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

Abstract

Inter-species 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 kb of nuclear sequence, in addition to complete mitochondrial genomes generated using light-coverage Illumina sequencing. We present the first robust felid time tree 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 cold spots, 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.

Figure 1.

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.

Figure 2.

Signatures of genome-wide phylogenetic discordance. (A) Results of sliding window-based approximately unbiased (AU) tests for each of the eight felid lineages (see Methods for details). Horizontal panels indicate genomic regions (vertical bars) that produced significantly better topologies than the species tree topology. Felid chromosomes are displayed in bars below the scale spanning the length of the feline genome. Abbreviations for lineages are as follows: (ALC) Asian leopard cat, (DOM) Domestic cat, (LYN) Lynx, (BAY) Bay cat, (PUM) Puma, (CAR) Caracal, (OCE) Ocelot, (PAN) Panthera. (B) Summary statistics for results in Figure 1A. The white bars represent the percentage of sliding windows supporting the species tree topology (black bars) with bootstrap support ≥ 70% (Hillis and Bull 1993). The gray bars indicate the proportion of nonspecies tree topologies identified by the AU test that were significantly better than the species tree (Fig. 1A).

Figure 3.

Patterns of hybridization within felid lineages. (A) Ocelot lineage, showing the discordant position of the northern tigrina (green) between nuclear (red) and mitogenome (black) phylogenies. Within the species tree is shown nuclear (red) and mitogenome (black) genealogies, with dashed red lines indicating genomic evidence for ancient hybridization (not scaled to time). (B) Asian leopard cat lineage, showing the discordant position of the fishing cat (green) relative to the Asian leopard cat populations in nuclear and mitogenome trees. (C) Domestic cat lineage, showing the results of admixture tests based on whole-genome SNV alignments which reveal two strong introgression signals (a and b) across the whole genome of Felis species. (D) Panthera lineage, showing the discordant position of the snow leopard (green) between nuclear and mitogenome phylogenies. Admixture tests from whole-genome SNV alignments support gene flow from the lion/leopard lineage to the snow leopard. Note the significantly skewed D-statistic for the X Chromosome (right).

Figure 4.

Evidence for admixture within Panthera genome sequences. (A) Species tree topology of the three Panthera species defined by black outline. Blue lines represent coalescent patterns of tiger + snow leopard shared alleles, green indicates lion + tiger shared alleles, and red represents lion + snow leopard shared alleles. (B) Distribution of trees supporting each topology from the genome-wide sliding window analysis (y-axis) plotted against divergence time (x-axis), shown for autosomes and the X Chromosome (see Supplemental Fig. S9 for individual chromosome plots). (C) Mean and standard error for divergence times for each category of sister-species relationship within the three taxa. (D) Phylogeny and relative divergence time (y-axis, in millions of years ago) for each window plotted along the largest autosome (Chromosome A1, above) and the X Chromosome (below). Dots are color-coded for each of the three sister-species relationships (see legend). The gray dots indicate the age of the base of Panthera. Note the drop in divergence times for both internal and basal nodes in regions corresponding to extremely low recombination rates (bottom). Recombination data are from the domestic cat linkage map (Schmidt-Kuntzel et al. 2009).