Topics & Lectures
Biogeochemistry - Mustafa Yücel
Lecture 1: Biogeochemistry I
Evolution of metabolism and emergence of biogeochemical cycles coupled to Earth Evolution.
Formation of Earth and differentiation of elements, the formation of atmosphere and oceans, early ocean geochemistry and emergence of life, the establishment of cycles of metals, sulfur, nitrogen and phosphorus, metabolism and enzymes
Lecture 2: Biogeochemistry II
Modern elemental biogeochemical cycles in the Earth System. Global cycles, photosynthesis vs respiration, redox-dependent metabolic processes, and a special lecture on the biogeochemistry of Turkish Seas.
Lecture 3: Biogeochemistry III
Deep-Sea Ecosystems. Seafloor sediments and benthic ecosystems, hydrothermal vents and cold seeps, chemosynthesis-based ecosystems, sustainability issues of seafloor resource utilization and Blue Growth
Molecular Ecology - Arzu Karahan
Lecture 1: Molecular Ecology Markers
Molecular ecology markers and defining their application methods
Lecture 2: Studying ecologically important characters
Ecogenomics, QTL Analysis, and reverse genetics, connecting genotype to phenotype.
Lecture 3: Molecular Evolution and Genome Evolution
Which mutations are more important in the genome, which changes cause speciation?
Introduction to Quantitative Ecology - ÇaÄŸatay TavÅŸanoÄŸlu
Lecture 1: Experimental design in ecology
Experimental design, hypothesis testing, randomization, replicate, confounding effects. Relationship between statistical analysis and experimental design.
Lecture 2: Datatypes and analyses in ecology
Data types obtained from ecological research and statistical analysis approaches for different data types. Basic statistical analyses, general linear models, generalized linear models, mixed models.
Lecture 3: Analysis of ecological data
Using sample datasets, analyses in relation to previous lecture's subjects in the R environment.
Extending the evolutionary theory - Manolis Ladoukakis
Lecture: The evolutionary theory is not restricted to explain the origin and diversification of life but it can be extended to any evolvable system such as microbial communities or languages.
Statistical analyses methods in community ecology: null model analyses using R - Korhan Ozkan
Lecture 1: Community ecology
Major concepts in community ecology
Lecture 2: Statistical methods in community ecology
A general overview of main statistical approaches in community ecology
Lecture 3: Null model analyses using R
Constructing null model analyses to test niche theories in a bird community
DNA-based taxonomy for ecological and evolutionary studies - Anna Papadopoulou
Lecture 1: DNA barcoding: main concepts, problems, and applications
The main concepts, problems, and applications of species identification using DNA barcodes will be explained and discussed and several practical examples will be provided.
Lecture 2: Species concepts and DNA-based species delimitation
An overview of the 'species problem' and the major species concepts will be provided. The main ideas, problems and applications of DNA-based species delimitation will be explained and discussed.
Lecture 3: DNA-based species delimitation methods
Several single-locus and multi-locus DNA-based species delimitation methods will be presented and practical examples will be provided using case studies and sample datasets.
Coalescent theory and analysis of DNA sequence data - Ä°smail Kudret SaÄŸlam
Monday Lecture 1: Summarizing DNA sequence data and the coalescent with two gene copies
Lecture 1.1 - Summarizing DNA Sequence Data
Lecture 1.2 - Pi, S, and the SFS
Lecture 1.3 Expected tMRCA With 2 Gene Copies
Lecture 1.4 Tajima’s Estimator
Monday Lecture 2: Coalescent process with n gene copies
Lecture 2.1 - Coalescent Process With n Gene Copies
Lecture 2.2 - Expected tMRCA Of n Gene Copies and total tree length
Lecture 2.3 - Segregating Sites And Watterson’s Theta
Lecture 2.4 - The Derived SFS and Tajima’s and Watterson’s Thetas in WF Model
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Tuesday Lecture 1: Understanding selection and demography from the site frequency spectrum
Lecture 3.1 - Selection On SFS and Tajima's D
Lecture 3.2 - Coalescent Effective Population Size
Tuesday Lecture 2: Understanding selection and demography from the site frequency spectrum
Lecture 3.3 - SFS And Changing Population Size
Lecture 3.4 - Demography Vs Selection
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Metabarcoding Workflow: Field, Laboratory and Bioinformatics - Emre Keskin
Lecture 1: Metabarcoding Workflow I: Fieldwork planning and sampling.
What should be considered in sampling planning for metabarcoding studies will be explained. In this context, the sampling points to be selected, the number and amount of samples to be taken, how the samples will be transported and stored will be explained.
Lecture 2: Metabarcoding Workflow II: Laboratory workflow.
Before and when working in the laboratory for metabarcoding studies, the issues that need to be considered while working will be explained. In this context, primer design, extraction protocol, enzyme selection, what to consider, and how to plan for library preparation and sequencing will be explained.
Lecture 3: Metabarcoding Workflow III: Bioinformatics
For metabarcoding studies, how to analyze the raw data obtained after sequencing will be explained. In this context, reading quality thresholds, what errors are to be filtered, how to separate tagged/indexed samples, how to identify them using OTU clustering and reference databases will be explained.
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Social Evolutionary Theory and Evolutionary Game Theory - Erol Akçay
Lecture 1: Introduction to methods used in modeling social interaction's evolution.
Price equation, Hamilton's rule, Inclusive fitness
Lecture 2: Introduction to methods used in modeling social interaction's evolution. -- continuing
Multi-level selection, Selection in group-structured populations
Lecture 3: Introduction to evolutionary game theory and its biological applications
Evolutionarily stable strategies, sequential and simultaneous games, the evolution of cooperation.
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Evolution of communication and bioacoustics, vocal sequence analysis, - ÇaÄŸlar Akçay
Lecture 1: Animal communication and bioacoustics
Behavioral ecology of communication and introduction to the bioacoustic analysis
Lecture 2: Bioacoustics and vocal sequence analysis
Vocal sequence models
Lecture 3: Bioacoustics and vocal sequence analysis
Vocal sequence models and applications
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A general introduction to ancient DNA analysis - Nikos Psonis
Lecture: A general introduction to ancient DNA analysis: lessons from case studies.
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Comparison of binary sequences - Ogün Adebali
Lecture 1: Alignment of two sequences
Local and global alignment, Needleman-Wunsch, BLAST algorithms
Lecture 2: Multiple Sequence Alignments
Algorithms to align 3 or more sequences. AFFT, MUSCLE, T-COFFEE, CLUSTAL, Profile-based methods
Lecture 3: Phylogenetics
Methods to create phylogenetic trees. UPGMA, Neighbor-joining, Maximum likelihood methods
Pavlos Pavlidis
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Forward genetic simulation analyses / SLiM - GülÅŸah Merve Kılınç
Lecture 1: Introduction to simulation analysis in population genetics
Importance of producing DNA sequence data for population genetics under various evolutionary and demographic scenarios.
Lecture 2: Introduction to SLiM
Introducing SLiM software, WF ve nonWF models
Lecture 3: Setting up a basic simulation scenario using SLiM.
Creating a simulation scenario.
Transcriptome comparisons in evolutionary analysis. - Mehmet Somel
Lecture 1: Introduction to transcriptome data. How is it produced and evaluated?
Searching varying phenotypes. Properties of RNA sequencing data. Information retrieval for adaptation from RNA sequencing comparisons between species.
Lecture 2: Transcriptome Data Analysis - Determining varying genes
Reading a published comparative transcriptome dataset in R environment. Determining genes varying between species. Using appropriate statistical tests and the importance of multiple test correction.
Lecture 3: Transcriptome Data Analysis - Determining varying pathways
Determining the frequent pathways of genes found in the previous lecture concentrate. Commentary on the results and discussion.
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You can download the course schedule from the "Concise Program" file below.
For detailed program you can download the excel file "Detailed Program".
Detailed program and lecture schedule can be downloaded here