DOI: 10.5061/dryad.bg79cnp9q
title: Demographic consequences of dispersal-related trait shift in two recently diverged taxa of montane grasshoppers

description: Although the pervasiveness of intraspecific wing-size polymorphism and
 transitions to flightlessness have long captivated biologists, the
 demographic outcomes of shifts in dispersal ability are not yet well
 understood and have been seldom studied at early stages of
 diversification. Here, we use genomic data to infer the consequences of
 dispersal-related trait variation in the taxonomically controversial
 short-winged (Chorthippus corsicus corsicus) and long-winged (Chorthippus
 corsicus pascuorum) Corsican grasshoppers. Our analyses revealed lack of
 contemporary hybridization between sympatric long- and short-winged forms
 and phylogenomic reconstructions supported their taxonomic
 distinctiveness, rejecting the hypothesis of intraspecific wing
 polymorphism. Statistical evaluation of alternative models of speciation
 strongly supported a scenario of Pleistocene divergence (&lt;1.5 Ma)
 with ancestral gene flow. According to neutral expectations from
 differences in dispersal capacity, historical effective migration rates
 from the long- to the short-winged taxon were three-fold higher than in
 the opposite direction. Although populations of the two taxa present a
 marked genetic structure and have experienced parallel demographic
 histories, our coalescent-based analyses suggest that reduced dispersal
 has fueled diversification in the short-winged C. c. corsicus.
 Collectively, our study illustrates how dispersal reduction can speed up
 geographical diversification and increase the opportunity for allopatric
 speciation in topographically complex landscapes.
description: <strong>Genomic library
 preparation</strong> We used NucleoSpin Tissue
 (Macherey-Nagel, Düren, Germany) kits to extract and purify DNA from a
 hind leg of each individual. We processed genomic DNA into one genomic
 library using the double-digestion restriction-site associated DNA
 sequencing procedure (ddRAD-seq) described in Peterson et al. (2012). In
 brief, we digested DNA with the restriction enzymes MseI and EcoRI (New
 England Biolabs, Ipswich, MA, USA) and ligated Illumina adaptors including
 unique 7-bp barcodes to the digested fragments of each individual. We
 pooled ligation products and size-selected them between 475-580 bp with a
 Pippin Prep instrument (Sage Science, Beverly, MA, USA). We amplified the
 fragments by PCR with 12 cycles using the iProofTM High-Fidelity DNA
 Polymerase (BIO-RAD, Veenendaal, Netherlands) and sequenced the library in
 a single-read 150-bp lane on an Illumina HiSeq2500 platform at The Centre
 for Applied Genomics (Toronto, ON, Canada). <strong>Genomic data
 assembling and filtering</strong> Raw sequences were demultiplexed
 and preprocessed using stacks v. 1.35
 (Catchen et al., 2013) and assembled using pyrad v. 3.0.66
 (Eaton, 2014). Libraries were demultiplexed and filtered for overall
 quality using <em>process_radtags </em>(Catchen et al., 2011,
 2013), retaining reads with a Phred score &gt; 10 (using a sliding
 window of 15%), no adaptor contamination, and that had an unambiguous
 barcode and restriction cut site. Raw sequence data quality was checked in
 fastqc
 v. 0.11.5 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and sequences were trimmed to 129 bp using seqtk (Heng Li, https://github.com/lh3/seqtk) in order to remove barcodes and low-quality reads near the 3´ ends. We assembled our sequences into <em>de novo</em> loci using pyrad v. 3.0.66 (Eaton, 2014). Briefly, reads retained after <em>process_radtags</em> were further quality-filtered with pyrad to convert base calls with a Phred score &lt;20 into <em>N</em>s and discard reads with &gt;2 <em>N</em>s. Retained reads were clustered within- and across samples considering a threshold of sequence similarity (<em>W</em><sub>clust</sub>) of 85% and clusters with a coverage depth &lt;5 were discarded. Loci containing one or more heterozygous sites across &gt;15% of individuals were excluded, as we expect that this represents a fixed difference among clustered paralogs rather than a true polymorphism (Eaton, 2014). Unless otherwise indicated, all downstream analyses were performed using datasets of unlinked SNPs (i.e., a single SNP per RAD locus) obtained with pyrad considering a clustering threshold of sequence similarity of 0.85 (<em>W</em><sub>clust</sub> = 0.85) and discarding loci that were not present in at least 50 % individuals (<em>minCov</em> = 50 %). <strong>References</strong> Catchen, J. M., A. Amores, P. Hohenlohe, W. Cresko, and J. H. Postlethwait. 2011. stacks: Building and genotyping loci <em>de novo</em> from short-read sequences. G3-Genes Genom. Genet. 1:171-182. Catchen, J., P. A. Hohenlohe, S. Bassham, A. Amores, and W. A. Cresko. 2013. stacks: an analysis tool set for population genomics. Mol. Ecol. 22:3124-3140. Eaton, D. A. R. 2014. pyrad: assembly of <em>de novo</em> RADseq loci for phylogenetic analyses. Bioinformatics 30:1844-1849. Peterson, B. K., J. N. Weber, E. H. Kay, H. S. Fisher, and H. E. Hoekstra. 2012. Double digest RADseq: An inexpensive method for <em>de novo</em> SNP discovery and genotyping in model and non-model species. PLoS One 7:e37135.
description: <strong>Samples.xlsx</strong>: Description of individual and population codes used in the different analyses and genomic datasets <strong>c85d5m9sh15.nex</strong>: Input file (NEXUS format) used for phylogenomic analyses in SNAPP <strong>c85d5m24sh15.unlinked_snps</strong>: Input file (NEXUS format) used for phylogenomic analyses in SVDQuartets <strong>c85d5m24sh15.treemix</strong>: Input file (TREEMIX format) used for phylogenomic analyses in TREEMIX <strong>STRUCTURE_PCA.zip</strong>: This ZIP folder contains the genetic datasets (STR format) used to perform clustering (STRUCTURE) and principal component analyses (PCA) <strong>BPP.zip</strong>: This ZIP folder contains the genetic dataset, control file and individual map file used to perform BPP analyses <strong>c85d5m24sh15_Outgroup.loci</strong>: Input file used to perform <em>D</em>-statistic (ABBA-BABA) tests in PYRAD <strong>Fastsimcoal2</strong><strong>.zip</strong>: Input files for the alternative models tested using FASTSIMCOAL2 <strong>StairwayPlot</strong><strong>.zip</strong>: Input files for demographic reconstructions in STAIRWAYPLOT <strong>PYRAD.zip</strong>: Output files from PYRAD obtained for populations of the two taxa (c85d5m24sh15) and only considering populations of <em>Chorthippus corsicus corsicus</em> (C_corsicus_corsicus_c85d5m12sh15) and <em>Chorthippus corsicus pascuorum</em> (C_corsicus_pascuorum_c85d5m12sh15)