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Abstract Phylogenomic analyses of closely related species allow important glimpses into their evolutionary history. Although recent studies have demonstrated that inter-species hybridization has occurred in several groups, incorporating this process in phylogenetic reconstruction remains challenging. Specifically, the most predominant topology across the genome is often assumed to reflect the speciation tree, but rampant hybridization might overwhelm the genomes, causing that assumption to be violated. The notoriously challenging phylogeny of the 5 extant Panthera species (specifically jaguar [P. onca], lion [P. leo], and leopard [P. pardus]) is an interesting system to address this problem. Here we employed a Panthera-wide whole-genome-sequence data set incorporating 3 jaguar genomes and 2 representatives of lions and leopards to dissect the relationships among these 3 species. Maximum-likelihood trees reconstructed from non-overlapping genomic fragments of 4 different sizes strongly supported the monophyly of all 3 species. The most frequent topology (76–95%) united lion + leopard as a sister species (topology 1), followed by lion + jaguar (topology 2: 4–8%) and leopard + jaguar (topology 3: 0–6%). Topology 1 was dominant across the genome, especially in high-recombination regions. Topologies 2 and 3 were enriched in low-recombination segments, likely reflecting the species tree in the face of hybridization. Divergence times between sister species of each topology, corrected for local-recombination-rate effects, indicated that the lion-leopard divergence was significantly younger than the alternatives, likely driven by post-speciation admixture. Introgression analyses detected pervasive hybridization between lions and leopards, regardless of the assumed species tree. This inference was strongly supported by multispecies-coalescence-with-introgression analyses, which rejected topology 1 (lion+leopard) or any model without introgression. Interestingly, topologies 2 (lion+jaguar) and 3 (jaguar+leopard) with extensive lion-leopard introgression were unidentifiable, highlighting the complexity of this phylogenetic problem. Our results suggest that the dominant genome-wide tree topology is not the true species tree but rather a consequence of overwhelming post-speciation admixture between lion and leopard. 

Genomic data from species of the cat family Felidae promise to stimulate veterinary and human medical advances, and clarify the coherence of genome organization. We describe how interspecies hybrids have been instrumental in the genetic analysis of cats, from the first genetic maps to propelling cat genomes toward the T2T standard set by the human genome project. Genotype-to-phenotype mapping in cat models has revealed dozens of health-related genetic variants, the molecular basis for mammalian pigmentation and patterning, and species-specific adaptations. Improved genomic surveillance of natural and captive populations across the cat family tree will increase our understanding of the genetic architecture of traits, population dynamics, and guide a future of genome-enabled biodiversity conservation. 

Habitat degradation and loss of genetic diversity are common threats faced by almost all of today’s wild cats. Big cats, such as tigers and lions, are of great concern and have received considerable conservation attention through policies and international actions. However, knowledge of and conservation actions for small wild cats are lagging considerably behind. The black-footed cat,Felis nigripes, one of the smallest felid species, is experiencing increasing threats with a rapid reduction in population size. However, there is a lack of genetic information to assist in developing effective conservation actions. A de novo assembly of a high-quality chromosome-level reference genome of the black-footed cat was made, and comparative genomics and population genomics analyses were carried out. These analyses revealed that the most significant genetic changes in the evolution of the black-footed cat are the rapid evolution of sensory and metabolic-related genes, reflecting genetic adaptations to its characteristic nocturnal hunting and a high metabolic rate. Genomes of the black-footed cat exhibit a high level of inbreeding, especially for signals of recent inbreeding events, which suggest that they may have experienced severe genetic isolation caused by habitat fragmentation. More importantly, inbreeding associated with two deleterious mutated genes may exacerbate the risk of amyloidosis, the dominant disease that causes mortality of about 70% of captive individuals. Our research provides comprehensive documentation of the evolutionary history of the black-footed cat and suggests that there is an urgent need to investigate genomic variations of small felids worldwide to support effective conservation actions. 

Abstract Even in the genomics era, the phylogeny of Neotropical small felids comprised in the genus Leopardus remains contentious. We used whole-genome resequencing data to construct a time-calibrated consensus phylogeny of this group, quantify phylogenomic discordance, test for interspecies introgression, and assess patterns of genetic diversity and demographic history. We infer that the Leopardus radiation started in the Early Pliocene as an initial speciation burst, followed by another in its subgenus Oncifelis during the Early Pleistocene. Our findings challenge the long-held notion that ocelot (Leopardus pardalis) and margay (L. wiedii) are sister species and instead indicate that margay is most closely related to the enigmatic Andean cat (L. jacobita), whose whole-genome data are reported here for the first time. In addition, we found that the newly sampled Andean tiger cat (L. tigrinus pardinoides) population from Colombia associates closely with Central American tiger cats (L. tigrinus oncilla). Genealogical discordance was largely attributable to incomplete lineage sorting, yet was augmented by strong gene flow between ocelot and the ancestral branch of Oncifelis, as well as between Geoffroy's cat (L. geoffroyi) and southern tiger cat (L. guttulus). Contrasting demographic trajectories have led to disparate levels of current genomic diversity, with a nearly tenfold difference in heterozygosity between Andean cat and ocelot, spanning the entire range of variability found in extant felids. Our analyses improved our understanding of the speciation history and diversity patterns in this felid radiation, and highlight the benefits to phylogenomic inference of embracing the many heterogeneous signals scattered across the genome. 

Clouded leopards (Neofelisspp.), a morphologically and ecologically distinct lineage of big cats, are severely threatened by habitat loss and fragmentation, targeted hunting, and other human activities. The long-held poor understanding of their genetics and evolution has undermined the effectiveness of conservation actions. Here, we report a comprehensive investigation of the whole genomes, population genetics, and adaptive evolution ofNeofelis. Our results indicate the genusNeofelisarose during the Pleistocene, coinciding with glacial-induced climate changes to the distributions of savannas and rainforests, and signatures of natural selection associated with genes functioning in tooth, pigmentation, and tail development, associated with clouded leopards’ unique adaptations. Our study highlights high-altitude adaptation as the main factor driving nontaxonomic population differentiation inNeofelis nebulosa. Population declines and inbreeding have led to reduced genetic diversity and the accumulation of deleterious variation that likely affect reproduction of clouded leopards, highlighting the urgent need for effective conservation efforts. 

Abstract Tree House Explorer (THEx) is a genome browser that integrates phylogenomic data and genomic annotations into a single interactive platform for combined analysis. THEx allows users to visualize genome-wide variation in evolutionary histories and genetic divergence on a chromosome-by-chromosome basis, with continuous sliding window comparisons to gene annotations, recombination rates, and other user-specified, highly customizable feature annotations. THEx provides a new platform for interactive phylogenomic data visualization to analyze and interpret the diverse evolutionary histories woven throughout genomes. Hosted on Conda, THEx integrates seamlessly into new or pre-existing workflows. 

Tree House Explorer (THEx) is a genome browser that integrates phylogenomic data and genomic annotations into a single interactive platform for combined analysis. THEx allows users to visualize genome-wide variation in evolutionary histories and genetic divergence on a chromosome-by-chromosome basis, with continuous sliding window comparisons to gene annotations, recombination rates, and other user-specified, highly customizable feature annotations. THEx provides a new platform for interactive phylogenomic data visualization to analyze and interpret the diverse evolutionary histories woven throughout genomes. Hosted on Conda, THEx integrates seamlessly into new or pre-existing workflows.