Download Biology 4E03: Population Genetics Course Outline: Term II, 2010

Biology 4E03: Population Genetics
Course Outline: Term II, 2010
Student Evaluation:
Mid Term : 20%
Tutorials: (problem assignments) : 20%
Final: 60%
Part I. Dr. Richard Morton
Week 1: Introduction to Population Genetics; Genetic Variation
Topics: Define population genetics and applications to other disciplines. Review basic genetic
background including genes and alleles, mitosis and meiosis, and replication, transcription, translation;
discuss types and causes of genetic variation
Readings: Halliburton Chapter 1, 2
Utami et al. (2002) Male bimaturism and reproductive success in Sumatran orang-utans. Behavioral
Ecology 13:5):643-652
Week 2: HWE
Topics:Assumptions of Hardy Weinberg Equilibrium and the implications of violating these
assumptions. Application to studies of genetic load and age-dependent natural selection. Chi square test,
degrees of freedom.
Readings:Halliburton Chapt 3
Laundey S. and Hedgecock D. (2001) High genetic load in the Pacific Oyster Crassostrea gigas .
Genetics 159: 255-265
Week 3: More HWE; Linkage Disequilibrium, Population Subdivision, Inbreeding, and Gene
Flow
Topics:Hardy-Weinberg Equilibrium, allelic expectations at X-linked loci and sex-biased allele
frequencies. Intro to linkage disequilibrium and applications to human evolution.
Readings:Halliburton Chapt 4 pp. 91-110; 120-125
Tishkoff et al. (1996) Global patterns of linkage disequilibrium at the CD4 locus and modern human
origins. Science 271: 1380-1387
Garrigan and Hammer (2006) Reconstructing human origins in the genomic era. Nature Reviews
Genetics 7: 669-680.
Week 4: Human evolution and the Out of Africa Hypothesis; Linkage Disequilibrium (continued),
Gene Flow, Genetic Drift
Topics:Out of Africa versus Multiregional hypotheses; evidence from mitochondrial and nuclear DNA.
D - the linkage disequilibrium coefficient, Dmax and Dmin, r - the recombination parameter. Linkage
disequeilibrium in humans. Tajima's D
Readings:Halliburton Chapt 6 (all),Chapt 7 pp. 221-262, Chapt. 10 pp. 405-407
Nordborg et al. (2005) The pattern of polymorphism in Arabidopsis thaliana. PLoS Biology 3(7):e196
Week 5: Genetic drift, non-random mating, inbreeding
Topics:The binomial coefficient and binomial equation. Application of binomial equation to HWE, LD,
and drift. The Poisson distribution and the impact of variance in reproductive success and the effective
population size.
Inbreeding, assortative and disassortative mating, inbreeding depression.
Readings:Halliburton Chapt 8, pp. 269-281; 286-294; Chapt. 9 (all)
Hoelzer, G. A. (1997) Inferring phylogenies from mtDNA variation: mitohondrial-gene trees versus
nuclear-gene trees revisited. Evolution 51(2):622-626.
Week 6: Neutral Theory; Coalescence
Topics:Discussion of the neutral model; fundamentals of coalescent theory.
Readings:Halliburton, Chapt 10 (all)
Week 7: Mid Term Break
Part II. Dr. Rama Singh
Week 8. Natural Selection I: Basic Theory
Meaning of natural selection, requirement for natural selection, life cycle and components of fitness,
basic models of selection, dynamics of allele frequency change, stability analysis and equlibrium
frequency, population fitness, maintenance of variation: overdominance, underdominance selection in
fitness, examples of natural selection in nature , concept of dminance in fitness, concept of marginal
fitness- of alleles and genotypes, evolution of population fitness, Fundamental theorem of natural
selection, Wrights concept of fitness landscape, and fitness peaks and valleys
Reading: Halliburton Chapter 5
Week 9. Natural Selection II. Maintenance of Genetic Variation
Two locus theory: Concept of linkage disequilibrium (LD), Role of selection and recombination in
maintaining variation, Balancing Selection: maintenance of variation/polymorphism, Overdominance
vs. under dominance, varying environment, Antagonistic selection, Selection in opposite direction in
males vs. females, Selection in temporally varying environment, Frequency Dependent Selection:
Negative frequency dependent selection, Examples of frequency Dependent Selection, Fitness at
Equilibrium, Sexual selection: Concept of male and female fitness, the need for sexual selection theory,
nature of sexual dimorphism, evolution of sexual dimorphism, female choice and other theories
Reading: Halliburton Chapter 12
Week 10: Gene Flow and Population differentiation
Concept of heterozygosity in hierarchical populations, Calculation and meaning of Fst, theoretical
derivation of Fst, relation between Fst and gene flow (Nm), relation between Fst, H and Nm, measuring
gene flow from Fst, distribution of Fst at loci and role of selection, gene flow between mainland and
Island.
Reading: Halliburton Chapter 9
Week 11: Molecular Evolution
Cost of selection (1-W) and limit to genetic polymorphisms, neutral theory of evolution, rates of
evolution and the concept of molecular clock (constant rates), rates of substitution (k), concept of
effective neutrality (mean s << 1/2N), effective neutrality and levels of H in small vs. large populations,
concept of synonymous (ks)and non-synonymous(ka) substitution, use of Ka/Ks ratio to test selection
within and between species, generation time effect on k, relation between population size, generation
time and substitution rate
Reading: Halliburton Chapter 10
Week 12: Quantitative Genetics and Phenotypic Evolution
Concept of genotype, phenotype and environment, Quantitative Trait Loci (QTL), components of
phenotypic variance, calculation of heritability, concept of covariance/ genetic correlation between
relatives, broad sense and narrow sense heritability, meaning of heritability, heritability of traits within
and between populations, calculation of heritability from selection experiment, relation between
selection response (R) and selection (S), selection response in quantitative traits, effects of long-term
selection on population fitness, phenotypic Selection in Nature, directional, stabilizing and disruptive
selection, stabilizing selection and maintenance of variation
Reading: Halliburton Chapter 13