Reconstruction of Family-Level Phylogenetic Relationships within Demospongiae (Porifera) Using Nuclear Encoded Housekeeping Genes

Background: Demosponges are challenging for phylogenetic systematics because of their plastic and relatively simple morphologies and many deep divergences between major clades. To improve understanding of the phylogenetic relationships within Demospongiae, we sequenced and analyzed seven nuclear housekeeping genes involved in a variety of cellular functions from a diverse group of sponges. Methodology/Principal Findings: We generated data from each of the four sponge classes (i.e., Calcarea, Demospongiae, Hexactinellida, and Homoscleromorpha), but focused on family-level relationships within demosponges. With data for 21 newly sampled families, our Maximum Likelihood and Bayesian-based approaches recovered previously phylogenetically defined taxa: Keratosap, Myxospongiaep, Spongillidap, Haploscleromorphap (the marine haplosclerids) and Democlaviap. We found conflicting results concerning the relationships of Keratosap and Myxospongiaep to the remaining demosponges, but our results strongly supported a clade of Haploscleromorphap+Spongillidap+Democlaviap. In contrast to hypotheses based on mitochondrial genome and ribosomal data, nuclear housekeeping gene data suggested that freshwater sponges (Spongillidap) are sister to Haploscleromorphap rather than part of Democlaviap. Within Keratosap, we found equivocal results as to the monophyly of Dictyoceratida. Within Myxospongiaep, Chondrosida and Verongida were monophyletic. A well supported clade within Democlaviap, Tetractinellidap, composed of all sampled members of Astrophorina and Spirophorina (including the only lithistid in our analysis), was consistently revealed as the sister group to all other members of Democlaviap. Within Tetractinellidap, we did not recover monophyletic Astrophorina or Spirophorina. Our results also reaffirmed the monophyly of order Poecilosclerida (excluding Desmacellidae and Raspailiidae), and polyphyly of Hadromerida and Halichondrida. Conclusions/Significance: These results, using an independent nuclear gene set, confirmed many hypotheses based on ribosomal and/or mitochondrial genes, and they also identified clades with low statistical support or clades that conflicted with traditional morphological classification. Our results will serve as a basis for future exploration of these outstanding questions using more taxon- and gene-rich datasets

An annotated and illustrated identification guide to common mesophotic reef sponges (Porifera, Demospongiae, Hexactinellida, and Homoscleromorpha) inhabiting Flower Garden Banks national marine sanctuary and vicinities

Sponges are recognized as a diverse and abundant component of mesophotic and deep-sea ecosystems worldwide. In Flower Garden Banks National Marine Sanctuary region within the northwestern Gulf of Mexico, sponges thrive among diverse biological and geological habitats between 16-200+ m deep (i.e., coral reefs and communities, algal nodule and coralline algae reefs, mesophotic reefs, patch reefs, scarps, ridges, soft substrate, and rocky outcrops). We present a synoptic guide developed by studying common sponge species in the region, through direct sampling and in situ photographic records.  A total of 63 species are included: 60 are Demospongiae (14 orders), 2 are Hexactinellida (1 order), 2 are Homoscleromorpha (1 order). Thirty-nine taxa are identified to species and 11 were identified to have affinity with, but are not identical to, a known species. Thirteen taxa could only be identified to genus level at this time, and the species remain as uncertain (incerta sedis), with the potential to constitute new species or variants of known species. One specimen received only a family assignation.  This study extends geographic or mesophotic occurrence data for 11 known species and includes several potentially new species. This work improves our knowledge of Gulf of Mexico sponge biodiversity and highlights the importance of the region for scientists and resource managers

An annotated and illustrated identification guide to common mesophotic reef sponges (Porifera, Demospongiae, Hexactinellida, and Homoscleromorpha) inhabiting Flower Garden Banks National Marine Sanctuary and vicinities

Sponges are recognized as a diverse and abundant component of mesophotic and deep-sea ecosystems worldwide. In Flower Garden Banks National Marine Sanctuary region within the northwestern Gulf of Mexico, sponges thrive among diverse biological and geological habitats between 16–200+ m deep (i.e., coral reefs and communities, algal nodules, and coralline algae reefs, mesophotic reefs, patch reefs, scarps, ridges, soft substrate, and rocky outcrops). A synoptic guide is presented, developed by studying common sponge species in the region, through direct sampling and in-situ photographic records. A total of 64 species is included: 60 are Demospongiae (14 orders), two are Hexactinellida (one order), and two are Homoscleromorpha (one order). Thirty-four taxa are identified to species and 13 were identified to have affinity with, but were not identical to, a known species. Fifteen taxa could only be identified to genus level, and the species remain as uncertain (incerta sedis), with the potential to represent new species or variants of known species. One specimen received only a family assignation. This study extends geographic or mesophotic occurrence data for eleven known species and includes several potentially new species. This work improves our knowledge of Gulf of Mexico sponge biodiversity and highlights the importance of the region for scientists and resource managers

Comparison of clades found in NHK7^* ML topology with those revealed in single-gene and other analyses.^*

*<p>NHK7 refers to the complete dataset, while NHK6-4 refer to datasets where the markers CAT, EF1A, and ATPB are successively removed.</p

Model cross validation performed using CAT-GTR as the reference model.

*<p>A negative cross validation score indicates that the reference model (CAT-GTR) fits the data better then the tested model. This table indicates that CAT-GTR provides the best fit to the data (as the standard deviations around the means are not sufficient to define a confidence intervals including positive values).</p

Amino acid model selection, used for maximum likelihood searches on different datasets^*.

*<p>NHK7 refers to the complete dataset, while NHK6-4 refer to datasets where the markers CAT, EF1A, and ATPB are successively removed.</p

Hypothesis of demosponge relationships based on maximum likelihood analysis of seven nuclear housekeeping genes.

<p>Topology rooted on three cnidarians and the placozoan <i>Trichoplax</i>. Bootstrap indices (400 replicates) are shown at each node, with those exceeding 70 in bold. New taxa added as part of the PorToL project are indicated in bold; new taxa added from EST/genomics projects are indicated with a single asterisk; and taxa with new identifications after examination of the voucher specimen are marked with two asterisks. Clade names in italics followed by a superscript p have been phylogenetically defined in other studies (see text).</p

Hypothesis of demosponge relationships based on Bayesian analysis of seven nuclear housekeeping genes.

<p>Topology rooted on three cnidarians and the placozoan <i>Trichoplax</i>. Posterior probabilities are shown at each node, with those exceeding 0.90 in bold. New taxa added as part of the PorToL project are indicated in bold; new taxa added from EST/genomics projects are indicated with a single asterisk; and taxa with new identifications after examination of the voucher specimen are marked with two asterisks. Clade names in italics followed by a superscript p have been phylogenetically defined in other studies (see text).</p