DOI: 10.5061/dryad.3tx95x6df
title: Data from: Dispersal barriers and opportunities drive multiple levels of phylogeographic concordance in the Southern Alps of New Zealand

description: Phylogeographic concordance, or the sharing of phylogeographic patterns
 among co-distributed species, suggests similar responses to topography or
 climatic history. While the orientation and timing of breaks between
 lineages are routinely compared, spatial dynamics within regions occupied
 by individual lineages provide a second opportunity for comparing
 responses to past events. In environments with complex topography and
 glacial history, such as New Zealand’s South Island, geographically nested
 comparisons can identify the processes leading to phylogeographic
 concordance between and within regional genomic clusters. Here, we used
 single nucleotide polymorphisms (obtained via ddRADseq) for two
 co-distributed forest beetle species, Agyrtodes labralis (Leiodidae) and
 Brachynopus scutellaris (Staphylinidae), to evaluate the role of
 climate change and topography in shaping phylogeographic concordance at
 two, nested spatial scales: do species diverge over the same geographic
 barriers, with similar divergence times? And within regions delimited by
 these breaks, do species share similar spatial dynamics of directional
 expansion or isolation-by-distance? We found greater congruence of
 phylogeographic breaks between regions divided by the strongest dispersal
 barriers (i.e., the Southern Alps). However, these shared breaks were not
 indicative of shared spatial dynamics within the regions they delimit, and
 the most similar spatial dynamics between species occurred within regions
 with the strongest gradients in historical climatic stability. Our results
 indicate that lack of concordance as traditionally detected by lineage
 turnover does not rule out the possibility of shared histories, and
 variation in the presence and type of concordance may provide insights
 into the different processes shaping phylogeographic patterns across
 geologically dynamic regions.    
description: <strong>localities_accessions
 files:</strong> A .csv file for each species
 includes extraction codes, region and population assignments for the
 Structure and Directionality Index analyses, respectively, geographic
 coordinates, BioSample accession numbers for raw reads, and Genbank
 accession numbers for corresponding mitochondrial sequences from Marske et
 al, 2012 (doi:10.1111/j.1558-5646.2011.01538.x). <strong>Structure (zipped directory):</strong> Files include a Structure input file allowing maximum 25% missing data, a parameters file, and zipped results from Structure Harvestor. For <em>Agyrtodes labralis</em>, inputs are given for a global analysis. For <em>Brachynopus scutellaris</em>, inputs are given for the global and two subStructure analyses. <strong>Procrustes (zipped directory):</strong> Files include a Structure-formatted input file allowing maximum 25% missing data, locality data for sequenced individuals, and locality data for populations. For each species, a .stru file and two .csv files are given for global and regional analyses. <strong>Directionality Index (zipped directory):</strong> Files include a SNAPP-formatted input file allowing maximum 25% missing data and locality data for each merged population (.txt). <strong>FastSimcoal (zipped directory):</strong> Separate folders with input files allowing maximum 25% missing dataand Python or R codes are given for calculating the site frequency spectrum (01_CalculateSFS), deriving the point estimates for divergence dates and other parameters (02_PointEstimates) and bootstrapping the model parameters for the divergence with migration model (03_Migration_model_Bootstrap).