Data from: Phylogeographic analysis of Ligia oceanica (Crustacea: Isopoda) reveals two deep divergent mitochondrial lineages

Raupach M, Bininda-Emonds O, Knebelsberger T, Laakmann S, Pfaender J, Leese F

Date Published: January 21, 2014

DOI: http://dx.doi.org/10.5061/dryad.mg606

 

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Title Bayes_phylogram_Ligia_oceanica_CO1
Downloaded 12 times
Description Bayesian 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.
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Title Ligia_oceanica_16S_haplotypes
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Description 16S rDNA haplotypes of the analysed isopod specimens.
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Title Ligia_oceanica_COI_haplotypes
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Description COI haplotypes of the analysed isopod specimens.
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Title Supporting_Information_Figure_S2
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Description Supporting 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.
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Title Supporting_Information_Table_S1
Downloaded 48 times
Description Supporting 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).
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Title AMOVA_COI_data
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Description Input file of COI data for the AMOVA analysis using Arlequin 3.5.1.2 (Excoffier & Lischer, 2010).
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When using this data, please cite the original publication:

Raupach M, Bininda-Emonds O, Knebelsberger T, Laakmann S, Pfaender J, Leese F (2014) Phylogeographic analysis of Ligia oceanica (Crustacea: Isopoda) reveals two deep divergent mitochondrial lineages. Biological Journal of the Linnean Society 112(1): 16-30. http://dx.doi.org/10.1111/bij.12254

Additionally, please cite the Dryad data package:

Raupach M, Bininda-Emonds O, Knebelsberger T, Laakmann S, Pfaender J, Leese F (2014) Data from: Phylogeographic analysis of Ligia oceanica (Crustacea: Isopoda) reveals two deep divergent mitochondrial lineages. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.mg606
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