title: Molecular phylogeny of the aquatic beetle family Noteridae (Coleoptera: Adephaga) with an emphasis on data partitioning strategies.
abstract: The first molecular phylogenetic hypothesis for the aquatic beetle family Noteridae is inferred using DNA sequence data from five gene fragments (mitochondrial and nuclear): COI, H3, 16S, 18S, and 28S. Our analysis is the most comprehensive phylogenetic reconstruction of Noteridae to date, and includes 53 species representing all subfamilies, tribes and 16 of the 17 genera within the family. We examine the impact of data partitioning on phylogenetic inference by comparing two different algorithm-based partitioning strategies: one using predefined subsets of the dataset, and another recently introduced method, which uses the k-means algorithm to iteratively divide the dataset into clusters of sites evolving at similar rates across sampled loci. We conducted both maximum likelihood and Bayesian inference analyses using these different partitioning schemes. Resulting trees are strongly incongruent with prior classifications of Noteridae. We recover variant tree topologies and support values among the implemented partitioning schemes. Bayes factors calculated with marginal likelihoods of Bayesian analyses support a priori partitioning over k-means and unpartitioned data strategies. Our study substantiates the importance of data partitioning in phylogenetic inference, and underscores the use of comparative analyses to determine optimal analytical strategies. Our analyses recover Noterini Thomson to be paraphyletic with respect to three other tribes. The genera Suphisellus Crotch and Hydrocanthus Say are also recovered as paraphyletic. Following the results of the preferred partitioning scheme, we here propose a revised classification of Noteridae, comprising two subfamilies, three tribes and 18 genera. The following taxonomic changes are made: Notomicrinae sensu n. (= Phreatodytinae syn. n.) is expanded to include the tribe Phreatodytini; Noterini sensu n. (= Neohydrocoptini syn. n., Pronoterini syn. n., Tonerini syn. n.) is expanded to include all genera of the Noterinae; The genus Suphisellus Crotch is expanded to include species of Pronoterus Sharp syn. n.; and the former subgenus Sternocanthus Guignot stat. rev. is resurrected from synonymy and elevated to genus rank.
authors: Department of Ecology and Evolutionary Biology and Division of Entomology, Biodiversity Institute, University of Kansas, Lawrence, KS 66045, USA. Electronic address: s953b810@ku.edu.
authors: Stephen M
authors: SM
authors: Baca
authors: Department of Ecology and Evolutionary Biology and Division of Entomology, Biodiversity Institute, University of Kansas, Lawrence, KS 66045, USA.
authors: Emmanuel F A
authors: EFA
authors: Toussaint
authors: Department of Biology and Museum of Southwestern Biology, University of New Mexico Albuquerque, NM 87131-0001, USA.
authors: Kelly B
authors: KB
authors: Miller
authors: Department of Ecology and Evolutionary Biology and Division of Entomology, Biodiversity Institute, University of Kansas, Lawrence, KS 66045, USA.
authors: Andrew E Z
authors: AEZ
authors: Short
mesh_terms: D000818:Animals; D059001:Aquatic Organisms / Q000235:genetics*; D001499:Bayes Theorem; D001517:Coleoptera / Q000145:classification* / Q000235:genetics*; D016013:Likelihood Functions; D008962:Models, Theoretical; D010802:Phylogeny
keywords: Bayes factors; PartitionFinder; Stepping-stone sampling; Tree Independent Generation of Evolutionary Rates; Water beetle systematics; k-means algorithm