title: Enlarged Multilocus Data set Provides Surprisingly Younger Time of Origin for the Plethodontidae, the Largest Family of Salamanders.
abstract: Deep phylogenetic relationships of the largest salamander family Plethodontidae have been difficult to resolve, probably reflecting a rapid diversification early in their evolutionary history. Here, data from 50 independent nuclear markers (total 48,582 bp) are used to reconstruct the phylogeny and divergence times for plethodontid salamanders, using both concatenation and coalescence-based species tree analyses. Our results robustly resolve the position of the enigmatic eastern North American four-toed salamander (Hemidactylium) as the sister taxon of Batrachoseps + Tribe Bolitoglossini, thus settling a long-standing question. Furthermore, we statistically reject sister taxon status of Karsenia and Hydromantes, the only plethodontids to occur outside the Americas, leading us to new biogeographic hypotheses. Contrary to previous long-standing arguments that plethodontid salamanders are an old lineage originating in the Cretaceous (more than 90 Ma), our analyses lead to the hypothesis that these salamanders are much younger, arising close to the K-T boundary (~66 Ma). These time estimates are highly stable using alternative calibration schemes and dating methods. Our data simulation highlights the potential risk of making strong arguments about phylogenetic timing based on inferences from a handful of nuclear genes, a common practice. Based on the newly obtained timetree and ancestral area reconstruction results, we argue that (i) the classic "Out of Appalachia" hypothesis of plethodontid origins is problematic; (ii) the common ancestor of extant plethodontids may have originated in northwestern North America in the early Paleocene; (iii) origins of Eurasian plethodontids likely result from two separate dispersal events from western North America via Beringia in the late Eocene (~42 Ma) and the early Miocene (~23 Ma), respectively.
authors.affiliation: State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China and.
authors.forename: Xing-Xing
authors.initials: XX
authors.lastname: Shen
authors.affiliation: State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China and.
authors.forename: Dan
authors.initials: D
authors.lastname: Liang
authors.affiliation: State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China and.
authors.forename: Meng-Yun
authors.initials: MY
authors.lastname: Chen
authors.affiliation: State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China and.
authors.forename: Rong-Li
authors.initials: RL
authors.lastname: Mao
authors.affiliation: Museum of Vertebrate Zoology and Department of Integrative Biology, 3101 Valley Life Sciences Bldg, University of California, Berkeley, CA 94720, USA alarzhang@gmail.com wakelab@berkeley.edu.
authors.forename: David B
authors.initials: DB
authors.lastname: Wake
authors.affiliation: State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China and alarzhang@gmail.com wakelab@berkeley.edu.
authors.forename: Peng
authors.initials: P
authors.lastname: Zhang
mesh_terms: D063147:Animal Distribution; D000818:Animals; D008969:Molecular Sequence Data; D009656:North America; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D013995:Time; D014562:Caudata / Q000145:classification* / Q000235:genetics*
keywords: Dispersal; molecular dating; paleogeography; phylogenomics; species tree; timetree