Expected learning outcomes:
Introduce, discuss, compare and apply molecular, statistical and computational methods for the analysis of genetic diversity which are most often used in population genetics, molecular ecology, spatial genetics, phylogenetics, biology conservation and epigenetic researches.
Course content broken down in detail by weekly class schedule (syllabus):
1. Introduction to the analysis of molecular diversity; overview of classical and molecular genetics; examples of scientific researches.
2. Genetic markers: basic molecular techniques in the analysis of genetic diversity; morphological and molecular markers; isoenzymes; molecular markers at the DNA level; randomly amplified molecular markers; molecular markers based on known sequences.
3. Descriptive statistics: informativeness of genetic markers; codominant and dominant markers; genotype and allelic frequency; polymorphism information contents; measures of intrapopulation diversity; allelic richness; observed and expected heterozygosity; fixation index; Shannon's information index; frequency of rare alleles; analysis of genetic bottleneck.
4. Measures of genetic distance: distances between populations; frequency of amplified fragments and allele frequency; distances based on evolutionary models; geometric distances; genetic distance between individuals; the proportion of shared alleles distance; similarity coefficients for binary data.
5. Multivariate methods: introduction; characteristics of mutlivariate data; classification of multivariate methods; cluster analysis; types of trees; UPGMA and related algorithms; neighbor joining method; bootstrap method; principal component and principal coordinate methods
6. Genetic structure: Hardy Weinberg equilibrium; Wrights F statistics; Wahlundov effect; index of genetic differentiation; method according Weir and Cockerham; analysis of of molecular variance; basic concept of Bayesian statistics; linkage disequilibrium; model based Bayesian analysis (STRUCTURE, BAPS).
7. Spatial and landscape genetics: spatial distribution of genetic diversity; isolation by distance; spatial autocorrelation; Moran s index; Bayesian analysis of spatial population structure (BAPS, TESS); genetic barriers; comparison of bioclimatic and genetic parameters; landscape genetics (POPS).
8. Phylogeography: impact of demographic processes on the geographical distribution of population or species; genetic genealogy; analysis of nested clad' vs. coalescent theory; analysis of haplotype and nucleotide diversity; neutrality test; phylogenetic networks; statistical parsimony; strict and relaxed molecular clock.
9. Adaptive genetic diversity: natural selection vs. neutral theory; genetic diversity and adaptive potential of populations/species; neutral genetic markers and markers under selection pressure; genetic drift; methods of identification of markers under selection pressure; marker deviation of the overall population genetic differentiation.
10. Epigenetic diversity of natural populations: analysis of epigenetic markers; the epigenetic structure of the population; the relationship between genetic and epigenetic diversity; the impact of environmental factors, genetic bottleneck, hybridization, polyploidization and inbreeding depression on epigenetic diversity
Student responsibilities:
Attendance of lectures, making and presentation of seminars, solving of homework exams. The final mark represents the sum of marks of seminars, homework and final written exam.
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