Biological Procedures Online

, Volume 10, Issue 1, pp 66–73 | Cite as

Characterizing gene family evolution

  • David A. Liberles
  • Katharina Dittmar
Open Access


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.

Indexing terms

genomics evolution, molecular phylogeny sequence homology 


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Copyright information

© Springer 2008

Authors and Affiliations

  1. 1.Department of Molecular BiologyUniversity of WyomingLaramieUSA

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