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:
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:
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.)?