10.5061/DRYAD.MG606
Raupach, Michael
Senckenberg am Meer
Bininda-Emonds, Olaf
Carl von Ossietzky University of Oldenburg
Knebelsberger, Thomas
Senckenberg am Meer
Laakmann, Silke
Senckenberg am Meer
Pfaender, Jobst
Zoological Research Museum Alexander Koenig
Leese, Florian
Ruhr University Bochum
Data from: Phylogeographic analysis of Ligia oceanica (Crustacea: Isopoda)
reveals two deep divergent mitochondrial lineages
Dryad
dataset
2014
glacial refugia
long-distance dispersal
16S rDNA
Wolbachia
cytochrome c oxidase subunit I
Ligia oceanica
Oniscidea
2014-01-21T19:16:04Z
2014-01-21T19:16:04Z
en
https://doi.org/10.1111/bij.12254
3305909 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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
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 (< 0.01) with 2 x 20,001 tree samples showed
good convergence after 5,000 sampled trees (split frequency <
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).
Northern Europe
North Sea