ArticleGenome biology and evolution2016
Capturing the Phylogeny of Holometabola with Mitochondrial Genome Data and Bayesian Site-Heterogeneous Mixture Models.
Article in Genome biology and evolution, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 90 papers, 1 of them a synthesis that pooled it.
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90 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Effects of immune challenge on expression of life-history and immune trait expression in sexually reproducing metazoans-a meta-analysis.BMC biology · 2020Pooled it
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- The first complete mitochondrial genome sequences ofFrontiers in veterinary science · 2026Article
- Characterization and deorphanization of RYamide signaling in Aedes aegypti: A potential regulator of hindgut-associated physiology.PloS one · 2026Article
- Mitochondrial Genome Features and Phylogenetic Analyses of Four Chrysochroinae Species (Coleoptera: Buprestidae).Biomolecules · 2025Article
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- Exploring the Mitogenomes of Acroneuriinae: The First Report of Gene Rearrangements in Plecoptera Species and Phylogenetic Analyses of Perlidae.Ecology and evolution · 2025Article
- A Comparative Analysis and Limited Phylogenetic Implications of Mitogenomes in Infraorder-Level Diptera.International journal of molecular sciences · 2025Article
- Genomic Insights into Basal Diptera Phylogeny: The Non-Monophyletic Nature of Blephariceromorpha.International journal of molecular sciences · 2025Article
- Complete Mitochondrial Genome ofBiology · 2025Article
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- The complete mitochondrial genomes ofFrontiers in veterinary science · 2025Article
- New Mitochondrial Genomes of Ithonidae (Neuroptera) and Higher Phylogenetic Implications.Insects · 2024Article
- The first mitogenome of the genusParasitology · 2024Article
- The first mitogenome of the subfamily Stenoponiinae (Siphonaptera: Ctenophthalmidae) and implications for its phylogenetic position.Scientific reports · 2024Article
- Phylogenetic placement and comparative analysis of the mitochondrial genomes of Idiostoloidea (Hemiptera: Heteroptera).Ecology and evolution · 2024Article
- Article
30 more citing papers are in PubMed but not listed here.
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8 authors.
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Abstract
After decades of debate, a mostly satisfactory resolution of relationships among the 11 recognized holometabolan orders of insects has been reached based on nuclear genes, resolving one of the most substantial branches of the tree-of-life, but the relationships are still not well established with mitochondrial genome data. The main reasons have been the absence of sufficient data in several orders and lack of appropriate phylogenetic methods that avoid the systematic errors from compositional and mutational biases in insect mitochondrial genomes. In this study, we assembled the richest taxon sampling of Holometabola to date (199 species in 11 orders), and analyzed both nucleotide and amino acid data sets using several methods. We find the standard Bayesian inference and maximum-likelihood analyses were strongly affected by systematic biases, but the site-heterogeneous mixture model implemented in PhyloBayes avoided the false grouping of unrelated taxa exhibiting similar base composition and accelerated evolutionary rate. The inclusion of rRNA genes and removal of fast-evolving sites with the observed variability sorting method for identifying sites deviating from the mean rates improved the phylogenetic inferences under a site-heterogeneous model, correctly recovering most deep branches of the Holometabola phylogeny. We suggest that the use of mitochondrial genome data for resolving deep phylogenetic relationships requires an assessment of the potential impact of substitutional saturation and compositional biases through data deletion strategies and by using site-heterogeneous mixture models. Our study suggests a practical approach for how to use densely sampled mitochondrial genome data in phylogenetic analyses.
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