title: Changing preferences: deformation of single position amino acid fitness landscapes and evolution of proteins.
abstract: The fitness landscape-the function that relates genotypes to fitness-and its role in directing evolution are a central object of evolutionary biology. However, its huge dimensionality precludes understanding of even the basic aspects of its shape. One way to approach it is to ask a simpler question: what are the properties of a function that assigns fitness to each possible variant at just one particular site-a single position fitness landscape-and how does it change in the course of evolution? Analyses of genomic data from multiple species and multiple individuals within a species have proved beyond reasonable doubt that fitness functions of positions throughout the genome do themselves change with time, thus shaping protein evolution. Here, I will briefly review the literature that addresses these dynamics, focusing on recent genome-scale analyses of fitness functions of amino acid sites, i.e. vectors of fitnesses of 20 individual amino acid variants at a given position of a protein. The set of amino acids that confer high fitness at a particular position changes with time, and the rate of this change is comparable with the rate at which a position evolves, implying that this process plays a major role in evolutionary dynamics. However, the causes of these changes remain largely unclear.
authors.affiliation: Institute for Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences, Moscow 127051, Russia Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia Pirogov Russian National Research Medical University, Moscow 117997, Russia gbazykin@iitp.ru.
authors.forename: Georgii A
authors.initials: GA
authors.lastname: Bazykin
mesh_terms: D000220:Adaptation, Biological; D000596:Amino Acids / Q000235:genetics*; D004843:Epistasis, Genetic; D019143:Evolution, Molecular; D056084:Genetic Fitness; D005838:Genotype; D011506:Proteins / Q000235:genetics*
chemical_list: D000596:Amino Acids; D011506:Proteins
keywords: epistasis; macroevolution; microevolution; proteins; selection