SubjectsSubjects(version: 861)
Course, academic year 2019/2020
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 [hours/week]
Capacity: 20
Min. number of students: 5
State of the course: taught
Language: English
Guarantor: Clément Lafon Placette, Dr.
Teacher(s): Mgr. Magdalena Bohutínská
RNDr. Filip Kolář, Ph.D.
Mgr. Veronika Konečná
Clément Lafon Placette, Dr.
RNDr. Antonín Macháč, Ph.D.
Ashish Kumar Pathak, Ph.D.
Manon Poignet
RNDr. Radka Reifová, Ph.D.
Roswitha Elisabeth Schmickl, Ph.D.
doc. Ing. Petr Smýkal, Ph.D.
Annotation -
Last update: Clément Lafon Placette, Dr. (13.12.2019)
This course will be held in English.
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.
Literature -
Last update: Clément Lafon Placette, Dr. (24.05.2019)

Bomblies K, Weigel D. 2007. Hybrid necrosis: autoimmunity as a potential gene-flow barrier in plant species. Nature Reviews Genetics 8: 382–393.

Coyne JA, Orr HA. 1997. ‘Patterns of Speciation in Drosophila’ Revisited. Evolution 51: 295.

Coyne JA, Orr HA. 2004. Speciation. Sinauer Associates, Incorporated Publishers.

Hopkins R. 2013. Reinforcement in plants. New Phytologist 197: 1095–1103.

Mayr E. 1996. What Is a Species, and What Is Not? Philosophy of Science 63: 262–277.

Moore JC, Pannell JR. 2011. Sexual selection in plants. Current Biology 21: R176–R182.

Poelstra JW, Vijay N, Bossu CM, Lantz H, Ryll B, Müller I, Baglione V, Unneberg P, Wikelski M, Grabherr MG, et al. 2014. The genomic landscape underlying phenotypic integrity in the face of gene flow in crows. Science 344: 1410–1414.

Schmickl R, Koch MA. 2011. Arabidopsis hybrid speciation processes. Proceedings of the National Academy of Sciences 108: 14192–14197.

Seehausen O, Butlin RK, Keller I, Wagner CE, Boughman JW, Hohenlohe PA, Peichel CL, Saetre G-P, Bank C, Brännström Å, et al. 2014. Genomics and the origin of species. Nature Reviews Genetics 15: 176–192.

Requirements to the exam -
Last update: Clément Lafon Placette, Dr. (29.10.2019)

- oral final exam for the theoretical part

- written reports for the practical part

Syllabus -
Last update: Clément Lafon Placette, Dr. (13.12.2019)

* Preliminary schedule:

Week 1. Lecture: Introduction to speciation and hybridization barriers [CLP]; no practical class.

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

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

Week 4. Lecture: Local adaptation & Ecological speciation [FK]; no practical class.

Week 5. Lecture: Speciation by domestication [PS]; no practical class.

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

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

Week 8. Lecture: Speciation genomics methodologies [RR]; no practical class.

Week 9. 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. [AKP] + [CLP]

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

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

Week 13. 4 hours practical class: Detecting gene flow between species. [MP] + [SS]



Antonin Macháč (Center for Theoretical Studies) [AM]

Ashish Kumar Pathak (Dpt of Botany) [AKP]

Clément Lafon Placette (Dpt of Botany) [CLP]

Filip Kolář (Dpt of Botany) [FK]

Magdalena Bohutínská (Dpt of Botany) [MB]

Manon Poignet (Dpt of Zoology) [MP]

Nelida Padilla (Dpt of Botany) [NP]

Petr Smykal (Palacky University in Olomouc) [PS]

Radka Reifová (Dpt of Zoology) [RR]

Roswitha Schmickl (Dpt of Botany) [RS]

Stephen Schlebush(Dpt of Zoology) [SS]

Veronika Konečná (Dpt of Botany) [VK]

Charles University | Information system of Charles University |