DOI: 10.5061/dryad.mg606
title: Data from: Phylogeographic analysis of Ligia oceanica (Crustacea: Isopoda) reveals two deep divergent mitochondrial lineages

description: Isopods of the species Ligia oceanica are typical inhabitants of the rocky
 intertidal of the northern European coastline. The aim of this study was
 to assess the genetic structure of this species using mitochondrial and
 nuclear sequence data. We analysed partial mitochondrial cytochrome c
 oxidase subunit I (CO1) and 16S rRNA gene sequence data of 161 specimens
 collected from ten sites ranging from Spain to Norway. For selected
 specimens, we also sequenced the hypervariable V7 expansion segment of the
 nuclear 18S rRNA gene as a supplementary marker. Furthermore, we studied
 the infection rate of all analysed specimens by the alphaproteobacterium
 Wolbachia. Our analyses revealed two deeply divergent mitochondrial
 lineages for Ligia oceanica that probably diverged in the late Pliocene to
 mid Pleistocene. One lineage comprised specimens from northern populations
 (‘lineage N’) and one primarily those from France and Spain (‘lineage S’).
 Distribution patterns of the haplotypes and the genetic distances between
 both lineages revealed two populations that diverged before the Last
 Glacial Maximum. Given that we found no homogenization of mitochondrial
 haplotypes, our present results also reject any influence of Wolbachia on
 the observed mtDNA variability
description: Bayes_phylogram_Ligia_oceanica_CO1Bayesian tree by MrBayes 3.2.1 (Ronquist et al., 2012) for the 61 CO1 haplotypes of Ligia oceanica. The most appropriate model was determined beforehand using the Bayesian information criterion (BIC) as implemented in jModeltest 2.1.1 (Darriba et al., 2012), indicating TPM1uf+I+G to be the optimal nucleotide substitution model with the following parameters: nucleotide frequencies A: 0.27, C: 0.19, G: 0.17, T: 0.37; substitution rates RAC: 1, RAG: 13.33, RAT: 4.63, RCG: 4.63, RCT: 13.33, RGT: 1; gamma distribution shape = 0.48; and proportion of invariable sites = 0.38. The Bayesian analysis employed 10,000,000 Markov chain Monte Carlo (MCMC) generations in two parallel runs, each with three cold chains and one hot chain. Trees were sampled every 500th generation, with the number of burn-in generations being determined using the likelihood scores over all generations in Tracer 1.5 (Rambaut & Drummond, 2007). The determination of the split frequencies in both independent runs (&lt; 0.01) with 2 x 20,001 tree samples showed good convergence after 5,000 sampled trees (split frequency &lt; 0.01), which was therefore set as the burn-in.Ligia_oceanica_16S_haplotypes16S rDNA haplotypes of the analysed isopod specimens.Ligia_oceanica_COI_haplotypesCOI haplotypes of the analysed isopod specimens.Supporting_Information_Figure_S2Supporting Information Figure S2. Geographical distributions of Wolbachia-infected specimens of Ligia oceanica (black, in %). The total number of specimens per population is given in the white boxes.Supporting_Information_Table_S1Supporting Information Table S1. Table of all specimens used in this study, including individual codes, GenBank accession numbers (left) and haplotype numbers (right) of both mitochondrial gene fragments, collection sites with coordinates and dates, gender and status of Wolbachia infection of the analysed isopod specimens. Specimens are marked with asterisks when nuclear V7 regions were additionally analysed (accession number JQ814405).AMOVA_COI_dataInput file of COI data for the AMOVA analysis using Arlequin 3.5.1.2 (Excoffier & Lischer, 2010).