June 07, 2013

Demographic history from distribution of shared IBS lengths

An interesting new paper has appeared in PLoS Genetics, with what appears to be a nice new method for inferring demographic history from genome-scale data. The authors observe that segments inherited from common ancestors are "broken up" by mutation as time goes by: initially there are long identical tracts, but these are "split" whenever a new mutation appears, so they study the distribution of lengths of the pieces between mutations that remain identical by state.

A practical application of the new technique is applied to European-African history:
We estimate that the European-African divergence occurred 55 kya and that gene flow continued until 13 kya. About 5.8% of European genetic material is derived from a ghost population that diverged 420 kya from the ancestors of modern humans. The out-of-Africa bottleneck period, where the European effective population size is only 1,530, lasts until 5.9 kya.
The authors use the "old" 2.5x10-8 mutation derived from a paleontological calibration of the human-chimp split, which renders their calculations comparable to many past papers on human demographic history, but at odds with many of the newer rates that are approximately twice slower. There is lingering controversy about the appropriateness of different rates.

The authors estimate that perhaps a 1.75x increase in their estimates will be effected if the slower rates are used; this is not 2x as one might expect from a 2x slower rate, because their age estimates depend on both the mutation rate (for which there is controversy) and the recombination rate. By applying the 1.75x correction factor, we may obtain a time for European-African split at 96 thousand years and a continuation of gene flow between Europeans and Africans down to 23 thousand years.

I suppose that things might be complicated by the occurrence of Amerindian-like admixture in some West Eurasians in the past, as well as the occurrence of intra-African admixture (which I've called "Palaeoafrican") in the ancestry of Yoruba, both of which do not appear to be modeled here: the former might have infused an "African-less" component of ancestry at a time when the authors suggest that there was continuing gene flow between West Eurasia and African; the latter would inflate the effective population size of the Yoruba and make the appear earlier diverged from non-Africans.

In any case, this is a useful addition to our understanding of human history and may tie in to some of my arguments about Eurasian back-migration into Africa (although the authors consider bidrectional gene flow in their model). The lack of non-M,N mitochondria in non-Africans makes the post-OoA gene flow from Africa->Eurasia difficult to stomach, while the opposing migration of Y-haplogroup E bearers into Africa (as I have suggested) seems too instantaneous to account for the authors' evidence for protracted gene flow.


PLoS Genet 9(6): e1003521. doi:10.1371/journal.pgen.1003521

Inferring Demographic History from a Spectrum of Shared Haplotype Lengths

Kelley Harris, Rasmus Nielsen

There has been much recent excitement about the use of genetics to elucidate ancestral history and demography. Whole genome data from humans and other species are revealing complex stories of divergence and admixture that were left undiscovered by previous smaller data sets. A central challenge is to estimate the timing of past admixture and divergence events, for example the time at which Neanderthals exchanged genetic material with humans and the time at which modern humans left Africa. Here, we present a method for using sequence data to jointly estimate the timing and magnitude of past admixture events, along with population divergence times and changes in effective population size. We infer demography from a collection of pairwise sequence alignments by summarizing their length distribution of tracts of identity by state (IBS) and maximizing an analytic composite likelihood derived from a Markovian coalescent approximation. Recent gene flow between populations leaves behind long tracts of identity by descent (IBD), and these tracts give our method power by influencing the distribution of shared IBS tracts. In simulated data, we accurately infer the timing and strength of admixture events, population size changes, and divergence times over a variety of ancient and recent time scales. Using the same technique, we analyze deeply sequenced trio parents from the 1000 Genomes project. The data show evidence of extensive gene flow between Africa and Europe after the time of divergence as well as substructure and gene flow among ancestral hominids. In particular, we infer that recent African-European gene flow and ancient ghost admixture into Europe are both necessary to explain the spectrum of IBS sharing in the trios, rejecting simpler models that contain less population structure.

Link

8 comments:

Jack said...

"About 5.8% of European genetic material is derived from a ghost population that diverged 420 kya from the ancestors of modern humans."
Ghosts? What the heck? They have genes too?

n/a said...

"I suppose that things might be complicated by the occurrence of Amerindian-like admixture in some West Eurasians [. . .] The lack of non-M,N mitochondria in non-Africans makes the post-OoA gene flow from Africa->Eurasia difficult to stomach, while the opposing migration of Y-haplogroup E bearers into Africa (as I have suggested) seems too instantaneous to account for the authors' evidence for protracted gene flow."

Obviously there was "post-OoA gene flow" from Africa to the Middle East. Eurasians brought Y haplogroup E (or its ancestor) to Africa, and Africans brought E back to the Middle East in pre-Neolithic times. There's also evidence from archaeology and physical anthropology of sub-Saharan influence in Mesolithic Near Easterners.

This is something that needs to be taken into account in any serious attempt at understanding what you refer to as "Amerindian-like admixture in some West Eurasians".

As for later gene flow from Eurasia to Africa, there's also evidence in the form R1b.

Steve Tubbs said...

"Ghost population" would be Neanderthal, Denisovan, etc., correct?

Jim said...

That looks like Neanderghosts they are talaking about

eurologist said...

I still think a factor of about ~2 (instead of 1.75) makes all the data fit much better.

Also, I always cringe when authors suggest major gene flow (or even a minor one) from far away into Europe during LGM (~26,500 ya onward!). That's just crazy talk. Again, a factor of ~2 fits much better, here.

Of course, gene flow from Africa could have continued (and probably did continue) into e.g. the Levant and other parts of SW Asia, which then got pushed into Europe during the Neolithic and Metal Ages.

However, this would be a much, much smaller percentage, and also carry a different signature.

halvorsonian said...

As is well known, Africans have really, really curly hair. So curly in fact, that even Europeans of only 1/8th African ancestry such as Pushkin are still noticeably much curlier than their countrymen. I've always wondered if you could explain Caucasoid variation in hair straightness solely as a function of African ancestry: maybe West Eurasians, even Arabians, were originally straight haired and acquired their curls more recently. I didn't really think this plausible before, because recent African gene flow from the Proto-Semites or the slave trade couldn't possibly explain why say, many Irish have curls, but if the admixture is as ancient as the paper implies it very well could.

Umi said...

@halvorsonian,

Curly hair is found in many 'Out of Africa' populations that have no African admixture such as certain Indians and Pacific Islanders. So, it is very possible that the curly hair in West Eurasians may be of an independent type. The reason why Mongoloids lack curly hair is because they have a post-OOA mutation affecting their hair type that reached near fixation in them. Hence, they can't be representative of the hair type diversity of the early Out-of-Africans population.

Unknown said...

" There's also evidence from archaeology and physical anthropology of sub-Saharan influence in Mesolithic Near Easterners."

This.

Also, the 55 kya divergence date is remarkably coincident with the development of a blade-producing culture in Taramsa, Egypt 70-60 kya. This industry is thought to have been ancestral to the proto-UP cultures appearing shortly afterwards in the Near East, which in turn are thought to be ancestral to the UP of Europe.

Both the 55 kya and 13 kya dates are strongly supported by archaeology, and the latter also by ancient DNA (mtdna L2 found at in the early Neolithic of Syria).