Demographic consequences of dispersal-related trait shift in two recently diverged taxa of montane grasshoppers

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 (<1.5 Ma) with ancestral gene flow. According to neutral expectations from differences in dispersal capacity, historic..., Genomic library preparation
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).
Genomic data assembling and filtering
..., Samples.xlsx: Description of individual and population codes used in the different analyses and genomic datasets
c85d5m9sh15.nex: Input file (NEXUS format) used for phylogenomic analyses in SNAPP
c85d5m24sh15.unlinked_snps: Input file (NEXUS format) used for phylogenomic analyses in SVDQuartets
c85d5m24sh15.treemix: Input file (TREEMIX format) used for phylogenomic analyses in TREEMIX
STRUCTURE_PCA.zip: This ZIP folder contains the genetic datasets (STR format) used to perform clustering (STRUCTURE) and principal component analyses (PCA)
BPP.zip: This ZIP folder contains the genetic dataset, control file and individual map file used to perform BPP analyses
c85d5m24sh15_Outgroup.loci: Input file used to perform D-statistic (ABBA-BABA) tests in PYRAD
Fastsimcoal2.zip: Input files for the alternative models tested using FASTSIMCOAL2
StairwayPlot.zip: Input files for demographic reconstructions in STAIRWAYPLOT
PYRAD.zip: Output files from PYRAD obtained for populations of the two taxa (c85d...