The Evolutionary Causes and Consequences of Base Composition Variation

Abstract

Every nucleotide position in a genome experiences a unique set of mutational and selective forces. Local sequence context, location in coding or noncoding regions, structure of the DNA, and timing of replication are just some of the diverse factors important in determining the evolutionary forces likely to act on a given base pair. One consequence of such complexity is that base composition (the relative usage of different DNA nucleotides and motifs) varies considerably both within and among genomes. Drawing accurate evolutionary inferences in the face of base composition variation is hugely challenging. First, we must decide which factors cannot be ignored when trying to model or interpret patterns of molecular evolution. Second, we must develop methods and models that address such factors explicitly. This chapter aims to discuss some of the key processes, both mutational and selective, influencing base composition variation and various models that have been proposed to describe their effects on molecular evolution. I will also explore how to measure base composition variation and discuss some of the pitfalls that can arise if such effects are ignored.