y chromosome researchers (e.g., Michael Hammer) have been noting that Southeast Asia, in particular, seems to be harbor the ancestral lineages for venerable branches such as R. These seem to derive from mutations in this area. For example, one can argue for a scenario where the ancestry of R & Q percolates up to Siberia, and shifts west, where R1 emerges among the “Ancient North Eurasians”, and eventually R1b and R1a diffuse across western and southern Eurasia. Today, R1a in Southeast Asia is an indication of migration from South Asia, closing the circle.
About ten years ago maps like the one to the right were all the rage. They are focused on uniparental haplogroups. The phylogenies are easily simply overlaid upon a map to trace out migrations. Implicit is the ‘serial bottleneck’ out of Africa framework.
But what if we have something seriously wrong? We now know there was lots of reticulation. Gene flow across populations. And it wasn’t unidirectional. Additionally, there is the weird fact that across the Middle East there seems to have a population now termed “Basal Eurasian” which split off from other non-Africans earlier, and probably had no Neanderthal ancestry at all. In contrast, Pleistocene Europeans, East Eurasians, the people of the New World and Oceanians, form a lineage.
So here is a hypothesis that I have minimal confidence in, but is not crazy as such
– “Basal Eurasians” are the primal population of the Near East
– “Eastern non-Africans” mix with Neanderthals on the way into southern and southeast Asia.
– One group of “Eastern non-Africans” moves into Oceania. Another group continues northward and eventually percolates back into the center of Eurasia, and gives rise to “West Eurasians.”
– This backflow population eventually mix with “Basal Eurasians” in the Near East.
The extremely ancient genomes from Europe, Siberia, and China are very strange in the results they present. Though the west vs. east bifurcation is evident, it looks have to occurred not much earlier than 40,000 years ago. The Goyet sample’s strange affinity to East Eurasians, as well as the fact that the first modern Europeans and Siberians seem to be not particularly more closely related to modern West and East Eurasians, also makes more sense.
Since 2010 the combination of improvements in genomic technology and ancient DNA have totally revolutionized our understanding of the human past through genetic techniques. In the 2000s there was a “live debate” about archaic introgression into modern human genomes, in large part because the techniques were not powerful enough to answer the questions that were being asked (nevertheless, many thought they really knew the answer already!).
– Lots of debate about whether greater estimated Neanderthal fraction in East Asians was due to a second admixture or dilution of the original admixture by later mixing in West Eurasians, or, differential natural selection in different populations (I lean toward the middle position)
The power of the Icelandic dataset is that they got really high coverage genomes, 30x, and phased them together to generate a lot of confident haplotypes. 3.3% Denisovan out of the 2-3% that’s archaic is really small. But if you have enough data you can find it.
Many years ago 
