Bi0999 Molecular ecology

Faculty of Science
Autumn 2023
Extent and Intensity
2/0/0. 2 credit(s) (plus extra credits for completion). Type of Completion: zk (examination).
Teacher(s)
prof. Mgr. et Mgr. Josef Bryja, Ph.D. (lecturer)
Mgr. Adam Konečný, Ph.D. (lecturer)
prof. RNDr. Miloš Macholán, CSc. (lecturer)
Guaranteed by
prof. Mgr. et Mgr. Josef Bryja, Ph.D.
Department of Botany and Zoology – Biology Section – Faculty of Science
Contact Person: prof. Mgr. et Mgr. Josef Bryja, Ph.D.
Supplier department: Department of Botany and Zoology – Biology Section – Faculty of Science
Timetable
Thu 8:00–9:50 D32/329
Prerequisites
( Bi1030 Inverteb. phylog. & divers. && Bi2090 Verteb. phylog. & divers. && Bi3060 Basic genetics && Bi4010 Essential molecular biology && Bi7900 Genetic methods in zoology && Bi7150 Mechanisms of Microevolution ) || SOUHLAS
Prerekvizity: Bi7900 (Genetické metody v zoologii - jarní semestr, ideálně 4. ročník) + Bi7150 (Mechanismy mikroevoluce - jarní semestr, ideálně 4. ročník)
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
Molecular ecology is recently established scientific discipline whose main aim is to resolve ecological problems by using molecular and genetic methodological tools. Despite its recent origin, molecular ecology is rapidly developing, the number of published articles is growing geometrically, highly-ranked scientific journal Molecular Ecology is now well established and first books focussed on these issues have been published.
The series of lectures should present the main questions and principles of molecular ecology with special attention devoted to interpretation of results obtained by genetic methods when answering ecological questions. It is expected that participants already have the basic knowledge of laboratory genetic techniques ("Genetic methods in zoology") and evolutionary principles in populations (new lectures "Mechanisms of microevolution").
Learning outcomes
Students will be able to apply genetic approaches to solve the problems of evolutionary biology, population and conservation genetics and species delimitations.
Syllabus
  • 1. Introduction. What is and what is not molecular ecology? Definition of the subject, overlap with other disciplines, short history. Genetic variation in natural populations, overview of methodological approaches. Collection and storage of samples, methods for detection of genetic polymorphism in free-living populations, genetic markers. (JB)
  • 2. Phylogenetic reconstructions - overview of phylogenetic approaches and programs for analysis of DNA sequences. Likelihood, Bayesian approaches, coalescence. (MM)
  • 3. Phylogenetic reconstructions - ecological inference using phylogenetic information. Phylogenetic contrasts and comparative methods. (MM)
  • 4. Genetic identification. DNA barcoding and its problems - cryptic species and hybridization; sex identification (CHD genes in birds, Y chromosome in mammals), identification of individuals (probability of identity, genetic fingerprinting). (JB)
  • 5. Genetic approaches in behavioural ecology. Metagenomics in the diet analysis. Relationships and mating systems, simple exclusion principle, categorical x fractional likelihood, overview of available software. Identification of parentage and relatedness. Genetic analysis of dispersal and migration, sex-biased dispersal, assignment test. (JB)
  • 6. Population genetics - analysis of genetic diversity. Consequences of Hardy-Weinberg principle, changes in allelic frequencies (mutations, migration, selection, effective population size, genetic drift). (AK)
  • 7. Population genetics - analysis of population structure. Wahlund´s principle, F-statistics, AMOVA, Bayesian clustering in STRUCTRE. (AK)
  • 8. Spatial genetics. Isolation by distance, Bayesian spatial clustering - examples with available software (Geneland, BAPs). Invasion genetics. (AK).
  • 9. Reconstructions of population history - changes in effective population size (bottlenecks, expansion), detection of admixture, etc. ABC approaches. (AK)
  • 10. Phylogeography: genetic history of species. Advantages of mitochodrial DNA and its alternatives (Y-chromosome), refugia and colonization routes, genetic drift vs. gene flow, phylogeography and co-evolution. (MM)
  • 11. Hybridization in nature, hybrid zones. Cline construction, selection against hybrids, differences in introgression pattern across genome. (MM)
  • 12. Conservation genetics. Non-invasive genetic methods, probability of identity, consequences of population fragmentation, evolutionary-significant units, inbreeding, genetic rescue, local adaptations, inbreeding and outbreeding depression. (JB)
  • 13. Genes and their biological function - examples of functional genes and their importance in ecology. Adaptive variation, immunogenetics, genes and behaviour, detection of selection at molecular and population level, -omics in ecology, gene ontology. (JB)
Literature
  • HARTL, Daniel L. and Andrew G. CLARK. Principles of population genetics. 4th ed. Sunderland, Mass.: Sinauer Associates, 2007, xv, 652. ISBN 9780878933082. info
  • FREELAND, Joanna. Molecular ecology. Chichester: John Wiley & Sons, 2005, x, 388. ISBN 0470090626. info
  • BEEBEE, Trevor J. C. and Graham ROWE. An introduction to molecular ecology. 1st pub. New York: Oxford University Press, 2004, xxii, 346. ISBN 0199248575. info
  • AVISE, John C. Phylogeography : the history and formation of species. Cambridge, Mass.: Harvard University Press, 2001, viii, 447. ISBN 0674666380. info
  • HARTL, Daniel L. A primer of population genetics. 3rd ed. Sunderland, Mass.: Sinauer Associates, 2000, xvii, 221. ISBN 0878933042. info
Teaching methods
Lectures, class discussion, homework and students´ presentations
Assessment methods
Lectures, class discussions, presentations. Oral exam.
Language of instruction
Czech
Further Comments
Study Materials
The course is taught annually.
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2005, Spring 2006, Spring 2007, Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2024.
  • Enrolment Statistics (Autumn 2023, recent)
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