Abstract
BackgroundDemosponges 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 FindingsWe 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/SignificanceThese 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.
Highlights
Sponges belong to an ancient metazoan lineage with a fossil record that stretches back to the late Cryogenian .635 Myr ago [1,2,3]
We report findings based on a significant expansion (38 new samples from 38 species representing 30 families, including 21 families newly sampled) of the nuclear housekeeping gene dataset first developed for metazoan-wide phylogenetic and molecular dating analyses [45,46] and later applied by Sperling et al [18,44] to sponges, with a thorough taxonomic vetting process and a slightly modified phylogenetic analysis focused on relationships within Demospongiaep
We evaluated single gene phylogenies (ALD, ATP synthase beta chain (ATPB), etc.) including all the members of each gene family that could be identified in GenBank to identify and remove potential paralogs
Summary
Sponges belong to an ancient metazoan lineage with a fossil record that stretches back to the late Cryogenian .635 Myr ago [1,2,3]. As a sister group (or groups) to all the other animals in the metazoan tree of life, sponges represent a fulcrum point in the history of animal life lying at the junction between single-celled ancestors and the rest of Metazoa. Sponges have been important ecosystem engineers throughout much of their history, e.g., as major reef-builders during the Upper Devonian, Upper Permian, and through a major portion of the Jurassic [6,7]. As one of the most diverse taxa of extant sessile invertebrates [16], a detailed exploration of poriferan evolutionary relationships will yield important insights into many phases of metazoan history. 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
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