© 2005 Society of Systematic Biologists
Partitioned Bayesian Analyses, Partition Choice, and the Phylogenetic Relationships of Scincid Lizards
1 Department of Biology, San Diego State University San Diego, California, 92182–4614 USA
2 Muséum d'histoirenaturelle, Department of Herpetology and Ichthyology C.P. 6434, CH-1211 Geneva 6, Switzerland
Edited by Frank Anderson: Associate Editor
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Abstract |
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Partitioned Bayesian analyses of 
2.2 kb of nucleotide sequence data (mtDNA) were used to elucidate phylogenetic relationships among 30 scincid lizard genera. Few partitioned Bayesian analyses exist in the literature, resulting in a lack of methods to determine the appropriate number of and identity of partitions. Thus, a criterion, based on the Bayes factor, for selecting among competing partitioning strategies is proposed and tested. Improvements in both mean–lnL and estimated posterior probabilities were observed when specific models and parameter estimates were assumed for partitions of the total data set. This result is expected given that the 95% credible intervals of model parameter estimates for numerous partitions do not overlap and it reveals that different data partitions may evolve quite differently. We further demonstrate that how one partitions the data (by gene, codon position, etc.) is shown to be a greater concern than simply the overall number of partitions. Using the criterion of the 2ln Bayes factor > 10, the phylogenetic analysis employing the largest number of partitions was decisively better than all other strategies. Strategies that partitioned the ND1 gene by codon position performed better than other partition strategies, regardless of the overall number of partitions. Scincidae, Acontinae, Lygosominae, east Asian and North American "Eumeces" + Neoseps; North African Eumeces, Scincus, and Scincopus, and a large group primarily from sub-Saharan Africa, Madagascar, and neighboring islands are monophyletic. Feylinia, a limbless group of previously uncertain relationships, is nested within a "scincine" clade from sub-Saharan Africa. We reject the hypothesis that the nearly limbless dibamids are derived from within the Scincidae, but cannot reject the hypothesis that they represent the sister taxon to skinks. Amphiglossus, Chalcides, the acontines Acontias and Typhlosaurus, and Scincinae are paraphyletic. The globally widespread "Eumeces" is polyphyletic and we make necessary taxonomic changes.
Keywords: Bayes factors; Bayesian hypothesis testing; "Eumeces"; mixed-model analyses; partitioning; "Scincinae."
Received March 17, 2004; Revised May 26, 2004; Accepted August 24, 2004
3 Current address: Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, California 94720–160, USA E-mail: brandley{at}berkeley.edu
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