Protein Structure, Models of Sequence Evolution, and Data Type Effects in Phylogenetic Analyses of Mitochondrial Data: A Case Study in Birds

Phylogenomic analyses have revolutionized the study of biodiversity, but they have revealed that estimated tree topologies can depend, at least in part, on the subset of the genome that is analyzed. For example, estimates of trees for avian orders differ if protein-coding or non-coding data are anal...

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Autores principales:	Emily L. Gordon, Rebecca T. Kimball, Edward L. Braun
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	mitogenome transmembrane proteins substitution matrix JTT matrix molecular evolution partitioned models Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/99bd2b8c38014dee9f718ad938629d98
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spelling	oai:doaj.org-article:99bd2b8c38014dee9f718ad938629d982021-11-25T17:22:38ZProtein Structure, Models of Sequence Evolution, and Data Type Effects in Phylogenetic Analyses of Mitochondrial Data: A Case Study in Birds10.3390/d131105551424-2818https://doaj.org/article/99bd2b8c38014dee9f718ad938629d982021-11-01T00:00:00Zhttps://www.mdpi.com/1424-2818/13/11/555https://doaj.org/toc/1424-2818Phylogenomic analyses have revolutionized the study of biodiversity, but they have revealed that estimated tree topologies can depend, at least in part, on the subset of the genome that is analyzed. For example, estimates of trees for avian orders differ if protein-coding or non-coding data are analyzed. The bird tree is a good study system because the historical signal for relationships among orders is very weak, which should permit subtle non-historical signals to be identified, while monophyly of orders is strongly corroborated, allowing identification of strong non-historical signals. Hydrophobic amino acids in mitochondrially-encoded proteins, which are expected to be found in transmembrane helices, have been hypothesized to be associated with non-historical signals. We tested this hypothesis by comparing the evolution of transmembrane helices and extramembrane segments of mitochondrial proteins from 420 bird species, sampled from most avian orders. We estimated amino acid exchangeabilities for both structural environments and assessed the performance of phylogenetic analysis using each data type. We compared those relative exchangeabilities with values calculated using a substitution matrix for transmembrane helices estimated using a variety of nuclear- and mitochondrially-encoded proteins, allowing us to compare the bird-specific mitochondrial models with a general model of transmembrane protein evolution. To complement our amino acid analyses, we examined the impact of protein structure on patterns of nucleotide evolution. Models of transmembrane and extramembrane sequence evolution for amino acids and nucleotides exhibited striking differences, but there was no evidence for strong topological data type effects. However, incorporating protein structure into analyses of mitochondrially-encoded proteins improved model fit. Thus, we believe that considering protein structure will improve analyses of mitogenomic data, both in birds and in other taxa.Emily L. GordonRebecca T. KimballEdward L. BraunMDPI AGarticlemitogenometransmembrane proteinssubstitution matrixJTT matrixmolecular evolutionpartitioned modelsBiology (General)QH301-705.5ENDiversity, Vol 13, Iss 555, p 555 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	mitogenome transmembrane proteins substitution matrix JTT matrix molecular evolution partitioned models Biology (General) QH301-705.5
spellingShingle	mitogenome transmembrane proteins substitution matrix JTT matrix molecular evolution partitioned models Biology (General) QH301-705.5 Emily L. Gordon Rebecca T. Kimball Edward L. Braun Protein Structure, Models of Sequence Evolution, and Data Type Effects in Phylogenetic Analyses of Mitochondrial Data: A Case Study in Birds
description	Phylogenomic analyses have revolutionized the study of biodiversity, but they have revealed that estimated tree topologies can depend, at least in part, on the subset of the genome that is analyzed. For example, estimates of trees for avian orders differ if protein-coding or non-coding data are analyzed. The bird tree is a good study system because the historical signal for relationships among orders is very weak, which should permit subtle non-historical signals to be identified, while monophyly of orders is strongly corroborated, allowing identification of strong non-historical signals. Hydrophobic amino acids in mitochondrially-encoded proteins, which are expected to be found in transmembrane helices, have been hypothesized to be associated with non-historical signals. We tested this hypothesis by comparing the evolution of transmembrane helices and extramembrane segments of mitochondrial proteins from 420 bird species, sampled from most avian orders. We estimated amino acid exchangeabilities for both structural environments and assessed the performance of phylogenetic analysis using each data type. We compared those relative exchangeabilities with values calculated using a substitution matrix for transmembrane helices estimated using a variety of nuclear- and mitochondrially-encoded proteins, allowing us to compare the bird-specific mitochondrial models with a general model of transmembrane protein evolution. To complement our amino acid analyses, we examined the impact of protein structure on patterns of nucleotide evolution. Models of transmembrane and extramembrane sequence evolution for amino acids and nucleotides exhibited striking differences, but there was no evidence for strong topological data type effects. However, incorporating protein structure into analyses of mitochondrially-encoded proteins improved model fit. Thus, we believe that considering protein structure will improve analyses of mitogenomic data, both in birds and in other taxa.
format	article
author	Emily L. Gordon Rebecca T. Kimball Edward L. Braun
author_facet	Emily L. Gordon Rebecca T. Kimball Edward L. Braun
author_sort	Emily L. Gordon
title	Protein Structure, Models of Sequence Evolution, and Data Type Effects in Phylogenetic Analyses of Mitochondrial Data: A Case Study in Birds
title_short	Protein Structure, Models of Sequence Evolution, and Data Type Effects in Phylogenetic Analyses of Mitochondrial Data: A Case Study in Birds
title_full	Protein Structure, Models of Sequence Evolution, and Data Type Effects in Phylogenetic Analyses of Mitochondrial Data: A Case Study in Birds
title_fullStr	Protein Structure, Models of Sequence Evolution, and Data Type Effects in Phylogenetic Analyses of Mitochondrial Data: A Case Study in Birds
title_full_unstemmed	Protein Structure, Models of Sequence Evolution, and Data Type Effects in Phylogenetic Analyses of Mitochondrial Data: A Case Study in Birds
title_sort	protein structure, models of sequence evolution, and data type effects in phylogenetic analyses of mitochondrial data: a case study in birds
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/99bd2b8c38014dee9f718ad938629d98
work_keys_str_mv	AT emilylgordon proteinstructuremodelsofsequenceevolutionanddatatypeeffectsinphylogeneticanalysesofmitochondrialdataacasestudyinbirds AT rebeccatkimball proteinstructuremodelsofsequenceevolutionanddatatypeeffectsinphylogeneticanalysesofmitochondrialdataacasestudyinbirds AT edwardlbraun proteinstructuremodelsofsequenceevolutionanddatatypeeffectsinphylogeneticanalysesofmitochondrialdataacasestudyinbirds
_version_	1718412422813843456

Protein Structure, Models of Sequence Evolution, and Data Type Effects in Phylogenetic Analyses of Mitochondrial Data: A Case Study in Birds

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