Data from: Do freshwater ecoregions and continental shelf width predict patterns of historical gene flow in the freshwater fish Poecilia butleri?

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.