Population and Ecological Genetics 01-POPGEN-PIE

The course begins with an overview of basic terms and concepts, including types of genetic variation and its measurement, and genetic structure of population. Emphasis will be placed on forces responsible for the origin and maintenance of genetic variation, i. e. systems of mating, genetic drift, migrations (models of the gene flow), mutations, and effect of natural selection on gene frequencies. The course introduces the most common computer software packages used in the data analysis. During the course students will read and analyze recent literature and will prepare short (2000 words) evaluation of the chosen article. The best student will be asked for 20` minutes lecture (last week). In the end there is a 1-hour test exam.

Week 1 Populations - basic terms and concepts; prosperities of population: size, density, dispersion, demographics, and growth;
Week 2 Pattern of human genetic variation from a population perspective; mutations: types of mutations, distribution of fitness effect of new mutations; fate of new mutations; allele frequency change caused by mutation; effect of dominance, mutational load, estimation of mutation rates; markers and data collection; SNP identification and screen; STR (short tandem repeats);
Week 3 Pattern of human genetic variation from a population perspective; measurement of genetic diversity:
DNA sequence variation (proportion of polymorphic sites; nucleotide diversity (π and Π); number of segregating (polymorphic) sites, the population scaled mutation rate Θ);
Arlequin: software for population genetics data analysis;
Week 4 Pattern of human genetic variation from a population perspective; Genetic population structure:
Wahlund effect, Wright’s F-Statistics; Estimating Fst, FIS; FIT
Week 5 Hardy-Weinberg “law”; Systems of mating and their genetic consequences: random mating and non-random mating (inbreeding incl. selfing; positive and negative assortative mating; consequences of mating systems on genotypic frequencies and allelic frequencies; system-of-mating inbreeding coefficient (Panmictic index) (f); pedigree inbreeding coefficient (F ); heterozygosity – fitness correlation; populations survive relative to inbreeding;
Week 6 Genetic drift:
causes of genetic drift; properties of genetic drift;
Week 7 Dispersal, gene flow:
principle models of population structure (panmictic model, one-way migration and genetic admixture, Wright’s island model, stepping-stone model, isolation-by-distance; metapopulation models; estimations of gene flow; software (DIST), STRUCTURE;
Week 8 Selection:
basic concepts, forms of selection, requirements for the evolution by natural selection; selection and mutation; selection and genetic drift; selection and gene flow;
Week 9 Selection and mutation; selection and genetic drift; selection and gene flow;
Week 10 The Neutral Theory
Modifications, the neutralist-selectionist controversy; tests of the Neutral Theory