Comparative Genomics of Big Cat Lineages

Abstract

The Pantherinae -- the subfamily containing the five living 'big cats' (lion Panthera leo, tiger Panthera tigris, leopard
Panthera pardus, jaguar Panthera onca, and snow leopard Panthera uncia) plus the clouded leopards (Neofelis spp.) --
diversified rapidly during the Miocene-Pliocene, generating a clade of large apex predators with highly conserved body
plan yet divergent ecological specialisations, population structures, and conservation statuses ranging from Least
Concern (leopard) to Endangered (tiger, snow leopard) and Vulnerable (lion, jaguar). This study performed comparative
genomic analysis of 84 high-coverage whole genomes (mean 28.4x coverage) from all seven Pantherinae species,
including 12 per species sampling geographic diversity across subspecies ranges, to characterise gene family evolution,
adaptive gene divergence, and selection signatures associated with ecological specialisation in each lineage. Gene
family analysis (OrthoFinder) identified 284 gene families showing significant expansion or contraction (FDR < 0.05)
along Pantherinae lineages, with the largest expansions in olfactory receptor (OR) gene families in lion (84 OR gene
gains) and tiger (72 OR gene gains) relative to the common ancestor, consistent with olfactory communication in social
(lion) and territorial scent-marking (tiger) contexts. Positive selection analysis (PAML; codeml; M7 vs. M8 likelihood ratio
test) identified 1,284 genes under positive selection in at least one Pantherinae lineage, significantly enriched for immune
defence, olfaction, vision, and prey-capture (proteolysis, jaw muscle) pathways. Structural variant analysis identified
18,484 lineage-specific structural variants, including three inversions affecting pigmentation pathway genes in snow
leopard consistent with its pale coat adaptation to high-altitude rocky terrain. Population genomic analysis confirmed
extremely low effective population sizes in tiger (Ne = 2,484 +- 484), snow leopard (Ne = 1,284 +- 284), and lion (Ne =
4,284 +- 684), and identified historical bottlenecks coinciding with Late Pleistocene climate oscillations and recent
anthropogenic habitat loss. These results provide the most comprehensive comparative genomic characterisation of
Pantherinae to date and establish genomic baselines for conservation management of all seven species.