DOI: 10.5061/dryad.np5hqc04s
title: Community assembly in subtidal epibenthic invertebrate communities in the Gulf of Maine: A community phylogenetic and functional trait approach

description: How organisms assemble to form a community is a central question in
 ecology, with commonly inferred mechanisms including environmental
 filtering, competitive exclusion, and random processes. Community
 phylogenetic and functional trait analyses have been used to identify the
 relative importance of these processes, most often in terrestrial
 angiosperm systems consisting of a single taxon (e.g., class). Here,
 community phylogenetic and functional trait analyses are applied to
 multiphyletic subtidal epibenthic invertebrate assemblages at eight sites
 in the Gulf of Maine, to investigate the relative importance of
 deterministic or stochastic forces in structuring these communities. At
 local sites, some communities were phylogenetically overdispersed,
 suggesting community assembly via competitive exclusion. Five traits
 exhibited phylogenetic signal and for these traits, phylogeny can be used
 as a proxy for ecological similarity. Functional trait diversity was
 overdispersed for one site and clustered for another, indicative of
 assembly via competitive exclusion and environmental filtering
 respectively. Regionally, taxonomic beta diversity was less than expected
 by chance but phylogenetic and functional trait beta diversity were
 greater than expected, indicating that species are not dispersal limited
 and that different environmental conditions among sites select for
 different species. These results suggest that subtidal epibenthic
 invertebrate assemblages in the Gulf of Maine are structured by
 deterministic forces and that different assembly processes operate at
 different spatial scales: locally, competitive exclusion appears to be
 important whereas regionally, environmental filtering plays a role.
description: To conduct a community phylogenetic analysis for subtidal
 epibenthic invertebrate species at 8 sites in the Gulf of Maine, 3 data
 sets were used: a phylogenetic tree, a species by site presence-absence
 matrix, and functional trait information. The site presence-absence matrix
 was created from data found in Table 1 from Miller and Etter (2011) using
 the species on vertical surfaces only, and the other two datasets are
 described below. Dataset 1—Bayesian newick
 tree DNA was extracted and amplified from 50
 invertebrate species or downloaded from GenBank and 18S sequences aligned,
 checked by eye, and trimmed at the beginning and end to minimize gaps. The
 general time-reversible (GTR) model of evolution was selected, with an
 estimated proportion of DNA sites invariant (I), and mutation rates among
 sites following a gamma distribution (G). The GTR+I+G model was then used
 to estimate a Bayesian gene tree with a ‘Bootstrapping procedure’ (100
 times) to assess support for tree nodes. Dataset
 2—Trait data Functional traits relevant to the study
 species were selected to cover a range of life history, morphological, and
 behavioral characteristics relating to space and food acquisition. All
 traits were divided into discrete categories and species were placed in
 categories based on their characteristics. For the one continuous trait,
 categories were assigned based on the species average. Trait information
 was obtained from a variety of sources including personal knowledge,
 on-line databases, natural history texts, and primary literature. To
 summarize, the trait data comprises five nominal traits (coloniality,
 reproduction, growth form, food capture, and defense), and one continuous
 trait (body size) divided into nominal categories.
 Miller, R. J., and R. J. Etter. 2011. “Rock walls: small–scale
 diversity hotspots in the subtidal Gulf of Maine.” <em>Marine
 Ecology Progress Series</em> 425: 153–165.
description: # Community assembly in subtidal epibenthic invertebrate communities in
 the Gulf of Maine: A community phylogenetic and functional trait approach
 [https://doi.org/10.5061/dryad.np5hqc04s](https://doi.org/10.5061/dryad.np5hqc04s) ## Description of the data and file structure These data represent files used to conduct a community phylogenetic analysis for subtidal epibenthic invertebrate species at 8 sites in the Gulf of Maine. ### Files and variables Dataset 1—Bayesian Newick tree (bayesian_newick_tree.txt) This is presented in Newick format and contains the names of the names of the species at the tips of the tree, the branching relationships between the species, and the length of each branch. Dataset 2—Trait data (trait_data.csv) This data is arranged in columns. The first column contains species names for subtidal epibenthic invertebrates in the Gulf of Maine. All other column headers represent an important functional trait that covers a range of life history, morphological, and behavioral characteristics relating to space and food acquisition for these species. Coloniality refers to whether the species is a colonial or solitary organism; Reproduction to reproductive mode; Body_size to the organism's typical size; Growth_form to whether the organism grows in an erect or encrusting manner; Food_capture to the organisms method of food capture; and Defense to the organism's primary mechanism of defense. Within the table are the various categories for each trait that the represents each species.  Species presence-absence data was derived from Table 1 in Miller and Etter (2011) using the species found on vertical surfaces only. It is not available here for copyright or licensing reasons. This data can be used by other researchers wanting to compare phylogenetic community structure between sessile marine invertebrates and other taxa, to examine the evolutionary relationships between subtidal epibenthic invertebrate species, and to see which functional trait categories different taxa fall into. Miller, R. J., and R. J. Etter. 2011. Rock walls: small–scale diversity hotspots in the subtidal Gulf of Maine. Marine Ecology Progress Series 425:153–165.