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

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

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

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

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

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

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

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

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

A comment below that captures my thoughts well:

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

“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).

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.

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.

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.