The objective of this course is to introduce students to the role of genomics sensu lato, as it applies to fundamental questions in ecology and evolution. Topics include genome evolution, adaptation, speciation, functional diversity genotype-phenotype interactions and conservation. Both eurkaryotic and prokaryotic systems are addressed. Attention is also given to theoretical and technical aspects of “omics” technologies, as well as current limitations and challenges. The course is divided into 4 modules, each lasting 4-6 days.
Module 1 reviews principles of population genetics (determinants of diversity, effective population size, gene flow, divergence, selection); types of molecular markers and gene sequences used in classical studies; classical analysis methods (identifying conservation units, close kin assignment, estimating dispersal, population structure, adaptation).
Module 2 extends the aforementioned topics in an advanced population genomics context, with an introduction to next generation sequencing technologies (genomic, transcriptomic); new classes of markers (EST-msats, RADS/SNPs, exome capture); comparative gene expression/transcriptomics; changing approaches to phylogenomics and phylogeography; advantages and limitations of working with non-model systems; general discussion of changing concepts of the gene and the genome with respect to the genotype-phenotype and adaptation.
Module 3 focuses on prokaryotic genomes (evolution, size, organization, stability); the important role of horizontal gene transfer (mechanisms, proclivity, impacts on evolution, selection); introduction to metagenomics and functional diversity (soils, marine systems) in microbial ecology; comparative genomics of ecotypes and the emerging significance of “microbiomes” associated with all life systems.
Module 4 focuses on quantitative genomics in the model systems Nasonia and Drosophila; introduction to mapping and analysis of QTL related to life history traits; genomic considerations of sex determination, speciation, epigenetics, host-parasite interactions.