Genome-wide signatures of complex introgression and adaptive evolution in the big cats

Abstract

The great cats of the genus Panthera comprise a recent radiation whose evolutionary history is poorly understood. Their rapid diversification poses challenges to resolving their phylogeny while offering opportunities to investigate the historical dynamics of adaptive divergence. We report the sequence, de novo assembly, and annotation of the jaguar (Panthera onca) genome, a novel genome sequence for the leopard (Panthera pardus), and comparative analyses encompassing all living Panthera species. Demographic reconstructions indicated that all of these species have experienced variable episodes of population decline during the Pleistocene, ultimately leading to small effective sizes in present-day genomes. We observed pervasive genealogical discordance across Panthera genomes, caused by both incomplete lineage sorting and complex patterns of historical interspecific hybridization. We identified multiple signatures of species-specific positive selection, affecting genes involved in craniofacial and limb development, protein metabolism, hypoxia, reproduction, pigmentation, and sensory perception. There was remarkable concordance in pathways enriched in genomic segments implicated in interspecies introgression and in positive selection, suggesting that these processes were connected. We tested this hypothesis by developing exome capture probes targeting ~19,000 Panthera genes and applying them to 30 wild-caught jaguars. We found at least two genes (DOCK3 and COL4A5, both related to optic nerve development) bearing significant signatures of interspecies introgression and within-species positive selection. These findings indicate that post-speciation admixture has contributed genetic material that facilitated the adaptive evolution of big cat lineages.

Fig. 1. Evolutionary history of the great cats.

(A) Species tree of the genus Panthera estimated from genome-wide data. All five extant species are represented as follows: lion (Panthera leo), leopard (P. pardus), jaguar (Panthera onca), snow leopard (Panthera uncia), and tiger (Panthera tigris). Numbers above branches indicate the estimated age [in million years ago (Ma)] of the adjacent node, averaged across all genomic windows (100-kb window size, 100-kb steps) that conform to the species tree (95% highest posterior density interval below the respective branch). Colored rectangles on terminal branches indicate phenotypic categories (defined below the tree; see Fig. 3B for more details) affected by species-specific episodes of positive selection. (B) PSMC plot depicting the demographic history of the five Panthera species inferred from genomic data. (C) Genealogical discordance across the genome of Panthera cats, demonstrated by a sliding window analysis (500-kb window size, 100-kb steps) of a full-genome alignment mapped to domestic cat chromosomes (gray lines at the bottom). The y axis indicates the percentage of overlapping windows within a given interval that conform to (blue) or reject (red) the species tree. Photo credits: D. Kantek (jaguar); C. Sperka (others).

Fig. 2. In-depth characterization of phylogenetic discordance in the Panthera.

(A) Frequencies of the species tree (Tree 1) and alternative topologies on pooled autosomes (blue) and the X chromosome (red). Trees 12 and 23 show the leopard in a basal position relative to the other species (tables S6 and S7). (B) Chromosome-wide mean divergence times (in Ma), calculated from 100-kb windows that yielded the three most frequent topologies (shown below the graphs; nodes are color-coded). Note the marked drop in divergence time on the X chromosome for non–species tree topologies. (C) Complex patterns of historical admixture among Panthera lineages, inferred from ABBA/BABA tests. Colored arrows indicate the phylogenetic position of significant D statistics (shown in the table) for different species trios, using the domestic cat as the outgroup. Species codes in bold types indicate pairs for which significant evidence of admixture was detected. (D) Patterns of phylogenetic discordance along the X chromosome (estimated in 100-kb windows) correlate with the recombination landscape (10). Regions depicting species tree relationships (Tree 1), shown in white, correspond to higher recombination rates, whereas recombination deserts are enriched for alternative topologies with reduced divergence times (a signature of introgression). Two terminal, lower-recombination regions are enriched for topologies 12 and 23, depicting a basal position for leopard. These regions also harbor tracts of windows with old divergence times between the leopard and the other Panthera.

Fig. 3. Genomic evidence of natural selection in the Panthera.

(A) Venn diagrams depicting shared genes (top) and pathways (bottom) among approaches that detect positive selection (site model and branch-site model) and interspecies introgression (Outlier window) (fig. S4 and tables S9 to S13 and S28 to S38). (B) Detailed results of the branch-site test, indicating genes bearing species-specific signatures of positive selection; phenotypic categories (color-coded as in Fig. 1A) were defined on the basis of Kegg and Pathway Commons enrichment results, along with additional literature searches. (C) Two genes with jaguar-specific signatures of positive selection affect craniofacial robustness. Silhouettes on the left depict a jaguar’s robust face relative to the inferred appearance of the Panthera ancestor. The positively selected I298Y substitution in the ESRP1 gene lies in the RRM1 domain, which is known to bind to the FGFR2IIIb gene isoform and affect craniofacial development (17). The two positively selected substitutions (R39A and R42E) in the SSTR4 gene imply substantial physicochemical amino acid changes (green, nonpolar; yellow, polar; blue, basic; red, acid). (D) Schematic representation of the Glypican pathway, showing only genes that were connected with, at most, one intermediate step (in gray) and that exhibited significant signatures of positive selection (purple, site model; orange, tiger branch-site model) or interspecies introgression (blue, outlier window test).

Fig. 4. Genomic evidence of positive selection following interspecific introgression.

(A to C) Graphs depicting variation in age estimates for the trio jaguar-lion-leopard in 100-kb windows across the length of three chromosomes (top) and specific chromosomal segments containing multiple outlier windows with ages significantly younger than the genome-wide average (bottom), indicating introgression. The gray lines in the top panels (gray circles in the bottom panels) represent the basal age of the trio, whereas colored circles represent the age of the internal node in each window (blue, lion-leopard; red, lion-jaguar; green, leopard-jaguar). Below the bottom panels, the annotated exons of a candidate gene located in each focal region are indicated. (D) Intraspecific signals of positive selection in jaguars affecting the three genes highlighted in (A) to (C). The graphs depict the null distribution of the number of segregating sites per gene based on 10,000 demographic simulations (see text); the gray shading indicates significant departure (P < 0.05) from the null expectation, and the red lines represent the observed value for each gene.