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20 September Tuesday

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09:00 - 10:00   Detecting signatures of selection within genomes: an introduction 

10:00 - 12:00  The impact of recombination on genome evolution

  • Hill-Robertson interference; impact of recombination on the efficacy of selection

  • BGC: Biased gene conversion 

Genome Evolution (Duret)

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21 September Wednesday

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09:00 - 12:00   Distinguishing the signatures of selective vs non-adaptive processes: case studies 

  • Hallmarks of positive selection in the human genome: gBGC clouds the clues

  • Codon usage

  • Alternative splicing: expansion of the functional repertoire or errors of the splicing machinery

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Population Genetics (Sezgin/Yanchukov/Sağlam)

19 September Monday

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09:00 - 10:00   Mutation, selection and fitness (Yanchukov) (lecture notes)

  • Genes, genotypes, allele frequencies & the mution process

  • Phenotypic space, fitness and heritability.

  • Natural selection in Darwinian model of evolution: deleterious, neutral and beneficial mutations, biological constrains of mutational effects.

  • Allelic fitness, mean fitness of populations and adaptive landscapes.

  • Directional and stabilising selection

  • Allelic replacement and Fisher’s fundamental theorem.

10:00 - 11:00  Genotypic variation, linkage disequilibrium, models of gene flow and characterizing                                       population subdivision under the Wright-Fisher Model (Yanchukov) (lecture notes)

  • Genotype as a selectable unit.

  • Diploid population and Hardy-Weinberg distribution.

  • Wahlund effect.

  • Linkage disequilibrium, its causes and decay.

  • Island-continent model of gene flow.

  • Wright-Fisher population, genetic drift, population subdivision and genetic variance.

  • Effective population size.

  • Calculation of FST as normalised variance

  • FST and time since population divergence.

  • FST and gene flow.

  • Limitations of F-statistics.

11:00 - 12:00  Estimating population genetic parameters from allelic data (Yanchukov) (lecture notes)

  • Calculate allele and genotype frequencies, allelic richness, FST and migration rates.

  • FST for haploid markers.

  • Other measures of expected versus observed heterozygosity:

    • PhiST, GST, Jost’s D.

  • Required materials & programs​

    • Pen and paper​

    • GenAlEx or PopGenKit in R​

20 September Tuesday

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13:00 - 15:00   Molecular population genetics (Sezgin) (lecture notes)

  • Mutations and the neutral theory of molecular evolution

  • The Infinite alleles and sites model

  • Neutrality tests (Tajima’s D, Fu and Li tests)

  • Estimating rates of molecular sequence divergence

  • The molecular clock

  • Coalescent theory

  • Measures of DNA polymorphism and estimation of population parameters

  • Detection of natural selection from sequence data

  • Polymorphism and divergence in nucleotide sequences: HKA and McDonald-Kreitman tests

15:30 - 16:30   Estimating molecular sequence divergence and population genetic parameters using                                              human and drosophila models (Sezgin) ​(practical)

  • Required materials & programs​ (Please download linked programs and read the documentation before class)

16:30 - 18:00   The site frequency spectrum for summarizing genome-wide sequence variation and                                                detecting selective and demographic change  (Sağlam) ​(Theory & practice) (lecture notes)

  • Demographic modeling and parameter estimation using the SFS (practical)

18:00 - 19:30   Modeling evolution  (Yanchukov) ​(practicals)

  • Natural selection and drift

  • Dynamics of multiple loci

  • Simulating genotype and allele frequency dynamics

  • Required materials & programs​

    • Pre-written code

    • Mathematica

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19 September Monday

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13:00 - 15:00   Community ecology and null models (Özkan) (lecture notes)

15:00 - 19:00  Introduction to R and a simple null models (Özkan) (practicals)​

 

Ecology (Özkan/Yücel)

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24 September Saturday

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09:00 - 12:00   Ecology of Biogeochemical Gradients (Yücel) (lecture notes)

15:00 - 18:00  Biogeochemical Reactive-Transport Modeling (Yücel) (practicals)

  • Required materials & programs​

    • Data sets

    • R packages & codes

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22 September Thursday

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09:00 - 10:30  Introduction to phylogenetics (lecture notes)

  • Tracing the origins of infectious disease: HIV and Zika as case studies for the importance of phylogenetics

  • Reconstructing evolutionary histories through variation

  • Questions addressed using phylogenetics (rabies virus transmission in Peruvian vampire bats)

  • Methods and R packages to apply phylogenetic approaches​

10:30 - 12:00  Introduction to the phylogenetic comparative method 

  • Why is controlling for phylogeny important? Examples

  • Basic conceptual background to phylogenetic comparative methods

  • Questions addressed using comparative methods (comparing the relative roles of parasite-mediated and sexual selection in explaining immune gene variation across mammals)

  • Methods to apply phylogenetic comparative approaches and their R packages

 

15:30 - 17:30  Introduction to the phylogenetic (comparative) method (practicals)

  • Build phylogenies from sequence data

  • Build and tailor phylogenies to interspecific datasets

  • Graphical methods for visualizing comparative data on phylogenies

  • Calculate measures of phylogenetic signal (λ and K)

  • Required materials & programs​

    • Data sets

    • R packages & codes

17:30 - 19:00  Putting theory into practice: testing evolutionary models controlling for/using                                         phylogeny

  • Independent contrasts

  • Phylogenetic Generalized Least Squares (PGLS) models

  • Bayesian approaches (MCMCglmm) using mixed models

  • Simulation of phylogenetic data

  • Bayesian skyline plots

  • Solve the mystery… Using what you have learned to answer an evolutionary question (simulated data)

  • Required materials & programs​

    • Data sets

    • R packages & codes

Phylogenetics (Winternitz)

Experimental Evolution (Bozdağ)

24 September Saturday

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13:00 - 15:00  A very brief introduction to experimental evolution (lecture notes)

  • The experimental approach to study evolution: watching evolution in action

  • How do we measure evolutionary adaptation?

  • The genetic basis of adaptation: lessons learnt from the experimental evolution studies

  • A look into the future from the present examples: using experimental evolution to address diverse questions in evolutionary biology

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Next Generation Sequencing (NGS) (Karakoç/Kılınç) (lecture notes)

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21 September Wednesday

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13:00 - 14:00  Next generation sequencing (Karakoç/Kılınç)

  • Introduction to DNA sequencing

  • History of sequencing

  • Next generation sequencing platforms

  • NGS data formats

14:00 - 15:00  Next generation sequencing data analysis (Karakoç/Kılınç)

  • Preprocessing

  • Mapping to the reference Genome

  • Algorithms and softwares

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23 September Friday

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09:00 - 12:00  Variation discovery (Karakoç/Kılınç)

  • SNV discovery

    • Methods for detecting SNVs

    • Algorithms and their limitations and advantages

  • CNV (Copy number variation) and SV (Structural variation) discovery

    • What are copy number variations and structural variations

    • Signatures of CNVs and SVs in the mapping data

    • Read depth methods

    • Read pair Methods

    • Split Read methods

  • De Novo Assembly methods

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Transcriptomics (Somel/Aravena)

22 September Thursday

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13:00 - 15:00  Comparative transcriptomics: overview of techniques and applications in evolutionary                           biology (Somel) (lecture notes)

  • RNA-seq: basics of RNA-sequencing, advantages over microarrays, common protocols (e.g. paired end), statistics (e.g. FPKM)

  • Comparative RNA-seq: genome and annotation orthology issues

  • Study design: species to include, environmental conditions, batch effects, other confounding factors

  • Differential expression: identifying DE, linear models, phylogeny-aware models

  • Differential expression: the multiple testing problem and the false discovery rate (with demo)

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23 September Friday

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13:00 - 15:00  Mathematics, probabilities and statistics in ecology and evolution (Aravena)

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15:30 - 19:30  Transcriptomics practicals using R (Somel) (practicals)

  • Preprocessing: quality control

  • Preprocessing: mapping and summarization

  • Preprocessing: normalization, transformation

  • Preprocessing: filtering genes and filtering individuals

  • Overview: principal components analysis

  • Differential expression: linear models and the DESeq package

  • Differential expression: correcting for multiple testing

  • Clustering DE genes

  • Functional enrichment using topGO

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