DOI: 10.5061/dryad.c1sd4
title: Data from: Climate oscillations, glacial refugia, and dispersal ability: factors influencing the genetic structure of the least salmonfly, Pteronarcella badia (Plecoptera), in Western North America

description: Background: Phylogeographic studies of aquatic insects provide valuable
 insights into mechanisms that shape the genetic structure of communities,
 yet studies that include broad geographic areas are uncommon for this
 group. We conducted a broad scale phylogeographic analysis of the least
 salmonfly Pteronarcella badia (Plecoptera) across western North America.
 We tested hypotheses related to mode of dispersal and the influence of
 historic climate oscillations on population genetic structure. In order to
 generate a larger mitochondrial data set, we used 454 sequencing to
 reconstruct the complete mitochondrial genome in the early stages of the
 project. Results: Our analysis revealed high levels of population
 structure with several deeply divergent clades present across the sample
 area. Evidence from five mitochondrial genes and one nuclear locus
 identified a potentially cryptic lineage in the Pacific Northwest. Gene
 flow estimates and geographic clade distributions suggest that overland
 flight during the winged adult stage is an important dispersal mechanism
 for this taxon. We found evidence of multiple glacial refugia across the
 species distribution and signs of secondary contact within and among major
 clades. Conclusions: This study provides a basis for future studies of
 aquatic insect phylogeography at the inter-basin scale in western North
 America. Our findings add to an understanding of the role of historical
 climate isolations in shaping assemblages of aquatic insects in this
 region. We identified several geographic areas that may have historical
 importance for other aquatic organisms with similar distributions and
 dispersal strategies as P. badia. This work adds to the ever-growing list
 of studies that highlight the potential of next-generation DNA sequencing
 in a phylogenetic context to improve molecular data sets from understudied
 groups.
description: Matrix.for.RAxML.AnalysisA NEXUS file written for Mesquite with a concatenated alignment and for all haplotypes which was used to reconstruct phylogenetic relationships (in RAxML) of populations of Pteronarcella badia and its sister species across western North America.BEAST.Divergence.DatingThe input file for BEAST containing all haplotypes which was used to infer divergence among populations of Pteronarcella badia across western North America.BEAST.BSPA BEAST input file used to infer recent demographic history via Bayesian Skyline analysis of Pteronarcella badia populations in western North America.Migrate.InfilesThree input files used to infer migration rates of Pteronarcella badia across, and within several major drainage basin boundaries in Western North America.TCS.mtConcatThe input file used to generate a haplotype network of Pteronarcella badia in TCS using a concatenated dataset of mitochondrial genes.TCS.28SThe input file used to generate a haplotype network of Pteronarcella badia in TCS using a portion of 28S rRNA.IBD.InfilesInput files for IBD (Isolation-by-Distance) web server (http://ibdws.sdsu.edu/~ibdws/distances.html) used to test for isolation-by-distance as a determinant of population structure within each major clade of Pteronarcella badia sequences.Sample Locality DataA table that includes sample locality for all specimens in the study.Table 2.docx