Computational protocol: Variation in species diversity and functional traits of sponge communities near human populations in Bocas del Toro, Panama

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Protocol publication

[…] Phylogenetic relatedness among surveyed sponge species was assessed using a phylogeny constructed from a partitioned alignment of gene sequences from GenBank coding for the small (18S) and large (28S) nuclear ribosomal subunits, which are common markers used for molecular identification of sponge species (; ; ). One sponge species, Verongula reiswigi, was not represented in GenBank, and we obtained sequence information from vouchers representing this species as part of the current study ().We reconstructed a phylogeny for all sponge species except Niphates caycedoi, for which we were unable to obtain sequence information. This species was rare, with only four individuals of this species found at one site. This species was excluded from phylogenetic analysis. For each gene, sequences were aligned using the default options of MAFFT 7.017 () in the program Geneious (version 6.1.8, Biomatters Limited). We concatenated the two alignments, treating them as two separate partitions with independent models of sequence evolution. We implemented a relaxed-clock model in MrBayes version 3.2.1 (), using the CIPRES computational resources (), and following recommended best practices for implementing partitioned analysis (; ). We constrained sponges in the genus Plakortis as an outgroup, using the independent gamma rate relaxed clock model with a birth-death process (, ). We included three parallel runs of 10 million generations, each using four Markov chains and sampling every 100 generations. A consensus phylogeny of the three parallel runs was summarized following a burn-in of 25% (). [...] We assessed phylogenetic diversity by calculating Faith’s phylogenetic diversity (PD), using the R package picante (). Faith’s PD measures the total branch length spanned by the sub-tree from each community, allowing for a comparison of total branch lengths between communities (). Additionally, Faith’s PD relaxes the diversity measurement assumption that all species are “equally different” by weighting species diversity based on phylogenetic similarity (). Phylogenetic diversity patterns (clustering, dispersion, or random) were assessed by measuring the mean pairwise distance (MPD) and mean nearest taxon distance (MNTD) scaled to the standard effect size among sponges within each site, accepting the default options in the models. MPD calculates the mean distance between two randomly chosen individuals in the community. Significant clustering measured by MPD implies a higher presence of species related to one another through interior nodes (away from the tips of the phylogeny) belonging to broader phylogenetic groups. MNTD calculates the mean distance separating one individual from its closest relative. MNTD describes clustering at the tips of the tree, and significant clustering by this metric indicates a higher presence of closely related species connected by nodes closer to the tips of the phylogeny. For both MPD and MNTD, we assessed differences in phylogenetic diversity patterns using two t-tests. We used a two-sample t-test to assess differences between sites, and a one-sample t-test to test whether each site differed from a null hypothesis of random phylogenetic relatedness (μ = 0, ; ). […]

Pipeline specifications

Software tools MAFFT, Geneious, MrBayes, Picante
Application Phylogenetics
Organisms Homo sapiens