Adaptive Molecular Evolution: Detection Methods

Modeling molecular evolution has become essential to many biological investigations. The wide variety of approaches fall into two broad categories: population analyses and comparative analyses. Comparative methods are further subdivided according to the source of information: codons, amino acids, and noncoding DNA. The majority of this entry is concerned with methods for detecting positive selection within sequences that code for proteins. This is partly due to the clear functional importance of proteins. But it is also because the 'footprint' of functional constraint is easier to detect in coding DNA. Eukaryotic genomes also contain vast amounts of noncoding DNA, and some unknown proportion is responsible for regulating protein expression. Indeed, many believe that evolution of regulatory sequences drives phenotypic evolution. Accordingly, a section of this entry is devoted to investigating noncoding sequence evolution between species. As existing methods are very diverse, the goal of this entry is to provide only a broad introduction. The entry also includes several brief prospectives of future research within each category.