ArticleMolecular biology and evolution2014
Decisive data sets in phylogenomics: lessons from studies on the phylogenetic relationships of primarily wingless insects.
Article in Molecular biology and evolution, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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41 citing papers in PubMed.
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- Phylogenomic analyses of echinoid diversification prompt a re-evaluation of their fossil record.eLife · 2022Article
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- HyRAD-X Exome Capture Museomics Unravels Giant Ground Beetle Evolution.Genome biology and evolution · 2021Article
- Resolving the Early Divergence Pattern of Teleost Fish Using Genome-Scale Data.Genome biology and evolution · 2021Article
- Beyond Drosophila: resolving the rapid radiation of schizophoran flies with phylotranscriptomics.BMC biology · 2021Article
- Target-capture phylogenomics provide insights on gene and species tree discordances in Old World treefrogs (Anura: Rhacophoridae).Proceedings. Biological sciences · 2020Article
- Four myriapod relatives - but who are sisters? No end to debates on relationships among the four major myriapod subgroups.BMC evolutionary biology · 2020Article
- New Methods to Calculate Concordance Factors for Phylogenomic Datasets.Molecular biology and evolution · 2020Article
- An integrative phylogenomic approach to elucidate the evolutionary history and divergence times of Neuropterida (Insecta: Holometabola).BMC evolutionary biology · 2020Article
- Model Choice, Missing Data, and Taxon Sampling Impact Phylogenomic Inference of Deep Basidiomycota Relationships.Systematic biology · 2020Article
- Gene markers for exon capture and phylogenomics in ray-finned fishes.Ecology and evolution · 2019Article
- Gene Selection and Evolutionary Modeling Affect Phylogenomic Inference of Neuropterida Based on Transcriptome Data.International journal of molecular sciences · 2019Article
- Evolutionary history of Polyneoptera and its implications for our understanding of early winged insects.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- An integrative phylogenomic approach illuminates the evolutionary history of cockroaches and termites (Blattodea).Proceedings. Biological sciences · 2019Article
- Article
- Phylogenomics and the evolution of hemipteroid insects.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Tetraconatan phylogeny with special focus on Malacostraca and Branchiopoda: highlighting the strength of taxon-specific matrices in phylogenomics.Proceedings. Biological sciences · 2018Article
- UFBoot2: Improving the Ultrafast Bootstrap Approximation.Molecular biology and evolution · 2018Article
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15 authors.
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Abstract
Phylogenetic relationships of the primarily wingless insects are still considered unresolved. Even the most comprehensive phylogenomic studies that addressed this question did not yield congruent results. To get a grip on these problems, we here analyzed the sources of incongruence in these phylogenomic studies by using an extended transcriptome data set. Our analyses showed that unevenly distributed missing data can be severely misleading by inflating node support despite the absence of phylogenetic signal. In consequence, only decisive data sets should be used which exclusively comprise data blocks containing all taxa whose relationships are addressed. Additionally, we used Four-cluster Likelihood Mapping (FcLM) to measure the degree of congruence among genes of a data set, as a measure of support alternative to bootstrap. FcLM showed incongruent signal among genes, which in our case is correlated neither with functional class assignment of these genes nor with model misspecification due to unpartitioned analyses. The herein analyzed data set is the currently largest data set covering primarily wingless insects, but failed to elucidate their interordinal phylogenetic relationships. Although this is unsatisfying from a phylogenetic perspective, we try to show that the analyses of structure and signal within phylogenomic data can protect us from biased phylogenetic inferences due to analytical artifacts.
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