November 25, 2010

Some Indians as genetically diverse as Africans, recent Out of Africa in serious trouble?

Razib alerts me to a very interesting new paper, which discovered that some Indian populations are more diverse than Africans in a sequenced 100kb region. I will have much more to say about this once I digest it fully, but as I said in my recent review of the Oceania paper, I don't believe in long "interludes" of humans living Africa and then spending tens of thousands of years camping in one place before starting to expand again. I don't believe that there is evidence for Neandertal admixture in Eurasians either; the title of my post hints at what I believe. Update to follow.

Thanks to the Jorde Lab for putting up their genotype data easily accessible online! They're an example for others to follow.


Here is the crux of the paper:
As previously observed, heterozygosity (a measure of genetic diversity) decreases with distance from East Africa (represented here by the Luhya LWK HapMap poopulation). The only trouble is, that this pattern disappears once the Indian populations are included in the analysis.

Things are even worse though: the Luhya are an admixed population. Thus, their level of heterozygosity is inflated because of their relatively recent admixture associated with the spread of Bantu languages. Remove them, and it's clear the pattern of diminution of genetic diversity from East Africa completely disappears. Indeed, I am convinced that this pattern may be completely due to the admixed status of East Africans; the Maasai are another HapMap population from East Africa that seems to be missing from this analysis, and it is less heterozygous than the Luhya.

Even though the pattern of diminution of genetic diversity from East Africa (in autosomal genes, at least) may be largely due to the admixed status of East Africans, the same could be true for the Indian groups, who are largely composed of an indigenous "Ancestral South Indian", and an invasive "Ancestral North Indian" component. But, the point is that these two groups must have been substantially differentiated to produce a larger level of heterozygosity than in the Africans.

A caveat should be registered: genetic diversity in African hunter-gatherers (Bushmen and Pygmies) may be even higher than in the Yoruba and Luhya. Also, the mtDNA phylogeny is pretty unambiguous about the matrilineal origin of humanity being in Africa. And, the earliest known fossils of anatomically modern humans are in Africa. Thus, some kind of Out-of-Africa scenario still finds support in the data.

What does no longer find support in the data is the idea of a recent Out-of-Africa exodus 40-60 thousand years ago. The authors of the current paper:
the divergence time between African and the ancestral Eurasian population (88-112 kya, CIs: 63-150 kya) is much older than the divergence time among the Eurasian groups (27-39 kya, CI: 20-59 kya).
A divergence between Africans and Eurasians 100ky is consistent with the paleoanthropological finds from the Levant and China, showing the presence of anatomically modern humans thousands of kilometers apart at that time outside Africa. If there was an Out of Africa, it happened 100 thousand years ago.

The second important point is that the supposed maintainance of a Eurasian population outside Africa in the Levant for tens of thousands of years before the breakup of the Eurasians:

There are serious reasons to doubt this hiatus:

First, the presence of AMH in China in the Levant and China 100,000 years ago is hardly consistent with the maintainance of a geographically circumscribed population of Eurasians in the Levant until 40,000 years ago.

Second, it is hardly parsimonious that such a population would maintain itself in a geographically circumscribed area for so long. If they moved from East Africa to the Near East, why on earth would they stop there?

In my opinion two underappreciated factors should be considered:
  • Gene flow within Eurasia reduces divergence times between Eurasians; West, South, and East Eurasians did not branch out from a common ancestor; there were episodes of gene flow between them, some of them very recent, some of them beyond any record. Such lateral gene flow did not abolish differences between them, but it would have reduced the inferred divergence time.
  • Gene flow between Afrasians (i.e., Eurasians' unadmixed ancestors in East Africa) and other Palaeoafricans inhabiting other parts of the continent would have increased the inferred divergence time between Africans and Eurasians.
These two factors might suffice to explain the observed pattern, without invoking a long hiatus.

Genome Biology 2010, 11:R113 doi:10.1186/gb-2010-11-11-r113

Genetic diversity in India and the inference of Eurasian population expansion

Jinchuan Xin et al.

Abstract (provisional)

Genetic studies of populations from the Indian subcontinent are of great interest because of India's large population size, complex demographic history, and unique social structure. Despite recent large-scale efforts in discovering human genetic variation, India's vast reservoir of genetic diversity remains largely unexplored.

To analyze an unbiased sample of genetic diversity in India and to investigate human migration history in Eurasia, we resequenced one 100 kb ENCODE region in 92 samples collected from three castes and one tribal group from the state of Andhra Pradesh in south India. Analyses of the four Indian populations, along with eight HapMap populations (692 samples), showed that 30% of all SNPs in the south Indian populations are not seen in HapMap populations. Several Indian populations, such as the Yadava, Mala/Madiga, and Irula, have nucleotide diversity levels as high as those of HapMap African populations. Using unbiased allele-frequency spectra, we investigated the expansion of human populations into Eurasia. The divergence time estimates among the major population groups suggest that Eurasian populations in this study diverged from Africans during the same time frame (approximately 90-110 thousand years ago). The divergence among different Eurasian populations occurred more than 40,000 years after their divergence with Africans.

Our results show that Indian populations harbor large amounts of genetic variation that have not been surveyed adequately by public SNP discovery efforts. Our data also support a delayed expansion hypothesis in which an ancestral Eurasian founding population remained isolated long after the out-of-Africa diaspora, before expanding throughout Eurasia.



eurologist said...

I think it makes sense. There is more and more evidence accumulating that there were two OOA - one of them around 120,000 years ago, and not as successful in spreading to other continents until the second one. Something was still missing, to accomplish that.

Toba clearly would have interfered --- but it would have only taken a very few thousand years to reach population saturation in India to then force further migration. We know the climate changed ~45,000 - 50,000 years ago, which helped - but something else happened shortly before to make things happen.

To me, it seems that the incredible flexibility modern humans showed after and only after ~50,000 years ago must have been caused by something tangible - be it a second OOA, or a first-time successful incorporation of local homo (Neanderthal, Heidelbergensis) contribution.

Anonymous said...

The Irulas are the ones that have sometimes African-like phenotypes, IIRC. (the ones on the right)

I'd like to see more studies about the Adaman islanders too (as they also have kind of African-like phenotypes).

terryt said...

"There is more and more evidence accumulating that there were two OOA - one of them around 120,000 years ago, and not as successful in spreading to other continents until the second one".

Interestingly mtDNA and Y-hap evidence provide different origin dates for the two. The mtDNA fits the 120,000 year date (somewhat anyway) and the Y-hap fits better a more recent OoA. Perhaps the dates can be taken at face value in fact. That would make sense of your other comment:

"it seems that the incredible flexibility modern humans showed after and only after ~50,000 years ago must have been caused by something tangible - be it a second OOA, or a first-time successful incorporation of local homo (Neanderthal, Heidelbergensis) contribution".

Anonymous said...

This is too premature to comment on this.

Africa has more diversity and more ancestral groups.

One of the groups may be OOA.

All these Irulas, Mala, Madigas have high percentages of C,F,H compared to other Indian cast groups and Eurasians. This can not discount Eurasian haplo group map. CF-T. ????.

Can we discount OOA based on this?.

Also another interesting thing is India offers very few skeletal remains to find these traces other than live dna. India is full of stories and there are lot of stories about cross population of different species. May be Neanderthal mixture happened there and spread.

Lank said...

The Luhya are among the least admixed populations in East Africa; they're almost unaltered Bantus. The ancestry of the Maasai, on the other hand, is very heterogeneous (Bantu, Nilotic, Afroasiatic).

I also don't understand how ancient paleoanthropological finds in parts of Eurasia disprove a more recent Out of Africa scenario. There could simply have been other OOA migrations, except that their lineages did not survive. Care to elaborate?

eurologist said...

What is a bit weird is that: (i) they emphasize an initial coastal rout with a subsequent northern Levant exit OOA, while archeology in the Levant and Saudi Arabia suggests the opposite, and (ii) they place the "hiatus" in either the Levant or Africa - but not in India, which of course makes much more sense. And, as Dienekes points out, such a central hiatus may be exaggerated in the data because of contact/gene transfer.