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Characterizing gene family evolution
Gene families are widely used in comparative genomics, molecular evolution, and in systematics. However, they are constructed in different manners, their data analyzed and interpreted differently, with different underlying assumptions, leading to sometimes divergent conclusions. In systematics, conc...
Autores principales: | , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
Biological Procedures Online
2008
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2683547/ https://www.ncbi.nlm.nih.gov/pubmed/19461954 http://dx.doi.org/10.1251/bpo144 |
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author | Liberles, David A. Dittmar, Katharina |
author_facet | Liberles, David A. Dittmar, Katharina |
author_sort | Liberles, David A. |
collection | PubMed |
description | Gene families are widely used in comparative genomics, molecular evolution, and in systematics. However, they are constructed in different manners, their data analyzed and interpreted differently, with different underlying assumptions, leading to sometimes divergent conclusions. In systematics, concepts like monophyly and the dichotomy between homoplasy and homology have been central to the analysis of phylogenies. We critique the traditional use of such concepts as applied to gene families and give examples of incorrect inferences they may lead to. Operational definitions that have emerged within functional genomics are contrasted with the common formal definitions derived from systematics. Lastly, we question the utility of layers of homology and the meaning of homology at the character state level in the context of sequence evolution. From this, we move forward to present an idealized strategy for characterizing gene family evolution for both systematic and functional purposes, including recent methodological improvements. |
format | Text |
id | pubmed-2683547 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2008 |
publisher | Biological Procedures Online |
record_format | MEDLINE/PubMed |
spelling | pubmed-26835472009-05-21 Characterizing gene family evolution Liberles, David A. Dittmar, Katharina Biol Proced Online Research Article Gene families are widely used in comparative genomics, molecular evolution, and in systematics. However, they are constructed in different manners, their data analyzed and interpreted differently, with different underlying assumptions, leading to sometimes divergent conclusions. In systematics, concepts like monophyly and the dichotomy between homoplasy and homology have been central to the analysis of phylogenies. We critique the traditional use of such concepts as applied to gene families and give examples of incorrect inferences they may lead to. Operational definitions that have emerged within functional genomics are contrasted with the common formal definitions derived from systematics. Lastly, we question the utility of layers of homology and the meaning of homology at the character state level in the context of sequence evolution. From this, we move forward to present an idealized strategy for characterizing gene family evolution for both systematic and functional purposes, including recent methodological improvements. Biological Procedures Online 2008-06-20 /pmc/articles/PMC2683547/ /pubmed/19461954 http://dx.doi.org/10.1251/bpo144 Text en © 2008 by the author(s). www.biologicalprocedures.com This paper is Open Access. Copying, printing, redistribution and storage permitted. Journal © 1997-2008 Biological Procedures Online |
spellingShingle | Research Article Liberles, David A. Dittmar, Katharina Characterizing gene family evolution |
title | Characterizing gene family evolution
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title_full | Characterizing gene family evolution
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title_fullStr | Characterizing gene family evolution
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title_full_unstemmed | Characterizing gene family evolution
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title_short | Characterizing gene family evolution
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title_sort | characterizing gene family evolution |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2683547/ https://www.ncbi.nlm.nih.gov/pubmed/19461954 http://dx.doi.org/10.1251/bpo144 |
work_keys_str_mv | AT liberlesdavida characterizinggenefamilyevolution AT dittmarkatharina characterizinggenefamilyevolution |