Authors

Malcolm S. Hill, University of Richmond
April L. Hill, University of Richmond
Jose V. Lopez, Nova Southeastern UniversityFollow
Kevin J. Peterson, Dartmouth College
Shirley Pomponi, Florida Atlantic UniversityFollow
Maria C. Diaz, Museo Marino de Margarita - Boca del Rio, Venezuela
Robert W. Thacker, University of Alabama - Birmingham
Maja Adamska, Sars International Centre for Marine Molecular Biology - Bergen, Norway
Nicole Boury-Esnault, Université d’Aix-Marseille - France
Paco Cárdenas, Uppsala University - Sweden
Andia Chaves-Fonnegra, Nova Southeastern UniversityFollow
Elizabeth Danka, University of Richmond
Bre-Onna De Laine, University of Richmond
Dawn Formica, Nova Southeastern University
Eduardo Hajdu, Universidade Federal do Rio de Janeiro - Brazil
Gisele Lobo-Hajdu, Universidade do Estado do Rio de Janeiro - Brazil
Sarah Klontz, Smithsonian Institution
Christine C. Morrow, Queen’s University - Belfast, United Kingdom
Jignasa Patel, Nova Southeastern University
Bernard Picton, National Museums Northern Ireland - United Kingdom
Davide Pisani, University of Bristol - United Kingdom
Deborah Pohlmann, University of Richmond
Niamh E. Redmond, Smithsonian Institution
John Reed, Florida Atlantic UniversityFollow
Stacy Richey, University of Richmond
Ana Riesgo, Harvard University
Ewelina Rubin, Nova Southeastern University
Zach Russell, University of Richmond
Klaus Rützler, Smithsonian Institution
Erik A. Sperling, Harvard University
Michael di Stefano, University of Richmond
James E. Tarver, University of Bristol - United Kingdom
Allen G. Collins, National Museum of Natural History, Smithsonian InstitutionFollow

Document Type

Article

Publication Date

1-2013

Publication Title

PLoS One

Keywords

Amino acid analysis, Animal phylogenetics, Bayes theorem, Mitochondria, Paleogenetics, Phylogeography, Sponges, Topology

ISSN

1932-6203

Volume

8

Issue/No.

1 e50437

First Page

1

Last Page

16

Abstract

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.

Comments

This is an open-access article, free of all This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

Additional Comments

NSF grant #s: DEB-0829763, DEB0829783, DEB0829791, DEB0829986

ORCID ID

0000-0002-1637-4125

ResearcherID

F-8809-2011

DOI

10.1371/journal.pone.0050437