Into the deep: A phylogenetic approach to the bivalve subclass Protobranchia

• Published in: Molecular phylogenetics and evolution 2013-10, Vol.69 (1), p.188-204
• Main Authors: Sharma, Prashant P., Zardus, John D., Boyle, Elizabeth E., González, Vanessa L., Jennings, Robert M., McIntyre, Erin, Wheeler, Ward C., Etter, Ron J., Giribet, Gonzalo
• Format: Article
• Language: English
• Subjects: Algorithms; Animals; Bivalvia; Bivalvia - classification; Bivalvia - genetics; Cladding; Constituents; cytochrome-c oxidase; Cytochromes; Electron Transport Complex IV - classification; Electron Transport Complex IV - genetics; End-Permian; Extinction; Extinction, Biological; genes; Genetic Speciation; Genetic Variation; Genetics; Histones; Histones - classification; Histones - genetics; Likelihood Functions; Loci; Models, Genetic; Molecular phylogeny; Mollusca; Nuculoidea; Oceans and Seas; Phylogeny; Protobranch gill; Reconstruction; ribosomal RNA; RNA, Ribosomal - classification; RNA, Ribosomal - genetics; Sequence Analysis, DNA; Signatures; Solemyidae; Tree alignment problem
• ISSN: 1055-7903; 1095-9513
• DOI: 10.1016/j.ympev.2013.05.018

•We investigated the internal phylogeny of the bivalve subclass Protobranchia using a multilocus dataset.•Four consistently recovered clades are Solemyoidea, Nucinellidae, Nuculoidea, and Nuculanoidea (including Sareptidae).•Sareptoidea is strongly supported as nested within or sister to Nuculanoidea.•The log-lineage through time plot of Protobranchia retains the signature of the end-Permian mass extinction. A molecular phylogeny of Protobranchia, the subclass of bivalve mollusks sister to the remaining Bivalvia, has long proven elusive, because many constituent lineages are deep-sea endemics, which creates methodological challenges for collecting and preserving genetic material. We obtained 74 representatives of all 12 extant protobranch families and investigated the internal phylogeny of this group using sequence data from five molecular loci (16S rRNA, 18S rRNA, 28S rRNA, cytochrome c oxidase subunit I, and histone H3). Model-based and dynamic homology parsimony approaches to phylogenetic reconstruction unanimously supported four major clades of Protobranchia, irrespective of treatment of hypervariable regions in the nuclear ribosomal genes 18S rRNA and 28S rRNA. These four clades correspond to the superfamilies Nuculoidea (excluding Sareptidae), Nuculanoidea (including Sareptidae), Solemyoidea, and Manzanelloidea. Salient aspects of the phylogeny include (1) support for the placement of the family Sareptidae with Nuculanoidea; (2) the non-monophyly of the order Solemyida (Solemyidae+Nucinellidae); (3) and the non-monophyly of most nuculoid and nuculanoid genera and families. In light of this first family-level phylogeny of Protobranchia, we present a revised classification of the group. Estimation of divergence times in concert with analyses of diversification rates demonstrate the signature of the end-Permian mass extinction in the phylogeny of extant protobranchs.