Unguided Species Delimitation Using DNA Sequence Data from Multiple Loci

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…

• UD
  Università degli Studi di Ferrara
• NI
  National Institutes of Health
• DF
  Directorate for Biological Sciences
• BA
  Biotechnology and Biological Sciences Research Council

  Award: BB/K000896/1
• BI
  Beijing Institute of Genomics, Chinese Academy of Sciences