Figure 3. Genome-wide phylogenetic discordance.

Bayesian concordance factors were calculated from the posterior probability distributions of 14,081 single-locus phylogenetic analyses. The concordance analysis is depicted using three different priors on gene tree concordance: complete independence among loci (α  =  infinity), a high probability of concordance among loci (α = 10⁻⁶), and an intermediate level of concordance (α = 1). The M. m. musculus/M. m. castaneus topology is supported by significantly more loci than the other two topologies regardless of the prior on gene tree concordance. Colors correspond to the three topologies. Error bars are 95% credibility intervals.