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March 3, 2019

Very ancient ghosts in the African genome

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

Here is the abstract:

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

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

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

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

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

Within the supplements, the authors are quite modest that many elements of their model are likely to be wrong. The bigger picture though is that they believe they are capturing some general dynamics. It seems rather clear from multiple lines of evidence in the preprint, as well as earlier work, that there are strong suggestions of very deep structure within Africa that assimilated into an expanding modern human population. They actually tested for a scenario of continuous gene flow, and a rapid pulse admixture of the 2-19% is a better fit to the data.

Additionally, there are peculiarities which they haven’t resolved in their results. The Luhya gives really bizarre numbers, and the authors don’t have a good explanation for it. It could be a problem with their model specification in some deep way, or, the history of East Africa (the Luhya are a Bantu group who mixed with East Africans) is more complicated than we may have understood.

They also did some cool things identifying possible introgressed segments. Their methods seem to agree on the regions, and with older literature which had earlier identified these as targets for introgression. Finally, there was also some validation of the finding that West Africans may have some “Basal modern human.” That is, the modern human lineage that split off first from everyone else.

As the coverage of populations and the number of genome sequences in Africa increases, we will probably get more resolution. I do wonder at how computationally intensive some of this work is, and how many moving parts there are. Replicating this work is doable, as all the code is provided, but it would take time.

In general, these results align with most of my priors, so I am pretty confident they’ve grasped onto a thread of reality here. I would, wouldn’t I? Basically, ~50,000 years ago there was a massive expansion of a core modern human lineage which absorbed other human groups as it expanded outward. Though the easiest explanation is that it was one group, the Holocene agricultural expansion should tell us that sometimes differently related groups in close proximity can undergo the sample cultural revolution and expand in different directions.

Note: It is clear “super-deep” lineages admixing is going to be the next big thing. See Alan Rogers recent work.

February 24, 2019

A more complex tree of recent human origins

Filed under: Human Evolution — Razib Khan @ 7:11 pm

Sometimes charts are useful. The above plot does not have branch lengths which are proportional to length. But, they capture I think the rough topology. I’ve also put notes on there.

Some of the branches are certainly wrong. We’ll know more in the next few years.

February 21, 2019

Reevaluating “multiple origins” for modern humans

Filed under: Human Evolution — Razib Khan @ 3:28 pm

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

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

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

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

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

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

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

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

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

February 19, 2019

Arabia between Africa & Eurasia

Filed under: Evolution,Genetics,Human Evolution,science — Razib Khan @ 1:57 am

Arabia between Africa and Eurasia

Shanidar cave in Iraq, once occupied by Neanderthals

For hundreds of thousands of years Neanderthals and the ancestors of modern humans interacted in the broad zone of territory we now call the “Middle East.” Neanderthals occupied sites across the Fertile Crescent, while Arabia and parts further north were settled on and off by people related to and possibly ancestral to modern humans. Before the expansion of our ancestors across Eurasia, and into Oceania, 50,000 years ago, a situation of dynamic equilibrium persisted as the Near East existed as an ecozone in flux between that of northern Eurasia and northern Africa. Between Neanderthal and modern human.

Though there is no doubt that Africa is the great reservoir for the vast majority of human ancestry today, by dint of their locations Arabia and the Fertile Crescent are essential pieces of the broader jigsaw puzzle of the human story. Modern humans either migrated north through the Sinai from Africa. Or, they crossed the straits that divide modern Yemen from Africa on the southern edge of the Red Sea. Of course, they could have done both!

But as modern humans were pushing north and east, this region was long occupied by Neanderthals. Today we know that all non-Africans carry Neanderthal ancestry. One of the simplest explanations for this is that the admixture occurred in the Middle East, as modern humans came into contact with their cousins. As they migrated onward, north and east, they did not mix so much with the Eurasian hominins that lived in those regions.

The problem with this theory is that different methods of analysis have shown that Neanderthal ancestry varies across many populations, even when you remove African ancestry from the equation. In short, many assessments conclude that East Asians have more Neanderthal ancestry than Europeans, who have more Neanderthal ancestry than people in the Middle East.

Why could this be? One of the most popular explanations is that East Asians have had more mixture with Neanderthal-like populations. That is, there was a later mixture event. Meanwhile, people in the Fertile Crescent and Arabia mixed with people who were not African but split from other “Out of Africa” populations before the admixture with Neanderthals. These people are awkwardly called “Basal Eurasians,” meaning they split off before the other groups diversified into all the lineages from Europe to Australia.

But new research suggests another possibility: all Africans may have ancestry from “West Eurasian” populations which moved back into Africa after the “Out of Africa” event ~50,000 years ago. For statistical reasons beyond the purview of this post, this affinity between West Eurasians and Africans may lead to incorrect estimates of Neanderthal ancestry varying across Eurasian groups, when in fact it is simply affinity to Africans which varies across groups. West Eurasians and Africans are simply genetically more similar than East Eurasians and Africans.

More work needs to be done about who these West Eurasians were. But, keep in mind that Arabians and Levantines do show less Neanderthal ancestry in the older framework than even Europeans, implying that the “West Eurasians” were likely from the Near East, which is the most reasonable scenario geographically in any case for a “back migration” to Africa.

Though it is certainly true that “we are all Africans” under the skin, least within the last 50,000 years, in some sense all Africans may be a bit Arabian….

Interested in learning where your ancestors came from? Check out Regional Ancestry by Insitome to discover various regional migration stories and more!

Arabia between Africa & Eurasia was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

February 16, 2019

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

Filed under: Europe,Human Evolution,Human Population Genetics,Paleolithic — Razib Khan @ 11:45 pm
Now things are coming into focus. Population dynamics and socio-spatial organization of the Aurignacian: Scalable quantitative demographic data for western and central Europe: Demographic estimates are presented for the Aurignacian techno-complex (~42,000 to 33,000 y calBP) and discussed in the context of socio-spatial organization of hunter-gatherer populations. Results of the analytical approach applied estimate a […]

January 16, 2019

How your Neanderthal functions in the human genome

Filed under: Human Evolution,Neanderthals,science,Selection — Razib Khan @ 2:28 pm

What does it mean that you have Neanderthal ancestry? Everyone agrees now that that ancestry exists, but does it make you any different from what you’d be otherwise? From a scientific perspective, one might ask what the function of Neanderthal genetic variants are. What do they do in your body?

The truth is that they do many things. The human genome has many genes. About 20,000. Across those genes, there are ~3 billion base-pairs. A, C, G, and T. The best estimate if you are not African is that there is a 1–2% chance that a base is from a Neanderthal ancestry. Modern humans don’t have the same 1–2%, so around 30% of the Neanderthal genome can be reconstructed from living people alone!

For many years researchers have examined patterns of Neanderthal admixture within the genome, and over time (looking at ancient DNA). Because the ancestors of Neanderthals separated from modern humans 700–900 thousand years ago, there are some genetic incompatibilities, and Neanderthal variants are likely to be selected against. The most recent research, though not the final word, indicates that much of this selection happened very early on.

In other words, most of the very incompatible Neanderthal variants were removed from the human genome within ~10,000 years of the admixture.

But within the genome, there are differences as to where Neanderthal genes are found. Early work indicated that Neanderthal ancestry was overrepresented in the vast majority of the genome that does not code for proteins (“junk DNA”). This was suggestive of the likely that Neanderthal ancestry was usually bad when it coded for proteins.

Today a closer look, as implied in the figure the left, suggest that selection against Neanderthal variants was less about protein coding, and more about regulation. Though the human genome has only about 20,000 genes, how those genes are expressed in tissues, and how they are expressed, plays an essential role in differentiating us from other mammals. This is why the vast majority of our genome can be similar to a chimpanzee, or a Neanderthal, and yet modern humans are creatures very different.

It may turn out that our unique Neanderthal ancestry may play a greater role in rearranging how genes express themselves more than anything else.

Discover your Neanderthal story today!

How your Neanderthal functions in the human genome was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

December 12, 2018

Most of human history was in Africa

Filed under: Africa,Genetics,Human Evolution,science — Razib Khan @ 12:31 am
Citation: Scerri, Eleanor ML, et al. “Did our species evolve in subdivided populations across Africa, and why does it matter?.” Trends in ecology & evolution (2018).

Over the last generation our understanding of the origin of what we term “modern humans” has undergone two revolutions. Or, perhaps more precisely, a revolution was won, and an evolution overturning much of the revolutionary orthodoxy is now occurring.

Starting with the emergence of “mitochondrial Eve” in the 1980s, and moving to with genome-wide analysis in subsequent decades, a certain narrative emerged that modern humans, Homo sapiens, evolved in a small region of East Africa ~60,000 years ago, and spread rapidly across the whole world. In the process, they replaced “archaic human” populations, the most famous of which were the Neanderthals. It was a “human revolution,” with some paleoanthropologists giving credit to our species’ special genius, perhaps even the invention of language.


Though there were those who disagreed, the dominant view that Neanderthals and our other human cousins were genetic dead-ends was so strong that it suffused many different fields. This changed in 2010, as the Neanderthal genome revealed that people outside of Africa seem to have had Neanderthal ancestry. A different genome from another human population called Denisovans, yielded the finding that Oceanians, and to a far lesser extent East and South Asians, have ancestry from this group of ancient humans.

The total replacement idea has now fallen by the wayside. But what about the idea that the dominant component of modern human ancestry expanded from East Africa 60,000 years ago? For several decades the Omo Kibish fossil from Ethiopia highlighted that the origins of modern humans were likely far older. Dated to 195,000 years ago, this individual was anatomically modern. The skull looks like that of contemporary peoples.

Omo reconstruction

A different argument was that “behavioral modernity” arose 40,000 years ago. Even if the physical characteristics we associated with modern humans were present earlier. The problem with this line of thought is that it seems that Neanderthals and Africans were engaging behavior we would define as “behaviorally modern” before 40,000 years ago. It could simply be that behavioral modernity was a quantitative change in the rate of cultural evolution.

Not only that, but a very early “proto-modern” human skull has now been found in Northwest Africa, in Morocco. One of the lynchpins for the East African origin of modern humanity was the antiquity of Omo Kibish, but the Jebel Irhoud remain dates to over 300,000 years ago! With a melange of modern and non-modern features, though this individual cannot be defined as strictly anatomically modern, it seems that a population proceeding in that direction flourished during this time in the north of the African continent.

San tribesman

The data from genetics has complicated our understanding of the origins of modern humans within Africa as well. Groups such as the San of southern Africa do not seem to have the same evidence of a rapid population expansion from a tight bottleneck as non-African populations. And even within Africa, the San maintained a relatively large population size over tens of thousands of years. The latest work suggests that they diverged from other modern populations at least 200,000 years ago.

All this points to the fact that though the story of modern human expansion from the edge of the Middle East ~60,000 years ago, into all of Eurasia, and then Oceania and finally New World, is one of explosive growth from a small founder group, and then some assimilation of Neanderthals and Denisovans. The emergence of modern humans in Africa is more complex. The story is not neat and tidy, and currently unfinished. Using genome analysis from a wide array of populations, modern geneticists are now uncovering evidence of “deep structure” within Africa.

Instead of a relatively recent explosion of humanity, the emergence of the modern lineage that we see around us today for most of its history seems to have been a more gradual affair, defined by the interconnection of populations with multiple geographical nodes. It may not “even be wrong” to assert that there was a particular region from which the dominant modern human lineage arose within Africa. If one takes the divergence of the Bushmen 200,000 years ago as a floor for the emergence and diversification of our lineage, then 70% of the time down to the present consisted of a purely African set of populations.

And, as modern humans spread out across Africa, it seems that just as in Eurasia, our ancestors interacted with cousin lineages of humans. Without ancient DNA there will be no smoking gun, but the circumstantial evidence is highly suggestive, and points in the direction of local admixture within the continent. The expansion out of Africa then may simply have recapitulated ancient patterns within our species.

Maybe you have some Neanderthal or Denisovan in your DNA. Discover your story today with Neanderthal by Insitome.

Most of human history was in Africa was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

October 23, 2018

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

Filed under: Human Evolution — Razib Khan @ 10:33 pm

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

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

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

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

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

August 3, 2018

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

Filed under: FOXP2,Human Evolution — Razib Khan @ 12:34 am

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

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

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

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

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

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

July 17, 2018

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

Filed under: Human Evolution,Multi-regionalism — Razib Khan @ 7:13 am

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

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

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

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

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

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

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

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

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

May 20, 2018

Beyond “Out of Africa” within Africa

Filed under: Human Evolution,Population genomics — Razib Khan @ 11:36 pm

It looks as if the vast majority (95% or more depending on the population) of the ancestry of non-African humans derives from a population expansion which began around ~60,000 years ago. Before this period some researchers argue there was a non-trivial period of isolation. The “long bottleneck” (David Reich alludes to this in Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past). For the vast majority of humans then the last 60,000 years is characterized by a branching process, some reticulation (e.g., South Asians merge West and East Eurasian lineages) between these branches from a common ancestor, as well as introgression from archaic lineages like Neanderthals and Denisovans.

Though I do accept that it seems that modern humans probably migrated out of Africa before 60,000 years ago, mostly due to the results from archaeology, I think the genetic evidence is strong that these groups contributed very little genetically to contemporary populations.

The situation within Africa is very different. Being conservative it seems likely that the Khoisan ancestral lineage diverged from some other Africans ~200,000 years ago. I say conservative because there are researchers who want to push the divergence much further back. Additionally, several different research groups are now converging in a result that West Africans are a mixture between eastern Sub-Saharan Africans (think the population ancestral to Mota in Ethiopia) and a lineage basal to all other humans. That means that the Khoisan are not the most basal, so even assuming the conservative 200,000 year divergence point for Khoisan, modern humans share a common ancestor earlier than 200,000 years ago.

The upshot here is that around 75 percent of the history of modern humans is within (greater)* Africa. The distinctive “Out of Africa” bottleneck and expansion defines most humans only in the last 25 percent of the history of our species. And, within Africa, the dynamics were very different. The biggest difference is that African populations are not defined by a large number of lineages emerging and diverging around the same period, because there wasn’t a massive and singular expansion within Africa analogous to what occurred outside of Africa (at least until the recent past, with the Bantu expansion). That’s why there’s deep structure within Africa today between groups as divergent as the Bantu, Mbuti, Hadza, and Khoisan.

The term “Basal Eurasian” kind of makes sense in the non-African context because of the singular importance of divergence between lineages in the first 10,000 years or so after the “Out of Africa” event. I’m not sure “Basal human” makes as much sense because there wasn’t a singular event within Africa that allowed for the emergence of modern humans. Rather, it was a process, and probably quite resembles something like multiregionalism.

* Some wiggle room here for the likelihood that modern humans were long present in the liminal Near East.

Beyond “Out of Africa” within Africa

Filed under: Human Evolution,Population genomics,Uncategorized — Razib Khan @ 11:36 pm

It looks as if the vast majority (95% or more depending on the population) of the ancestry of non-African humans derives from a population expansion which began around ~60,000 years ago. Before this period some researchers argue there was a non-trivial period of isolation. The “long bottleneck” (David Reich alludes to this in Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past). For the vast majority of humans then the last 60,000 years is characterized by a branching process, some reticulation (e.g., South Asians merge West and East Eurasian lineages) between these branches from a common ancestor, as well as introgression from archaic lineages like Neanderthals and Denisovans.

Though I do accept that it seems that modern humans probably migrated out of Africa before 60,000 years ago, mostly due to the results from archaeology, I think the genetic evidence is strong that these groups contributed very little genetically to contemporary populations.

The situation within Africa is very different. Being conservative it seems likely that the Khoisan ancestral lineage diverged from some other Africans ~200,000 years ago. I say conservative because there are researchers who want to push the divergence much further back. Additionally, several different research groups are now converging in a result that West Africans are a mixture between eastern Sub-Saharan Africans (think the population ancestral to Mota in Ethiopia) and a lineage basal to all other humans. That means that the Khoisan are not the most basal, so even assuming the conservative 200,000 year divergence point for Khoisan, modern humans share a common ancestor earlier than 200,000 years ago.

The upshot here is that around 75 percent of the history of modern humans is within (greater)* Africa. The distinctive “Out of Africa” bottleneck and expansion defines most humans only in the last 25 percent of the history of our species. And, within Africa, the dynamics were very different. The biggest difference is that African populations are not defined by a large number of lineages emerging and diverging around the same period, because there wasn’t a massive and singular expansion within Africa analogous to what occurred outside of Africa (at least until the recent past, with the Bantu expansion). That’s why there’s deep structure within Africa today between groups as divergent as the Bantu, Mbuti, Hadza, and Khoisan.

The term “Basal Eurasian” kind of makes sense in the non-African context because of the singular importance of divergence between lineages in the first 10,000 years or so after the “Out of Africa” event. I’m not sure “Basal human” makes as much sense because there wasn’t a singular event within Africa that allowed for the emergence of modern humans. Rather, it was a process, and probably quite resembles something like multiregionalism.

* Some wiggle room here for the likelihood that modern humans were long present in the liminal Near East.

April 26, 2018

The Ancient Neanderthal Mariner

Filed under: Human Evolution,Human Population Genetics — Razib Khan @ 10:35 pm

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

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

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

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

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

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

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

April 18, 2018

The braided estuary of human evolution

Filed under: Genetics,Human Evolution,paleontology,science — Razib Khan @ 2:22 pm

Metaphors matter because they evoke images, and images are often one of the best ways to understand something in a deep fashion. Consider Charles Darwin’s musing:

“It is interesting to contemplate a tangled bank…

He brought something memorable and familiar to make evocative the dynamics at play in his novel theory of evolutionary change through natural selection. The tangled bank has haunted us for over 150 years, though as a friendly apparition to be sure.

Other metaphors are less useful, and even downright destructive. The great chain of being hooks into deep human intuitions about our “special” place in nature and centrality in the universe. “Previously made in the image of our Creator” in the 19th century, science confirmed peoples’ expectations that modern humans are the pinnacle of evolution and the end of a long process of change; from the slouching ape, to the shuffling caveman, and finally, to the upright and thinking man.

The earlier view of Neanderthals was typical and illustrative of where we once were. Originally relegated to a primitive dead-end of our family tree, Neanderthals were depicted as bestial half-men at best. As late as the 2000s many researchers, such as the influential paleoanthropologist Richard Klein, doubted that humans and Neanderthals could produce offspring. There was skepticism from these quarters that Neanderthals could speak, or that they even used fire!

With the confirmation through myriad genetic analyses published from 2010 onward that in fact humans outside of Africa carry 1–2% Neanderthal ancestry, a transformation occurred in our perceptions of our cousins…or rather, our ancestors.

Clearly our understanding of human evolution is conditioned by our cultural preconceptions, our biases. Evolutionary biologists have long warned of the tendency to see in the “tree of life” directionality or purpose, but in the public’s mind the purpose of the universe is manifested in our own lineage. All of the pitfalls that we’ve attempted to avoid when considering evolutionary biology became stark and endemic in the study of humanity.

Unfortunately, paleoanthropology often fed into this narrative because of the paucity of remains.There was very little data, and an empire of theory and supposition cropped up in its place. The prominence of superstar researchers and their associated singular remains, Raymond Dart and the Taung child, Richard Leakey and the Turkana boy, and Donald Johansen and Lucy, highlighted the almost artisanal quality of the field.

As a result of only a few individuals being able to analyze the material evidence for the evolution of our own species, we eventually assembled a relatively neat ascending tree, with a few stray side branches. Like modernist architecture, paleoanthropology constructed a spare and elegant scaffold within which to understand the emergence of what we call humanity. Our story was simple, singular, and implicitly progressive. All paths led to us.

But just as genetics has changed our understanding of the origins of our species, so paleoanthropology itself is undergoing a revolution of sorts because of the veritable flood of data. Remains.

At the end of 2013 I happened to have been present when Lee Berger, a South African paleoanthropologist, presented work that reported on a deep cave where copious remains of a new hominin, Homo naledi, were being assembled and analyzed. Whereas previous researchers often focused on fragments, or the skeleton of a single individual, Berger explain that many remains were to be found in the cave system. This was going to be statistically-sound science, because he had much more than one sample.

To assemble the team that was small and nimble enough to venture into the cave, he reached out to paleoanthropology researchers via social media. And once the data came in, he published it quickly, at the same time releasing the information to other researchers.

The implications for paleoanthropology as it was practiced were revolutionary in and of themselves, but the results were also ground-breaking. H. naledi stood at five feet or shorter. Their cranial capacities were 30% those of modern humans. Meanwhile, their skeletal features were an assemblage of characteristics which seemed both very modern or very ancient. A simple role in a simple story did not present itself.

H. naledi reconstruction

This hominin confounded expectations. If the sample was singular, no doubt there would be skeptics. But Berger had the numbers, so that could not be denied. When the dates came back there was also another shocker: H. naledi flourished a bit over ~200,000 years ago. The reality though is that species invariably are found after and before the datings of particular remains. H. naledi almost certainly occupied the same landscape as early modern humans, who were developing within Africa 200-300 thousand years ago.

Meanwhile, far to east, on the island of Flores, were the Hobbits — H. floresiensis, a diminutive hominin that flourished until modern humans arrived in the region more than 50,000 years ago.

H. floresiensis

The reason that naledi and the Hobbits are important is that they shatter our image of an ascending chain of evolution progressing from lower to higher. The reality that modern human have genes from ancient Eurasian hominins, such as Denisovans and Neanderthals, also refute a simple model whereby humans were born, they came, and they conquered. Humans were both the conquered and conqueror.

Hundreds of thousands of years ago our lineage was highly speciose, with many diverse branches. Modern genetic technology implies that human lineages branch and come back together again and again, like an eternal cycle. The proliferation of ancient remains that are startling in their novelty and shocking in their recency also suggests that the shift in human evolution from slouching, small-brained apes to tall, large-brained apes was not the only way to be human. After all, the largest-brained hominins of all were Neanderthals, who eventually merged back into the much more massive stream of African humans who are our primary forebears.

Maybe you have some Neanderthal or Denisovan in your DNA. Discover your story today with Neanderthal by Insitome.

The braided estuary of human evolution was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

April 16, 2018

What did modern humans look like during the “Out of Africa” event?

Recently I was having an email exchange with a friend (a prominent public intellectual who is not a scientist), and we were thinking about what “ancestral Africans” looked like. More precisely, the populations which were resident around ~100,000 to ~200,000 years before the present. These are the people who are depicted in paleoanthropology documentaries. Here were some of my major contentions:

1) We don’t know what they looked like
2) They probably were more likely to look like modern Africans than non-Africans
3) But modern Africans are diverse in their looks and we could expect that ancient Africans were too

The neighbor-joining tree above is generated with a naive model of successive bifurcation.

1) Khoisan split off 200,000 years ago
2) Mbuti split off 150,000 years ago
3) Mende split off 100,000 years ago
4) Japanese about 50,000 years ago
5) While Pathan and Basque only 15,000 years ago

The model is wrong in the details. Pathan and Basque have some ancestry is which recently diverged, and much that is deeply diverged. The 15,000 year value is just an average. Similarly, the Khoisan have some Eurasian ancestry. But in the broad sketch it illustrates that some African populations diverged a very long time ago from other groups.

Ancient Africans date to ~200,000 years before the present for all the modern populations. Khoisan to Japanese. You could probably use phylogenetic character reconstruction methods to attempt to infer what ancient Africans looked like…but I’m not sure that it would be useful since modern humans have spread over so many ecologies over such a short span of time.

Outside of Sub-Saharan Africa perhaps on the order of 95% of the ancestry derives from an expansion from a small founder group between 60 and 80 thousand years ago. Removing the “Basal Eurasian” component, groups as diverse as Native Americans, Oceanians and East Asians probably derive their ancestry from a common group which flourished between 50 and 60 thousand years ago (this pulse is the majority of the ancestry of Europeans and South and West Asians as well).

The point here is to illustrate that 50,000 years is definitely sufficient for a great deal of diversity to have emerged in human physical variation. And yet the Khoisan are ~200,000 years diverged from their ancestors within Africa. We actually know that indigenous southern Africans have been selected for lighter pigmentation. We also know that loci associated with pigmentation in modern humans exhibits a lot of variation in Africans, and this variation is likely an ancestral feature of our species.

In sum, the number of generations between ancestral Africans and all modern descendent populations is great enough that I’m not uncertain that we can predict what they look like in anything except their skeletal features. Additionally, most of the history of anatomically modern humans was likely highly structured within Africa. That’s another way of saying that ancient Africans themselves were probably physically diverse.

With all that being said, all things equal ancient Africans probably are more likely to look like modern Africans than modern non-Africans. The main reason is simply that modern Africans occupy the same broad ecological landscape as ancient Africans, and many of our features, from our build to our complexion seem dependent upon environmental pressures. There’s lot of evidence that very light skin is probably a derived characteristic of our species (there are consistent signatures of sweeps around pigmentation loci). And, there is also evidence that some of the archaic introgression into non-Africans may have consequences in our morphology and external physical characteristics. For example, Eurasians seem to have very high frequencies of Neanderthal variants of the keratin gene. This is implicated in hair, skin and nail development.

Addendum: Note that even if we have ancient genomes, polygenic characteristics are still hard to predict. Even today common SNPs only explain a minority of the variation in hair color in Europeans.

April 9, 2018

Arabia as Africa-across-the-sea

Filed under: Evolutionary Genomics,Human Evolution — Razib Khan @ 8:35 pm

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

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

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

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

The maximum range of Neanderthals


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

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

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

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

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

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

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

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

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

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

March 21, 2018

The Others were people too

Filed under: Genetics,Human Evolution,paleontology,science — Razib Khan @ 12:25 pm
Neanderthals, cousins we knew.

In 2010, our understanding of Neanderthals, our human cousins, changed forever. Before this year, there was a live debate about whether they were human at all, whether they had fully elaborated language, or even culture.

When A Draft Sequence of the Neanderthal Genome was published in Science, we found out that all humans outside of Africa, and some within Africa, had some ancestors who were Neanderthal. In the wake of this finding, a renaissance of Neanderthal humanization occurred. Previously, Neanderthals were just a ‘dead-end’ in our ancestral lineage.

Denisova Cave

In December of the same year, Nature published Genetic history of an archaic hominin group from Denisova Cave in Siberia. While Neanderthals had been part of our cultural landscape for over 150 years, these hominins discovered in Denisova cave were a shot out of the dark. Debates about Neanderthals’ humanity raged for years, and this discovery certainly promoted more.

Called Denisovans, after the Siberian cave they were discovered in, what we know about these mysterious people comes from only a few bones and teeth.

The Denisovans were a total surprise scientifically. The result was not answering any questions because there was no foreknowledge of them. It turned out that about 5 percent of the ancestry of people in places like Papua New Guinea came down from the Denisovans!

Later work, which looked far more closely at mainland populations, showed that there were traces of Denisovan ancestry across the whole of South, Southeast, and East Asia — as well as into the New World. All these populations presumably descend from an African migration which swept east until it reached the Pacific, and then north and south. While Papuans had about 5 percent Denisovan ancestry, these groups had less: 0.1% to 0.5%.

Oddly, the only evidence we have for the Denisovans is in Siberia, but the greatest proportion of their ancestry is found beyond Wallace’s Line, in Oceania. It is very likely then that the Denisovan sequence from Siberia is from a particular population, and this species ranged far and wide across eastern Eurasia — just as Neanderthals did to the west.

A new paper in Cell, Analysis of Human Sequence Data Reveals Two Pulses of Archaic Denisovan Admixture, adds a further twist by reporting that there were two interbreeding events with Denisovans. One group of Denisovans contributed to Papuans, Southeast Asians, South Asians, and some of the ancestry of East Asians. It turn out, however, that another group contributed ancestry only to East Asians — up to half the Denisovan ancestry is in Han Chinese.

The way the authors did this is by first compiling a list of sequences, which likely came from Denisovans or Neanderthals. They did this by looking for regions which were anomalously different from modern Africans, who have no Denisovan or Neanderthal ancestry. Once they had this list, they compared them to the genomes of the Neanderthals and Denisovans.

Not surprisingly, Europeans had matches with Neanderthals only. Papuans had more matches with Denisovans than Neanderthals. South, Southeast, and East Asian populations had many more matches with Neanderthals, but a small number with Denisovans.

So far so good.

But the authors noticed that some of the populations had Densiovan matches to the Siberian sequence that were much better than those in other populations. In South and Southeast Asia, and Oceania, there were no high quality matches with the Denisovans. In the Han Chinese, about half the matches were much better with the Siberian Denisovan genome — while half the matches were similar to the ones found in other populations.

This could mean that in Northeast Asian populations, two groups of Denisovans contributed their ancestry, while in southern Asia and Oceania only one did.

These results show us that the human past was complicated even if the early genetic results painted a simple picture. Modern humans in eastern Asia interacted with Denisovans twice. We know from a genome in Europe that there were several admixture events with Neanderthals, but it seems only one persists down to the present — as the first Europeans with additional admixture left no descendants. Perhaps the same is true in Asia, maybe there were more than two admixtures with Denisovans.

The pattern of where Denisovan admixture is found is intriguing. It is found in highest frequency among Han Chinese and somewhat lower in Japanese and the Dai people of South China. It is entirely absent in the Vietnamese. Combined with the fact that Tibetans obtained a high altitude adaptation from Denisovans, this is circumstantial evidence that the admixture occurred in the interior of Eurasia.

Denisovans are a major twist in the understanding of our species, but their widespread distribution, and multiple interactions with modern humans, points to intriguing possibilities. Perhaps the Denisovans persisted down to relatively recent times, and interacted a fair amount with modern humans? We know they interacted enough to mix with us twice. Denisovans complexify our understanding of the past, but they may simplify and illuminate myth!

Maybe you have some Neanderthal or Denisovan in your DNA. Discover your story today with Neanderthal by Insitome.

The Others were people too was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

March 19, 2018

Denisovans, Neanderthals, Yetis, oh my!

Filed under: denisovan,Human Evolution — Razib Khan @ 12:47 am

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

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

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

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

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

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

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

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

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

Pontus Skoglund immediately made a very interesting observation:

And Alexander Kim followed up:

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

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

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

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

February 28, 2018

Who We Are and How We Got Here, a book worth reading

Filed under: Human Evolution,Human Genetics — Razib Khan @ 7:18 am

Yesterday I talked to a friend who has a review copy of Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past. They gave me a preview (their overall assessment was positive).

I haven’t personally asked to get a copy because, to be honest, I thought there wouldn’t be anything new in it. If you “read the supplements” what more could there be in 368 pages? So I was waiting until the end of the month to buy the book and read it in my own sweet time as due diligence.

Well, this morning I asked a publicist to send me a copy. I will be getting it next week. The reason is that I’m told the latter portions of the book are quite challenging and candid as to what genetics may tell us in the 21st century. Who We Are and How We Got Here is a 21st-century revision and update of The History and Geography of Human Genes. But it’s apparently a lot more.

Also, I make a small cameo in the book, as does Eurogenes and Dienekes. I have always appreciated how the David Reich and Nick Patterson and their whole lab has taken people outside of the halls of the academy seriously. They didn’t need to as a matter of professional necessity but often engage as a matter of decency and seriousness.

January 25, 2018

Out of Africa to Out of Eden (well, perhaps not yet)

Filed under: Human Evolution,Out-of-Africa — Razib Khan @ 10:05 pm

The recent African origins hypothesis for modern humans had several things going for it. First, most of the old fossils that look like modern humans were in Africa. Chris Stringer and others were pushing the African origins of our modern lineage before genetics came to the fore. But of course, you also have DNA. The mtDNA, Y, and autosomal DNA, which tends to show a pattern where Africans are more diverse, and non-Africans are nested within phylogenies of Africans.

In the 2000s the “Out of Africa” model got a little out of control. The stylized narrative was that a small tribe of East Africans developed some genetic mutation that allowed them to exterminate all other human lineages (e.g., language). This is best encapsulated in Richard Klein’s The Dawn of Human Culture. The British science fiction author Stephen Baxter used this idea as a frame in his novel Evolution (the innovation in this novel was religion though). In this view modern humanity was an African saltation, a great leap forward.

We’re at a different point now. The idea of admixture and/or introgression from non-African lineages into African modern humans is widely accepted. Additionally, both genomic inference and paleontology are pushing the roots of modern humanity much further than ~50,000-60,000 years before the present.

So it’s not as surprising to see a paper like this, The earliest modern humans outside Africa:

To date, the earliest modern human fossils found outside of Africa are dated to around 90,000 to 120,000 years ago at the Levantine sites of Skhul and Qafzeh. A maxilla and associated dentition recently discovered at Misliya Cave, Israel, was dated to 177,000 to 194,000 years ago, suggesting that members of the Homo sapiens clade left Africa earlier than previously thought. This finding changes our view on modern human dispersal and is consistent with recent genetic studies, which have posited the possibility of an earlier dispersal of Homo sapiens around 220,000 years ago. The Misliya maxilla is associated with full-fledged Levallois technology in the Levant, suggesting that the emergence of this technology is linked to the appearance of Homo sapiens in the region, as has been documented in Africa.

Now, the reality is that Israel is arguably part of “Greater Africa” biogeographically. So it isn’t that surprising. Or it shouldn’t be.

But, this reinforces the reality that anatomically modern humans were geographically already widespread ~200,000 years ago. I would say that this informs and updates our estimation of the plausibility of the Jebel Irhoud modern humans in Morocco, who flourished ~300,000 years ago. It also makes more sense of the reality that most of the ancestors of the Khoisan likely diverged from other modern lineages ~200,000 years ago (or more, depending on who you talk to). Finally, it makes recent archaeological finds of modern humans or their artifacts in East Asia tens of thousands of years before the great expansion of neo-African humanity50,000-60,000 years before the present much more plausible.

There has been some genetic evidence for modern(ish) human expansion before the 50,000 year date. So this isn’t resting only on paleontological evidence.

Where does this leave us? In The Guardian David Reich observes that ‘It’s important to distinguish between the migration out of Africa that’s being discussed here and the “out-of-Africa” migration that is most commonly discussed when referring to genetic data. This [Misliya] lineage contributed little if anything to present-day people.’

Obviously, this is an important point. But we know that the first modern humans to settle Europe did not leave any descendants either.  The modern human settlement of Europe was still nevertheless important. Second, these early wave humans may have given modern populations adaptive variants that are present at high frequencies in modern lineages.

Finally, there’s the issue that this may reorient our understanding about the demographic origins of human populations. Ever so slightly our priors as to an African genesis for our modern lineage are getting weaker. You have two very old modern fossils on the northwest and northeast fringe of the continent. Ten years back the arguments was between those who argued for an East African origin (most), or a minority who favored a Southern Africa one. Now the whole continent, and perhaps even Arabia, are game.

Ultimately, as always, ancient DNA is going to be the final arbiter.

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