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Molecular systematics of the Eastern Fence Lizard (Sceloporus undulatus): a comparison of Parsimony, Likelihood, and Bayesian approaches.
Syst Biol. 2002 Feb; 51(1):44-68.SB

Abstract

Phylogenetic analysis of large datasets using complex nucleotide substitution models under a maximum likelihood framework can be computationally infeasible, especially when attempting to infer confidence values by way of nonparametric bootstrapping. Recent developments in phylogenetics suggest the computational burden can be reduced by using Bayesian methods of phylogenetic inference. However, few empirical phylogenetic studies exist that explore the efficiency of Bayesian analysis of large datasets. To this end, we conducted an extensive phylogenetic analysis of the wide-ranging and geographically variable Eastern Fence Lizard (Sceloporus undulatus). Maximum parsimony, maximum likelihood, and Bayesian phylogenetic analyses were performed on a combined mitochondrial DNA dataset (12S and 16S rRNA, ND1 protein-coding gene, and associated tRNA; 3,688 bp total) for 56 populations of S. undulatus (78 total terminals including other S. undulatus group species and outgroups). Maximum parsimony analysis resulted in numerous equally parsimonious trees (82,646 from equally weighted parsimony and 335 from weighted parsimony). The majority rule consensus tree derived from the Bayesian analysis was topologically identical to the single best phylogeny inferred from the maximum likelihood analysis, but required approximately 80% less computational time. The mtDNA data provide strong support for the monophyly of the S. undulatus group and the paraphyly of "S. undulatus" with respect to S. belli, S. cautus, and S. woodi. Parallel evolution of ecomorphs within "S. undulatus" has masked the actual number of species within this group. This evidence, along with convincing patterns of phylogeographic differentiation suggests "S. undulatus" represents at least four lineages that should be recognized as evolutionary species.

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Authors+Show Affiliations

Leaché AD
Department of Biology, San Diego State University, San Diego, California 92182-4614, USA. aleach1@lsu.edu
Reeder TW
No affiliation info available

MeSH

AnimalsBayes TheoremDNA, MitochondrialData Interpretation, StatisticalDatabases, Nucleic AcidLikelihood FunctionsLizardsMexicoModels, GeneticPhylogenySequence AlignmentUnited States

Pub Type(s)

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

Language

eng

PubMed ID

11943092

Citation

Leaché, Adam D., and Tod W. Reeder. "Molecular Systematics of the Eastern Fence Lizard (Sceloporus Undulatus): a Comparison of Parsimony, Likelihood, and Bayesian Approaches." Systematic Biology, vol. 51, no. 1, 2002, pp. 44-68.
Leaché AD, Reeder TW. Molecular systematics of the Eastern Fence Lizard (Sceloporus undulatus): a comparison of Parsimony, Likelihood, and Bayesian approaches. Syst Biol. 2002;51(1):44-68.
Leaché, A. D., & Reeder, T. W. (2002). Molecular systematics of the Eastern Fence Lizard (Sceloporus undulatus): a comparison of Parsimony, Likelihood, and Bayesian approaches. Systematic Biology, 51(1), 44-68.
Leaché AD, Reeder TW. Molecular Systematics of the Eastern Fence Lizard (Sceloporus Undulatus): a Comparison of Parsimony, Likelihood, and Bayesian Approaches. Syst Biol. 2002;51(1):44-68. PubMed PMID: 11943092.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Molecular systematics of the Eastern Fence Lizard (Sceloporus undulatus): a comparison of Parsimony, Likelihood, and Bayesian approaches. AU - Leaché,Adam D, AU - Reeder,Tod W, PY - 2002/4/12/pubmed PY - 2002/7/23/medline PY - 2002/4/12/entrez SP - 44 EP - 68 JF - Systematic biology JO - Syst Biol VL - 51 IS - 1 N2 - Phylogenetic analysis of large datasets using complex nucleotide substitution models under a maximum likelihood framework can be computationally infeasible, especially when attempting to infer confidence values by way of nonparametric bootstrapping. Recent developments in phylogenetics suggest the computational burden can be reduced by using Bayesian methods of phylogenetic inference. However, few empirical phylogenetic studies exist that explore the efficiency of Bayesian analysis of large datasets. To this end, we conducted an extensive phylogenetic analysis of the wide-ranging and geographically variable Eastern Fence Lizard (Sceloporus undulatus). Maximum parsimony, maximum likelihood, and Bayesian phylogenetic analyses were performed on a combined mitochondrial DNA dataset (12S and 16S rRNA, ND1 protein-coding gene, and associated tRNA; 3,688 bp total) for 56 populations of S. undulatus (78 total terminals including other S. undulatus group species and outgroups). Maximum parsimony analysis resulted in numerous equally parsimonious trees (82,646 from equally weighted parsimony and 335 from weighted parsimony). The majority rule consensus tree derived from the Bayesian analysis was topologically identical to the single best phylogeny inferred from the maximum likelihood analysis, but required approximately 80% less computational time. The mtDNA data provide strong support for the monophyly of the S. undulatus group and the paraphyly of "S. undulatus" with respect to S. belli, S. cautus, and S. woodi. Parallel evolution of ecomorphs within "S. undulatus" has masked the actual number of species within this group. This evidence, along with convincing patterns of phylogeographic differentiation suggests "S. undulatus" represents at least four lineages that should be recognized as evolutionary species. SN - 1063-5157 UR - https://www.unboundmedicine.com/medline/citation/11943092/Molecular_systematics_of_the_Eastern_Fence_Lizard__Sceloporus_undulatus_:_a_comparison_of_Parsimony_Likelihood_and_Bayesian_approaches_ L2 - https://academic.oup.com/sysbio/article-lookup/doi/10.1080/106351502753475871 DB - PRIME DP - Unbound Medicine ER -