ArticleBMC evolutionary biology2017
Improved mitochondrial amino acid substitution models for metazoan evolutionary studies.
Article in BMC evolutionary biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed.
- Bottom-up reconstruction of synthetic pyrenoids provides insights into the mechanisms and evolution of carbon concentration by EPYC1 proteins.Nature plants · 2026Article
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- Multiple Horizontal Transfers of Immune Genes Between Distantly Related Teleost Fishes.Molecular biology and evolution · 2025Article
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- Next-generation development and application of codon model in evolution.Frontiers in genetics · 2023Review
- The complete mitochondrial genome of a wild-collectedMitochondrial DNA. Part B, Resources · 2023Article
- Consequences of Substitution Model Selection on Protein Ancestral Sequence Reconstruction.Molecular biology and evolution · 2022Article
- A thermodynamic model of protein structure evolution explains empirical amino acid substitution matrices.Protein science : a publication of the Protein Society · 2021Article
- Long rDNA amplicon sequencing of insect-infecting nephridiophagids reveals their affiliation to the Chytridiomycota and a potential to switch between hosts.Scientific reports · 2021Article
- FLAVI: An Amino Acid Substitution Model for Flaviviruses.Journal of molecular evolution · 2020Article
- Relative Model Fit Does Not Predict Topological Accuracy in Single-Gene Protein Phylogenetics.Molecular biology and evolution · 2020Article
- Characterization of the complete mitochondrial genome of Amblyomma ovale, comparative analyses and phylogenetic considerations.Experimental & applied acarology · 2020Article
- MtOrt: an empirical mitochondrial amino acid substitution model for evolutionary studies of Orthoptera insects.BMC evolutionary biology · 2020Article
- Characterization of the Complete Mitochondrial Genomes of Two Sibling Species of Parasitic Roundworms,Frontiers in genetics · 2020Article
- Simulation data for the estimation of numerical constants for approximating pairwise evolutionary distances between amino acid sequences.Data in brief · 2019Article
- Relative Evolutionary Rates in Proteins Are Largely Insensitive to the Substitution Model.Molecular biology and evolution · 2018Article
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3 authors.
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Abstract
backgroundAmino acid substitution models play an essential role in inferring phylogenies from mitochondrial protein data. However, only few empirical models have been estimated from restricted mitochondrial protein data of a hundred species. The existing models are unlikely to represent appropriately the amino acid substitutions from hundred thousands metazoan mitochondrial protein sequences.
resultsWe selected 125,935 mitochondrial protein sequences from 34,448 species in the metazoan kingdom to estimate new amino acid substitution models targeting metazoa, vertebrates and invertebrate groups. The new models help to find significantly better likelihood phylogenies in comparison with the existing models. We noted remarkable distances from phylogenies with the existing models to the maximum likelihood phylogenies that indicate a considerable number of incorrect bipartitions in phylogenies with the existing models. Finally, we used the new models and mitochondrial protein data to certify that Testudines, Aves, and Crocodylia form one separated clade within amniotes.
conclusionsWe introduced new mitochondrial amino acid substitution models for metazoan mitochondrial proteins. The new models outperform the existing models in inferring phylogenies from metazoan mitochondrial protein data. We strongly recommend researchers to use the new models in analysing metazoan mitochondrial protein data.
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