[LINK] "Genetic diversity among chimpanzees reveals just how closely related humans really are"

[rfmcdonald]

io9 linked to a very interesting study of chimpanzee genetics suggesting that humans--by comparison, and notwithstanding their substantially larger numbers--are genetically much less diverse than their nearest relatives.

There are four genetically distinct chimpanzee populations, all found in two relatively small regions of Africa. And yet these populations, which are sometimes less than a mile apart, are more genetically diverse than humans that live on different continents.

Three of the common chimpanzee groups are found in very close quarters[.] While the distinct bonobo subspecies in in red on the southern side of the Congo River, the Eastern, Central, and Cameroonian subspecies form a nearly contiguous region in Central Africa, with only the Western population isolated from the others by any considerable geographic distance.

That's why the results of a new genomic study conducted by an international team of researchers is so surprising. Based on the DNA from 54 chimps taken from across these four populations, these chimps really are genetically distinct from each other despite often being so close together. What's more, the genetic diversity of these different chimp populations, even those who are practically right on top of each other, is significantly greater than that found in humans separated by entire continents. Oxford professor Peter Donnelly explains:

"Relatively small numbers of humans left Africa 50,000-100,000 years ago. All non-African populations descended from them, and are reasonably similar genetically. That chimpanzees from habitats in the same country, separated only by a river, are more distinct than humans from different continents is really interesting. It speaks to the great genetic similarities between human populations, and to much more stability, and less interbreeding, over hundreds of thousands of years, in the chimpanzee groups."

The poster links to the PLoS Genetics paper "Genomic Tools for Evolution and Conservation in the Chimpanzee: Pan troglodytes ellioti Is a Genetically Distinct Population", of which a noteworthy portion is posted below.

We have applied a number of different analytical methods to an extensive set of SNP data from 54 chimpanzees. All of the methods point clearly to the existence of three distinct population groups, corresponding to three of the previously-described “subspecies” of chimpanzee P. t. verus, P. t. troglodytes, and P. t. ellioti, with the latter two groups sharing somewhat more similarity with each other than either does with P. t. verus. P. t. troglodytes and P. t. verus are two securely defined populations estimated to have diverged 0.4–0.6 million years ago. Our analyses show P. t. ellioti to be clearly distinct from P. t. troglodytes with both groups equally distinct from P. t. verus, so that whatever terminology (“population” or “subspecies”) is applied to verus and troglodytes should equally be applied to ellioti.

By way of comparison, we have shown that these three chimpanzee populations are more differentiated than even continental human populations, and also that in spite of the relatively close geographic proximity of the groups, particularly troglodytes and ellioti, the chimpanzee populations are considerably more distinct than the African populations sampled in HapMap III, suggesting rather differing demographic histories for the two sister species.

In order to compare population comparisons based on the copying model with those based on more traditional FST approaches, we also calculated pairwise FST values for each of the 100 resamples of individuals and SNPs in our analyses of the three continental population samples. The results are summarized in Table 2. We note that while the average values of pairwise FST across the 100 samples show the same pattern as copying proportions in the copying model, the sample-to-sample variation is larger. For example, the FST intervals for the central 95% of resamples for Europe-East Asia overlap those of Africa-Europe and Africa-East Asia, and for example for five of the 100 resamples the pairwise FST between Africa and Europe was actually smaller than that between Europe and East-Asia. In contrast, for the copying model analysis the 95% intervals for the proportion that Europe and East Asia copy from each other do not overlap with the 95% intervals for either copying from Africa, and the proportion that Europe copied from Africa was lower than the proportion Europe copied from East Asia in each of the 100 re-samples. This accurately reflects the fact that on average East Asia and Europe share more recent ancestry with each other than with Africa.

One weakness of our study (and some others) is that we do not have definitive information on the geographic origin of all of the chimpanzees we have studied. All our analyses point to two very distinct population groups for the chimpanzees originating from eastern Nigeria and Cameroon. In the light of other genetic evidence for distinctiveness of individuals sampled from either side of the Sanaga Riverour assignment of one of our sampled groups as troglodytes and one as ellioti seems reasonable. Whilst our data alone could not rule out two distinct populations, one or both of which extends across the Sanaga River, this seems a priori unlikely – the river provides a natural barrier between the distinct populations, whereas if both were to exist on the same side of the river there seems no reason for their reproductive isolation—and at variance to other available evidence. Notwithstanding our lack of complete geographical information on sampled chimpanzees, the clear separation between all three populations, relative to the similarities within the populations, seems hard to reconcile with the suggestion that chimpanzee genetic variation is distributed more or less continuously across the species range.

There's a certain irony in all this: although chimpanzees currently face the threat of extinction from we their near-cousins, who are smarter or more capable generally than chimpanzees whatever their subspecies, chimpanzees don't seem to have gone through the near-extinction events that human beings seem to have gone through at least once.