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      Estimation of the Origin of Polypedates leucomystax (Amphibia: Anura: Rhacophoridae) Introduced to the Ryukyu Archipelago, Japan

      1 , 1 , 2
      Pacific Science
      Pacific Science

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          Molecular systematics of the Eastern Fence Lizard (Sceloporus undulatus): a comparison of Parsimony, Likelihood, and Bayesian approaches.

          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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            Geographic patterns of endemism and speciation in amphibians and reptiles of the Ryukyu Archipelago, Japan, with special reference to their paleogeographical implications

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              An Empirical Test of Bootstrapping as a Method for Assessing Confidence in Phylogenetic Analysis

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                Author and article information

                Journal
                Pacific Science
                Pacific Science
                Pacific Science
                0030-8870
                1534-6188
                July 2009
                July 2009
                : 63
                : 3
                : 317-325
                Affiliations
                [1 ]Graduate School of Human and Environmental Studies, Kyoto University, Sakyo, Kyoto 606–8501, Japan.
                [2 ]Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa 903–0213, Japan.
                Article
                10.2984/049.063.0302
                69c0b805-6809-4920-b768-12b59df87f93
                © 2009

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