Genomics of adaptation and speciation - MB120P165

• Title: Genomics of adaptation and speciation
• Czech title: Genomika adaptací a speciací
• Guaranteed by: Department of Botany (31-120)
• Faculty: Faculty of Science
• Actual: from 2020
• 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
• Additional information: https://lab-allience.natur.cuni.cz/plantreproevo/teaching/speciation
• Note: enabled for web enrollment
• Guarantor: doc. Clément Lafon Placette, Dr.
• Teacher(s): Mgr. Magdalena Bohutínská, Ph.D.; RNDr. Filip Kolář, Ph.D.; doc. Clément Lafon Placette, Dr.; RNDr. Veronika Lipánová, Ph.D.; RNDr. Antonín Macháč, Ph.D.; Nelida Maria Padilla Garcia, Ph.D.; Manon Poignet, Ph.D.; RNDr. Radka Reifová, Ph.D.; Stephen Schlebusch; Roswitha Elisabeth Schmickl, Ph.D.

Annotation

English

Last update: doc. Clément Lafon Placette, Dr. (11.01.2022)

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 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 hybridization barriers, detection of gene flow... 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.

Czech

Last update: Mgr. Michal Štefánek (07.06.2019)

Jak vznikají nové druhy? Současné technologické pokroky umožňující sekvenovat kompletní genomy,
charakterizovat transkriptomy a metabolomy nás k odpovědi na předchozí otázku velmi přiblížily. Tento
technologický pokrok obohatil naše znalosti procesů, které vedou k adaptacím a diferenciaci populací. Kurs se
zabývá teoretickými aspekty souvisejícími s adaptacemi, speciací a hybridizačními bariérami u živočichů a rostlin.
Studenti absolvují praktickou výuku moderních genomických analýz s tématikou adaptací a speciace zahrnující
designování výzkumu, analýzy transkriptomu hybridních taxonů, QTL ke stanovení genetické podstaty
hybridizačních bariér, skenování genomu. Pracovat se bude s upravenými daty z probíhajícího výzkumu. Výuka
celéhu kurzu bude probíhat v angličtině.

Výstupy vzdělávání: Studenti budou schopni popsat hlavní evoluční mechanismy, které podmiňují adaptace a
speciace, identifikovat genomické důsledky těchto mechanismů pomocí moderních technik, analyzovat data v
prostředí R.

Aim of the course

Last update: Mgr. Michal Štefánek (07.06.2019)

Výstupy vzdělávání: Studenti budou schopni popsat hlavní evoluční mechanismy, které podmiňují adaptace a

speciace, identifikovat genomické důsledky těchto mechanismů pomocí moderních technik, analyzovat data v

prostředí R.

Literature

English

Last update: doc. 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.

Czech

Last update: Mgr. Michal Štefánek (10.06.2019)

Abbott R. et al (2013); Hybridization and speciation. - Journal of Evolutionary Biology. 26:229.

Coyne, J. A., & Orr, H. A. (2004). Speciation. Sunderland, Mass: Sinauer

Savolainen O, Lascoux M, Merilä J (2013). Ecological genomics of local adaptation. - Nature Reviews Genetics 14, 807

Requirements to the exam

English

Last update: doc. Clément Lafon Placette, Dr. (12.10.2020)

- analysis of figures and written essay as final exam, with a process called "calibrated peer review" for the theoretical part

- written reports for the practical part

Czech

Last update: doc. Clément Lafon Placette, Dr. (12.10.2020)

- rozbor čísel a písemná práce pro závěrečnou zkoušku teoretické části

- písemné zprávy pro praktickou část

Syllabus

English

Last update: doc. Clément Lafon Placette, Dr. (07.01.2022)

Block I: basic concepts in speciation and case study of a hybridization barrier, the triploid block

·       Week 1. Lecture: Introduction to speciation and hybridization barriers; no practical class.

·       Week 2. Lecture: Postzygotic barriers, Bayeson-Dobzhansky-Müller incompatibilities, genomic conflicts; no practical class.

·       Week 3. Lecture: Knowledge consolidation I: group work on the concept of species; 4 hours practical class: reminders on R.

·       Week 4. Lecture: Polyploid speciation, triploid block; no practical class.

·       Week 5. Lecture: Transcriptomics, a method to understand the functional basis of hybridization barriers; 4 hours practical class: Transcriptomics of a hybridization barrier, the triploid block.

 

Block II: the population genomics of speciation, or how allele frequency changes lead to hybridization barriers

·       Week 6. Lecture: Methodologies and concepts in population genomics I; no practical class.

·       Week 7. Lecture: Methodologies and concepts in population genomics II; no practical class.

·       Week 8. Lecture: Knowledge consolidation II, essay writing on a case study: the population genomics of speciation by domestication; no practical class.

·       Week 9. Lecture: Genotype-phenotype associations, a method to discover speciation genes; 4 hours practical class: Hybrid necrosis in Capsella. Revealing the genetic basis using a QTL approach.

 

Block III: gene flow, the other side of the speciation coin

·       Week 10. Lecture: Gene flow, the rule rather than the exception of speciation; no practical class.

·       Week 11. Lecture: Evolutionary consequences of gene flow between species: hybrid speciation, adaptive introgression; no practical class.

·       Week 12. Lecture: A method to detect gene flow; 4 hours practical class: Detecting gene flow between species.

Entry requirements

Last update: doc. Clément Lafon Placette, Dr. (06.05.2021)

This course requires a completed Licence in biology, and is therefore for Master and PhD students only. A basic knowledge in R is also recommended for the practicals.