Poslední úprava: 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.
Poslední úprava: 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.
Cíl předmětu
Poslední úprava: 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.
Literatura -
Poslední úprava: 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
Poslední úprava: 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 Genetics8: 382–393.
Coyne JA, Orr HA. 1997. ‘Patterns of Speciation in Drosophila’ Revisited. Evolution51: 295.
Coyne JA, Orr HA. 2004. Speciation. Sinauer Associates, Incorporated Publishers.
Hopkins R. 2013. Reinforcement in plants. New Phytologist197: 1095–1103.
Mayr E. 1996. What Is a Species, and What Is Not? Philosophy of Science63: 262–277.
Moore JC, Pannell JR. 2011. Sexual selection in plants. Current Biology21: 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. Science344: 1410–1414.
Schmickl R, Koch MA. 2011. Arabidopsis hybrid speciation processes. Proceedings of the National Academy of Sciences108: 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 Genetics15: 176–192.
Požadavky ke zkoušce -
Poslední úprava: doc. Clément Lafon Placette, Dr. (12.10.2020)
- rozbor čísel a písemná práce pro závěrečnou zkoušku teoretické části
- písemné zprávy pro praktickou část
Poslední úprava: 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
Sylabus -
Poslední úprava: 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 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.
Poslední úprava: 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 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.
Vstupní požadavky - angličtina
Poslední úprava: 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.
