Phylogenomics of the superfamily Dytiscoidea (Coleoptera: Adephaga) with an evaluation of phylogenetic conflict and systematic error
| Autor: | Shanlin Liu, David R. Maddison, Fenglong Jia, Xin Zhou, Bernhard Misof, Rolf G. Beutel, Yves Alarie, Christoph Mayer, Karen Meusemann, Ralph S. Peters, Lars Podsiadlowski, Hermes E. Escalona, Lars Hendrich, Alexandros Vasilikopoulos, Michael Balke, Robert M. Waterhouse, Alexander Donath, Oliver Niehuis, David T. Bilton, James M. Pflug |
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| Jazyk: | angličtina |
| Rok vydání: | 2019 |
| Předmět: |
0106 biological sciences
0301 basic medicine Amino Acids/genetics Animals Base Sequence Classification Codon/genetics Coleoptera/classification Coleoptera/genetics Genome Genomics Likelihood Functions Phylogeny Transcriptome/genetics Aspidytidae Compositional bias Hydradephaga RNA-seq Transcriptomics 010603 evolutionary biology 01 natural sciences Adephaga Coalescent theory 03 medical and health sciences Monophyly Phylogenetics Phylogenomics Genetics Amino Acids Codon Clade Molecular Biology Ecology Evolution Behavior and Systematics biology Phylogenetic tree biology.organism_classification Coleoptera 030104 developmental biology Sister group Evolutionary biology Transcriptome |
| Zdroj: | Molecular phylogenetics and evolution, vol. 135, pp. 270-285 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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