DOI: 10.5061/dryad.0dg5h
title: Data from: Do freshwater ecoregions and continental shelf width predict patterns of historical gene flow in the freshwater fish Poecilia butleri?

description: We examined historical patterns of gene flow in the freshwater fish
 Poecilia butleri in western Mexico. We tested the hypothesis that the
 boundaries between four freshwater ecological communities (ecoregions)
 might have limited the movement of P. butleri because changes in species
 compositions might restrict establishment between adjacent ecoregions,
 even in situations where a physical barrier is absent. Hence, we predicted
 that boundaries between ecoregions should correspond to phylogeographical
 breaks in P. butleri. We also tested the hypothesis that the width of the
 continental shelf affected historical gene flow in P. butleri because a
 broad continental shelf provides a greater opportunity for rivers to
 coalesce during historical episodes of low sea levels as opposed to a
 narrow continental shelf that should restrict the potential for gene flow
 among adjacent rivers. Hence, we predicted greater amounts of historical
 gene flow among neighbouring river basins in the region of western Mexico
 where the continental shelf is wider, whereas, in the region where the
 continental shelf is narrower, we expected to detect limited levels of
 historical gene flow. We analyzed mitochondrial DNA sequence data
 (cytochrome b) taken from 264 individuals of P. butleri collected from 34
 locations distributed across four different ecoregions in western Mexico.
 To examine patterns of phylogenetic diversification and historical gene
 flow in P. butleri, we employed several analytical approaches, including
 traditional tree-based phylogenetic analyses (likelihood and parsimony),
 haplotype network reconstruction, analyses of molecular variance, and
 spatial analysis of molecular variance. We found genetic breaks coinciding
 with two out of three different ecoregion boundaries, suggesting limited
 historical gene flow. In addition to different species compositions
 between these adjacent ecoregions, geological features such as the
 Trans-Mexican Volcanic Belt and the mountainous topography in
 south-western Mexico, likely contributed to these observed genetic breaks.
 By contrast, no genetic break was evident between two other ecoregions, a
 result that partially rejects our first hypothesis. Several results were
 consistent with our second hypothesis. Changes in the width of the
 continental shelf in western Mexico are associated with the observed
 patterns of historical gene flow. Our results indicate that the
 interactions among multiple geological and biological factors affect the
 spatial patterns of genetic diversity of widespread freshwater species.
description: Poecilia butleri
 cytochrome b data for all individuals in nexus formatpoecilia.butt.only.cb.nexPoecilia butleri cytochrome b data for all haplotypes in nexus formatPbutleri only HAPLOTYPES.nexPoecilia butleri cytochrome b data for all individuals in arlequin formatThe haplotype data are in a second file which should be placed in the same directory as the .arp fileFINAL_Pbutleri_arlequin.arpPoecilia butleri cytochrome b data for all individuals in arlequin haplotype formatThese data contain the haplotype information and should be placed in the same directory as the .arp fileFINAL_Pbutleri_arlequin_haplotype.hapPoecilia butleri cytochrome b data for all individuals in samova / arlequin formatThe haplotype data are in a second file which should be placed in the same directory as the .arp filePbutleri_SAMOVA_inputfile.arpPoecilia butleri cytochrome b data for all individuals in samova / arlequin geography formatThese data contain the geographic information and should be placed in the same directory as the .arp filePbutleri_SAMOVA_inputfile_geography.geoPoecilia butleri cytochrome b data for all sequences in *BEAST XML formatpbutt.xmlTable 1 from paper, with population codes addedAll sequences in data files use the population code, this table defines which populations those codes belong to.table1.rtf