A new ancient DNA preprint, this time using the sequence of a 34,000-year-old sample from Northeastern Mongolia. The preprint is Denisovan ancestry and population history of early East Asians:

We present analyses of the genome of a ~34,000-year-old hominin skull cap discovered in the Salkhit Valley in North East Mongolia. We show that this individual was a female member of a modern human population that, following the split between East and West Eurasians, experienced substantial gene flow from West Eurasians. Both she and a 40,000-year-old individual from Tianyuan outside Beijing carried genomic segments of Denisovan ancestry. These segments derive from the same Denisovan admixture event(s) that contributed to present-day mainland Asians but are distinct from the Denisovan DNA segments in present-day Papuans and Aboriginal Australians.

There are two major points in this preprint. First, as noted in the title, this adds weight to the inference that there were multiple admixtures between “Denisovan” populations and the peoples of south and east Eurasia. I put Denisovan in quotations because there is more and more evidence now that this was a diverse and variegated lineage of humans, not a simple classification such as Neanderthals, who often seem to have been closely related due to periodic population bottlenecks. This individual carries segments similar to the Altai Denisovan, and something different from the segments in the Papuans.

I think the second major aspect here is east-west gene flow in Eurasia in a bidirectional sense. It seems more and more likely that the “Ancient North Eurasians” (ANE) reflect two dynamics. First, the rapid expansion of an ancient West Eurasian branch of humans pushing up through the Near East and into Central Asia, and then Siberia, very early. Second, the assimilation and admixture with a minority element of incipient East Asian populations pushing up from the south. Though the trend was patchy and uneven, eventually the East Asian ancestral component kept increasing, until you have “Neo-Siberian” modern populations which are overwhelmingly East Asian.

Why the difference? As with Denisovans, I think the answer is a function of biogeography. Though West Eurasians had an easier “straight shot,” East Asians had a much larger reservoir population near at hand to the south over the late Pleistocene. Over time this resulted in a difference, whereby Siberian populations become more and more East Asians, with relatively little influx of West Eurasian genes until the Russian colonization.

In 2005 Dienekes Pontikos had a post up, The mitochondrial time depth of humanity:

It is common to distinguish between Africans and non-Africans, with the former being much more genetically diverse than the latter. But, the real “gap” in human origins seems to be between the really old Africans (“Paleoafricans”) and the rest (“Afrasians”).

The Paleoafrican element is entirely confined to Africa, while the Afrasian one is found in both Africa and Eurasia. Indeed, modern humans can be entirely split into two groups: (i) a group of “pure” Afrasians which includes all non-Africans, and (ii) a group of Afrasian-Paleoafricans which includes all non-Caucasoid Africans. Human groups of entirely Paleoafrican origin, unhybridized with the younger Afrasians are no longer in existence.

Today, a preprint with very sophisticated computational methods of data analysis was posted, Ancient admixture into Africa from the ancestors of non-Africans. The figure to the right shows the proportion of deep “Eurasian” admixture into each major Sub-Saharan African population. Basically this preprint very formally breaks down the high likelihood that Dienekes’ model outlined in the mid-aughts was correct. Even back in 2008, there was an mtDNA phylogeny and coalescence that aligned well with his hypothesis: The Dawn of Human Matrilineal Diversity. Finally, there is the fact Y haplogroup E is dominant among non-hunter-gatherers in Africa, and it is within the “Eurasian-clade” DE.

The abstract of the new preprint makes the genome-wide results pretty clearly in alignment with the older uniparental evidence, as well as some interesting twists that one can infer from population genomics:

Genetic diversity across human populations has been shaped by demographic history, making it possible to infer past demographic events from extant genomes. However, demographic inference in the ancient past is difficult, particularly around the out-of-Africa event in the Late Middle Paleolithic, a period of profound importance to our species’ history. Here we present SMCSMC, a Bayesian method for inference of time-varying population sizes and directional migration rates under the coalescent-with-recombination model, to study ancient demographic events. We find evidence for substantial migration from the ancestors of present-day Eurasians into African groups between 40 and 70 thousand years ago, predating the divergence of Eastern and Western Eurasian lineages. This event accounts for previously unexplained genetic diversity in African populations, and supports the existence of novel population substructure in the Late Middle Paleolithic. Our results indicate that our species’ demographic history around the out-of-Africa event is more complex than previously appreciated.

The reason I put “Basal Eurasian” in the headline is that this is the “ghost population” postulated by the Reich group researchers in the first half of the teens to account for the fact that Mesolithic European hunter-gatherers seem to share more genetically with people such as Oceanians and Han Chinese in some ways that European “first farmers.” More precisely, the early West Asian farmer groups seem to be a mix of a population that is distinct as the “first branch” of non-African humanity, “Basal Eurasians”, and people related to West Eurasian Mesolithic hunter-gatherers. The latter place West Asians in the clade with Pleistocene Europeans and early Siberians, as a “western” group, while the former means that West Asians have ancestry that is more distant to Papuans and Amerindians than Mesolithic European hunter-gatherers.

Another thing that notable about Basal Eurasians is there is some circumstantial evidence that this population did not undergo much admixture with Neanderthals. This is important because the authors above report that the dominant signal of admixture between “40 and 70 thousand years ago” didn’t contribute Neanderthal admixture. Additionally, there’s the symmetrical distance from Han and European, which means that the gene-flow predates that divergence. Europeans have some Basal Eurasian admixture, so the symmetry might imply that this admixture is even basal to the Basal Eurasians (a Lazaridis et al. preprint suggests that there might be such a thing), though I’m not sure they have the statistical power to ascertain this. Rather, whatever this back-migration was, it probably doesn’t extend to a population beyond the Near East, and, it was probably just a bit before the massive “Out of Africa” break that happened ~55,000 years ago and is synchronous with Neanderthal admixture that we currently detect.

There are some things to reflect on in light of these data. First, crazy ideas sometimes are true. Reading Dienekes’ 2005 post today is not that exciting. It is quite plausible, perhaps right even. But in 2005 it seemed crazy. The “dogma” of a tree-like phylogeny and explosive “Out-of-Africa” event all over the world was pretty strong then. It was a robust prior and hard to entertain alternative models. But science advances, so here we are.

Second, terms like “Eurasian” and “African” do a little too much work. The ancestral lineages that we are thinking of here may not have been geographically where we assume using the geographical term. There is a good amount of evidence that the ancestors of the non-African lineage went through a protracted bottleneck. But we don’t know where this bottleneck occurred. We call it “non-African,” but perhaps the bottleneck occurred in Kenya? We don’t know. The bottleneck includes Basal Eurasians, so it predated Neanderthal admixture, and the massive radiation ~55-60,000 years ago. The most likely region is probably the Levant and Arabia. Sub-Saharan Africa seems to be lacking the geographic barriers such as a mega-desert or bodies to water to sustain barriers to gene-flow for thousands of years. But “most likely” does not mean overwhelmingly likely.

Preprints like the one above fill in a lot of general dynamics, but I think ancient DNA is going to be necessary to nail down the model tightly.

What can we expect? Honestly, we don’t know, but here is my general sense of what ancient DNA + better methods + more compute time (look at all the simulations!) + non-genetic information (paleontology, paleoclimate, paleo-everything) might tell us. Below is my best guess outline…

• Proto-modern humans diversified in Africa 100 to 200 thousand years ago.
• One branch related to eastern modern humans becomes isolated from other populations 75 to 100 thousand years ago
• This branch is ancestral “non-Africans.” They are probably located in the southern Near East
• But, in southeast Asia, there are other earlier expansions of modern human-related groups, which have mixed with local hominins
• The expansion of the primary non-African group means that most of the signal of earlier Asian “moderns” is gone, though perhaps some of them are responsible for the Denisovan and other archaic signals
• At the same time that the non-basal non-Africans are pushing east, the basal non-Africans are pushing west. The admixture between Basal Eurasians and African hunter-gatherers of various sorts results in the emergence of what we term Africans qua Africans. My working assumption is that the non-African ancestry in hunter-gatherer populations is due to continuous gene-flow from the primary synthetic groups
• Archaic admixture everywhere there were earlier human groups

As Iain Mathieson once said, the story of the last few hundred thousand years is the collapse of old structure.

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!

Add to that list a new paper, The nature of Neanderthal introgression revealed by 27,566 Icelandic genomes:

…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.

Meanwhile, ancient protein is marching onward. A new paper in Nature, The dental proteome of Homo antecessor:

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.

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.

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…