Searching for Closure in the Quest for a Phylogeny of the Panthera Genus

Background: The evolutionary relationships within the genus Panthera —which includes the lion ( P. leo ), tiger ( P. tigris ), leopard ( P. pardus ), jaguar ( P. onca ), and snow leopard ( P. uncia )—remain unresolved despite decades of molecular and morphological research. Conflicting phylogenetic models, particularly regarding the placement of the snow leopard, have created persistent taxonomic uncertainty. This study sought to evaluate protein-level similarities among all Panthera species using amino acid sequences from five mitochondrial genes (ND1–ND5) “to determine whether protein-based distances support or differ from published mitochondrial DNA relationships.” Results: A total of 785 amino acid differences were identified across the five mitochondrial proteins analyzed. Pairwise comparison matrices and position-specific scoring profiles revealed that interspecies distances derived from protein data were consistent with previously reported mitochondrial DNA patterns. The highest similarity was observed between the tiger and snow leopard, followed by close clustering of the lion and leopard. Phylogenetic reconstructions generated from protein data reinforced the inclusion of the snow leopard within the Panthera genus rather than its historical classification as Uncia uncia . Conclusions: This study demonstrates strong concordance between protein and mitochondrial sequence analyses, strengthening the case for recognizing Panthera uncia as a valid member of the genus Panthera . The integration of amino acid–based data offers a complementary molecular approach for resolving phylogenetic disputes and contributes to the long-standing goal of establishing a stable, evidence-based evolutionary framework for the great cats.