July 03, 2013

The history of great apes

Nature (2013) doi:10.1038/nature12228

Great ape genetic diversity and population history

Javier Prado-Martinez et al.

Most great ape genetic variation remains uncharacterized1, 2; however, its study is critical for understanding population history3, 4, 5, 6, recombination7, selection8 and susceptibility to disease9, 10. Here we sequence to high coverage a total of 79 wild- and captive-born individuals representing all six great ape species and seven subspecies and report 88.8 million single nucleotide polymorphisms. Our analysis provides support for genetically distinct populations within each species, signals of gene flow, and the split of common chimpanzees into two distinct groups: Nigeria–Cameroon/western and central/eastern populations. We find extensive inbreeding in almost all wild populations, with eastern gorillas being the most extreme. Inferred effective population sizes have varied radically over time in different lineages and this appears to have a profound effect on the genetic diversity at, or close to, genes in almost all species. We discover and assign 1,982 loss-of-function variants throughout the human and great ape lineages, determining that the rate of gene loss has not been different in the human branch compared to other internal branches in the great ape phylogeny. This comprehensive catalogue of great ape genome diversity provides a framework for understanding evolution and a resource for more effective management of wild and captive great ape populations.

Link

5 comments:

Timmay said...

The human-chimpanzee divergance postulated by that graph is far to recent.

I thought that recent discoveries concerning the human mutation rate had pushed back the divergance well past 5 million years.

Palisto said...

Does the figure say that our human ancestors started to diverge from the Chimp/Bonobo ancestors 10 million years ago, but for another 3 million years there was still gene flow (a.k.a. mating) between them?

GARMALL said...

Timmay, the actual value of the chimp-human split was estimated to be almost 4myr with a mutation rate of 1e-9. This estimate is really dependent on the mutation rate which can double to 8myr the split. (you can find the values of this figure here: http://www.nature.com/nature/journal/vaop/ncurrent/extref/nature12228-s2.xlsx)

Palisto, the two lines correspond to the divergence (light brown) and the actual split time (dark brown). The divergence time should be the sum of the split time and twice the ancestral Ne at that time.

Grognard said...

Wow, this is just way off. Complete fantasy. Along the lines of saying humans and chimps share 97.5% of their DNA (which isn't even true between most human individuals).

terryt said...

"Along the lines of saying humans and chimps share 97.5% of their DNA (which isn't even true between most human individuals)".

Humans actually share a considerable proportion of their DNA even with fungi, and even more with mice and other mammals.

"Does the figure say that our human ancestors started to diverge from the Chimp/Bonobo ancestors 10 million years ago, but for another 3 million years there was still gene flow (a.k.a. mating) between them?"

A period of gene flow between chimp and human ancestors after they first split was claimed some years ago:

http://www.ncbi.nlm.nih.gov/pubmed/16710306

Although the finding has been disputed:

http://mbe.oxfordjournals.org/content/early/2011/09/07/molbev.msr172.abstract

But this paper mentioned:

"Our analysis provides support for genetically distinct populations within each species, signals of gene flow, and ..."

It surely makes sense that the two species did not separate over a single night.