Resolving tricky nodes in the tree of life through amino acid recoding

Genomic data allowed a detailed resolution of the Tree of Life, but ''tricky nodes'' such as the root of the animals remain unresolved. Genome-scale datasets are heterogeneous as genes and species are exposed to different pressures, and this can negatively impacts phylogenetic ac...

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Authors: Giacomelli, Mattia, Rossi, Maria Eleonora, Lozano-Fernandez, Jesus, Feuda, Roberto, Pisani, Davide
Format: article
Status:Published version
Publication Date:2022
Country:España
Institution:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
Repository:Recercat. Dipósit de la Recerca de Catalunya
OAI Identifier:oai:recercat.cat:2445/193866
Online Access:https://hdl.handle.net/2445/193866
Access Level:Open access
Keyword:Evolució (Biologia)
Filogènia
Aminoàcids
Evolution (Biology)
Phylogeny
Amino acids
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repository_id_str
spelling Resolving tricky nodes in the tree of life through amino acid recodingGiacomelli, MattiaRossi, Maria EleonoraLozano-Fernandez, JesusFeuda, RobertoPisani, DavideEvolució (Biologia)FilogèniaAminoàcidsEvolution (Biology)PhylogenyAmino acidsGenomic data allowed a detailed resolution of the Tree of Life, but ''tricky nodes'' such as the root of the animals remain unresolved. Genome-scale datasets are heterogeneous as genes and species are exposed to different pressures, and this can negatively impacts phylogenetic accuracy. We use simulated genomic- scale datasets and show that recoding amino acid data improves accuracy when the model does not account for the compositional heterogeneity of the amino acid alignment. We apply our findings to three datasets addressing the root of the animal tree, where the debate centers on whether sponges (Porifera) or comb jellies (Ctenophora) represent the sister of all other animals. We show that results from empirical data follow predictions from simulations and suggest that, at the least in phylogenies inferred from amino acid sequences, a placement of the ctenophores as sister to all the other animals is best explained as a tree reconstruction artifact.Elsevier2023202320222023info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersion24 p.application/pdfhttps://hdl.handle.net/2445/193866Articles publicats en revistes (Genètica, Microbiologia i Estadística)reponame:Recercat. Dipósit de la Recerca de Catalunyainstname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)InglésReproducció del document publicat a: https://doi.org/10.1016/j.isci.2022.105594iScience, 2022, vol. 25, num. 12, p. 105594https://doi.org/10.1016/j.isci.2022.105594cc-by (c) Giacomelli, Mattia et al., 2022https://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:recercat.cat:2445/1938662026-05-29T05:05:01Z
dc.title.none.fl_str_mv Resolving tricky nodes in the tree of life through amino acid recoding
title Resolving tricky nodes in the tree of life through amino acid recoding
spellingShingle Resolving tricky nodes in the tree of life through amino acid recoding
Giacomelli, Mattia
Evolució (Biologia)
Filogènia
Aminoàcids
Evolution (Biology)
Phylogeny
Amino acids
title_short Resolving tricky nodes in the tree of life through amino acid recoding
title_full Resolving tricky nodes in the tree of life through amino acid recoding
title_fullStr Resolving tricky nodes in the tree of life through amino acid recoding
title_full_unstemmed Resolving tricky nodes in the tree of life through amino acid recoding
title_sort Resolving tricky nodes in the tree of life through amino acid recoding
dc.creator.none.fl_str_mv Giacomelli, Mattia
Rossi, Maria Eleonora
Lozano-Fernandez, Jesus
Feuda, Roberto
Pisani, Davide
author Giacomelli, Mattia
author_facet Giacomelli, Mattia
Rossi, Maria Eleonora
Lozano-Fernandez, Jesus
Feuda, Roberto
Pisani, Davide
author_role author
author2 Rossi, Maria Eleonora
Lozano-Fernandez, Jesus
Feuda, Roberto
Pisani, Davide
author2_role author
author
author
author
dc.subject.none.fl_str_mv Evolució (Biologia)
Filogènia
Aminoàcids
Evolution (Biology)
Phylogeny
Amino acids
topic Evolució (Biologia)
Filogènia
Aminoàcids
Evolution (Biology)
Phylogeny
Amino acids
description Genomic data allowed a detailed resolution of the Tree of Life, but ''tricky nodes'' such as the root of the animals remain unresolved. Genome-scale datasets are heterogeneous as genes and species are exposed to different pressures, and this can negatively impacts phylogenetic accuracy. We use simulated genomic- scale datasets and show that recoding amino acid data improves accuracy when the model does not account for the compositional heterogeneity of the amino acid alignment. We apply our findings to three datasets addressing the root of the animal tree, where the debate centers on whether sponges (Porifera) or comb jellies (Ctenophora) represent the sister of all other animals. We show that results from empirical data follow predictions from simulations and suggest that, at the least in phylogenies inferred from amino acid sequences, a placement of the ctenophores as sister to all the other animals is best explained as a tree reconstruction artifact.
publishDate 2022
dc.date.none.fl_str_mv 2022
2023
2023
2023
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv https://hdl.handle.net/2445/193866
url https://hdl.handle.net/2445/193866
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Reproducció del document publicat a: https://doi.org/10.1016/j.isci.2022.105594
iScience, 2022, vol. 25, num. 12, p. 105594
https://doi.org/10.1016/j.isci.2022.105594
dc.rights.none.fl_str_mv cc-by (c) Giacomelli, Mattia et al., 2022
https://creativecommons.org/licenses/by/4.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv cc-by (c) Giacomelli, Mattia et al., 2022
https://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv 24 p.
application/pdf
dc.publisher.none.fl_str_mv Elsevier
publisher.none.fl_str_mv Elsevier
dc.source.none.fl_str_mv Articles publicats en revistes (Genètica, Microbiologia i Estadística)
reponame:Recercat. Dipósit de la Recerca de Catalunya
instname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
instname_str Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
reponame_str Recercat. Dipósit de la Recerca de Catalunya
collection Recercat. Dipósit de la Recerca de Catalunya
repository.name.fl_str_mv
repository.mail.fl_str_mv
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