10.5061/DRYAD.053M3
Chen, Xin
Queens College, CUNY
Jiang, Ke
Kunming Institute of Zoology
Guo, Peng
Yibin University
Huang, Song
Huangshan University
Rao, Dingqi
Kunming Institute of Zoology
Ding, Li
Kunming Institute of Zoology
Takeuchi, Hirohiko
Kyoto University
Che, Jing
Kunming Institute of Zoology
Zhang, Yaping
Myers, Edward A.
Queens College, CUNY
Burbrink, Frank T.
Queens College, CUNY
Zhang, Ya-ping
Kunming Institute of Zoology
Data from: Assessing species boundaries and the phylogenetic position of
the rare Szechwan Ratsnake, Euprepiophis perlacea (Serpentes: Colubridae),
using coalescent-based methods
Dryad
dataset
2013
Euprepiophis perlacea
Coalescence
Gene tree
2013-09-26T13:42:34Z
2013-09-26T13:42:34Z
en
https://doi.org/10.1016/j.ympev.2013.09.003
914924 bytes
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CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Delimiting species and clarifying phylogenetic relationships are the main
goals of systematics. For species with questionable taxonomic status,
species delimitation approaches using multi-species coalescent models with
multiple loci are recommended if morphological data are unavailable or
unhelpful. Moreover, these methods will also reduce subjectivity based on
genetic distance or requirement of monophyletic genetic lineages. We
determine the validity and phylogenetic position of a rare and long
controversial species of Chinese reptile, the Szechwan ratsnake
(Euprepiophis perlacea), using multi-locus data from multiple individuals
and coalescent-based approaches. Species were first delimited using
Bayesian Phylogenetics & Phylogeography (BP&P), Brownie
and Bayes Factor model comparison approaches, while relationships among
species were estimated using species tree inference in *BEAST. Results
indicate that Euprepiophis perlacea is a distinct species sister to
Euprepiophis mandarinus. Despite gene tree discrepancy, the coalescent
model-based approaches used here demonstrate the taxonomic validity and
the phylogenetic position of Euprepiophis perlacea. These approaches
objectively test the validity of questionable species diagnoses based on
morphological characters and determine their phylogenetic position.
Perlaceaspeciestreexml for inferring specie tree in *BEAST using one
mitochondria gene and three nuclear genesperlspeciestree_nuclearonlyxml
for inferring specie tree in *BEAST using three nuclear genesmodel1_1xml
file for running species tree in *BEAST based on model 1 (assuming
Euprepiophis perlacea and Euprepiophis manderinus are two independent
species)model2_1xml file for running species tree in *BEAST based on model
2 (assuming Euprepiophis perlacea and Euprepiophis manderinus are one
species)m1_1pathSamplingxml file for calculating marginal likelihood of
model 1 (Euprepiophis perlacea and Eupreophis manderinus are two species)
using path-sampling estimatorm1_1stepstonexml file for calculating
marginal likelihood of model 1 (Euprepiophis perlacea and Eupreophis
manderinus are two species) using stepstone estimatorm2_1pathSamplingxml
file for calculating marginal likelihood of model 2 (Euprepiophis perlacea
and Eupreophis manderinus are one species) using path-sampling
estimatorm2_1stepstonexml file for calculating marginal likelihood of
model 2 (Euprepiophis perlacea and Eupreophis manderinus are one species)
using stepstone estimator
Southeast Asia
China
Japan