Adaptive Evolutionary Genetics

ID	Subject (Credit)	Instructor	Availability 2024	Term	Day	Hours	Place
47140-21E	Adaptive Evolutionary Genetics	Shoji Kawamura	Available	A2	Dec 3, 4, 10, 11, 17, 18 (6 days)	8:30-12:10	Lecture Room, Bioscience BLDG / On Line

<Theme & Objectives>

The purpose of this lecture is to provide theoretical framework for studying adaptive evolution of gene function. Since it is the population and genes that change over evolutionary time, it is essential to acquire basic knowledge of population genetics to understand molecular evolution. I shall review several basic concepts of population genetics such as gene frequencies, natural selection and random genetic drift, then introduce the neutral theory of molecular evolution. On the basis of the theorem, methods and their limitations for detecting adaptive evolution are discussed. Finally, direction of evolutionary genetic study will be discussed.

<Description>

1. Introduction: history of life, continental drift, extinction, chance events
2. Population genetics I: genetic variation, gene frequency, natural selection
3. Population genetics II: random genetic drift, population differentiation, coalescence, drift-mutation equilibrium
4. Population genetics III: DNA sequence data, nucleotide diversity, coalescence simulation and maximum likelihood estimation, Tajima's D test, linkage disequilibrium
5. Molecular evolution I: nucleotide substitution, evolutionary rate
6. Molecular evolution II: evolutionary distance, phylogenetic tree
7. Neutral theory of molecular evolution: standard null model of genetic variation and evolution
8. Adaptive evolution: within-species polymorphism, between-species divergence, within vs between species variation, nonsynonymous vs synonymous nucleotide substitutions, convergent evolution, methodological limitations, adaptive evolution vs functional evolution
9. Perspectives: testing inference of functional evolution, evolution of gene-interacting system

<Grading>

Examination every after the time unit

<Textbook and References>

• A Primer of Population Genetics, 3rd ed., D.L. Hartl, Sinauer Publishers (2000)
• Principles of Population Genetics, 4th ed., D.L. Hartl and A.G. Clark, Sinauer Publishers (2007)
• Molecular Evolution and Phylogenetics, M. Nei and S. Kumar, Oxford University Press (2000)
• Fundamentals of Molecular Evolution, 2nd ed., D. Graur and W.-H. Li, Sinauer Publishers (2000)
• Molecular Evolutionary Genetics, M. Nei, Columbia University Press (1987)
• The Neutral Theory of Molecular Evolution, M. Kimura, Cambridge University Press (1983)
• On the Origin of Species, C. Darwin, Harvard University Press

<Prerequisites>