5007014
doi
10.5061/dryad.4p7n5
oai:zenodo.org:5007014
user-dryad
Li, Shou-Hsien
National Taiwan Normal University
Wang, Hurng-Yi
National Taiwan University
Lin, Si-Min
National Taiwan Normal University
Hsieh, Chia-Hung
Chinese Culture University
Data from: Influence of gene flow on divergence dating – implications for speciation history of Takydromus grass lizards
Tseng, Shu-Ping
National Taiwan University
doi:10.1111/mec.12889
info:eu-repo/semantics/openAccess
Creative Commons Zero v1.0 Universal
https://creativecommons.org/publicdomain/zero/1.0/legalcode
Reptiles
population demography
parapatric speciation
Takydromus spp.
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.
<div class="o-metadata__file-usage-entry">alignment<div class="o-metadata__file-description">DNA sequence alignments</div><div class="o-metadata__file-name"></div></div><div class="o-metadata__file-usage-entry">Species tree files in this study<div class="o-metadata__file-description">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</div><div class="o-metadata__file-name">speciestree files.zip<br></div></div><div class="o-metadata__file-usage-entry">12S sequence alignment<div class="o-metadata__file-description">12S sequence alignment used in this study</div><div class="o-metadata__file-name">12S.fas<br></div></div>
Zenodo
2014-08-19
info:eu-repo/semantics/other
5007013
user-dryad
1653826946.490255
51917
md5:e63117ca30e7e65390a9a9ad032ffb1c
https://zenodo.org/records/5007014/files/12S.fas
8117
md5:6004ca4d8f60eba10d16869173e30601
https://zenodo.org/records/5007014/files/speciestree files.zip
57894
md5:e9025adbc7b3c4e45af186ff12f6e922
https://zenodo.org/records/5007014/files/alignment.zip
public
10.1111/mec.12889
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