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Simple evolutionary pathways to complex proteins

Department of Biology, Indiana University, Bloomington, Indiana 47405, USA

(RECEIVED October 8, 2004; FINAL REVISION October 8, 2004; ACCEPTED June 16, 2005)

A recent paper in this journal has challenged the idea that complex adaptive features of proteins can be explained by known molecular, genetic, and evolutionary mechanisms. It is shown here that the conclusions of this prior work are an artifact of unwarranted biological assumptions, inappropriate mathematical modeling, and faulty logic. Numerous simple pathways exist by which adaptive multi-residue functions can evolve on time scales of a million years (or much less) in populations of only moderate size. Thus, the classical evolutionary trajectory of descent with modification is adequate to explain the diversification of protein functions.

Keywords: evolutionary theory; gene duplication; microevolutionary theory; multi-residue functions; mutation; neofunctionalization; population genetics; protein evolution; random genetic drift

Article and publication are at http://www.proteinscience.org/cgi/doi/10.1110/ps.041171805.

Reprint requests to: Michael Lynch, Department of Biology, Indiana University, Bloomington, IN 47405, USA; e-mail: mlynch{at}bio.indiana.edu; fax: (812) 855-6705.

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