The pantherine lineage of cats diverged from the remainder of modern Felidae less
than 11 million years ago and consists of the five big cats of the genus Panthera,
the lion, tiger, jaguar, leopard, and snow leopard, as well as the closely related
clouded leopard. A significant problem exists with respect to the precise phylogeny
of these highly threatened great cats. Despite multiple publications on the subject,
no two molecular studies have reconstructed Panthera with the same topology. These
evolutionary relationships remain unresolved partially due to the recent and rapid
radiation of pantherines in the Pliocene, individual speciation events occurring within
less than 1 million years, and probable introgression between lineages following their
divergence. We provide an alternative, highly supported interpretation of the evolutionary
history of the pantherine lineage using novel and published DNA sequence data from
the autosomes, both sex chromosomes and the mitochondrial genome. New sequences were
generated for 39 single-copy regions of the felid Y chromosome, as well as four mitochondrial
and four autosomal gene segments, totaling 28.7 kb. Phylogenetic analysis of these
new data, combined with all published data in GenBank, highlighted the prevalence
of phylogenetic disparities stemming either from the amplification of a mitochondrial
to nuclear translocation event (numt), or errors in species identification. Our 47.6
kb combined dataset was analyzed as a supermatrix and with respect to individual partitions
using maximum likelihood and Bayesian phylogenetic inference, in conjunction with
Bayesian Estimation of Species Trees (BEST) which accounts for heterogeneous gene
histories. Our results yield a robust consensus topology supporting the monophyly
of lion and leopard, with jaguar sister to these species, as well as a sister species
relationship of tiger and snow leopard. These results highlight new avenues for the
study of speciation genomics and understanding the historical events surrounding the
origin of the members of this lineage.
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