MAE-50806 Advanced Molecular Ecology

Course

Credits 6.00

Teaching methodContact hours
Individual Paper0
Lecture16
Tutorial18
Practical28
Course coordinator(s)dr. R Nijland
Lecturer(s)prof. dr. AJ Murk
dr. ir. BA Pannebakker
dr. R Nijland
prof. dr. ir. J Komen
dr. ir. HJ Megens
J van den heuvel
Examiner(s)prof. dr. AJ Murk

Language of instruction:

English

Assumed knowledge on:

This course is aimed at MSc students that are interested to combine genomics and transcriptomics approaches including hands on bioinformatics to assess biodiversity, non-indigenous species, genetic heterogeneity, population genomics, adaptations to changing environments, with organisms ranging from microbes to fish and insects. Especially MSc students Biology (MBI) and Aquaculture and Marine Resource Management (MAS) are expected to profit from this course.
Basic knowledge molecular biology and genetics, builds upon BSc courses like;
GEN-20306 Molecular and Evolutionary Ecology
GEN-11806 Fundamentals of Genetics and Molecular Biology
BIF-20306 Introduction to Bioinformatics 
MIB-10306 Microbiology & Biochemistry
Builds upon MSc course: GEN-30806 Population and quantitative genetics


Continuation courses:

MAE-Thesis ABG/GEN/MAE, and Internship ABG/GEN/MAE, MAE-50306 Short Research Projects in Marine Animal Ecology




Contents:

The course discusses how to obtain data on the biodiversity, genetic heterogeneity and adaptation of organisms to changing environments including human induced changes using DNA sequencing technology on a diversity of samples including eDNA from water samples. Through lectures and tutorials, this course will introduce the main principles underlying biodiversity and genetic diversity assessment using DNA sequencing technology. Characterisation of diversity, from within species to species community, will be used to infer ecosystem functioning and infer response to a changing environment. These techniques are for example applied to understand how species can invade new environments, how animals adapt to climate change, and how isolated populations change genetically. In this advanced course the focus lies on approaches to obtain and analyse complex datasets, and interpret their biological meaning. During the tutorials / practical's, which are scheduled throughout the course, students will work in pairs on several case studies to analyse a specific biodiversity dataset. Since advanced tools for analysing genomic datasets usually require Linux and command-line skills, an introduction to acquiring basic competences in this area will be included. 
The topics that are treated cover: 
- population genetic diversity;
- DNA metabarcoding;
- environmental DNA;
- microbiome diversity;
- data-analysis  (also using command line tools);
- next generation/third generation DNA sequencing technologies.

Learning outcomes:

After successful completion of this course students are expected to be able to:
- describe the different DNA sequencing methods available survey biodiversity;
- assess biodiversity using metagenomic or metabarcoding sequencing data;
- reconstruct evolutionary processes using genomic data;
- design appropriate sampling and sequencing approaches in order to collect meaningful data;
- interpret and convert the raw sequencing data into clear information on the ecosystem studied using appropriate bioinformatics tools;
- analyse the ecological status of the sampled ecosystem based on a metagenomics sequencing experiment.

Activities:

- lectures;
- tutorials;
- practical (DNA isolation+ metabarcode amplification+ sequencing).

Examination:

The students have to pass two self-tests with >80% score. Examination is based on participation in tutorials, reporting and defense of own work  (poster) on a selected topic, and an electronic exam.
Results from the participation in tutorials, poster and defence, and the exam all count for the final mark (10:40:50). The minimum mark for the exam is 5.5

Literature:

The contents of the computer exercises and self tests are available via BrightSpace. Additional material on BrightSpace consists of links to relevant websites, to the presentations of the lectures and reference to further background information in review papers. Optional book for this course: environmental DNA (ISBN: 978-0-19-876728-2)?