title: Phylogeny and biogeography of the family Salamandridae (Amphibia: Caudata) inferred from complete mitochondrial genomes.
abstract: Phylogenetic relationships of members of the salamander family Salamandridae were examined using complete mitochondrial genomes collected from 42 species representing all 20 salamandrid genera and five outgroup taxa. Weighted maximum parsimony, partitioned maximum likelihood, and partitioned Bayesian approaches all produce an identical, well-resolved phylogeny; most branches are strongly supported with greater than 90% bootstrap values and 1.0 Bayesian posterior probabilities. Our results support recent taxonomic changes in finding the traditional genera Mertensiella, Euproctus, and Triturus to be non-monophyletic species assemblages. We successfully resolved the current polytomy at the base of the salamandrid tree: the Italian newt genus Salamandrina is sister to all remaining salamandrids. Beyond Salamandrina, a clade comprising all remaining newts is separated from a clade containing the true salamanders. Among these newts, the branching orders of well-supported clades are: primitive newts (Echinotriton, Pleurodeles, and Tylototriton), New World newts (Notophthalmus-Taricha), Corsica-Sardinia newts (Euproctus), and modern European newts (Calotriton, Lissotriton, Mesotriton, Neurergus, Ommatotriton, and Triturus) plus modern Asian newts (Cynops, Pachytriton, and Paramesotriton).Two alternative sets of calibration points and two Bayesian dating methods (BEAST and MultiDivTime) were used to estimate timescales for salamandrid evolution. The estimation difference by dating methods is slight and we propose two sets of timescales based on different calibration choices. The two timescales suggest that the initial diversification of extant salamandrids took place in Europe about 97 or 69Ma. North American salamandrids were derived from their European ancestors by dispersal through North Atlantic Land Bridges in the Late Cretaceous ( approximately 69Ma) or Middle Eocene ( approximately 43Ma). Ancestors of Asian salamandrids most probably dispersed to the eastern Asia from Europe, after withdrawal of the Turgai Sea ( approximately 29Ma).
authors.affiliation: Department of Integrative Biology, Museum of Vertebrate Zoology, 3101 Valley Life Sciences Building, University of California, Berkeley, CA 94720-3160, USA. alarzhang@gmail.com
authors.forename: Peng
authors.initials: P
authors.lastname: Zhang
authors.forename: Theodore J
authors.initials: TJ
authors.lastname: Papenfuss
authors.forename: Marvalee H
authors.initials: MH
authors.lastname: Wake
authors.forename: Lianghu
authors.initials: L
authors.lastname: Qu
authors.forename: David B
authors.initials: DB
authors.lastname: Wake
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D004272:DNA, Mitochondrial / Q000235:genetics; D019143:Evolution, Molecular; D049810:Genetic Speciation; D054629:Genome, Mitochondrial; D005843:Geography; D016013:Likelihood Functions; D008928:Mitochondria / Q000235:genetics; D008957:Models, Genetic; D010802:Phylogeny; D012455:Salamandridae / Q000145:classification* / Q000235:genetics*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
chemical_list: D004272:DNA, Mitochondrial