DOI: 10.5061/dryad.v2n38
title: Data from: Considering gene flow when using coalescent methods to delimit lineages of North American pitvipers of the genus Agkistrodon

description: Examining species diversity and mechanisms of speciation using coalescent
 models provides a framework for how regional diversity is accrued, even in
 well-studied areas such as the Nearctic. It is likely, that gene flow
 among closely-related species with adjacent distributions may be common.
 However, the absence of gene flow is a primary assumption of many
 phylogeographical methods that produce species trees and delimit species
 using Bayesian or likelihood functions in a coalescent framework. In the
 present study, we examine delimitation when gene flow between species is
 present using empirical datasets from two species of North American
 pitvipers of the genus Agkistrodon. We also use niche modelling to
 determine whether these young lineages occur in distinct environmental
 niches. To manage the problem of gene flow between species, we first
 identify admixed individuals, demonstrate that gene flow has occurred, and
 then identify the impact of alternative population assignments of admixed
 individuals on delimitation posterior probabilities. In addition, we
 examine the influence of mitochondrial genes relative to other loci
 combined in coalescent analyses that delimit species. Here, we find that
 the copperheads (Agkistrodon contortrix) and the cottonmouths (Agkistrodon
 piscivorus) are each composed of two distinct species, with each occupying
 different niches. Importantly, we find that species can be delimited when
 the amount of gene flow between lineages is low, although the methods are
 acutely sensitive to population assignment of individuals.
description: cont11a.phy
 2Nexus file for
 Agkistrodon contortrix for anonymous locus 11.cont51a.phyNexus file for Agkistrodon contortrix for anonymous locus 51.contaa.phyNexus file for Agkistrodon contortrix for anonymous locus a.contcytb.phyNexus file for Agkistrodon contortrix for Cytochrome b.contnt3a.phyNexus file for Agkistrodon contortrix for anonymous locus 3.contsptbn1.phyNexus file for Agkistrodon contortrix for sptbn1.piscanon11.nex 3Nexus file for Agkistrodon piscivorus for anonymous locus 11.pisccytb1.nex 2Nexus file for Agkistrodon piscivorus for Cytochrome b.piscnt3.nex 3Nexus file for Agkistrodon piscivorus for NT3.piscsptbn1.nex 3Nexus file for Agkistrodon piscivorus for sptbn1.piscvim56.nex 4Nexus file for Agkistrodon piscivorus for Vimentin 5-6.piscwl.nex 3Nexus file for Agkistrodon piscivorus for AHR.anon 11d outgroupsNexus file for species tree estimates for anonymous locus 11.anon 51d outgroupsNexus file for species tree estimates for anonymous locus 51.anon ad outgroupNexus file for species tree estimates for anonymous locus a.cytbd outgroupsNexus file for species tree estimates for Cytochrome b.nav56d outgroupsNexus file for species tree estimates for Nav5-6.nt3d outgroupsNexus file for species tree estimates for NT3.sptbn1d outgroupsNexus file for species tree estimates for sptbn1.vim56d outgroupNexus file for species tree estimates for Vim5-6.wld outgroupNexus file for species tree for AHR gene.Agk collection master_Burbrink&GuiherSpreadsheet of voucher numbers and collecting localities (georeferenced) for tissues of Agkistrodon contortrix and A. piscivorus used in this study. In the Nexus data files only the numbers prior to the "^" match up to the TG numbers in this list. For example TG103^9 is TG 103 in this list. Nuclear genes have been phased so there may be two copies in the Nexus files (second copy labeled b).