Phylogeny and classification of the tribe Hydaticini (Coleoptera: Dytiscidae): partition choice for Bayesian analysis with multiple nuclear and mitochondrial protein-coding genes

Miller, K. B., Bergsten, J. & Whiting M. F. (2009). Phylogeny and classification of the tribe Hydaticini (Coleoptera: Dytiscidae): partition choice for Bayesian analysis with multiple nuclear and mitochondrial protein-coding genes. - Zoologica Scripta 38, 591-615. A phylogenetic analysis of the diving beetle tribe Hydaticini Sharp (Coleoptera: Dytiscidae: Dytiscinae) is presented based on data from adult morphology, two nuclear (histone III and wingless) and two mitochondrial (cytochrome c oxidase I and II) protein-coding genes. We explore how to best partition a data set of multiple nuclear and mitochondrial protein-coding genes by using Bayes factor and a penalized modification of Bayes Factor. Ten biologically relevant partitioning strategies were identified ranging from all DNA analysed under a single model to each codon position of each gene treated with a separate model. Model selection criteria AIC, AICc, BIC and four ways of traversing parameter space in a hierarchical likelihood ratio test were applied to each partition. All unique partitioning and model combinations were analysed with Bayesian methods. Results show that partitioning by codon position and genome source (nuclear vs. mitochondrial) is strongly favoured over partitioning by gene. We also find evidence that Bayes Factor can penalize overparameterization even when comparing nested models. Species groups showing a strong geographical pattern were generally highly supported, however, the sister group relationship of an isolated Madagascan and Australian species were shown to be artefactual with a long-branch extraction test. The following conclusions were supported in both the selected method of partitioning the Bayesian analysis and combined parsimony analyses: (i) the tribe Hydaticini is monophyletic (ii) the genus Hydaticus Leach is paraphyletic with respect to Prodaticus Sharp (iii) the subgenus Hydaticus (Hydaticus) is monophyletic, and (iv) the subgenus H. (Guignotites) Brinck is paraphyletic with respect to Prodaticus and the subgenera H. (Pleurodytes) Regimbart and H. (Hydaticinus) Guignot. Based on these results, Hydaticus and Prodaticus are each recognized as valid genera and Guignotites, Hydaticinus and Pleurodytes are each placed as junior synonyms of Prodaticus (new synonymies).