Data from: Phylogenomic evidence for ancient hybridization in the genomes of living cats (Felidae)

Interspecies hybridization has been recently recognized as potentially
common in wild animals, but the extent to which it shapes modern genomes
is still poorly understood. Distinguishing historical hybridization events
from other processes leading to phylogenetic discordance among different
markers requires a well-resolved species tree that considers all modes of
inheritance, and overcomes systematic problems due to rapid lineage
diversification by sampling large genomic character sets. Here we assessed
genome-wide phylogenetic variation across a diverse mammalian family,
Felidae (cats). We combined genotypes from a genome-wide SNP array with
additional autosomal, X- and Y-linked variants to sample ~150 kilobases of
nuclear sequence, in addition to complete mitochondrial genomes generated
using light-coverage Illumina sequencing. We present the first robust
felid timetree that accounts for unique maternal, paternal, and biparental
evolutionary histories. Signatures of phylogenetic discordance were
abundant in the genomes of modern cats, in many cases indicating
hybridization as the most likely cause. Comparison of big cat whole-genome
sequences revealed a substantial reduction of X-linked divergence times
across several large recombination coldspots, which were highly enriched
for signatures of selection-driven post-divergence hybridization between
the ancestors of the snow leopard and lion lineages. These results
highlight the mosaic origin of modern felid genomes and the influence of
sex chromosomes and sex-biased dispersal in post-speciation gene flow. A
complete resolution of the Tree of Life will require comprehensive genomic
sampling of biparental and sex-limited genetic variation to identify and
control for phylogenetic conflict caused by ancient admixture and
sex-biased differences in genomic transmission.