10.5061/dryad.4p7n5
https://zenodo.org/records/5007014
oai:zenodo.org:5007014
Tseng, Shu-Ping
Shu-Ping
Tseng
National Taiwan University
Li, Shou-Hsien
Shou-Hsien
Li
National Taiwan Normal University
Wang, Hurng-Yi
Hurng-Yi
Wang
National Taiwan University
Lin, Si-Min
Si-Min
Lin
National Taiwan Normal University
Hsieh, Chia-Hung
Chia-Hung
Hsieh
Chinese Culture University
Data from: Influence of gene flow on divergence dating – implications for speciation history of Takydromus grass lizards
Zenodo
2014
Reptiles
population demography
parapatric speciation
Takydromus spp.
2014-08-19
10.1111/mec.12889
https://zenodo.org/communities/dryad
Creative Commons Zero v1.0 Universal
Dating the time of divergence and understanding speciation processes are central to the study of the evolutionary history of organisms but are notoriously difficult. The difficulty is largely rooted in variations in the ancestral population size or in the genealogy variation across loci. To depict the speciation processes and divergence histories of three monophyletic Takydromus species endemic to Taiwan, we sequenced 20 nuclear loci and combined with one mitochondrial locus published in GenBank. They were analyzed by a multispecies coalescent approach within a Bayesian framework. Divergence dating based on the gene tree approach showed high variation among loci, and the divergence was estimated at an earlier date than when derived by the species tree approach. To test whether variations in the ancestral population size accounted for the majority of this variation, we conducted computer inferences using isolation-with-migration (IM) and approximate Bayesian computation (ABC) frameworks. The results revealed that gene flow during the early stage of speciation was strongly favored over the isolation model, and the initiation of the speciation process was far earlier than the dates estimated by gene- and species-based divergence dating. Due to their limited dispersal ability, it is suggested that geographic isolation may have played a major role in the divergence of these Takydromus species. Nevertheless, the current study reveals a more complex situation and demonstrates that gene flow during the speciation process cannot be overlooked and may have a great impact on divergence dating. By using multilocus data and incorporating Bayesian coalescence approaches, we provide a more biologically realistic framework for delineating the divergence history of Takydromus.
alignment
DNA sequence alignments
Species tree files in this study
Species tree of Takydromus constructed by (A) mtDNA and 16 nuclear loci (B) mtDNA only (C) nuclear loci only using substitution rate prior. Divergence times are shown at the nodes with 95% highest posterior densities in brackets. Bayesian posterior probabilities are shown above the branches
speciestree files.zip
12S sequence alignment
12S sequence alignment used in this study
12S.fas
Taiwan