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Revisiting metazoan phylogeny with genomic sampling of all phyla
Proper biological interpretation of a phylogeny can sometimes hinge on the placement of key taxa—or fail when such key taxa are not sampled. In this light, we here present the first attempt to investigate (though not conclusively resolve) animal relationships using genome-scale data from all phyla....
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
The Royal Society
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6650721/ https://www.ncbi.nlm.nih.gov/pubmed/31288696 http://dx.doi.org/10.1098/rspb.2019.0831 |
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author | Laumer, Christopher E. Fernández, Rosa Lemer, Sarah Combosch, David Kocot, Kevin M. Riesgo, Ana Andrade, Sónia C. S. Sterrer, Wolfgang Sørensen, Martin V. Giribet, Gonzalo |
author_facet | Laumer, Christopher E. Fernández, Rosa Lemer, Sarah Combosch, David Kocot, Kevin M. Riesgo, Ana Andrade, Sónia C. S. Sterrer, Wolfgang Sørensen, Martin V. Giribet, Gonzalo |
author_sort | Laumer, Christopher E. |
collection | PubMed |
description | Proper biological interpretation of a phylogeny can sometimes hinge on the placement of key taxa—or fail when such key taxa are not sampled. In this light, we here present the first attempt to investigate (though not conclusively resolve) animal relationships using genome-scale data from all phyla. Results from the site-heterogeneous CAT + GTR model recapitulate many established major clades, and strongly confirm some recent discoveries, such as a monophyletic Lophophorata, and a sister group relationship between Gnathifera and Chaetognatha, raising continued questions on the nature of the spiralian ancestor. We also explore matrix construction with an eye towards testing specific relationships; this approach uniquely recovers support for Panarthropoda, and shows that Lophotrochozoa (a subclade of Spiralia) can be constructed in strongly conflicting ways using different taxon- and/or orthologue sets. Dayhoff-6 recoding sacrifices information, but can also reveal surprising outcomes, e.g. full support for a clade of Lophophorata and Entoprocta + Cycliophora, a clade of Placozoa + Cnidaria, and raising support for Ctenophora as sister group to the remaining Metazoa, in a manner dependent on the gene and/or taxon sampling of the matrix in question. Future work should test the hypothesis that the few remaining uncertainties in animal phylogeny might reflect violations of the various stationarity assumptions used in contemporary inference methods. |
format | Online Article Text |
id | pubmed-6650721 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | The Royal Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-66507212019-07-28 Revisiting metazoan phylogeny with genomic sampling of all phyla Laumer, Christopher E. Fernández, Rosa Lemer, Sarah Combosch, David Kocot, Kevin M. Riesgo, Ana Andrade, Sónia C. S. Sterrer, Wolfgang Sørensen, Martin V. Giribet, Gonzalo Proc Biol Sci Evolution Proper biological interpretation of a phylogeny can sometimes hinge on the placement of key taxa—or fail when such key taxa are not sampled. In this light, we here present the first attempt to investigate (though not conclusively resolve) animal relationships using genome-scale data from all phyla. Results from the site-heterogeneous CAT + GTR model recapitulate many established major clades, and strongly confirm some recent discoveries, such as a monophyletic Lophophorata, and a sister group relationship between Gnathifera and Chaetognatha, raising continued questions on the nature of the spiralian ancestor. We also explore matrix construction with an eye towards testing specific relationships; this approach uniquely recovers support for Panarthropoda, and shows that Lophotrochozoa (a subclade of Spiralia) can be constructed in strongly conflicting ways using different taxon- and/or orthologue sets. Dayhoff-6 recoding sacrifices information, but can also reveal surprising outcomes, e.g. full support for a clade of Lophophorata and Entoprocta + Cycliophora, a clade of Placozoa + Cnidaria, and raising support for Ctenophora as sister group to the remaining Metazoa, in a manner dependent on the gene and/or taxon sampling of the matrix in question. Future work should test the hypothesis that the few remaining uncertainties in animal phylogeny might reflect violations of the various stationarity assumptions used in contemporary inference methods. The Royal Society 2019-07-10 2019-07-10 /pmc/articles/PMC6650721/ /pubmed/31288696 http://dx.doi.org/10.1098/rspb.2019.0831 Text en © 2019 The Authors. http://creativecommons.org/licenses/by/4.0/ Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited. |
spellingShingle | Evolution Laumer, Christopher E. Fernández, Rosa Lemer, Sarah Combosch, David Kocot, Kevin M. Riesgo, Ana Andrade, Sónia C. S. Sterrer, Wolfgang Sørensen, Martin V. Giribet, Gonzalo Revisiting metazoan phylogeny with genomic sampling of all phyla |
title | Revisiting metazoan phylogeny with genomic sampling of all phyla |
title_full | Revisiting metazoan phylogeny with genomic sampling of all phyla |
title_fullStr | Revisiting metazoan phylogeny with genomic sampling of all phyla |
title_full_unstemmed | Revisiting metazoan phylogeny with genomic sampling of all phyla |
title_short | Revisiting metazoan phylogeny with genomic sampling of all phyla |
title_sort | revisiting metazoan phylogeny with genomic sampling of all phyla |
topic | Evolution |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6650721/ https://www.ncbi.nlm.nih.gov/pubmed/31288696 http://dx.doi.org/10.1098/rspb.2019.0831 |
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