Fig. 5

Tree topology changes with variation in recombination rate and introgression. a The frequency distribution of the four most common topologies in the high- and low-recombination regions of the autosomal and Z chromosomes, respectively. b, c Interplay between the topological distribution and recombination rate variation (left) as well as between the topological distribution and genetic introgression (right) in the Z chromosome (b) and autosomes (c). Topology 4 (blue), which is congruent with the phylogeny inferred from the intron-set, is enriched in the genomic regions with high-recombination rate and high level of gene flow, while the topology 3 (reddish) is more common in the genomic regions with low-recombination rates and less signature of gene flow. d ASTRAL species trees reconstructed for the low-recombination regions within the Z chromosome (left) and for the high-recombination regions within the autosomes (right), respectively. The two phylogenies differ in the position of P. montanella/P. rubida, P. fulvescens/P. koslowi, and P. modularis (indicated by reddish branches). The phylogeny of high recombination regions within autosomes is similar to those of intron-set