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This article is part of the supplement: Selected articles from the 9th Annual Biotechnology and Bioinformatics Symposium (BIOT 2012)

Open Access Open Badges Research

Directional Darwinian Selection in proteins

David A McClellan

Author Affiliations

Department of Biology, University of Arkansas-Fort Smith, Fort Smith, AR 72913, USA

Bigelow Laboratory for Ocean Sciences, East Boothbay, ME 04544, USA

BMC Bioinformatics 2013, 14(Suppl 13):S6  doi:10.1186/1471-2105-14-S13-S6

Published: 1 October 2013



Molecular evolution is a very active field of research, with several complementary approaches, including dN/dS, HON90, MM01, and others. Each has documented strengths and weaknesses, and no one approach provides a clear picture of how natural selection works at the molecular level. The purpose of this work is to present a simple new method that uses quantitative amino acid properties to identify and characterize directional selection in proteins.


Inferred amino acid replacements are viewed through the prism of a single physicochemical property to determine the amount and direction of change caused by each replacement. This allows the calculation of the probability that the mean change in the single property associated with the amino acid replacements is equal to zero (H0: μ = 0; i.e., no net change) using a simple two-tailed t-test.


Example data from calanoid and cyclopoid copepod cytochrome oxidase subunit I sequence pairs are presented to demonstrate how directional selection may be linked to major shifts in adaptive zones, and that convergent evolution at the whole organism level may be the result of convergent protein adaptations.


Rather than replace previous methods, this new method further complements existing methods to provide a holistic glimpse of how natural selection shapes protein structure and function over evolutionary time.