title: Resolving deep phylogenetic relationships in salamanders: analyses of mitochondrial and nuclear genomic data.
abstract: Phylogenetic relationships among salamander families illustrate analytical challenges inherent to inferring phylogenies in which terminal branches are temporally very long relative to internal branches. We present new mitochondrial DNA sequences, approximately 2,100 base pairs from the genes encoding ND1, ND2, COI, and the intervening tRNA genes for 34 species representing all 10 salamander families, to examine these relationships. Parsimony analysis of these mtDNA sequences supports monophyly of all families except Proteidae, but yields a tree largely unresolved with respect to interfamilial relationships and the phylogenetic positions of the proteid genera Necturus and Proteus. In contrast, Bayesian and maximum-likelihood analyses of the mtDNA data produce a topology concordant with phylogenetic results from nuclear-encoded rRNA sequences, and they statistically reject monophyly of the internally fertilizing salamanders, suborder Salamandroidea. Phylogenetic simulations based on our mitochondrial DNA sequences reveal that Bayesian analyses outperform parsimony in reconstructing short branches located deep in the phylogenetic history of a taxon. However, phylogenetic conflicts between our results and a recent analysis of nuclear RAG-1 gene sequences suggest that statistical rejection of a monophyletic Salamandroidea by Bayesian analyses of our mitochondrial genomic data is probably erroneous. Bayesian and likelihood-based analyses may overestimate phylogenetic precision when estimating short branches located deep in a phylogeny from data showing substitutional saturation; an analysis of nucleotide substitutions indicates that these methods may be overly sensitive to a relatively small number of sites that show substitutions judged uncommon by the favored evolutionary model.
authors.affiliation: Department of Biology, Campus Box 1137, Washington University, St. Louis, Missouri, 63130, USA. weisrock@uky.edu
authors.forename: David W
authors.initials: DW
authors.lastname: Weisrock
authors.forename: Luke J
authors.initials: LJ
authors.lastname: Harmon
authors.forename: Allan
authors.initials: A
authors.lastname: Larson
mesh_terms: D000818:Animals; D001483:Base Sequence; D001499:Bayes Theorem; D003198:Computer Simulation; D017931:DNA Primers; D004272:DNA, Mitochondrial / Q000235:genetics; D016013:Likelihood Functions; D008957:Models, Genetic; D008969:Molecular Sequence Data; D010802:Phylogeny; D012107:Research Design; D017422:Sequence Analysis, DNA; D014562:Caudata / Q000235:genetics*
chemical_list: D017931:DNA Primers; D004272:DNA, Mitochondrial