DOI: 10.5061/dryad.g0v02
title: Data from: A new integrative framework for large-scale assessments of biodiversity and community dynamics, using littoral gastropods and crabs of British Columbia, Canada

description: Improving our understanding of species responses to environmental changes
 is an important contribution ecologists can make to facilitate effective
 management decisions. Novel synthetic approaches to assessing biodiversity
 and ecosystem integrity are needed, ideally including all species living
 in a community and the dynamics defining their ecological relationships.
 Here we present and apply an integrative approach that links
 high-throughput, multi-character taxonomy with community ecology. The
 overall purpose is to enable the coupling of biodiversity assessments with
 investigations into the nature of ecological interactions in a
 community-level data set. We collected 1,195 gastropods and crabs in
 British Columbia. First, the General mixed Yule-coalescent (GMYC) and the
 Poisson Tree Processes (PTP) methods for proposing primary
 species-hypotheses based on cox1 sequences were evaluated against an
 integrative taxonomic framework. We then used data on the geographic
 distribution of delineated species to test species co-occurrence patterns
 for non-randomness using community-wide and pairwise approaches. Results
 showed that PTP generally outperformed GMYC and thus constitutes a more
 effective option for producing species-hypotheses in community-level
 datasets. Non-random species co-occurrence patterns indicative of
 ecological relationships or habitat preferences were observed for grazer
 gastropods, whereas assemblages of opportunistic omnivorous gastropods and
 crabs appeared influenced by random processes. Species-pair associations
 were consistent with current ecological knowledge, thus suggesting that
 applying community assembly within a large taxonomical framework
 constitutes a valuable tool for assessing ecological interactions.
 Combining phylogenetic, morphological and co-occurrence data enabled an
 integrated view of communities, providing both a conceptual and pragmatic
 framework for biodiversity assessments and investigations into community
 dynamics.
description: DNA sequence alignments
 per superfamilyCox1 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.DNA
 Alignments.zipTree
 figuresFigures 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).Presence-absence
 matricesSix 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.presence-absence
 matrices.xls