ArticleBMC evolutionary biology2009
Can comprehensive background knowledge be incorporated into substitution models to improve phylogenetic analyses? A case study on major arthropod relationships.
Article in BMC evolutionary biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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37 citing papers in PubMed.
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- Arthropod Phylotranscriptomics With a Special Focus on the Basal Phylogeny of the Myriapoda.Genome biology and evolution · 2024Article
- Molecular Apomorphies in the Secondary and Tertiary Structures of Length-Variable Regions (LVRs) of 18S rRNA Shed Light on the Systematic Position of the Family Thaumastellidae (Hemiptera: Heteroptera: Pentatomoidea).International journal of molecular sciences · 2023Article
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- The Genome of the Blind Soil-Dwelling and Ancestrally Wingless Dipluran Campodea augens: A Key Reference Hexapod for Studying the Emergence of Insect Innovations.Genome biology and evolution · 2020Article
- Phylomitogenomic analyses on collembolan higher taxa with enhanced taxon sampling and discussion on method selection.PloS one · 2020Article
- The mitochondrial genomes of palaeopteran insects and insights into the early insect relationships.Scientific reports · 2019Article
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- Molecular Phylogeny and Revision of Copepod Orders (Crustacea: Copepoda).Scientific reports · 2017Article
- Evolutionary origin of type IV classical cadherins in arthropods.BMC evolutionary biology · 2017Article
- Progress, pitfalls and parallel universes: a history of insect phylogenetics.Journal of the Royal Society, Interface · 2016Review
- Origin and higher-level diversification of acariform mites - evidence from nuclear ribosomal genes, extensive taxon sampling, and secondary structure alignment.BMC evolutionary biology · 2015Article
- A histological evaluation of development and axis formation in freshwater fish ectoparasite Argulus bengalensis Ramakrishna, 1951 (Crustacea: Branchiura).Parasitology research · 2015Article
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- Molecular phylogeny of Myriapoda provides insights into evolutionary patterns of the mode in post-embryonic development.Scientific reports · 2014Article
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14 authors.
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Abstract
backgroundWhenever different data sets arrive at conflicting phylogenetic hypotheses, only testable causal explanations of sources of errors in at least one of the data sets allow us to critically choose among the conflicting hypotheses of relationships. The large (28S) and small (18S) subunit rRNAs are among the most popular markers for studies of deep phylogenies. However, some nodes supported by this data are suspected of being artifacts caused by peculiarities of the evolution of these molecules. Arthropod phylogeny is an especially controversial subject dotted with conflicting hypotheses which are dependent on data set and method of reconstruction. We assume that phylogenetic analyses based on these genes can be improved further i) by enlarging the taxon sample and ii) employing more realistic models of sequence evolution incorporating non-stationary substitution processes and iii) considering covariation and pairing of sites in rRNA-genes.
resultsWe analyzed a large set of arthropod sequences, applied new tools for quality control of data prior to tree reconstruction, and increased the biological realism of substitution models. Although the split-decomposition network indicated a high noise content in the data set, our measures were able to both improve the analyses and give causal explanations for some incongruities mentioned from analyses of rRNA sequences. However, misleading effects did not completely disappear.
conclusionAnalyses of data sets that result in ambiguous phylogenetic hypotheses demand for methods, which do not only filter stochastic noise, but likewise allow to differentiate phylogenetic signal from systematic biases. Such methods can only rely on our findings regarding the evolution of the analyzed data. Analyses on independent data sets then are crucial to test the plausibility of the results. Our approach can easily be extended to genomic data, as well, whereby layers of quality assessment are set up applicable to phylogenetic reconstructions in general.
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