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

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.