@ARTICLE{TreeBASE2Ref18092, author = {David W. Weisrock and Luke J. Harmon and Allan Larson}, title = {Resolving Deep Phylogenetic Relationships in Salamanders: Analyses of Mitochondrial and Nuclear Genomic Data.}, year = {2005}, keywords = {}, doi = {10.1080/10635150500234641}, url = {}, pmid = {}, journal = {Systematic Biology}, volume = {54}, number = {5}, pages = {758--777}, abstract = {Phylogenetic relationships among salamander families illustrate analytical challenges inherent to inferring phylogenies in which terminal branches have a very long temporal duration relative to internal ones. To examine these relationships, we present new mitochondrial-DNA sequences, approximately 2100 base-pairs from the genes encoding ND1, ND2, COI, and the intervening tRNA genes for 34 species representing all 10 salamander families. 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 Bayesian posterior probabilities provide statistical support for interfamilial groupings that preclude monophyly of the internally fertilizing salamanders, suborder Salamandroidea. Bayesian analysis of mtDNA data strongly supports a clade containing the internally fertilizing families Ambystomatidae, Dicamptodontidae, Proteidae, and Salamandridae, and the externally fertilizing family Sirenidae; both molecular data sets strongly place all of these families in a clade excluding the internally fertilizing families Amphiumidae, Plethodontidae, and Rhyacotritonidae. These analyses also support monophyly of suborder Cryptobranchoidea (Cryptobranchidae and Hynobiidae), whose fertilization is external. Computer simulations and analyses of our data indicate that ancestral lineages shared by two or more families would need to have been at least 23 million years and in some cases much longer in duration for statistical recovery using parsimony, but that Bayesian methods may correctly infer groupings whose common ancestral lineage is shorter. Branch support for such nodes in our likelihood and Bayesian analyses of mtDNA derives largely from occurrence of a small number of relatively rare substitutions in categories heavily weighted by the favored evolutionary model. Our molecular phylogenetic results challenge the interpretation that internal-fertilization systems of salamandroid families are homologous and that functional burden precludes evolutionary loss of internal fertilization.} }

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