Chapter 1 Thinking like a Population Geneticist 1.1 Expectations What do we expect to happen? Expectations are the basis of understanding cause and effect. 1.2 Theory and Assumptions What is a "theory" and what are assumptions? How can theories be useful with so many assumptions? 1.3 Simulation A method of practice, trial and error learning and exploration. Chapter 2 Genotype Frequencies 2.1 Mendel''s model of particulate genetics Mendel''s breeding experiments. Independent assortment of alleles.
Independent segregation of loci. Some common genetic terminology. 2.2 Hardy-Weinberg Expected Genotype Frequencies Hardy-Weinberg and its assumptions. Each assumption is a population genetic process. Hardy-Weinberg is a null model. Hardy-Weinberg in haplo-diploid systems. Interact Box 2.
1 Genotype frequencies. 2.3 Why does Hardy-Weinberg work? A simple proof of Hardy-Weinberg. Hardy-Weinberg with more than 2 alleles. 2.4 Applications of Hardy-Weinberg Apply Hardy-Weinberg to estimate the frequency of an observed genotype in a forensic DNA typing case. The 2 test to gauge if observed and expected differ more than expected by chance. Assume Hardy-Weinberg to compare two genetic models.
Problem 2.1 The expected genotype frequency for a DNA profile Box 2.1 DNA Profiling Interact Box 2.2 2 test Problem 2.2 Proving allele frequencies are obtained from expected genotype frequencies Problem 2.3 Inheritance for corn kernel phenotypes 2.5 The Fixation Index and Heterozygosity The fixation index (F) measures deviation from Hardy-Weinberg expected heterozygote frequencies. Examples of mating systems and F in wild populations.
Observed and expected heterozygosity. Interact Box 2.3 Assortative mating and genotype frequencies Box 2.2 Protein locus or allozyme genotyping 2.6 Mating among relatives Consanguineous mating alters genotype frequencies but not allele frequencies. Mating among relatives and the probability that two alleles are identical by descent. Inbreeding depression and its possible causes. The many meanings of inbreeding.
2.7 Gametic Disequilibrium Estimating gametic disequilibrium with D. Approach to gametic equilibrium over time Causes of gametic disequilibrium. Interact Box 2.4 Decay of gametic disequilibrium and a 2 test Interact Box 2.5 Gametic disequilibrium under both recombination and natural selection Interact Box 2.6 Estimating genotypic disequilibrium Chapter 3 Genetic Drift and Effective Population Size 3.1 The effects of sampling lead to genetic drift Biological populations are finite.
A simple sampling experiment with microfuge tube "populations." Wright-Fisher model of sampling. Sampling error and genetic drift in biological populations. Interact Box 3.1 Genetic drift 3.2 Models of genetic drift An introduction to the binomial and Markov chains. The diffusion approximation of genetic drift. Problem 3.
1 Applying the binomial formula Math Box 3.1 Variance of a Binomial Variable Interact Box 3.2 Genetic drift simulated with a Markov chain model Problem 3.2 Constructing a transition probability matrix 3.3 Effective population size Defining genetic populations. Census and effective population size. Example of bottleneck and harmonic mean to demonstrate effective population size versus census size. Effective population size due to unequal sex ratio and variation in family size.
Problem 3.3 Estimating Ne from information about N 3.4 Parallelism between drift and inbreeding Autozygosity due to sampling in a finite gamete population. The relationship between the fixation index (F) and heterozygosity (H). Decline in heterozygosity over time due to genetic drift. Heterozygosity in island and mainland populations. Interact Box 3.3 Heterozygosity and inbreeding over time in finite populations 3.
5 Estimating effective population size Variance and inbreeding effective population size. Breeding effective population size in continuous populations. Effective population sizes for different genomes. Problem 3.4 Estimating Ne from observed heterozygosity over time 3.6 Gene genealogies and the coalescent model Modeling the branching of lineages to predict the time to the most recent common ancestor. Math Box 3.2 Approximating the probability of a coalescent event with the exponential distribution Interact Box 3.
4 Build your own coalescent genealogies 3.6 Effective population size in the coalescent model The coalescent model effective population size. Coalescent genealogies and population bottlenecks. Coalescent genealogies in growing and shrinking populations. Interact Box 3.5 Simulating gene genealogies in populations with different effective sizes Interact Box 3.6 Coalescent Genealogies in Populations with Changing Size Chapter 4 Population Structure and Gene Flow 4.1 Genetic populations Genetic versus geographic organization of populations.
Isolation by distance and divergence of populations. Gene flow and migration. Direct and indirect measures of gene flow. Method Box 4.1 Are allele frequencies random or clumped in two dimensions? 4.2 Direct measures of gene flow Genetic marker based parentage analysis. Problem Box 4.1 Calculate the probability of a random haplotype match and the exclusion probability Interact Box 4.
1 Average exclusion probability for a locus 4.3 Fixation indices to measure the pattern of population subdivision Extending the fixation index to measure the pattern of population structure through FIS, FST and FIT. Problem Box 4.2 Compute FIS, FST and FIT. Method Box 4.2 Estimating fixation indices. 4.4 Population subdivision and the Wahlund effect Genetic variation can be present as heterozygosity within a panmictic population or as differences in allele frequency among diverged subpopulations.
Interact Box 4.2 Simulating the Wahlund effect Problem Box 4.3 Account for population structure in a DNA profile match probability 4.5 Models of population structure Continent-island, two island and infinite island models. Stepping stone and metapopulation population models. General expectations and conclusions from the different migration models. Interact Box 4.3 Continent-island model of gene flow Interact Box 4.
4 Two island model of gene flow Math Box 4.1 The expected value of FST in the infinite island model Problem Box 4.4 Expected levels of FST for Y-chromosome and organelle loci Interact Box 4.5 Finite island model of gene flow 4.6 The impact of population structure on genealogical branching Bugs in many boxes. Event times with population subdivision. Sample configurations. Mean and variance of waiting time in a two demes.
Interact Box 4.6 Coalescent events in two demes Math Box 4.2 Solving two equations with two unknowns for average coalescence times Chapter 5 Mutation 5.1 The source of all genetic variation Types of mutations and rates of mutation. How can a low probability event like mutation account for genetic variation? The spectrum of fitness for mutations. 5.2 The fate of a new mutation The chance a neutral or beneficial is lost due to Mendelian segregation. Mutations fixed by natural selection.
Frequency of a mutant allele in a finite population. Accumulation of deleterious mutations by Muller''s ratchet without recombination. Interact Box 5.1 Frequency of neutral mutations in a finite population Interact Box 5.2 Muller''s ratchet 5.3 Mutation models The infinite alleles, k alleles and stepwise mutation models. Understanding the implications of mutation models using the standard genetic distance and RST. The infinite sites and finite sites mutation models for DNA sequences.
Interact Box 5.3 RST and FST as examples of the consequences of different mutation models 5.4 The influence of mutation on allele frequency and autozygosity Irreversible and bi-directional mutation models. The parallels between the processes of mutation and gene flow. Expected autozygosity at equilibrium under mutation and genetic drift. Expected heterozygosity and the biological interpretation of . Math Box 5.1 Equilibrium allele frequency with two-way mutation Interact Box 5.
4 Simulating irreversible and bi-directional mutation 5.5 The coalescent model with mutation Adding the process of mutation to coalescence. Longer genealogical branches experience more mutations. Genealogies under the infinite alleles and infinite sites models of mutation. Interact Box 5.5 Build your own coalescent genealogies with mutation Chapter 6 Fundamentals of Natural Selection 6.1 Natural Selection Translating Darwin''s ideas into a model. Natural selection as differential population growth.
Natural selection with clonal reproduction. Natural selection with sexual reproduction and its assumptions. Problem Box 6.1 Relative fitness of human immunodeficiency virus (HIV) genotypes Math Box 6.1 The change in allele frequency each generation under natural selection 6.2 General results for natural selection on a diallelic locus Selection against a recessive phenotype. Selection against a dominant phenotype. The general effects of dominance.
Heterozygote disadvantage and advantage. The strength of natural selection. M.