More on chimpanzee population structure

A reader reminded me of a second paper on chimpanzee population structure, using a different Bayesian framework, which came out shortly after the study by Jody Hey I cited in my previous post (“Return of the Neanderchimps”). This paper, by Daniel Wegmann and Laurent Excoffier (2010) confirms many of Hey’s findings but diverges from that paper’s conclusions in some important respects. Here’s most of the abstract:

Here, we present a novel attempt at globally inferring the detailed evolution of the Pan genus based on approximate Bayesian computation, an approach preferentially applied to complex models where the likelihood cannot be computed analytically. Based on two microsatellite and DNA sequence data sets and adjusting simulated data for local levels of inbreeding and patterns of missing data, we find support for several new features of chimpanzee evolution as compared with previous studies based on smaller data sets and simpler evolutionary models. We find that the central chimpanzees are certainly the oldest population of all P. troglodytes subspecies and that the other two P. t. subspecies diverged from the central chimpanzees by founder events. We also find an older divergence time (1.6 million years [My]) between common chimpanzee and Bonobos than previous studies (0.91.3 My), but this divergence appears to have been very progressive with the maintenance of relatively high levels of gene flow between the ancestral chimpanzee population and the Bonobos. Finally, we could also confirm the existence of strong unidirectional gene flow from the western into the central chimpanzee. These results show that interesting and innovative features of chimpanzee history emerge when considering their whole evolutionary history in a single analysis, rather than relying on simpler models involving several comparisons of pairs of populations.

The difference in timing of the chimpanzee-bonobo speciation is not very great, considering the difference in mode of speciation inferred. This study prefers an older speciation time with subsequent gene flow; Hey had arrived at a later speciation time (around a million years ago, compared to 1.6 million here). This difference is a semantic one coming from the model of speciation – if there’s meaningful gene flow after a “speciation”, detectable in samples of 20 or fewer bonobos, it’s hard to say that was really a “speciation”. Restricted gene flow in an earlier, geographically structured population seems like an alternative way to describe the same model.

Possibly, the higher value for speciation time found by Wegman and Excoffier reflects the nonzero migration they infer between bonobos and eastern chimpanzees. It would be interesting to see the speciation time under the constraint of no migration; alternatively it would be interesting to strongly test the hypothesis of no migration itself. A demonstration of interbreeding in the wild between eastern chimpanzees and bonobos would be newsworthy.

One relatively large difference between the two studies is in the time inferred for the establishment of the East African chimpanzee subspecies, P. t. schweinfurthii. Hey had inferred a time of 93,000 years for this population’s founding; Wegman and Excoffier infer a much older origin, 440,000 years ago. In Wegman and Excoffier’s analysis, the East African subspecies is almost as old as the west African one.

It’s not obvious why the studies differ so greatly in this conclusion, when other conclusions are broadly equivalent (including the date of the west-central African population divergence, the asymmetrical pattern of gene flow from west into central African populations, and the much greater effective size of the central African population compared to the other two. It’s possible that Hey’s inclusion of genetic markers excluded by Wegman and Excoffier make the difference – one or two recent shared markers might greatly increase the apparent likelihood of a recent population divergence. Or the additional parameters explored by Wegman and Excoffier – they allow the populations to have grown over time – may have influenced this branch point. That assumption certainly seems to have influenced the effective size of central African chimpanzees, which Wegman and Excoffier infer to have been four times higher than Hey (135,000 versus less than 30,000).

All these estimates are scaled to generation time and mutation rate, and these differ between the two studies – Wegman and Excoffier assume that human and chimpanzee genes diverged 7 million years ago; Hey had assumed 6 million. That difference is not great, but reminds us that the present demographic results depend on a particular model of human and chimpanzee differences which is certainly in error to some extent.

Both sets of conclusions actually share most of their underlying data, although they depend on different assumptions and slightly different datasets. You can see how fast we will be able to make progress on chimpanzee population history given only a little bit more sampling. Using the chimpanzee genome to find a set of markers and genotyping them in 100 wild chimpanzees of each subspecies would provide the chimpanzee equivalent of the HapMap, and would be comparatively inexpensive. Still, I think some progress will depend on a better understanding of the pattern of human and chimpanzee (and gorilla) speciation.

References:

Gagneux P, Gonder MK, Goldberg TL, Morin PA. 2001. Gene flow in wild chimpanzee populations: what genetic data tell us about chimpanzee movement over time and space. Phil Trans R Soc Lond B 356:889-897.

Goldberg TL, Ruvolo M. 1997. Molecular phylogenetics and historical biogeography of east African chimpanzees. Biol J Linn Soc 61:301-324.

Hey J. 2010. The divergence of chimpanzee species and subspecies as revealed in multipopulation isolation-with-migration analyses. Mol Biol Evol 27:921-933. doi:10.1093/molbev/msp298

McBrearty S, Jablonski NG. 2005. First fossil chimpanzee. Nature 437:105-108. doi:10.1038/nature04008

Wegmann D, Excoffier L. 2010. Bayesian inference of the demographic history of chimpanzees. Mol Biol Evol 27:1425-1435. doi:10.1093/molbev/msq028