Phylogenetic analysis of four nuclear protein-encoding genes largely corroborates the traditional classification of Bivalvia (Mollusca)

Sharma, Prashant P. and González, Vanessa L. and Kawauchi, Gisele Y. and Andrade, Sónia C.S. and Guzmán, Alejandra and Collins, Timothy M. and Glover, Emily A. and Harper, Elizabeth M. and Healy, John M. and Mikkelsen, Paula M. and Taylor, John D. and Bieler, Rüdiger and Giribet, Gonzalo (2012) Phylogenetic analysis of four nuclear protein-encoding genes largely corroborates the traditional classification of Bivalvia (Mollusca). Molecular Phylogenetics and Evolution, 65 (1). pp. 64-74. ISSN ISSN: 1055-7903 DOI 10.1016/j.ympev.2012.05.025

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Abstract

Revived interest in molluscan phylogeny has resulted in a torrent of molecular sequence data from phylogenetic, mitogenomic, and phylogenomic studies. Despite recent progress, basal relationships of the class Bivalvia remain contentious, owing to conflicting morphological and molecular hypotheses. Marked incongruity of phylogenetic signal in datasets heavily represented by nuclear ribosomal genes versus mitochondrial genes has also impeded consensus on the type of molecular data best suited for investigating bivalve relationships. To arbitrate conflicting phylogenetic hypotheses, we evaluated the utility of four nuclear protein-encoding genes—ATP synthase β, elongation factor-1α, myosin heavy chain type II, and RNA polymerase II—for resolving the basal relationships of Bivalvia. We sampled all five major lineages of bivalves (Archiheterodonta, Euheterodonta [including Anomalodesmata], Palaeoheterodonta, Protobranchia, and Pteriomorphia) and inferred relationships using maximum likelihood and Bayesian approaches. To investigate the robustness of the phylogenetic signal embedded in the data, we implemented additional datasets wherein length variability and/or third codon positions were eliminated. Results obtained include (a) the clade (Nuculanida + Opponobranchia), i.e., the traditionally defined Protobranchia; (b) the monophyly of Pteriomorphia; (c) the clade (Archiheterodonta + Palaeoheterodonta); (d) the monophyly of the traditionally defined Euheterodonta (including Anomalodesmata); and (e) the monophyly of Heteroconchia, i.e., (Palaeoheterodonta + Archiheterodonta + Euheterodonta). The stability of the basal tree topology to dataset manipulation is indicative of signal robustness in these four genes. The inferred tree topology corresponds closely to those obtained by datasets dominated by nuclear ribosomal genes (18S rRNA and 28S rRNA), controverting recent taxonomic actions based solely upon mitochondrial gene phylogenies.

Item Type:	Article
Uncontrolled Keywords:	2012AREP; IA64;
Subjects:	04 - Palaeobiology
Divisions:	04 - Palaeobiology
Journal or Publication Title:	Molecular Phylogenetics and Evolution
Volume:	65
Page Range:	pp. 64-74
Identification Number:	10.1016/j.ympev.2012.05.025
Depositing User:	Sarah Humbert
Date Deposited:	18 Jul 2012 11:08
Last Modified:	23 Jul 2013 10:04
URI:	http://eprints.esc.cam.ac.uk/id/eprint/2558

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