I’ve been thinking about the concordance of genomes between the two lineages of pink salmon and between populations of Chinook salmon originating in Beringia and Cascadia.  I’ve found a lot of studies ranging from Ruth Phillips’ original karyotype work to complete genome comparisons in model species.

Here is a study looking at subspecies of mice in the early stages of species divergence:

http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1000729

This situation might be a good comparison for Wes’ island sockeye work (detecting islands in that early sweet spot of divergence).  They used an approach called Bayesian concordance analysis that estimates a concordance factor among gene clades:

http://www.stat.wisc.edu/~ane/bucky/index.html

As we collect more genome-scale data from populations across the ranges of species, and among lineages and species, could this be a useful tool to characterize genome concordance and complement standard outlier tests?  Do you have other suggestions for methods to quantify genome concordance outside of standard approaches (# linkage groups, Fst and outlier tests, etc.)?

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