Gene Expression

Check out this cool paper in PLOS Genetics:

In this first application of the approximate Bayesian computation approach using the serial coalescent, we demonstrated the estimation of historical demographic parameters from ancient DNA. We estimated the timing and severity of a population bottleneck in an endemic subterranean rodent, Ctenomys sociabilis, over the last 10,000 y from two cave sites in northern Patagonia, Argentina….We found a decrease from a female effective population size of 95,231 to less than 300 females at 2,890 y before present: a 99.7% decline. Our study demonstrates the persistence of a species depauperate in genetic diversity for at least 2,000 y and has implications for modes of speciation in the incredibly diverse rodent genus Ctenomys. Our approach shows promise for determining demographic parameters for other species with ancient and historic samples and demonstrates the power of such an approach using ancient DNA.

I hope John Hawks and the gang can get their buddies to lend them some ancient DNA! The character of human evolutionary bottlenecks is a major issue in how we view the origin of our own species. There is other cool stuff about founder effect speciation (founder flush?) and the evolution of sociality via kin selection.

Here’s the Eureka Alert summation.


  1. #1 windy
    April 20, 2006

    I don’t think they pointed out, that lack of variation in neutral genes does not always mean that the population lacks adaptive variation as well:

    ‘High MHC diversity maintained by balancing selection in an otherwise genetically monomorphic mammal’

    (Although MHC is a bit of a special case.)

    It seems that the subject areas of the different PLOS journals are still evolving – there’s stuff on orang-utan bottlenecks in “Biology” but this was in “Genetics”. Or is that because the former is for slightly more high-profile stuff? Interesting, anyway.

  2. #2 RPM
    April 21, 2006

    I think they’re overhyping this. Havn’t Beth Shapiro and colleagues been doing coalescent’s on ancient DNAs for a couple of years now ( Note that the authors of this paper do not cite the Shapiro paper, which seems a bit odd to me.

    I’m also a bit bothered by the application of the coalescent to ancient DNA. I believe the coalescent requires the assumption of sampling from the tips of a genealogy. When some of the chromosomes/haplotypes in your sample are located internally, I would think that you’re violating a key assumption of the model. I have limited knowledge of the theory and practice of coalescent simulations, so I may be wrong. I should have asked Shapiro about this when I saw her speak last year.

  3. #3 razib
    April 21, 2006

    MHC is a very special case though. remember, this i a complex of loci where diversity has been preserved for tens of millions of years, so that alleles span species. and even in this case some mammals have been MHC homogenized. the northern elephant seal and the cheetah are two cases.

  4. #4 RPM
    April 21, 2006

    Razib, I posted a comment about how this result seems trivial in light of work published by Beth Shapiro a couple of years ago, but the comment never showed up. I’m adding this comment (sans the links from the original which may have upped the junk score) so that I have something written down here.

    I’m also bothered by coalescent simulations that use samples from multiple generations (especially when they come from ancient DNA). I’m not all to familiar with the serial coalescent, so I should probably look into it before criticizing this aspect of the paper.

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