This is only tangentially related to our theme, but interesting nonetheless…
Orangutans are separated into two populations (Sumatran and Bornean) and, according to many researchers, are distinct species. A recent study in Nature provides us with a draft genome from a single Sumatran individual and shorter sequences from a handful of Sumatran and Bornean individuals. What is really interesting here is that the Sumatran/Bornean speciation time is estimated to be about 400,000 years ago, which is much, much more recent than the estimate provided by mitochondrial DNA from a previous study (about 3.5 million years ago). As the authors of the new study point out, this “underscores the complexity of the orang-utan speciation process.”
We run into the same sort of issues when estimating divergence times for humans and chimps and when we compare the genomes of modern humans. It really does depend on what part of the genome you are looking at.
Arora, N. et al. (2010). Effects of Pleistocene glaciations and rivers on the population structure of Bornean oragutans (Pongo pygmaeus). Proceedings of the National Academy of Sciences 107: 21376-21381.