Basics in Molecular Evolution

Molecular evolution is the study of the process of evolution at the level of DNA, RNA, and proteins, in which the neutral or nearly neutral evolution model has provided the theoretical basis. Yet, the role of positive selection at the molecular level remains a controversial issue. Recent advances in genomics, including whole-genome sequencing, high-throughput protein characterization, and bioinformatics have led to a dramatic increase in studies in comparative and evolutionary genomics. This chapter introduces some widely-used methods in genomic analysis. These include distance method,...

Molecular evolution is the study of the process of evolution at the level of DNA, RNA, and proteins, in which the neutral or nearly neutral evolution model has provided the theoretical basis. Yet, the role of positive selection at the molecular level remains a controversial issue. Recent advances in genomics, including whole-genome sequencing, high-throughput protein characterization, and bioinformatics have led to a dramatic increase in studies in comparative and evolutionary genomics. This chapter introduces some widely-used methods in genomic analysis. These include distance method, parsimony methods, maximum-likelihood methods, Bayesian methods, and ancestral sequence inference.