Data from: A new integrative framework for large-scale assessments of biodiversity and community dynamics, using littoral gastropods and crabs of British Columbia, Canada

Castelin M, Van Steenkiste N, Pante E, Harbo R, Lowe G, Gilmore SR, Therriault TW, Abbott CL

Date Published: March 28, 2016

DOI: http://dx.doi.org/10.5061/dryad.g0v02

 

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Title DNA sequence alignments per superfamily
Description Cox1 and 28S DNA sequence alignments of each superfamily of shelled gastropods and brachyuran crabs analyzed in the study. Cox1 alignments include only haplotypes. Cox1 datasets were supplemented with DNA sequences from Canadian marine shelled gastropods and North East Pacific brachyuran crabs available on BOLD. Cox1 and 28S alignments include an outgroup. Alignments were generated using MAFFT v. 7 (Katoh et al. 2002; Katoh & Toh 2010) with the FFT-NS-I option. Alignments were used to generate Maximum Likelihood implementations.
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Title Tree figures
Description Figures of the phylogenetic trees produced in this study using Cox1 and 28S datasets. For each superfamily are represented the ML tree based on 28S dataset, and the PTP and GMYC trees produced using Cox1 datasets. Trees were built using Maximum Likelihood (ML) implementations using the GTR+GAMMA model of rate substitution (the most inclusive model) inferred using RAxML HPC2 (Stamatakis 2006) on Teragrid v.7.2.7, implemented in the Cyber Infrastructure for Phylogenetic Research (CIPRES) portal v.3.1. (Miller et al. 2011). One hundred independent searches, each starting from distinct random trees, were conducted. Robustness of the nodes was assessed using nonparametric bootstrapping (Felsenstein 1985) with 1000 replicates. For Cox1 datasets, the resulting tree served as input for the PTP model. For GMYC, the ML trees were made ultra-metric using r8s (Sanderson 2003). Trees were calibrated using divergence time and absolute rate of substitution between roots (fixed to have an arbitrary age of 1.0) and all unfixed nodes. Calibrations were reconstructed using the Langley-Fitch method and Powell’s algorithm (Sanderson 2003). PTP and GMYC analyses were both run using the ETE package (Huerta-Cepas et al. 2010).
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Title Presence-absence matrices
Downloaded 3 times
Description Six presence-absence matrices generated to detect non-random species co-occurrence patterns using EcoSim (Gotelli & Entsminger 2004). Rows correspond to the species sampled in this study. Columns correspond to the sampled sites analyzed.
Download presence-absence matrices.xls (77.82 Kb)
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When using this data, please cite the original publication:

Castelin M, Van Steenkiste N, Pante E, Harbo R, Lowe G, Gilmore SR, Therriault TW, Abbott CL (2016) Data from: A new integrative framework for large-scale assessments of biodiversity and community dynamics, using littoral gastropods and crabs of British Columbia, Canada. Molecular Ecology Resources 16(6): 1322–1339. http://dx.doi.org/10.1111/1755-0998.12534

Additionally, please cite the Dryad data package:

Castelin M, Van Steenkiste N, Pante E, Harbo R, Lowe G, Gilmore SR, Therriault TW, Abbott CL (2016) Data from: A new integrative framework for large-scale assessments of biodiversity and community dynamics, using littoral gastropods and crabs of British Columbia, Canada. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.g0v02
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