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Dental characters used in phylogenetic analyses of mammals show higher rates of evolution, but not reduced independence

Accurate reconstructions of phylogeny are essential for studying the evolution of a clade, and morphological characters are necessarily used for the reconstruction of the relationships of fossil organisms. However, variation in their evolutionary modes (for example rate variation and character non-i...

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Autores principales: Brocklehurst, Neil, Benevento, Gemma Louise
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7100591/
https://www.ncbi.nlm.nih.gov/pubmed/32231876
http://dx.doi.org/10.7717/peerj.8744
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author Brocklehurst, Neil
Benevento, Gemma Louise
author_facet Brocklehurst, Neil
Benevento, Gemma Louise
author_sort Brocklehurst, Neil
collection PubMed
description Accurate reconstructions of phylogeny are essential for studying the evolution of a clade, and morphological characters are necessarily used for the reconstruction of the relationships of fossil organisms. However, variation in their evolutionary modes (for example rate variation and character non-independence) not accounted for in analyses may be leading to unreliable phylogenies. A recent study suggested that phylogenetic analyses of mammals may be suffering from a dominance of dental characters, which were shown to have lower phylogenetic signal than osteological characters and produced phylogenies less congruent with molecularly-derived benchmarks. Here we build on this previous work by testing five additional morphological partitions for phylogenetic signal and examining what aspects of dental and other character evolution may be affecting this, by fitting models of discrete character evolution to phylogenies inferred and time calibrated using molecular data. Results indicate that the phylogenetic signal of discrete characters correlate most strongly with rates of evolution, with increased rates driving increased homoplasy. In a dataset covering all Mammalia, dental characters have higher rates of evolution than other partitions. They do not, however, fit a model of independent character evolution any worse than other regions. Primates and marsupials show different patterns to other mammal clades, with dental characters evolving at slower rates and being more heavily integrated (less independent). While the dominance of dental characters in analyses of mammals could be leading to inaccurate phylogenies, the issue is not unique to dental characters and the results are not consistent across datasets. Molecular benchmarks (being entirely independent of the character data) provide a framework for examining each dataset individually to assess the evolution of the characters used.
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spelling pubmed-71005912020-03-30 Dental characters used in phylogenetic analyses of mammals show higher rates of evolution, but not reduced independence Brocklehurst, Neil Benevento, Gemma Louise PeerJ Computational Biology Accurate reconstructions of phylogeny are essential for studying the evolution of a clade, and morphological characters are necessarily used for the reconstruction of the relationships of fossil organisms. However, variation in their evolutionary modes (for example rate variation and character non-independence) not accounted for in analyses may be leading to unreliable phylogenies. A recent study suggested that phylogenetic analyses of mammals may be suffering from a dominance of dental characters, which were shown to have lower phylogenetic signal than osteological characters and produced phylogenies less congruent with molecularly-derived benchmarks. Here we build on this previous work by testing five additional morphological partitions for phylogenetic signal and examining what aspects of dental and other character evolution may be affecting this, by fitting models of discrete character evolution to phylogenies inferred and time calibrated using molecular data. Results indicate that the phylogenetic signal of discrete characters correlate most strongly with rates of evolution, with increased rates driving increased homoplasy. In a dataset covering all Mammalia, dental characters have higher rates of evolution than other partitions. They do not, however, fit a model of independent character evolution any worse than other regions. Primates and marsupials show different patterns to other mammal clades, with dental characters evolving at slower rates and being more heavily integrated (less independent). While the dominance of dental characters in analyses of mammals could be leading to inaccurate phylogenies, the issue is not unique to dental characters and the results are not consistent across datasets. Molecular benchmarks (being entirely independent of the character data) provide a framework for examining each dataset individually to assess the evolution of the characters used. PeerJ Inc. 2020-03-24 /pmc/articles/PMC7100591/ /pubmed/32231876 http://dx.doi.org/10.7717/peerj.8744 Text en ©2020 Brocklehurst and Benevento https://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
spellingShingle Computational Biology
Brocklehurst, Neil
Benevento, Gemma Louise
Dental characters used in phylogenetic analyses of mammals show higher rates of evolution, but not reduced independence
title Dental characters used in phylogenetic analyses of mammals show higher rates of evolution, but not reduced independence
title_full Dental characters used in phylogenetic analyses of mammals show higher rates of evolution, but not reduced independence
title_fullStr Dental characters used in phylogenetic analyses of mammals show higher rates of evolution, but not reduced independence
title_full_unstemmed Dental characters used in phylogenetic analyses of mammals show higher rates of evolution, but not reduced independence
title_short Dental characters used in phylogenetic analyses of mammals show higher rates of evolution, but not reduced independence
title_sort dental characters used in phylogenetic analyses of mammals show higher rates of evolution, but not reduced independence
topic Computational Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7100591/
https://www.ncbi.nlm.nih.gov/pubmed/32231876
http://dx.doi.org/10.7717/peerj.8744
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