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Biological Procedures Online

, Volume 10, Issue 1, pp 66–73

Received: 18 September 2007Revised: 17 March 2008Accepted: 07 April 2008DOI: 10.1251-bpo144

Cite this article as: Liberles, D.A. & Dittmar, K. Biol. Proced. Online 2008 10: 66. doi:10.1251-bpo144


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 termsgenomics evolution, molecular phylogeny sequence homology  Download to read the full article text

Autor: David A. Liberles - Katharina Dittmar


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