Tuesday, June 28, 2011

Ascertainment bias data sets?

Hi folks,
I'm working on a simulation study looking at the effects of using ascertained SNP data for phylogenetic and phylogeographic reconstruction. I'm basing my simulations on real data sets. I have a few but am looking for more!
Have any of you seen studies recently that use single nucleotide loci that were selected based on being polymorphic is some ascertainment panel? Mostly SNP chip based data sets are what I was thinking of, but there are others too.
For example, Decker et al. 2009 used marker loci that are known to be polymorphic in cattle to reconstruct divergences up to 29 mya across bovidae.
SNP chip data are cheap and easy to get- I want to figure out how far you can push using them!
Send me an email! ejmctavish [at] utexas.edu

Fig. 1 from Decker et al 2009. Strict consensus cladogram (no branch lengths) of 17 most parsimonious trees based on 40,843 SNP genotypes. *, Denotes paraphyletic group.


  1. Have you seen this paper?


  2. This paper on Haitian cholera uses 30 SNP's obtained from a previously defined reference panel:

    Chin et al. 2011. The origin of the Haitian cholera outbreak strain. New England Journal of Medicine. 364: 33-42.