relation: https://eprints.uet.vnu.edu.vn/eprints/id/eprint/2519/
title: Improved mitochondrial amino acid substitution models for metazoan   evolutionary studies
creator: Le, Sy Vinh
creator: Dang, Cuong
creator: Le, Quang
subject: Information Technology (IT)
subject: ISI-indexed journals
description: Background: Amino 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.  Results: We 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.  Conclusions: We 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.
date: 2017
type: Article
type: PeerReviewed
format: application/pdf
language: en
identifier: https://eprints.uet.vnu.edu.vn/eprints/id/eprint/2519/1/Vinh_2017a.pdf
identifier:   Le, Sy Vinh and Dang, Cuong and Le, Quang  (2017) Improved mitochondrial amino acid substitution models for metazoan evolutionary studies.  BMC Mol Evol, 17  (136).