Yang, Z;
Rannala, B;
(2014)
Unguided Species Delimitation Using DNA Sequence Data from Multiple Loci.
Molecular Biology and Evolution
, 31
(12)
pp. 3125-3135.
10.1093/molbev/msu279.
Preview |
Text
Yang et al. last version Unguided species delimitation .pdf Download (670kB) | Preview |
Abstract
A method was developed for simultaneous Bayesian inference of species delimitation and species phylogeny using the multispecies coalescent model. The method eliminates the need for a user-specified guide tree in species delimitation and incorporates phylogenetic uncertainty in a Bayesian framework. The nearest-neighbor interchange algorithm was adapted to propose changes to the species tree, with the gene trees for multiple loci altered in the proposal to avoid conflicts with the newly proposed species tree. We also modify our previous scheme for specifying priors for species delimitation models to construct joint priors for models of species delimitation and species phylogeny. As in our earlier method, the modified algorithm integrates over gene trees, taking account of the uncertainty of gene tree topology and branch lengths given the sequence data. We conducted a simulation study to examine the statistical properties of the method using six populations (two sequences each) and a true number of three species, with values of divergence times and ancestral population sizes that are realistic for recently diverged species. The results suggest that the method tends to be conservative with high posterior probabilities being a confident indicator of species status. Simulation results also indicate that the power of the method to delimit species increases with an increase of the divergence times in the species tree, and with an increased number of gene loci. Reanalyses of two data sets of cavefish and coast horned lizards suggest considerable phylogenetic uncertainty even though the data are informative about species delimitation. We discuss the impact of the prior on models of species delimitation and species phylogeny and of the prior on population size parameters (θ) on Bayesian species delimitation.
| Type: | Article |
|---|---|
| Title: | Unguided Species Delimitation Using DNA Sequence Data from Multiple Loci |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.1093/molbev/msu279 |
| Publisher version: | http://dx.doi.org/10.1093/molbev/msu279 |
| Language: | English |
| Additional information: | © The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
| Keywords: | Bayesian species delimitation, species tree, multispecies coalescent, reversible-jump MCMC, guide tree, nearest-neighbor interchange |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Genetics, Evolution and Environment |
| URI: | https://discovery.ucl.ac.uk/id/eprint/1470712 |
Loading...
Loading...Loading...Loading...Archive Staff Only
 |
View Item |
