Evolutionary Genomics

URL study guide

https://studiegids.vu.nl/en/courses/2025-2026/AM_1231

Course Objective

For modern biologists it becomes increasingly important to have genomics in their professional toolbox. During these 4 weeks students will learn about the possibilities of genome sequencing
- how we can read the genome like a history book, learning about past bottlenecks during the ice age, local adaptation and how hybridization is defying species boundaries. There will be a focus on conservation genomics, how we can use genomics information to protect endangered species. During the practical you will extract dna from an iconic species in Artis and use that to inform the studbook keeper, contributing to conservation in practice. After the course, student will be able to:Understand genome architecture of prokaryotes and eukaryotes. Comparing genomes to understand evolutionary change in genome architecture.Describe different molecular genetic techniques to study transcriptomes and genomic variation in response to environmental stimuli and natural selection. Analyze experimental data generated by genomics research and knowing the possibilities for follow-up research.Find and analyze genomic data in databases on internet.Describe the evolutionary significance of functional genomic variation.Explain the evolutionary consequences of such variation for species abundance, community diversity, and speciation.Understand and describe the relevant genomic measures for conservation.Setup, execute, analyze and report a conservation-genetics study using dna from zoo animals.

Course Content

Nowadays, researchers in evolutionary biology and ecology are making extensive use of molecular techniques. Genomics technology can be used to advance our understanding of how selection acts on genomic variation to adapt to local environments, which will in turn affect species abundance, community diversity, and the evolution of speciation. In this course we will focus on:Differences in the molecular basis of fitness among individuals. Is there intraspecific genomic variation in response to environmental change, and is this variation adaptive?Evolutionary consequences of genomic variation. What proportion of genomic variation is associated with phenotypic change and how does this affect evolution of species?the difference between long-term evolutionary divergence and molecular adaptation to (changing) environments as driver of adaptive evolution. The use of genomics for conservation; which genomic measures are relevant, how to interpret them and use them to better protect endangered populations/speciesWe will discuss the methodology and applications of various genomic analyses, but mostly whole genome sequencing, genome-wide association studies, phylogenomic analysis and analyses on diversity.

Teaching Methods

The following working forms with expected amount of hours will be applied during the course:
- 25 hours Lectures, including some guest lectures of leading specialists in the field
- Practical conservation genomics, four afternoons of each 3 hours, in total 12 hours.
- Computer exercise evolutionary relationships, evolutionary genomics, selection & functional genomics. Four afternoons of 3 hours, in total 12 hours.
- Journal club, including paper presentation. one day part, maximum 4 hours. Journal club preparation is estimated to be 8 hours.

Method of Assessment

A practical report will be written by the student reflecting the execution of a conservation genomics experiment followed by data analysis and interpretation/discussion of the results. The report includes introduction/background, material and methods, results and discussion. The form of tuition is an assessment of the practical report, performed by the course coordinator and the course assistant. It relates to dublin descriptors 1 and 2: knowledge and understanding & application of knowledge Weight: 30% of the final grade.The Journal club presentation will be assessed using a standardized rubric performed by a panel of the course lecturer, participating lecturers and course assistants. It related to dublin desciptors 3 and 4: critical judgement and communication. Weight: 10% of the final gradeThe written exam will be assessed by the course coordinator using model answers. It relates to dublin descriptors 1 and 5: Knowledge and understanding & learning skills.Weight: 60% of final grade and needs to be 5.5 or higher to successfully pass the course.

Literature

Recommended literature (but NOT absolutely required): Evolutionary Genetics / Concepts, Analysis, and Practice / Glenn-Peter Sætre and Mark Ravinet ISBN: 9780198830924

Recommended background knowledge

It is highly recommended to have followed and passed the BSc course 'Evolutionary Genetics' AB_1022 (or an equivalent 6 EC).