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Supermatrix and species tree methods resolve phylogenetic relationships within the big cats, Panthera (Carnivora: Felidae).
Mol Phylogenet Evol. 2010 Jul; 56(1):64-76.MP

Abstract

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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Authors+Show Affiliations

Davis BW
Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843-4458, USA.
Li G
No affiliation info available
Murphy WJ
No affiliation info available

MeSH

AnimalsBayes TheoremCatsCell NucleusDNA, MitochondrialEvolution, MolecularGenome, MitochondrialLikelihood FunctionsModels, GeneticPantheraPhylogenyPrealbuminSequence AlignmentSequence Analysis, DNAY Chromosome

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

Language

eng

PubMed ID

20138224

Citation

Davis, Brian W., et al. "Supermatrix and Species Tree Methods Resolve Phylogenetic Relationships Within the Big Cats, Panthera (Carnivora: Felidae)." Molecular Phylogenetics and Evolution, vol. 56, no. 1, 2010, pp. 64-76.
Davis BW, Li G, Murphy WJ. Supermatrix and species tree methods resolve phylogenetic relationships within the big cats, Panthera (Carnivora: Felidae). Mol Phylogenet Evol. 2010;56(1):64-76.
Davis, B. W., Li, G., & Murphy, W. J. (2010). Supermatrix and species tree methods resolve phylogenetic relationships within the big cats, Panthera (Carnivora: Felidae). Molecular Phylogenetics and Evolution, 56(1), 64-76. https://doi.org/10.1016/j.ympev.2010.01.036
Davis BW, Li G, Murphy WJ. Supermatrix and Species Tree Methods Resolve Phylogenetic Relationships Within the Big Cats, Panthera (Carnivora: Felidae). Mol Phylogenet Evol. 2010;56(1):64-76. PubMed PMID: 20138224.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Supermatrix and species tree methods resolve phylogenetic relationships within the big cats, Panthera (Carnivora: Felidae). AU - Davis,Brian W, AU - Li,Gang, AU - Murphy,William J, Y1 - 2010/02/04/ PY - 2009/08/10/received PY - 2010/01/28/revised PY - 2010/01/29/accepted PY - 2010/2/9/entrez PY - 2010/2/9/pubmed PY - 2010/7/24/medline SP - 64 EP - 76 JF - Molecular phylogenetics and evolution JO - Mol Phylogenet Evol VL - 56 IS - 1 N2 - 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. SN - 1095-9513 UR - https://www.unboundmedicine.com/medline/citation/20138224/Supermatrix_and_species_tree_methods_resolve_phylogenetic_relationships_within_the_big_cats_Panthera__Carnivora:_Felidae__ L2 - https://linkinghub.elsevier.com/retrieve/pii/S1055-7903(10)00047-3 DB - PRIME DP - Unbound Medicine ER -