Genetics of orangutan demographic collapse

I'm reading a new paper by Benoit Goossens and colleagues (2006) in PLoS Biology, called "Genetic signature of anthropogenic population collapse in orang-utans". The abstract:

Great ape populations are undergoing a dramatic decline, which is predicted to result in their extinction in the wild from entire regions in the near future. Recent findings have particularly focused on African apes, and have implicated multiple factors contributing to this decline, such as deforestation, hunting, and disease. Less well-publicised, but equally dramatic, has been the decline in orang-utans, whose distribution is limited to parts of Sumatra and Borneo. Using the largest-ever genetic sample from wild orang-utan populations, we show strong evidence for a recent demographic collapse in North Eastern Borneo and demonstrate that this signature is independent of the mutation and demographic models used. This is the first demonstration that genetic data can detect and quantify the effect of recent, human-induced deforestation and habitat fragmentation on an endangered species. Because current demographic collapses are usually confounded by ancient events, this suggests a much more dramatic decline than demographic data alone and emphasises the need for major conservation efforts.

Basically, the claims are that genetic variation shows that orangutans on Borneo began crashing in population size within the past century or so, and that disputed census figures from the 1980's that estimated a very large population of orangutans (then) may have been accurate, since the ongoing collapse has been very rapid.

I have to say, I'm not sure about this one. There's quite a bit of "fighting with the method" in this paper which to me is never a good sign. The main analysis is a Boolean method, and they emphasize repeatedly how conservative their prior assumptions are. They could be right, but that's not really the problem.

The biggest potential problem is population structure, which previous studies (e.g., Warren et al. 2001) suggested was very strong among Bornean orangutans. This study notes that population structure within the population that they sampled is relatively slight, with low FST between groups. Of course, that doesn't quite answer the question, since the analysis of demographic structure depends on a paucity of young rare alleles and an excess of old intermediate-frequency ones. Since populations on Borneo haven't necessarily been historically isolated, these old alleles might easily come from other Bornean populations, the ones that according to Warren et al. (2001) have a mean genetic divergence over 800,000 years ago.

So I'm not so sure about the demographic interpretations here. Hard to say that the problem of population structure would result in the signature of very recent collapse (instead of, say, a more ancient event), but collapses are tricky to interpret -- expansions are much more straightforward.

In this case, there is no chance that genetics are picking up a population crash that has been going on since the 1980's -- that is so recent that there should be barely any new rare alleles to miss in a sample. The idea that a collapse since 1980 is supported by a collapse ongoing since 1900 is pretty tenuous. The paper's best claim is that population collapse didn't start a long time ago -- say when humans first reached Borneo, for example. Their analyses certainly support that point -- orangutans may have coexisted with humans well enough as long as people weren't cutting down the forest. But I'm not sure that the analyses aren't affected by population structure in a way that would mess up these estimates.

References:

Goossens B, Chikhi L, Ancrenaz M, Lackman-Ancrenaz I, Andau P, Bruford MW. 2006. Genetic signature of anthropogenic population collapse in orang-utans. PLoS Biol 4:e25. Full text

Warren KS et al. 2001. Speciation and intrasubspecific variation of Bornean orangutans, Pongo pygmaeus pygmaeus. Mol Biol Evol 10:472-480.