The deep(er) roots of Eukaryotes and Akaryotes [version 2; peer review: 2 approved, 1 approved with reservations]
Background: Locating the root node of the “tree of life” (ToL) is one of the hardest problems in phylogenetics, given the time depth. The root-node, or the universal common ancestor (UCA), groups descendants into organismal clades/domains. Two notable variants of the two-domains ToL (2D-ToL) have ga...
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| Format: | Article |
| Language: | English |
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F1000 Research Ltd
2020-06-01
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| Series: | F1000Research |
| Online Access: | https://f1000research.com/articles/9-112/v2 |
| _version_ | 1829113136777527296 |
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| author | Ajith Harish David Morrison |
| author_facet | Ajith Harish David Morrison |
| author_sort | Ajith Harish |
| collection | DOAJ |
| description | Background: Locating the root node of the “tree of life” (ToL) is one of the hardest problems in phylogenetics, given the time depth. The root-node, or the universal common ancestor (UCA), groups descendants into organismal clades/domains. Two notable variants of the two-domains ToL (2D-ToL) have gained support recently. One 2D-ToL posits that eukaryotes (organisms with nuclei) and akaryotes (organisms without nuclei) are sister clades that diverged from the UCA, and that Asgard archaea are sister to other archaea. The other 2D-ToL proposes that eukaryotes emerged from within archaea and places Asgard archaea as sister to eukaryotes. Williams et al. ( Nature Ecol. Evol. 4: 138–147; 2020) re-evaluated the data and methods that support the competing two-domains proposals and concluded that eukaryotes are the closest relatives of Asgard archaea. Critique: The poor resolution of the archaea in their analysis, despite employing amino acid alignments from thousands of proteins and the best-fitting substitution models, contradicts their conclusions. We argue that they overlooked important aspects of estimating evolutionary relatedness and assessing phylogenetic signal in empirical data. Which 2D-ToL is better supported depends on which kind of molecular features are better for resolving common ancestors at the roots of clades – protein-domains or their component amino acids. We focus on phylogenetic character reconstructions necessary to describe the UCA or its closest descendants in the absence of reliable fossils. Clarifications: It is well known that different character types present different perspectives on evolutionary history that relate to different phylogenetic depths. We show that protein structural-domains support more reliable phylogenetic reconstructions of deep-diverging clades in the ToL. Accordingly, Eukaryotes and Akaryotes are better supported clades in a 2D-ToL. |
| first_indexed | 2024-12-12T15:30:18Z |
| format | Article |
| id | doaj.art-f1791acfa7ca4bd382b343aa2f2744b6 |
| institution | Directory Open Access Journal |
| issn | 2046-1402 |
| language | English |
| last_indexed | 2024-12-12T15:30:18Z |
| publishDate | 2020-06-01 |
| publisher | F1000 Research Ltd |
| record_format | Article |
| series | F1000Research |
| spelling | doaj.art-f1791acfa7ca4bd382b343aa2f2744b62022-12-22T00:20:08ZengF1000 Research LtdF1000Research2046-14022020-06-01910.12688/f1000research.22338.227407The deep(er) roots of Eukaryotes and Akaryotes [version 2; peer review: 2 approved, 1 approved with reservations]Ajith Harish0David Morrison1Independent Researcher, Uppsala, 756 57, SwedenDepartment of Organismal Biology, Systematic Biology, Uppsala University, Uppsala, 752 36, SwedenBackground: Locating the root node of the “tree of life” (ToL) is one of the hardest problems in phylogenetics, given the time depth. The root-node, or the universal common ancestor (UCA), groups descendants into organismal clades/domains. Two notable variants of the two-domains ToL (2D-ToL) have gained support recently. One 2D-ToL posits that eukaryotes (organisms with nuclei) and akaryotes (organisms without nuclei) are sister clades that diverged from the UCA, and that Asgard archaea are sister to other archaea. The other 2D-ToL proposes that eukaryotes emerged from within archaea and places Asgard archaea as sister to eukaryotes. Williams et al. ( Nature Ecol. Evol. 4: 138–147; 2020) re-evaluated the data and methods that support the competing two-domains proposals and concluded that eukaryotes are the closest relatives of Asgard archaea. Critique: The poor resolution of the archaea in their analysis, despite employing amino acid alignments from thousands of proteins and the best-fitting substitution models, contradicts their conclusions. We argue that they overlooked important aspects of estimating evolutionary relatedness and assessing phylogenetic signal in empirical data. Which 2D-ToL is better supported depends on which kind of molecular features are better for resolving common ancestors at the roots of clades – protein-domains or their component amino acids. We focus on phylogenetic character reconstructions necessary to describe the UCA or its closest descendants in the absence of reliable fossils. Clarifications: It is well known that different character types present different perspectives on evolutionary history that relate to different phylogenetic depths. We show that protein structural-domains support more reliable phylogenetic reconstructions of deep-diverging clades in the ToL. Accordingly, Eukaryotes and Akaryotes are better supported clades in a 2D-ToL.https://f1000research.com/articles/9-112/v2 |
| spellingShingle | Ajith Harish David Morrison The deep(er) roots of Eukaryotes and Akaryotes [version 2; peer review: 2 approved, 1 approved with reservations] F1000Research |
| title | The deep(er) roots of Eukaryotes and Akaryotes [version 2; peer review: 2 approved, 1 approved with reservations] |
| title_full | The deep(er) roots of Eukaryotes and Akaryotes [version 2; peer review: 2 approved, 1 approved with reservations] |
| title_fullStr | The deep(er) roots of Eukaryotes and Akaryotes [version 2; peer review: 2 approved, 1 approved with reservations] |
| title_full_unstemmed | The deep(er) roots of Eukaryotes and Akaryotes [version 2; peer review: 2 approved, 1 approved with reservations] |
| title_short | The deep(er) roots of Eukaryotes and Akaryotes [version 2; peer review: 2 approved, 1 approved with reservations] |
| title_sort | deep er roots of eukaryotes and akaryotes version 2 peer review 2 approved 1 approved with reservations |
| url | https://f1000research.com/articles/9-112/v2 |
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