Abstract 153 7.1 Introduction 153 7.2 Cataloging Genes and Other Sequences and Understanding Their Placement

in Gene Families 154 7.2.1 Gene Families 155

7.3 Comparative Genomics: Molecular Evolution and Natural Selection 158 7.3.1 Coding Sequences 158 7.3.2 Directional Selection, Molecular Adaptation and Evolution

of New Functions 159 7.3.3 Noncoding Sequences 161

7.4 Patterns in Genomes 162 7.5 Conclusions 163 References 164

Evolution is very important in modern biology, and with the appearance of complete genome sequences it is becoming more important than ever before. An understanding of the concepts and findings of important molecular evolution is now essential for molecular biologists, and evolutionary arguments are increasingly being used as part of functional studies of individual genes and of genomes. Population genetics concepts are involved in most aspects of genome analysis, such as cataloging genes and other sequences, understanding gene families and their behavior, examining genome data for evidence of the action of natural selection (including detecting molecular adaptation) and understanding patterns that are emerging in levels of sequence diversity within species and divergence between species. This chapter reviews some of these concepts and describe some of the diversity of studies by using these approaches.