Genomics of adaptation and speciation - MB120P165

• Title: Genomics of adaptation and speciation
• Guaranteed by: Department of Botany (31-120)
• Faculty: Faculty of Science
• Actual: from 2018 to 2019
• Semester: summer
• E-Credits: 4
• Examination process: summer s.:combined
• Hours per week, examination: summer s.:2/2, C+Ex [HT]
• Capacity: 20
• Min. number of students: 5
• 4EU+: no
• Virtual mobility / capacity: no
• State of the course: taught
• Language: English
• Note: enabled for web enrollment
• Guarantor: doc. Clément Lafon Placette, Dr.
• Teacher(s): Gianluca Chimetto; RNDr. Filip Kolář, Ph.D.; doc. Clément Lafon Placette, Dr.; RNDr. Veronika Lipánová, Ph.D.; RNDr. Antonín Macháč, Ph.D.; RNDr. Radka Reifová, Ph.D.; Roswitha Elisabeth Schmickl, Ph.D.; Camille Pauline Sottas, Ph.D.

Annotation

Last update: doc. Clément Lafon Placette, Dr. (29.10.2019)

How does a new species arise? With the recent advances in -omics technologies and the ability to sequence
complete genomes, characterize full transcriptomes or metabolomes, we have never been as close to the answer
as now. This technological boom not only revived the interest of the scientific community for speciation research,
but also enriched our knowledge of the processes underlying adaptation and population differentiation. This
course will cover up-to-date theoretical aspects of adaptation, speciation and hybridization barriers in animals and
plants, as well as the modern approaches to address these questions. Students will have hands-on practical
classes involving state-of-the-art genomic analyses applied to the topics of speciation and adaptation: study
design, transcriptomic analyses in hybrids, QTL to determine the genetic basis of adaptation/hybridization barriers,
genome scans searching for selective sweeps... They will be based on data adapted from actual recent research
works. The course will be taught exclusively in English.

Learning outcomes: At the end of the course, the students will be able to:
- explain the main evolutionary mechanisms driving adaptation and speciation.
- identify the genomic consequences of such mechanisms using state-of-the-art –omics methodologies.
- use R to do so.

Syllabus

Last update: doc. Clément Lafon Placette, Dr. (24.05.2019)

* Preliminary schedule:

Week 1 (18/2). Lecture: Introduction to speciation and hybridization barriers [CLP]; no practical class.

Week 2 (25/2). Lecture:Sexual selection and speciation [CLP]; no practical class.

Week 3 (4/3). Lecture: Postzygotic barriers, Bayeson-Dobzhansky-Müller incompatibilities, genomic conflicts [RR]; no practical class.

Week 4 (11/3). Lecture: Local adaptation &Ecological speciation [FK]; no practical class.

Week 5 (18/3). Lecture: Chromosome speciation [RR]; no practical class.

Week 6 (25/3). Lecture: Methodologies and concepts in population genomics and adaptomics [CLP] ; 4 hours practical class: reminders on R. ?

Week 7 (1/4). Lecture: Polyploid speciation [FK]; 4 hours practical class: local adaptation/ecological speciation I. Genome scans searching for adaptation genes. [FK] + [VK]

Week 8 (8/4). Lecture: Speciation genomics methodologies [RR]; no practical class.

Week 9 (15/4). Lecture: Evolutionary consequences of gene flow between species: hybrid speciation, adaptive introgression [CLP]; 4 hours practical class: Hybrid necrosis in Capsella. Revealing the genetic basis using a QTL approach. [GC] + [CLP]

Week 10 (22/4). Lecture: Secondary contact: relations between hybridization barriers, interspecific competition and fitness [RR]; 4 hours practical class: Reconstructing phylogeny despite hybridization (etc.). [RS]

Week 12 (6/5). Lecture: Species in a macro-context: out of the gene-oriented view on speciation [AM]

Week 13 (13/5). 4 hours practical class: Detecting gene flow between species. [RR] + [CS]

 

Teachers:

Clément Lafon Placette (Dpt of Botany) [CLP]

Radka Reifová (Dpt of Zoology) [RR]

Filip Kolář (Dpt of Botany) [FK]

Roswitha Schmickl (Dpt of Botany) [RS]

Antonin Macháč (Center for Theoretical Studies) [AM]

Gianluca Chimetto (Dpt of Botany) [GC]

Veronika Konečná (Dpt of Botany) [VK]

Camille Sottas [CS]