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Characterizing gene family evolution

Biological Procedures Online volume 10, pages 66–73 (2008)Cite this article

Abstract

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.

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Author notes

  1. Katharina Dittmar

    Present address: Department of Biological Sciences, State University of New York - Buffalo, 14260, Buffalo, NY, USA

Authors and Affiliations

  1. Department of Molecular Biology, University of Wyoming, 82071, Laramie, WY, USA

    David A. Liberles & Katharina Dittmar

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  1. David A. Liberles
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  2. Katharina Dittmar
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Correspondence to David A. Liberles.

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Open Access This article is published under license to BioMed Central Ltd. This is an Open Access article is distributed under the terms of the Creative Commons Attribution License ( https://creativecommons.org/licenses/by/2.0 ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Liberles, D.A., Dittmar, K. Characterizing gene family evolution. Biol. Proced. Online 10, 66–73 (2008). https://doi.org/10.1251/bpo144

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  • DOI: https://doi.org/10.1251/bpo144

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Biological Procedures Online

ISSN: 1480-9222

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