How biogeography will be more important in understanding human evolutionary history

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…


The complex origins of our species in Africa

The figure to the right illustrates a model that is put forward in a new paper, Recovering signals of ghost archaic introgression in African populations. This was originally a preprint, Recovering signals of ghost archaic introgression in African populations. So we’ve discussed the implications extensively. Carl Zimmer has covered the story in The New York Times, while Georbe Busby did so in The Conversation.

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.

This work seems more a question than an answer.


Neanderthal ancestry in Africa and West Eurasian gene flow

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!


All narratives are wrong, some are just less wrong

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 modern human back-sweep from Southeast Asia

The Insight is 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.


The Asian human species that we lost

A new paper, The GenomeAsia 100K Project enables genetic discoveries across Asia:

The underrepresentation of non-Europeans in human genetic studies so far has limited the diversity of individuals in genomic datasets and led to reduced medical relevance for a large proportion of the world’s population. Population-specific reference genome datasets as well as genome-wide association studies in diverse populations are needed to address this issue. Here we describe the pilot phase of the GenomeAsia 100K Project. This includes a whole-genome sequencing reference dataset from 1,739 individuals of 219 population groups and 64 countries across Asia. We catalogue genetic variation, population structure, disease associations and founder effects. We also explore the use of this dataset in imputation, to facilitate genetic studies in populations across Asia and worldwide.

This is a paper where you need to jump to the supplementary note. The really interesting thing about this paper is the Denisovan aspect. They had a lot of whole genomes of Asians. Large sample sizes and good coverage genome-wide.Here’s the relevant selection:

The high levels of Denisovan ancestry in Melanesians and the Aeta are consistent with an admixture event into a population that is ancestral to both…however, two lines of evidence suggest that the ancestors of the Aeta experienced a second Denisovan admixture event. First, multiple analyses found that the Aeta are genetically more similar to populations without appreciable Denisovan ancestry (for example, Igorot, Malay and Malay Negrito groups) than they are to Melanesians [Aeta are at least 25% Austronesian -Razib].his can be explained by more recent gene flow from other populations without Denisovan ancestry. However, such gene flow would reduce the levels of Denisovan admixture below that found in Melanesians. More directly, we find that putative Denisovan haplotypes that are unique to the Aeta (n = 962) are significantly longer than putative Denisovan haplotypes shared between Aeta and Papuans (n = 596, mean = 16.1 kb compared with mean = 14.1 kb, Mann–Whitney U-test, P ≪ 10−10), or putative Denisovan haplotypes unique to Papuans (n = 727, mean = 16.1 kb compared with mean = 14.9 kb, Mann–Whitney U-test, P ≪ 10−1,000)…supporting a scenario in which a second admixture event between the Aeta and Denisovans happened after the separation of the Aeta and Melanesians. Two distinct Denisovan admixture events are most consistent with Homo sapiens and Denisovans interacting within southeast Asia…making it likely that admixture occurred within Sundaland…or even farther east….

Longer haplotypes in the Aeta indicates that the Denisovan admixture unique to them happened later than the one that might be common or contemporaneous with the Papuans.

But that’s not the only interesting pattern. In the supplements, they have an estimate of Denisovan ancestry in various Asian populations, and some patterns jump out. As found in other work, Northeast Asians have Denisovan ancestry. In the 0.20-0.25% range. South Asians have a wider range, from 0.10%-0.30%. The Andamanese are above 0.3%, though not much over. Some of the Malaysian Negritos are on the 0.35%-0.40% range. West Asians, like Europeans, are basically at ~0%.

It seems likely that Northeast Asians obtain their Denisovan admixture from a population closely related to the Altai sample. Populations from southern Eurasia and Oceania, less so. But, now there is good evidence that the Aeta, and Phillippine Paleolithic populations in general, mixed with a Denisovan group later than the event that led to the high fraction in Oceanians. Finally, there is evidence that Papuans carry two mixture of events. One west of the Wallace Line, and another east of it. The eastern admixture is recent, possibly less than 20,000 years ago (though the authors in the linked paper suggest these are unadmixed, I think a modern population with a high load of Denisovan could be another option).

There is suggestive evidence across these papers of admixture with Denisovans in Northeast Asia, the Phillippines, and New Guinea (or at least Wallacea). And, evidence of admixture more generally across southern Eurasians.

Whereas a single Neanderthal admixture still a viable explanation for that hominin’s ancestry in modern humans, it seems very unlikely for the deeply diverged lineages which are termed “Denisovan.”


We don’t know much about deep East Asian paleogenetics

A comment below that captures my thoughts well:

The deeper I dig into the Tianyuan discussions posted online, the less I seem to understand… seriously, we NEED more samples from east Asia, specifically China to piece together the east Eurasian developments and to understand where Tianyuan fits in all of this. Is it even more divergent than Papuans and Onge? Is it somewhere between them and east Asians in a very broad term (this includes east, southeast Asians and native Americans) or is it in the broad east Asian ‘protomongoloid’ nest…. I have no clue at this point.

The reality is it is only in Europe do we have a really robust and well-supported graph of human population history over the last 40,000 years. Even in West Asia, there is some fuzziness (at least until the Reich group comes out with their West Asia paper, which has new samples according to Iosif Lazaridis), and what we know about South Asia is ancillary to what we know about West Asia and Europe (ergo, non-West Eurasian ancestry in South Asians gets thrown into a big bucket).

If you read papers about the Jomon one thing that seems clear is that there are lots of “basal” lineages in the past. It’s hard to place them robustly on a modern graph.  What this really reflects is that rapid demographic expansion in the Holocene of farming groups seems to have obscured a lot of the deep structure that had existed in the Pleistocene. The erratic results on the Jomon, the “Australo-Melanesian” ancestry in Amazonians, and the distribution of Y haplogroup D is all part of this bigger puzzle.

D is found at high frequency among Japanese, some Siberians, Tibetans, and Andamanese natives. To me, this isn’t due to close relationships, but the fact that these groups relate somehow to the near polytomic diversification of “East Eurasian” lineages ~45,000 years ago. Oceanian people are clearly part of this, and some ancient Southeast Asian people seem to be closer to Oceanian people than Northeast Asians. This is not surprising seeing as Oceanians almost certainly derive from ancient Southeast Asians (or, that that was the last bifurcation).

Finally, there’s the issue with “Denisovans.” The most likely hypothesis to me is that this was a highly divergent group of human populations, which occupied a much more ecologically diverse territory than Neanderthals. And, unlike Neanderthals, they were not genetically homogeneous, as southern “Denisovans” had larger population sizes and did not suffer periodic extinctions in the meta-population.


Answers to questions we don’t need to answer about human origins

For many years I have been arguing that there isn’t a specific genetic variant associated with “modern humanity.” If most selection is on standing variation in the form of soft sweeps, then what distinguishes our “modern” lineage from older hominin lineages which flourished 200,000 years ago is more a matter of degree than kind. The reason that our lineage, which we label “modern humans,” has ancestry from various “archaic” lineages is that they were recognizable as human too. And, their genetic differences were not that great from us.

If Denisovans and Neanderthals were discovered in a remote part of the Altai today, they would be given human rights, not put in a zoo.

Of course, how we understand the emergence of what we term modern humans, the mode and tempo of the population substructure that we see across our species, has evolved over the past generation. It is no surprise to anyone who reads this weblog that ancient DNA helped reshape our understanding. But, it has to be said that some of the proponents of multi-regionalism in the late 20th-century were not entirely wrong in the process, even if they were very wrong in the nature of the phenomenon over the last 50,000 years.

The old debate between the multi-regionalists and proponents of “out of Africa” was framed in part as one between continuity and rupture. As it happens, the “out of Africa” model got something big right insofar as 50,000 years ago there was a massive expansion from a small founding population which contributes to the overwhelming majority of the ancestry of all living hominins. A subset of anatomically modern humans.

There is an important nuance here in that outside of Africa the vast majority of ancestry derives from a small founding population. Within Africa, the ancestry is more complex. Some groups, like the San Bushmen of the Kalahari, have strands of ancestry which diverged from other human lineages on the order of 200,000 years ago. Other Sub-Saharan African groups are closer to non-Africans, possibly due to admixture (gene flow between Africa and non-Africa in either direction) or ancient population structure (i.e., the pro-non-African group was more closely related to some proto-African groups than others).

A punctuated demographic origin for non-African humanity makes some sense. But it is less clear it makes sense within Africa, especially before the Holocene, when agricultural and pastoral populations expanded across most of the continent, marginalizing the hunter-gatherer populations. This is why “African multi-regionalism” is a thing. With very little ancient DNA to go on and researchers unsure about the inferences one can make into deep time from modern variation, genetics can’t easily adjudicate the “original homeland.” And now, neither can archaeology.

The remaining African hunter-gatherers, in particular, the San Bushmen, exhibit evidence in their DNA that they did not undergo a significant period of being within a very small breeding population, as can be seen in the case of all non-Africans, and to a lesser extent in agricultural Africans. This is not to say that 150,000 years ago most of the people alive on earth were San Bushmen. Not only were there Neanderthals and Denisovans, but there were many other African populations. Unlike the ancestors of most modern humans the ancestors of the San Bushmen did not experience a near-extinction event during the Pleistocene, nor did they undergo a transition to agriculture, which favored a few “early adopters” at the expanse of most humans.

Such a complex landscape and model has many lacunae, which ancient DNA is attempting to fill. There are obvious technical limitations (Africa is hot, and it isn’t as if > 100,000-year-old remains are copious even in cold Eurasia).

But let’s go forward and backward in time for a moment. In 2006 a paper was published, Genetic evidence for complex speciation of humans and chimpanzees, which argued that the emergence of our human (hominin) lineage was subject to periods of reciprocal gene flow with the ancestors of chimpanzees. Though this thesis is still somewhat controversial, that is due to the arguments around the limitations of the resolution of statistical genetic power, not the idea of “complex speciation.” Second, we now know that the genetic characteristics which are clear and evident in modern samples as “European” have a relatively late Holocene origin, threaded together from very distinct ancestral populations.

What both of these phenomena have in common is admixture, reticulation, and an “edge” in the abstract, rather than a “tree.”

The “out of Africa” model ascendent in public imagination, and to a lesser extent among human evolutionary biologists (yes, I am aware that there were savvy geneticists who were always skeptical of some details), presented a simple model of a diversifying tree of modern humans expanding across the world. In contrast, multi-regionalists posited deep regional continuities, with the human species tied together through gene flow. It turns out that multi-regionalism was wrong in suggesting that as a null hypothesis we should assume continuity. Turnover is common. Ubiquitous even. But, “out of Africa” made us dismiss the importance of admixture.

The admixture with deeply diverged lineages, such as Neanderthals and Denisovans, did happen. But arguably even more important has been admixture between more closely related lineages. This is how West Africans, Europeans, West Asians, and South Asians came about, through the admixture of lineages which have diverged only in the last 20,000 to 200,000 years.

All this is to set the stage for the reaction to this paper in Nature, Human origins in a southern African palaeo-wetland and first migrations:

Anatomically modern humans originated in Africa around 200 thousand years ago (ka)1,2,3,4. Although some of the oldest skeletal remains suggest an eastern African origin2, southern Africa is home to contemporary populations that represent the earliest branch of human genetic phylogeny5,6. Here we generate, to our knowledge, the largest resource for the poorly represented and deepest-rooting maternal L0 mitochondrial DNA branch (198 new mitogenomes for a total of 1,217 mitogenomes) from contemporary southern Africans and show the geographical isolation of L0d1’2, L0k and L0g KhoeSan descendants south of the Zambezi river in Africa. By establishing mitogenomic timelines, frequencies and dispersals, we show that the L0 lineage emerged within the residual Makgadikgadi–Okavango palaeo-wetland of southern Africa7, approximately 200 ka (95% confidence interval, 240–165 ka). Genetic divergence points to a sustained 70,000-year-long existence of the L0 lineage before an out-of-homeland northeast–southwest dispersal between 130 and 110 ka. Palaeo-climate proxy and model data suggest that increased humidity opened green corridors, first to the northeast then to the southwest. Subsequent drying of the homeland corresponds to sustained effective population size (L0k), whereas wet–dry cycles and probable adaptation to marine foraging allowed the southwestern migrants to achieve population growth (L0d1’2), as supported by extensive south-coastal archaeological evidence8,9,10. Taken together, we propose a southern African origin of anatomically modern humans with sustained homeland occupation before the first migrations of people that appear to have been driven by regional climate changes.

Ed Yong reports on some of the negative comments, as well as the defenses from the authors themselves. Twitter pretty much exploded.

In light of what I have stated above, a paper like this answers questions that are not really asked because they are not seen as relevant. The question of the “original home” of “modern humans” within Africa is not totally a sensical query in light of what we know now (i.e., the likely polycentric character of anatomically modern humans within Africa). What this paper likely discovered, with the deeply diverged branches of mtDNA haplogroup L0, is to confirm that the San Bushmen of southern Africa have a unique history in comparison to other modern humans. It’s not that they are particularly ancient. They aren’t. It’s that they did not undergo the demographic trauma of the Pleistocene that left its mark in the genomes of non-Africans, and they are not predominantly descended from a small group of founding populations which underwent rapid expansion due to adoption of agriculture and pastoralism.

I believe that this paper would have benefited greatly from being a preprint first because the feedback would have been immediate. The reviewers that Nature selected also clearly were either not skeptical or aware of the literature in human evolutionary genetics because there would have been some immediate comments that they should have made (I suppose the editor could have overruled them). Because of the high visibility in Nature and the claims, you have pieces like this on the BBC now: Origin of modern humans ‘traced to Botswana’.

At this point I think most researchers in this field would say that such an assertion is “not even wrong.”


Late Denisovan admixture?

From A method for genome-wide genealogy estimation for thousands of samples, this section jumped out at me:

In the East and South Asian groups, the data suggest a very recent arrival of Denisovan DNA (mainly <15,000 YBP). In non-Africans, Neanderthal sharing remains high for branches with lower-end age younger than ~30,000 YBP. These dates are only lower bounds on the introgression time, and an accurate arrival date of Neanderthal DNA would require estimating a joint genealogy that requires further work….

Comparing YRI, GBR, BEB (Bengali in Bangladesh) and CHB to expectations under panmixia, we observe a strong excess of mutations on deep branches with lower coalescence age <40,000 YBP in all cases, which is almost entirely explained by Neanderthals/Denisovans in the non-African populations, but not in YRI (Fig. 4d, Methods). In panmictic simulations with matched population size histories, we observed no such excess (Supplementary Fig. 6). This gives evidence for ancient but uncharacterized population structure within Africa, as suggested elsewhere…Figure 4b shows one example consistent with an introgression event in YRI, not involving a closely relative of Neanderthals.

The inference of deep structure within Africa is not a great surprise. But note that their estimate for Denisovan admixture is that on the whole, it could be half as old as Neanderthal admixture. I don’t put much stock in the specific estimate of the date, but rather the relative time.


The vines around the tree trunks

A lot of the understanding of scientific theories and models in the public domain is communicated by evocative metaphors and turns of phrase. For example, Charles Darwin famously wrote:

It is interesting to contemplate a tangled bank, clothed with many plants of many kinds, with birds singing on the bushes, with various insects flitting about, and with worms crawling through the damp earth, and to reflect that these elaborately constructed forms, so different from each other, and dependent upon each other in so complex a manner, have all been produced by laws acting around us….

When it comes to understanding the origin of our own species and the broader human lineage over the past two million years, I’ve started to come to a mental model of a weighted-graph with edges. Some of the edges traverse time and have strong weights. These are analogous to the normal phylogenetic tree model, representing phyletic gradualism and anagenesis along each branch before some bifurcation event. But, some of the edges move horizontally between others. These represent migration and/or gene flow between the primary lineages.

I’m not sure though that a graph theory derived mental model helps many people, so I’ll use another one: imagine large trunks defining the primary lineages, and vines tying them together representing gene flow events. The above figure is from a new preprint, Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph. This is a methods-heavy preprint. It utilizes an “ancestral recombination graph” (so a model of the genealogy of genes in the genome) and MCMC generate Bayesian probabilities of particular events (e.g., introgression of a lineage that diverged x years ago at fraction y).

The abstract presents some specific findings:

…While much attention has been paid to the relatively recent gene flow from Neanderthals and Denisovans into modern humans, other instances of introgression leave more subtle genomic evidence and have received less attention. Here, we present an extended version of the ARGweaver algorithm, ARGweaver-D, which can infer local genetic relationships under a user-defined demographic model that includes population splits and migration events. This Bayesian algorithm probabilistically samples ancestral recombination graphs (ARGs) that specify not only tree topology and branch lengths along the genome, but also indicate migrant lineages…We show that this method is well powered to detect the archaic migration into modern humans, even with only a few samples…We apply it to human, Neanderthal, and Denisovan genomes, looking for signatures of older proposed migration events, including ancient humans into Neanderthal, and unknown archaic hominins into Denisovans. We identify 3% of the Neanderthal genome that is putatively introgressed from ancient humans, and estimate that the gene flow occurred between 200-300kya. We find no convincing evidence that negative selection acted against these regions. We also identify 1% of the Denisovan genome which was likely introgressed from an unsequenced hominin ancestor, and note that 15% of these regions have been passed on to modern humans through subsequent gene flow.

ARGweaver-D is gnarly. Not in a bad way. But you should never really trust computational wizard of this sort unless you’ve taken it for a test drive, or it’s been around decades and people have validated it. A “play with the parameters” phase is necessary for these packages to become more than magic.

That being said, for about half a decade people have been detecting evidence of a “super-archaic” lineage within Denisovans. This is just another confirmation with another method. The super-archaic hypothesis seems plausible as an explanation of the patterns in the data (there may be other explanations). Second, there’s a lot of circumstantial evidence for gene flow into Neanderthals from moderns. E.g., mtDNA replacement in Neanderthals. Though not in the abstract, the preprint mentions the likelihood of “super-archaic” introgression into Neanderthals as well. From a recent ancient DNA paper on Nuclear DNA from two early Neandertals reveals 80,000 years of genetic continuity in Europe:

We find that population split times between HST and other Neandertals of less than 150 ka ago make the occurrence of a mitochondrial time to the most recent common ancestor (TMRCA) of 270 ka ago unlikely (1.2% of all simulated loci have such a deep TMRCA; note S11). We note that this result is robust to uncertainties in the estimates of the Neandertal population size and of the mitochondrial TMRCA (note S11). The presence of this deeply divergent mtDNA in HST thus suggests a more complex scenario in which HST carries some ancestry from a genetically distant population.

It seems entirely likely that we’re going to see “shadows of forgotten ancestors” in our genomes. But wait, there’s more!

…ARGweaver-D only detected a small amount of Sup→Afr introgression, which was somewhat lower than our estimated false positive rate. One aspect to note here is that the power to identify introgression from an unsequenced population is highly dependent on the population size of the recipient population. The larger the population, the deeper the coalescences are within that population, making it more difficult to discern which long branches might be explained by super-archaic introgression…If we had used a smaller population size, ARGweaver-D would have produced more Sup→Afr predictions, but most of these would be false positives unless that smaller population size is closer to the truth. Overall, we caution that the problem of detecting super-archaic introgression into a large and structured population such as Africas is very difficult and that claims of such introgression need to be robust to the demographic model used in analysis. It may not be possible to address the question of ancient introgression into Africans without directly sequencing fossils from the introgressing population.

In northern Eurasia, in particular, one might imagine a scenario with large fluctuations in population size, and patchy landscapes. This would reduce gene flow between populations, and also foster drift to produce distinct lineages. Simple stylized models of gene flow at particular times across disparate lineages makes a great deal of sense in this context. But if Africa had larger populations of humans, with more interconnected networks with continuous, if variable, levels of gene flow then the stylized models will mislead in important features.

This preprint is likely reporting some true robust results that will hold up. But I think the bigger picture is that it will lead us toward moving beyond the extremely simple models in vogue a generation ago, to a more subtle understanding of complex emergence and collapse of human population structure over the last two million years.