Xin Ma, Joanna L. Kelley, Kirsten Eilertson, Shaila Musharoff, Jeremiah D. Degenhardt, Andre L. Martins, Tomas Vinar, Carolin Kosiol, Adam Siepel, Ryan N. Gutenkunst, Carlos D. Bustamante. Population Genomic Analysis Reveals a Rich Speciation and Demographic History of Orang-utans (Pongo pygmaeus and Pongo abelii). PLoS One, 8(10):e77175. 2013.

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To gain insights into evolutionary forces that have shaped the history of Bornean
and Sumatran populations of orang-utans, we compare patterns of variation across 
more than 11 million single nucleotide polymorphisms found by previous
mitochondrial and autosomal genome sequencing of 10 wild-caught orang-utans. Our 
analysis of the mitochondrial data yields a far more ancient split time between
the two populations ( approximately 3.4 million years ago) than estimates based
on autosomal data (0.4 million years ago), suggesting a complex speciation
process with moderate levels of primarily male migration. We find that the
distribution of selection coefficients consistent with the observed frequency
spectrum of autosomal non-synonymous polymorphisms in orang-utans is similar to
the distribution in humans. Our analysis indicates that 35% of genes have evolved
under detectable negative selection. Overall, our findings suggest that purifying
natural selection, genetic drift, and a complex demographic history are the
dominant drivers of genome evolution for the two orang-utan populations.