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Canis dirus lived during the Rancholabrean land mammal age of North America (240,000–10,000 years BP) and was among the many large carnivores and megaherbivores that became extinct in North and South America near the end of the Pleistocene epoch.

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 Gen Bank, 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., 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 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.

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.

The dire wolf (Canis dirus, "fearsome dog") is an extinct carnivorous mammal of the genus Canis, roughly the size of the extant gray wolf, but with a heavier build.

It evolved in the New World and was its most evolutionary derived species of Canis.

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