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Inferring evolutionary processes from DNA sequence data

The allelic evolutionary genetic models explored so far are applicable to genetic markers. However, DNA sequences harbor a lot of information about the evolutionary past that would be missed if different sequences were simply treated as different alleles. This chapter introduces some important methods and concepts applicable to the analysis of DNA-sequence data. The null models for analyzing sequence data are derived from the neutral theory of molecular evolution. Historically, however, the neutral theory has made a large impact on evolutionary genetics. Therefore, this chapter starts by reviewing its important contribution. Then, important parameters and statistics for analyzing sequence variation are introduced, including a plethora of neutrality tests. The chapter ends with a cautious focus on the powerful tool of genome scan analysis and its utility for identifying regions of the genomes potentially under selection. This includes a section on more recently derived statistics which incorporate information on haplotype structure.