On the causes of evolutionary transition:transversion bias

Arlin Stoltzfus; Ryan W. Norris

Presumably no biochemical factor, nor any simple combination of factors, fully captures the effects of replacements in complex proteins operating in a complex milieu. Indeed, the use of biochemical surrogates would seem unnecessary, given the availability of more direct measurements. Systematic laboratory studies of the effects of amino acid replacements in proteins have been carried out for 25 years (e.g., Kleina and Miller 1990) . Whereas early studies summarized by Yampolsky and Stoltzfus (2005) typically reported crude measures of biochemical or growth effects (e.g., a 2-valued scale of "-" and "+"), a number of more recent studies report a continuous measure of fitness for each mutant (e.g., Sanjuan, et al. 2004; Carrasco, et al. 2007; Domingo-Calap, et al. . CC-BY 4 .0 International license is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It . https://doi.org/10.1101/027722 doi: bioRxiv preprint 2009; Peris, et al. 2010; Jacquier, et al. 2013; Roscoe, et al. 2013; Acevedo, et al. 2014; Bloom 2014; Firnberg, et al. 2014; Thyagarajan and Bloom 2014; Wu, et al. 2014) .