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Mol Phylogenet Evol. 2019 Feb 26;135:270-285. doi: 10.1016/j.ympev.2019.02.022. [Epub ahead of print]

Phylogenomics of the superfamily Dytiscoidea (Coleoptera: Adephaga) with an evaluation of phylogenetic conflict and systematic error.

Author information

1
Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 53113 Bonn, Germany. Electronic address: a.vasilikopoulos@leibniz-zfmk.de.
2
Department of Entomology, SNSB-Bavarian State Collections of Zoology, Münchhausenstr. 21, 81247 Munich, Germany; GeoBio-Center, Ludwig-Maximilians-Universität Munich, Richard-Wagner-Str. 10, 80333 Munich, Germany.
3
Institut für Zoologie und Evolutionsforschung, Friedrich-Schiller-Universität Jena, Ebertstr. 1, 07743 Jena, Germany.
4
Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 53113 Bonn, Germany.
5
Department of Integrative Biology, Oregon State University, 3029 Cordley Hall, Corvallis, 97331 OR, USA.
6
Department of Ecology and Evolution, University of Lausanne and Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
7
Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 53113 Bonn, Germany; Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), Albert-Ludwigs-Universität Freiburg, Hauptstr. 1, 79104 Freiburg, Germany; Australian National Insect Collection, National Research Collections Australia, CSIRO, ACT 2601, Canberra, Australia.
8
Center of Taxonomy and Evolutionary Research, Department of Arthropoda, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 53113 Bonn, Germany.
9
Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), Albert-Ludwigs-Universität Freiburg, Hauptstr. 1, 79104 Freiburg, Germany.
10
China National GeneBank, BGI-Shenzhen, Shenzhen, Guangdong Province 518083, PR China.
11
Department of Entomology, SNSB-Bavarian State Collections of Zoology, Münchhausenstr. 21, 81247 Munich, Germany.
12
Department of Biology, Laurentian University, P3E2C6 Sudbury, Ontario, Canada.
13
Marine Biology and Ecology Research Center, School of Biological and Marine Sciences, University of Plymouth, Drake Circus, PL48AA, UK; Department of Zoology, University of Johannesburg, PO Box 524, Auckland Park, 2006 Johannesburg, South Africa.
14
Institute of Entomology, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, PR China.
15
Department of Entomology, China Agricultural University, 100193 Beijing, PR China.
16
Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 53113 Bonn, Germany. Electronic address: b.misof@leibniz-zfmk.de.

Abstract

The beetle superfamily Dytiscoidea, placed within the suborder Adephaga, comprises six families. The phylogenetic relationships of these families, whose species are aquatic, remain highly contentious. In particular the monophyly of the geographically disjunct Aspidytidae (China and South Africa) remains unclear. Here we use a phylogenomic approach to demonstrate that Aspidytidae are indeed monophyletic, as we inferred this phylogenetic relationship from analyzing nucleotide sequence data filtered for compositional heterogeneity and from analyzing amino-acid sequence data. Our analyses suggest that Aspidytidae are the sister group of Amphizoidae, although the support for this relationship is not unequivocal. A sister group relationship of Hygrobiidae to a clade comprising Amphizoidae, Aspidytidae, and Dytiscidae is supported by analyses in which model assumptions are violated the least. In general, we find that both concatenation and the applied coalescent method are sensitive to the effect of among-species compositional heterogeneity. Four-cluster likelihood-mapping suggests that despite the substantial size of the dataset and the use of advanced analytical methods, statistical support is weak for the inferred phylogenetic placement of Hygrobiidae. These results indicate that other kinds of data (e.g. genomic meta-characters) are possibly required to resolve the above-specified persisting phylogenetic uncertainties. Our study illustrates various data-driven confounding effects in phylogenetic reconstructions and highlights the need for careful monitoring of model violations prior to phylogenomic analysis.

KEYWORDS:

Aspidytidae; Compositional bias; Hydradephaga; RNA-seq; Transcriptomics

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