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    Characterizing gene family evolution

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    Genre
    Journal Article
    Date
    2008-06-30
    Author
    Liberles, DA
    Dittmar, K
    Subject
    genomics
    evolution
    molecular
    phylogeny
    sequence homology
    Permanent link to this record
    http://hdl.handle.net/20.500.12613/5605
    
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    DOI
    10.1251/bpo144
    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.
    Citation to related work
    Springer Science and Business Media LLC
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    Biological Procedures Online
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    http://dx.doi.org/10.34944/dspace/5587
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