Razib Khan One-stop-shopping for all of my content

May 1, 2019

The natural history of song – a human universal

Filed under: Human Evolution — Razib Khan @ 11:18 pm


“I am human, and I think nothing human is alien to me.”
– Terrence

One of the bizarre things about modern cultural anthropology is that its tendency toward extreme relativism means that it engages in so much “thick description” that generalities of humanity disappear in the avalanche of prose. A deep sense of ontological incommensurability creeps into the discussions of cross-cultural patterns. The prestige, what there is, of academic anthropology, then infects normal people, so that some can say that religion, as understood in the West, is qualitatively different from religion understand in the East. With a straight face.

I think this is wrong and leads us down a path to intellectual nihilism (well, actually, we’re at the end of that path today aren’t we!).

This sort of thing applies to other cultural phenomena as well. Consider music and in particular song. A new preprint uses the Human Area Relation Files (an ethnographic database) to statistically analyze patterns in songs across many societies, A natural history of song:

What is universal about music across human societies, and what varies? We built a corpus of ethnographic text on musical behavior from a representative sample of the world’s societies and a discography of audio recordings of the music itself. The ethnographic corpus reveals that music appears in every society observed; that variation in musical behavior is well characterized by three dimensions, which capture the formality, arousal, and religiosity of song events; that musical behavior varies more within societies than across societies on these dimensions; and that music is regularly associated with behavioral contexts such as infant care, healing, dance, and love. The discography, analyzed through four representations (machine summaries, listener ratings, expert annotations, expert transcriptions), revealed that identifiable acoustic features of songs predict their primary behavioral function worldwide, and that these features fall along two dimensions, melodic and rhythmic complexity. These analyses show how applying the tools of computational social science to rich bodies of humanistic data can reveal both universal features and patterns of variability in culture, addressing longstanding debates about each.

The figure at the top reports the three largest components of variation, formality, arousal, and religiosity. Not surprisingly, some types of songs are more weighted toward one feature than another. Lullabies are not particularly religious, arousing, or formal.

Interestingly, the vast majority of variation in songs is found within societies, not between them. There is some difference, with some societies lacking formal songs, at least in the ethnographic record. But, this illustrates that the basic repertoire for this cultural feature was probably present by the late Pleistocene in our species.

Songs seem to be aspects of human behavior which are both consumption and production goods. That is, on the individual and social level we consume songs for pleasure. On the individual level songs are essential parts of the parental toolkit to soothe the infant beast. They also serve a purpose in society to generate cohesion and produce fellow feeling. This is clear in a confessional religious context, but consider that drummers were important elements of the Ottoman war machine. Human cultural phenomena are so often multivalent that they need to be inspected and examined from a variety of dimensions.

I’m not a very musical person myself, so there is obviously individual variation in the ability to appreciate or produce music. But the basic cognitive toolkit seems to emerge out of a concert of neurological processes, somewhat distinct from common language (as evident by aphasics who can sing but can not speak).

It’s a Denisovan world, and paleoanthropology just lives in it!

Filed under: Human Evolution — Razib Khan @ 9:07 pm


Unless you’ve been sleeping under a rock, you may have seen a new paper, A late Middle Pleistocene Denisovan mandible from the Tibetan Plateau. The reason it is a big deal is that except for a fragment of a skull reported on at a conference, this is the first remains outside of Denisova cave identified as “Denisovan.” Part of the identification was morphological. Both this find and those in Denisova cave, are characterized by very large teeth.

But the really interesting aspect is that they used analysis of proteins to place this sample phylogenetically. You can see the results above. Proteins don’t degrade as fast as DNA, from what I know, so this isn’t surprising. This individual, from high altitude Tibet, dated to at least 160,000 years ago, is in the same clade as the Denisovan that has been sequenced in the broader context of hominin evolution. This is not a rock-solid inference…there wasn’t that much informative variation (I believe Janet Kelso said on Twitter that one particular position where the Denisovan were derived compared to all other hominins in particular matched this paleo-Tibetan sample). But, if you had to guess, it does seem likely that this was an individual related to the Denisovans that we’ve come to know and love.

Finally, there is an important twist that the high altitude adaptation in Tibetans due to EPAS1 seems to have arrived from an introgressed haplotype from Denisovans. Perhaps then the introgression occurred 40 to 50 thousand years ago, as modern humans replaced Denisovans. The majority of the ancestry of Tibetans though seems to share rather recent Holocene origins with groups such as the Han Chinese. Therefore, rather than absorption of an old substrate in Tibet, it could be that you are looking at a variant widely found in the northern Denisovans.

I’ve been talking a lot about Denisovans recently. Why? It seems that the investigations prompted by the original surprise sequencing of 2010 are finally yielding results. But one thing that is clear is that our understanding of the origin of our lineage, and how various hominins interacted with each other, and who they were, is much sketchier than we might like to think. Though the Tibetan and Denisova cave Denisovans were both robust, if the lineage began to diversify ~400,000 years ago, that’s certainly enough time for various morphological types to have emerged in different parts of Asia.

It could simply be we’ll never be able to specifically understand a lot of the detailed processes that occurred in terms of how different hominin groups related to each other. But, we will probably be able to get a better general picture in the near future. As Spencer mentioned in our podcast last week, the Neanderthals in some ways may have been atypical for ancient hominins, and not a good guide to the long term trajectory of the Denisovans.

April 27, 2019

African genomics tells us about deep structure and history

Filed under: African Genetics,Human Evolution,Human Genetics — Razib Khan @ 11:36 pm


Two interesting papers in Genome Biology that are open access, Whole-genome sequence analysis of a Pan African set of samples reveals archaic gene flow from an extinct basal population of modern humans into sub-Saharan populations and African evolutionary history inferred from whole genome sequence data of 44 indigenous African populations. Since they are open access you should just read both of them.

I believe they are the first in a series of papers over the next few years using whole-genome analysis to understand the population structure within Africa, and how it relations to the people who branched off from Africans. Eventually, this will also lead to research focused on medical and population genomics, looking at characteristics and forces beyond phylogeny.

The results confirm at a finer-grain and with more precision what we’ve known before. The strangest result (to me), which has been confirmed over the past several decades or so (starting with uniparental lineages), is that the hunter-gatherers of Sub-Saharan Africa are broadly related more closely related to each other than they are to the agriculturalists of Sub-Saharan Africa. The relationship is deep (see the figure of the NJ-tree). The Baka and Mbuti Pygmies of the west and east of the Congo are deeply diverged themselves from each other, and even more so from the Khoisan people of southern Africa, or the Hadza of Tanzania.

But the missing piece of the puzzle has to be the “Bantu expansion.” As was pointed out to me by Nick Patterson about a decade ago, the Bantu-speaking people are genetically very closely related, as benefits a demographic expansion that began on the order of ~3,000 years ago from a small region of the Cameroon-Nigeria border. Curiously, a similar expansion did not occur to the west, as West Africa remains linguistically much more diverse, though genetically it is broadly similar to “Bantu Africa.”

Even on the furthest southern edge of the Bantu expansion, the majority of the ancestry remains similar to their linguistic relatives in Cameroon-Nigeria region, even if a substantial minority of the ancestry is Khoisan. Similarly, the Bantu speakers of East Africa often have some Eurasian ancestry, probably mediated by pastoralist Cushitic-speaking people who were already present.

The genetic variation of contemporary Africa is an artifact of the recent Holocene. This was clear after the publication of Skoglund et al. a few years ago. It also means that a lot of the fine-grained inferences from modern populations must be taken with a grain of salt, as there was probably more admixture and movement in the early Holocene which is not visible to us, let alone in the Pleistocene.

That being said, the figure at the top of the post captures the major features since 1) they’re in keeping with our understanding of the interaction of deeply diverged lineages 2) there has been other work with other methods detecting the same dynamics.

Most scholars did not accept the likelihood of Neanderthal admixture until the genome of this ancient hominin was published. Then we discovered the Denisovan contribution due to another genome. Both of these discoveries should update our prior expectations of any given model. The model above utilizes a complex ABC-framework. If you know what that means, you know I’m not going to get into the details. But I trust computers only to a point… I expect the ABC model does reflect realities of archaic admixture, but I’m not sure that the typology of the tree is totally settled.

That’s because of the reality that human genealogies are more like graphs with edges of different thicknesses. There’s always some gene flow, especially between close lineages. These models often infer that the Khoisan diverged ~200,000 years ago from other lineages. And, that the African ancestors of modern Eurasians diverged ~100,000 years ago. The model above even suggests that there is “anatomically modern human” (so African) admixture into Neanderthals. It is highly likely that this was detected in the Altai genome, so I think this is likely.

But is it likely that the Khoisan were a long and isolated branch over 198,500 years ago when some admixture with a Nilotic or Cushitic populace broad Eurasian ancestry? I doubt it. I suspect these divergence/coalescence times mask deeper and more recent branches, which fused together, and so give us an average mid-point coalescence. Archaics aside, I suspect that some of the Khoisan ancestry is probably deeply basal, and some of it is less basal.

Finally, the divergence time of the ancestors of Eurasians is  ~100,000 years ago. Archaeology tells us that the expansion of the ancestors of modern non-Africans occurred 50-60,000 years ago. What was going on in that interval? First, of course, all these estimates need to be taken with a grain of salt, even beyond the confidence intervals. But, I’ve read enough of these papers to see a number >>>60,000 years for the divergence to think it’s real. It strikes me that the ancestral proto-Eurasians were on the fringe of Africa or in Arabia for a long time before the expansion. A deep divergence between Eurasians and Sub-Saharan Africans is probably a function of the fact that most ancient African populations left no descendants (or very few). This seems common in large parts of Eurasia. If the proto-Eurasians were liminal, it is possible all the intervening populations between it and the ancestors of West Africans just went extinct.

The structure and history of African genetics is not just important for medical and population work. It is probably also essential to scaffold some of our inferences about cultural evolutionary processes. At a minimum, half of modern human man history has been within Africa (if modern humans were outside Africa in Arabia 100,000 years ago).

April 23, 2019

Denisovans and the human story

Filed under: Denisovans,Human Evolution,Neanderthals,science — Razib Khan @ 1:38 pm
The Siberian cave where a new human species was discovered

We are all aware of the iconic fossil finds which mark the various milestones of our understanding of human evolution. The story of how our species became what it is today. Raymond Dart’s Taung Child helped establish that Africa might be the original home of our species. Lucy, which put the spotlight on some of the earliest upright ancestors of hominins. Even frauds like Piltdown Man go down in the history books, at least reflecting something of a particular Zeitgeist, wrong as it was.

And yet our past is haunted by a very small collection of remains indeed. Humans were never numerous (until recently). Our ancestors were fossilized thanks to luck, giving us a sense of the shape their form and bearing. The fossil trail of the upright line of apes which eventually lost their fur, and left Africa two million years ago, is quite tenuous.

Denisovan teeth from which DNA was extracted

But in the 21st-century new varieties of humans, species perhaps, are not discovered just by fossils alone. Rather, genetic science has now become adept at retrieving DNA from even the most ancient of human remains. Geneticists can then reconstruct the history of peoples long gone from their sequence, and compare them to modern people or other ancient genomes.

In the spring of 2010, the first whole Neanderthal genome was published, a landmark in the development of paleogenetics. Of course, Neanderthals have a long and storied history in paleoanthropology. They’ve been dehumanized and rehumanized and dehumanized many times. The surprise results out of the Neanderthal genome was that humans outside of Africa were all related to the Neanderthals. In other words, a few percent of the genome of non-Africans could be attributed to descent from them.

But wait! 2010 had more surprises in store for us. At the end of the year, a paper reported the genome of a new species of human. Previously unknown to science, these were the Denisovans, named after the cave in Siberia in which the remains were found. Because there was a genome of Neanderthals already sequenced, scientists could tell that the Denisovans were closer to Neanderthals than to modern humans. About ~750,000 years ago the ancestors of Neanderthals and Denisovans left Africa, separating from our own ancestors. Soon after, the Neanderthals and Denisovans began to diverge, becoming two distinct lineages, far more distinct than any two modern groups.

But why were they distinct?

To answer the question one must look at a map. While Neanderthals occupied Europe and ranged east into the heart of Eurasia, Denisovans likely inhabited the zone between eastern Siberia down into Southeast Asia. Differences develop between populations with common ancestors when they are geographically separated, and by and large (though not exclusively), Denisovans and Neanderthals were separated by the vast arid heart of Eurasia.

While the Neanderthals were a northern population, despite the discovery of Denisovans in a Siberian cave, they may have been used to warmer climes more often than not.

Papuan Woman and Child

One reason this seems likely is that Denisovans have descendants today. But they are not an obscure group in Siberia…they are the Papuans of New Guinea! This population has about ~5 percent of its genome from Denisovans. The descendants of these ancient people are also more widely scattered across Oceania, though to varying degrees.

While the Australian Aboriginals and Negritos of the Philippines have significant Denisovan ancestry, the native tribes of the Andaman Islands have little. This suggests that not all indigenous peoples of South and South Asia mixed equally with Denisovans.

More recent work has revealed that much lower levels of Denisovan ancestry are present across much of South and East Asia. And, importantly, the Denisovan ancestry in groups like the Chinese seems to be from a different group than that mixed into the Papuans. The genome from Denisova cave likely belongs to the people who mixed with East Asians and contributed adaptative functions such as high altitude adaptation in Tibetans.

So what we know now is that for hundreds of thousands of years a widespread group of humans, Denisovans, occupied eastern Eurasia. Unlike Neanderthals, they were not a single homogeneous group. Some research groups have detected three different Denisovan populations mixing into modern humans, while others have suggested that the Denisovans carry ancestry from even earlier hominins, who likely arrived in Asia before them.

But unlike Neanderthals or our African forebears, we have not been able to reconstruct a full skeleton of an individual who is Denisovan.

There are skullcaps, teeth, and stray bones, but not enough identified remains which could give us a sense of what these people looked like, how they were built (though the fragments from Denisova cave indicate to many the Siberian population was robust). Despite what we know was their expansive range, and the fact that they lived in eastern Eurasia for hundreds of thousands of years, to a great extent Denisovans remain genetic ghosts. They are digital shadows of their physical bodies, telling us about their relationships to other humans, details of their physiology, and immune system, but elusive in corporeal form.

The discovery of a new human on the island of Luzon, the existence of hobbits on Flores, and the diversity of Denisovans suggest that the eastern range of humanity during the Pleistocene was filled with many species of humans. The very existence of the Denisovans was window upon the vast ignorance of science in regards to the complexity of the Pleistocene world.

While Neanderthals have been the subjects of many books, they may have been a relatively homogeneous population with very precise adaptations to their northern Eurasian abode. A literal evolutionary sideshow. In contrast, Denisovans ranged from Siberia to the islands of Southeast Asia. From the edge of the tundra to the hot savanna of Sundaland.

They reflect in greater fullness the range of human experience.

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

April 21, 2019

The expansion of modern humans ~50,000 as part of a regular Poisson process

Filed under: Human Evolution,Uncategorized — Razib Khan @ 4:58 pm

Last of the giants: What killed off Madagascar’s megafauna a thousand years ago?:

The first job is to understand exactly when the megafauna died out.

Radiocarbon dating of over 400 recent fossils demonstrates that animals under 22 pounds lived on Madagascar throughout the last 10,000 years. For animals over 22 pounds, there are abundant fossils up to 1,000 years ago, but relatively few since. The biggest decline in number of large animals occurred rapidly between A.D. 700 and 1000 – practically instantaneous given the long history of their existence on the island.

According to new dates on fossil bones with cut marks on them, humans arrived on Madagascar 10,500 years ago, much earlier than previously believed. But whoever these early people were, there’s no genetic evidence of them left on the island. New analysis of the human genetic diversity in modern Madagascar suggests the current population derives primarily from two waves of migration: first from Indonesia 3,000 to 2,000 years ago, and later from mainland Africa 1,500 years ago.

So it seems that people lived alongside the megafauna for thousands of years. How did the humans interact with the large animals?

Our new study found dozens of fossils with butchery marks. Cut and chop marks provide compelling evidence as to which species people were hunting and eating. Evidence of butchery of animals that are now extinct continues right up to the time of the megafaunal crash. Some people on Madagascar hunted and ate the megafauna for millennia without a population crash.

The abrupt land use change might hold some clues. The transition from a forest-dominated ecosystem to a grassland-dominated ecosystem appears to be widespread….

This research about Madagascar is important. If it turns out correct, I think it gives us deep insights about the expansion of modern humans outside of Africa ~50,000 years ago, and why their arrival resulted in the extinction of so many other human lineages. A generation ago we might have posited that some massive bio-behavioral change is what triggered this, but I am coming closer to the idea that cultural changes are punctuated enough that that may actually explain things. The culture changes first, then genes follow the culture.

Perhaps one might posit a model with massive turnovers in the hominin lineage due to this cultural dynamic occurs periodically, as if it’s a Poisson process.

April 19, 2019

The teleos of modern humans

Filed under: Denisovans,Human Evolution — Razib Khan @ 3:15 pm
Credit: Luke Jostins

Next week’s episode of The Insight is going to be on Denisovans. It’s a long one because so much has come out in the last few months on the specific topic, as well as the broader framing issues (e.g., the discovery of a new human species on Luzon).

One of the major points Spencer and I discussed is how important it is to understand general trends in the hominin lineage, that is, humans, before the great expansion ~60,000 years ago. For example, Neanderthals and Denisovans were very different in their paleoecology and biogeography. Neanderthals seem relatively homogeneous (probably due to repeated mass die-offs). In contrast, the “Denisovans” look to have been very deeply diverged within their clade. If the latest work is correct, and some Denisovan lineages split more than 400,000 years ago and persisted down to >100,000 years ago, then the differences between Denisovans may have been considerably greater than between any modern human lineages. For example, the Khoisan diverged from all other humans ~200,000 years ago, and there are possible deeper lineages, but not that much deeper.

Right now what you know about the Denisovans are from genomes in the Altai region. Imagine if we extrapolated to all modern humans from Altaians? It seems entirely likely that the Denisovan lineage was very diverse because it occupied very diverse territory geographically.

But diversity aside, one of the things I like to point out to people, is that there was an overall trend of encephalization among hominins. Neanderthal brains were growing larger too. We need to understand the natural history of all human lineages to understand what happened 60,000 years ago. I am coming to the conclusion that it wasn’t some incredible miracle of a behavioral big bang, but the inevitable outcome of systemic forces in hairless ape evolution that started ~2 million years ago.

The teleos of modern humans

Filed under: Denisovans,Human Evolution — Razib Khan @ 3:15 pm
Credit: Luke Jostins

Next week’s episode of The Insight is going to be on Denisovans. It’s a long one because so much has come out in the last few months on the specific topic, as well as the broader framing issues (e.g., the discovery of a new human species on Luzon).

One of the major points Spencer and I discussed is how important it is to understand general trends in the hominin lineage, that is, humans, before the great expansion ~60,000 years ago. For example, Neanderthals and Denisovans were very different in their paleoecology and biogeography. Neanderthals seem relatively homogeneous (probably due to repeated mass die-offs). In contrast, the “Denisovans” look to have been very deeply diverged within their clade. If the latest work is correct, and some Denisovan lineages split more than 400,000 years ago and persisted down to >100,000 years ago, then the differences between Denisovans may have been considerably greater than between any modern human lineages. For example, the Khoisan diverged from all other humans ~200,000 years ago, and there are possible deeper lineages, but not that much deeper.

Right now what you know about the Denisovans are from genomes in the Altai region. Imagine if we extrapolated to all modern humans from Altaians? It seems entirely likely that the Denisovan lineage was very diverse because it occupied very diverse territory geographically.

But diversity aside, one of the things I like to point out to people, is that there was an overall trend of encephalization among hominins. Neanderthal brains were growing larger too. We need to understand the natural history of all human lineages to understand what happened 60,000 years ago. I am coming to the conclusion that it wasn’t some incredible miracle of a behavioral big bang, but the inevitable outcome of systemic forces in hairless ape evolution that started ~2 million years ago.

March 29, 2019

Deep Denisovan population structure

Filed under: Denisovans,Human Evolution — Razib Khan @ 5:09 pm


The Denisovan session at the American Society of Physical Anthropology meeting was very interesting. In Science Anne Gibbons reports on the findings, Our mysterious cousins—the Denisovans—may have mated with modern humans as recently as 15,000 years ago:

The elusive Denisovans, the extinct cousins of Neanderthals, are known from only the scraps of bone they left in Siberia’s Denisova Cave in Russia and the genetic legacy they bequeathed to living people across Asia. A new study of that legacy in people from New Guinea now suggests that, far from being a single group, these mysterious humans were so diverse that their populations were as distantly related to each other as they were to Neanderthals.

The finding of two Denisovan lineages in Southeast Asia adds to results reported in Cell last year by Sharon Browning of the University of Washington in Seattle and her colleagues. They had suggested that New Guineans had a separate source of Denisovan DNA than people in East Asia, suggesting at least two mixing events.

“I’m skeptical,” added Cosimo Posth of the Max Planck Institute for the Science of Human History in Jena, Germany. He suggests the hints of a late mating could reflect an encounter of previously isolated modern populations rather than of moderns and Denisovans. In this scenario, modern humans mated with Denisovans, then the modern populations diverged, with each branch retaining a different set of Denisovan genes. The moderns then reconnected, mixing the two sets of Denisovan DNA together again.

Here is one thing that I think is important to remember: unlike Western Eurasia parts of Eastern Eurasia were better insulated from extreme climatic events. Neanderthals show strong evidence of repeated die-offs and population expansion so that in general Neanderthal relatedness is more a function of time than location (i.e., Neanderthals tended to go extinct in much of their range periodically, to be repopulated from refuges).

In contrast, the Denisovan range likely went far into Southeast Asia. It is not surprising that this is a highly structured population, with deep lineages. This is exactly what we see in Africa for the same time period. Tropical Southeast Asia is not as extensive as Africa, but it was more expensive during the Pleistocene due to lower sea levels. Hominins with low population densities occupying a huge range of territory almost certainly had developed local lineages and traditions.

As should be clear in the quotes we shouldn’t take these presented results as definitive. But they are suggestive and align well with earlier work that there were several Densiovan admixtures across Eurasia.

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.

Neanderthal

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.

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