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.”
Related to the last discussion about East Asians, the Denisovan admixture shows that the East Asian core group, which had little to no archaic Denisovan, pushed the preceding populations, which were once much more widespread, to the edges.
Like in Central and Southern Africa, European colonisation brought a replacement to a halt or at least slowdown, which took place for thousands of years. Its remarkable that the expansion from the East Asian geostrategic center of the Eastern steppe and especially the Hwangho expanded in all directions. And by now it seems a large portion of the fringe groups pushed aside had Denisovan admixture. Wonder about the Ainu in this respect, but they seem to be without it.
Most likely the Denisovan too lived and survived mostly along the coasts and on islands, similar to Austronesians later, which were just one wave from the center I talked about.
The Wallace line was just a temporary halt and obstacle. Once the next push over the SEA sea worlds, caused by demographic build up or a new wave from the North, would have increased the pressure in the West, the East Asian colonists would have entered the Eastern sphere and ultimately reaching Australia.
Obviously the Negritos and Melanesians were once part of a much larger human population of which they are just the remnants.
In Tibet and North Eastern Sibiria or Japan the same is true. All regions being successfully colonised by the East Asian center. And if one wave failed, the next might have broken the resistence.
Like in Central and Southern Africa, European colonisation brought a replacement to a halt or at least slowdown, which took place for thousands of years.
huh?
Looks like some tribes (Abujmaria, Muria) in Chattisgarh have 0.4% Denisovan, surpassing Andamanese.
@Razib: I was referring to CA Pygmies and San primarily. For the Khoikhoi Europeans were no help obviously, but they too would have been replaced by Bantu people eventually.
Like Negritos, ASI and Melanesian groups, Khoisan and CA Pygmies were once much wider spread.
When the European colonisation started, the small scale expansions replacing fringe groups in difficult positions were slowed down, like Muslim slave trade as well.
For some regions of Central Africa for example the pressure rather increased again with the Europeans departure. Similarly Indonesia will increase, sooner or later, the pressure on New Guinea.
For some regions at least, the arrival of the Europeans meant a slowdown of replacement. Obviously with the modern means it might resume even at a faster pace depending on political and demographic pressure.
This is a superb review. I am literally amazed at these new findings. They should be all over NatGeo, Scientific American, Origins and other human evolution sites this morning.
One thing that hugely jumps out at me, is the sentence towards the end. Two tribes in south central India have even larger percentages of Denisovan DNA than the Andaman islanders? Wow. Wouldn’t that make them the most Denisovan living humans on the planet?
Eric, Houston TX
Razib,
“This is a paper where you need to jump to the supplementary note.”
You said it best. There’s a nugget of great interest, if you look at the South Asian PCA.
The Toda people of southern India do not cluster among South Indians. Instead, they cluster near north Indian Brahmins, yet still very distinct from them too (probably because the Toda lack Steppe_MLBA admixture).
Confirms my suspicions (based on phenotype) that the Toda are West Eurasians, of a distinctly South Asian kind (probably only 20%-25% AASI, max)… perhaps the closest living population to our Indus_perhiphery samples.
@Commentator, looks like a nice find – those people’s sequences could perhaps tell us even more if they were analyzed with formal stats and ancient dna. They look quite heavily ASI in the ADMIXTURE (until they form their own component) but not in the PCA so wonder what’s up with that. It’s not unusual for groups with very strong isolation like Kalash to form their own component or have unusual PCA position in large numbers so a check on that would be useful.
Though speaking of Kalash, I wonder if this paper has merged in the HGDP whole genome preprint samples in some of their supplementary analyses? (https://www.biorxiv.org/content/10.1101/674986v1). They certainly seem to have used in some analyses samples of Kalash, and some other HDGP populations that it does not look that they have independently sampled.
@Commentator
Also Kota tribe is quite distinct from other Nilgiri hill tribes.
“Confirms my suspicions (based on phenotype) that the Toda are West Eurasians, of a distinctly South Asian kind (probably only 20%-25% AASI, max)…”
Phenotype-wise they look pan south Asian unlike other tribes in the region. Not sure about 20-25% AASI, they might have more.
Nice to see some sampling of NE Indian Tibeto-Burman populations here (Chakma, Jamatia, Manipur, Mog, Toda).
It seems like a shame that they did not sample the Naga / Nyishi population though. These people show up in HarappaWorld (ADMIXTURE from 2012) as having a very North East Asian genetic profile and very little ASI. Ratios – https://imgur.com/a/dkK1tmf (More “NE Asian” than Northern Han, in their ratios of SE Asian:NE Asian:Siberian).
While these samples taken seem more to the Garo / Burmese with a good ratio of SE Asian component:NE Asian component and a fair level of ASI.
Matt,
I’ve always had an interest in seeing some samples from these people; if you ever get a chance to peruse the anthropological literature on southern India, you’ll find that the Toda people are very culturally distinctive. They’re outside the Hindu caste system (so “tribal”)… yet their traditional lifeways and social structure are highly distinct from their “tribal” neighbors. Lots of fascinating details.
And then, there’s the fact of their physical differentiation from almost everyone else in South India (in terms of phenotype, many Toda seem to resemble Baloch or Brahui from far away on the eastern edge of the Iranian plateau, rather than their own neighbors in the Nilgiri hills!).
The cultural and phenotypic distinctiveness always gave the expectation of these people being genetically unique… so it’s a pleasant surprise, seeing that pan out. (And if turns out that they really are only 20%-30% AASI, but with no Steppe_MLBA, it’ll be pretty awesome/cool to know that there’s still West Eurasian Indus_Periphery-like people in India)
But I absolutely agree that some analyses with aDNA and some formal stats could provide considerable insight. And I’ve always found David’s scaled G25 (in conjunction with nMonte) to be very effective as well (often showing patterns which are later presented in the literature as new findings).
I might try some things with qpAdm and these samples. If I do, I’ll make sure to share the output here, or on Brown Pundits. We’ll also keep a lookout for these samples being presented on David’s proprietary PCA.
But yeah, if I’m not mistaken, these are the Kalasha from the HGDP paper.
@Commentator,
The Toda’s neighbors and reputed relatives Kota are also in the paper, with 8 genomes against Toda’s 20. It’s hard to make out their position on the admixture graph, although there is one population “somewhere in the general vicinity of Kota samples” which has an unusual spike of Toda-like ancestry…
Of course with as drifted a group as the Toda, it’s just hard to imagine getting good answers with tools like ADMIXTURE. Some sort of haplotype IBD may be more helpful, perhaps?
dx, f/dstats less drift impacted. why i’d like to see that
@Commentator
“And if turns out that they really are only 20%-30% AASI, but with no Steppe_MLBA, it’ll be pretty awesome/cool to know that there’s still West Eurasian Indus_Periphery-like people in India”
20-30% is still lots of AASI to compare them with Baloch-Brahui groups.
An isolated community of 2k individuals obviously would look distinct. There are some individuals, even in Vellalar-Reddy like groups who phenotype-wise can pass as Balochi. If one of the individuals marries a Balochi looking girl from Vellalar or Reddy community, their offspring have a higher chance to look like Balochi.