ArticlePloS one2011
Sources of signal in 62 protein-coding nuclear genes for higher-level phylogenetics of arthropods.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Reinvestigating the phylogeny of Myriapoda with more extensive taxon sampling and novel genetic perspective.PeerJ · 2021Article
- Phylogenomics illuminates the backbone of the Myriapoda Tree of Life and reconciles morphological and molecular phylogenies.Scientific reports · 2018Article
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- Phylogenomic analysis of Copepoda (Arthropoda, Crustacea) reveals unexpected similarities with earlier proposed morphological phylogenies.BMC evolutionary biology · 2017Article
- Origin and higher-level diversification of acariform mites - evidence from nuclear ribosomal genes, extensive taxon sampling, and secondary structure alignment.BMC evolutionary biology · 2015Article
- Conflicting phylogenies for early land plants are caused by composition biases among synonymous substitutions.Systematic biology · 2014Article
- Statistical tests to identify appropriate types of nucleotide sequence recoding in molecular phylogenetics.BMC bioinformatics · 2014Article
- Article
- Parsimony and model-based analyses of indels in avian nuclear genes reveal congruent and incongruent phylogenetic signals.Biology · 2013Article
- The hymenopteran tree of life: evidence from protein-coding genes and objectively aligned ribosomal data.PloS one · 2013Article
- A large-scale, higher-level, molecular phylogenetic study of the insect order Lepidoptera (moths and butterflies).PloS one · 2013Article
- Phylogenetic analysis and DNA-based species confirmation in Anopheles (Nyssorhynchus).PloS one · 2013Article
- Article
- Can RNA-Seq resolve the rapid radiation of advanced moths and butterflies (Hexapoda: Lepidoptera: Apoditrysia)? An exploratory study.PloS one · 2013Article
- Article
- Phylogeographic analysis elucidates the influence of the ice ages on the disjunct distribution of relict dragonflies in Asia.PloS one · 2012Article
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThis study aims to investigate the strength of various sources of phylogenetic information that led to recent seemingly robust conclusions about higher-level arthropod phylogeny and to assess the role of excluding or downweighting synonymous change for arriving at those conclusions. METHODOLOGY/PRINCIPAL
findingsThe current study analyzes DNA sequences from 68 gene segments of 62 distinct protein-coding nuclear genes for 80 species. Gene segments analyzed individually support numerous nodes recovered in combined-gene analyses, but few of the higher-level nodes of greatest current interest. However, neither is there support for conflicting alternatives to these higher-level nodes. Gene segments with higher rates of nonsynonymous change tend to be more informative overall, but those with lower rates tend to provide stronger support for deeper nodes. Higher-level nodes with bootstrap values in the 80% - 99% range for the complete data matrix are markedly more sensitive to substantial drops in their bootstrap percentages after character subsampling than those with 100% bootstrap, suggesting that these nodes are likely not to have been strongly supported with many fewer data than in the full matrix. Data set partitioning of total data by (mostly) synonymous and (mostly) nonsynonymous change improves overall node support, but the result remains much inferior to analysis of (unpartitioned) nonsynonymous change alone. Clusters of genes with similar nonsynonymous rate properties (e.g., faster vs. slower) show some distinct patterns of node support but few conflicts. Synonymous change is shown to contribute little, if any, phylogenetic signal to the support of higher-level nodes, but it does contribute nonphylogenetic signal, probably through its underlying heterogeneous nucleotide composition. Analysis of seemingly conservative indels does not prove useful.
conclusionsGenerating a robust molecular higher-level phylogeny of Arthropoda is currently possible with large amounts of data and an exclusive reliance on nonsynonymous change.
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