FOR 842. Population Genetics, Genealogy, and Genomics

3 credits (3,0) Two one and a half hour lectures
(Tentative, could be changed to accommodate students: T,Th 2:40-4:00).

Prerequisites: Graduate standing (although there are no formal prerequisites students should have algebraic skills and have had a course in genetics).

Population genetic processes underlying patterns of molecular genetic variation. Spatial statistics. Genealogical approaches to the study of genomic diversity, phylogenetic reconstruction and molecular ecology.

Main emphasis is on developing understanding of the population genetic processes underlying patterns of molecular variation. Special attention is paid to the relationship of genealogical approaches to population genetics, and thus aspects of genomic diversity, lines of descent and the coalescent, phylogenetic reconstruction, and molecular ecology. The course concentrates on models as tools for illustrating the processes underlying patterns of genetic variation. Students are expected to discern qualitative results from models--the key is conceptual (verbal) understanding. Exercises will include "hands on" statistical analysis using software packages, such as spatial statistical software.

Main subject areas (approximate number of class hours in parentheses):

Introduction/Review of basic population genetics, single locus processes, selection, random processes, mutation and migration. (7 hours)

Plant and animal mating systems. (5 hours)

Multilocus genotypes, including linkage disequilibrium and transmission disequilibrium. (4 hours)

Lines of descent, and genealogies, coalescence theory, spatial patterns. (9 hours)

Genetic diversity, genomic diversity, geographical genetics. (6 hours)

Spatial statistics. (3 hours)

Quantitative traits, QTL analysis. (4 hours)

Molecular ecology. (4 hours)

Grading: Exercises (40%), Quizzes (20%), Midterm exam (20%), Final exam (20%).

1. Tu. 8/28 Introduction: population genetics viewed as genealogy or in terms of means and variances (of traits or allele frequencies). Review: Hardy-Weinberg
2. Th. 8/30 Review: Hardy-Weinberg; single locus models of selection, mutation, and migration
3. Tu. 9/4 Review: single locus models of selection, mutation, and migration
4. 9/6 Review: small populations and deviations from random mating
5. 9/11 Review: balances among directed and random processes
6. 9/13 Classical pedigree analysis
7. 9/18 Animal mating systems; Mixed mating systems--plants **Exercises, set 1 due**
8. 9/20 Modern pedigree analysis
9. 9/25 Multilocus genotypes--linkage disequilibrium under random processes and under natural selection
10. 9/27 Correlations of marker genes with genes with important effects on health and fitness
11. 10/2 Transmission disequilibrium **QUIZ 1**
12. 10/4 Lines of descent; Probabilities of identity by descent
13. 10/9 Kinship chains
14. 10/11 Basic "coalescence theory"
15. 10/16 Coalescence theory for DNA sequence data; Coalescence theory for phylogenetic reconstruction
16. 10/18 Examples of coalescence analysis of DNA sequence data: Origins of anatomically modern humans **Exercises, set 2 due**
17. 10/23 Examples of coalescence analysis of DNA sequence data: Origins of anatomically modern humans, continued.
18. 10/25 Measures of genetic diversity--introduction, experimental data **MIDTERM**
19. 10/30 Genomic Diversity and measures of within versus between population genetic diversity
20. 11/1 Genomic Diversity and spatial patterns of variation within populations
21. 11/6 Geographical Genetics--spatial patterns of variation among populations
22. 11/8 Spatial statistics
23. 11/13 Spatial statistics
24. 11/15 Patterns of variation caused by environment and selection
25. 11/20 Genotype by environment interactions; Norms of Reaction; Quantitative Traits in populations. **QUIZ 2**
26. 11/22 THANKSGIVING BREAK
27. 11/27 Quantitative Genetics; Quantitative Trait Locus, QTL, analysis
28. 11/29 Molecular ecology, classical approaches **Exercises, set 3 due**
29. 12/4 Molecular ecology, correlations of DNA sequences with environment
30. 12/6 Review

 Finals week - FINAL EXAM