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Ribosomal ITS Sequences Allow Resolution of Freshwater Sponge Phylogeny with Alignments Guided by Secondary Structure Prediction

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Abstract

Freshwater sponges include six extant families which belong to the suborder Spongillina (Porifera). The taxonomy of freshwater sponges is problematic and their phylogeny and evolution are not well understood. Sequences of the ribosomal internal transcribed spacers (ITS1 and ITS2) of 11 species from the family Lubomirskiidae, 13 species from the family Spongillidae, and 1 species from the family Potamolepidae were obtained to study the phylogenetic relationships between endemic and cosmopolitan freshwater sponges and the evolution of sponges in Lake Baikal. The present study is the first one where ITS1 sequences were successfully aligned using verified secondary structure models and, in combination with ITS2, used to infer relationships between the freshwater sponges. Phylogenetic trees inferred using maximum likelihood, neighbor-joining, and parsimony methods and Bayesian inference revealed that the endemic family Lubomirskiidae was monophyletic. Our results do not support the monophyly of Spongillidae because Lubomirskiidae formed a robust clade with E. muelleri, and Trochospongilla latouchiana formed a robust clade with the outgroup Echinospongilla brichardi (Potamolepidae). Within the cosmopolitan family Spongillidae the genera Radiospongilla and Eunapius were found to be monophyletic, while Ephydatia muelleri was basal to the family Lubomirskiidae. The genetic distances between Lubomirskiidae species being much lower than those between Spongillidae species are indicative of their relatively recent radiation from a common ancestor. These results indicated that rDNA spacers sequences can be useful in the study of phylogenetic relationships of and the identification of species of freshwater sponges.

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Acknowledgments

We thank E. Weinberg and Y. Takemon for help with the collection of samples. This work was supported by an Obuchi fellowship, the Deutsche Forschungsgemeinschaft (DFG 436 RUS/17/20/01), and Federal Agency for Science and Innovations (FASI) Grant MK-4167.2007.4. We also thank G. McCormack for her help with the first version of the text. Two anonymous reviewers are acknowledged for critical comments on the manuscript.

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  1. Laboratory of Analytical Bio-Organic Chemistry, Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664 033, Irkutsk, Russia

    Valeria Itskovich & Sergey Belikov

  2. Institute of Biology and Soil Science of the Far Eastern Branch of the Russian Academy of Sciences, pr. 100-leti Vladivostoka 159, 690022, Vladivostok, Russia

    Andrey Gontcharov

  3. Department of Biology, Kawasaki Medical School, Kurashiki, 701-0192, Japan

    Yoshiki Masuda & Tsutomu Nohno

  4. Laboratory of Ontogenesis, Biological Research Institute, St. Petersburg State University, Oranienbaumskoe sch. 2, Stary Peterhoff, 198 904, St. Petersburg, Russia

    Sofia Efremova

  5. SMB, R.- Breitscheidstr. 70, 15562, Ruёdersdorf, Germany

    Martin Meixner

  6. Forschungsinstitut und Naturmuseum Senckenberg, Frankfurt am Main, Germany

    Dorte Janussen

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  1. Valeria Itskovich
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Itskovich, V., Gontcharov, A., Masuda, Y. et al. Ribosomal ITS Sequences Allow Resolution of Freshwater Sponge Phylogeny with Alignments Guided by Secondary Structure Prediction. J Mol Evol 67, 608–620 (2008). https://doi.org/10.1007/s00239-008-9158-5

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