Fig. 4.

Pairwise comparison of species phylogenies inferred by breakpoint-based and LD-based methods on the empirical dataset. A species phylogeny was inferred for each mouse autosome using either the breakpoint-based method (“Breakpoint-based”) or an LD-based method. For the latter, sampled locus length varied between 1 SNP and at most 15 SNPs (which corresponds to an average genomic distance of around 100 kb, as shown in Additional file 1: Figure S5; each LD-based method is labeled by its sampled locus length (“1” through “15”). Pairwise topological comparisons are reported based upon average RF distance [26] across all mouse autosomes (n=19). Only upper triangular entries in the matrix are shown. Each cell is colored in a shade ranging from white to blue, corresponding to average normalized RF distance ranging from 0 to 1, respectively