Freak Felids - A Discussion of History's Largest Felines

[Ngala]

Genome-wide signatures of complex introgression and adaptive evolution in the big cats Figueiro et al., 2017

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(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).

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." Reply