Discordant phylogenetic patterns across maternal, paternal, and biparentally inherited subgenomic partitions. (A) Comparison of nuclear genome and mitogenome phylogenies. The nuclear phylogeny/time tree excludes the Y Chromosome partition. Lines between the two trees indicate alternative placement of particular species (black) or clades (red). Dashed lines represent poorly supported alternative placements. The time tree is based on the average divergence times across eight individual MCMCtree analyses (Supplemental Table S3). Lineages are color-coded based on their current/historical distributions (see inset map). Dashed lines indicate hypothesized dispersal events out of Eurasia. Gray vertical bars indicate periods of extended low sea level (Haq et al. 1987) that may have facilitated dispersal between continents/islands. Asterisks indicate ML bootstrap support values of 100 in all analyses (all SNPs/binary-coded SNPs/SNP + gene supermatrix). (B) Phylogenies showing relationships and bootstrap support values for eight felid lineages based on the mitogenome, X Chr (5761-bp), Y Chr (5352-bp), and autosomal (123,906-bp) SNP + gene supermatrix partitions. Bootstrap support for monophyly of each lineage is 100% (data not shown). The Bay cat clade is displayed in boldface to highlight the different topological positions based on different modes of inheritance.