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 accuracy. We use simul...
| Authors: | ; ; ; ; |
|---|---|
| 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 |
| _version_ | 1878733229980123137 |
|---|---|
| author | Giacomelli, Mattia |
| author2 | Rossi, Maria Eleonora Lozano-Fernandez, Jesus Feuda, Roberto Pisani, Davide |
| author2_role | author author author author |
| author_browse | Feuda, Roberto Giacomelli, Mattia Lozano-Fernandez, Jesus Pisani, Davide Rossi, Maria Eleonora |
| author_facet | Giacomelli, Mattia Rossi, Maria Eleonora Lozano-Fernandez, Jesus Feuda, Roberto Pisani, Davide |
| author_role | author |
| collection | Recercat. Dipósit de la Recerca de Catalunya |
| 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. |
| eu_rights_str_mv | openAccess |
| format | article |
| id | ES_524e916c8495c2ec0016ed4a1d699c56 |
| institution | 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) |
| network_acronym_str | ES |
| network_name_str | España |
| oai_identifier_str | oai:recercat.cat:2445/193866 |
| publishDate | 2022 |
| publishDateSort | 2022 |
| publisher | Elsevier |
| publisherStr | Elsevier |
| reponame_str | Recercat. Dipósit de la Recerca de Catalunya |
| spelling | Resolving tricky nodes in the tree of life through amino acid recoding Giacomelli, Mattia Rossi, Maria Eleonora Lozano-Fernandez, Jesus Feuda, Roberto Pisani, Davide Evolució (Biologia) Filogènia Aminoàcids Evolution (Biology) Phylogeny Amino acids 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. Elsevier https://hdl.handle.net/2445/193866 |
| spellingShingle | Resolving tricky nodes in the tree of life through amino acid recoding Giacomelli, Mattia Evolució (Biologia) Filogènia Aminoàcids Evolution (Biology) Phylogeny Amino acids |
| status_str | publishedVersion |
| title | 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_short | 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 |
| topic | Evolució (Biologia) Filogènia Aminoàcids Evolution (Biology) Phylogeny Amino acids |
| topic_facet | Evolució (Biologia) Filogènia Aminoàcids Evolution (Biology) Phylogeny Amino acids |
| url | https://hdl.handle.net/2445/193866 |