Bi0999 Molecular ecology

Faculty of Science
Autumn 2024
Extent and Intensity
2/0/0. 2 credit(s) (plus extra credits for completion). Type of Completion: zk (examination).
In-person direct teaching
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 D31/238
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
  • Block 1: Genetic identifications in zoology (Josef Bryja) 1. Introduction – what is and what is not molecular ecology? Overlap with other subjects, brief history. Genetic variability in natural populations, main field and laboratory approaches. Sampling, methods for quantification of genetic polymorphism in free-living animals, genetic markers. 2. Species concepts, DNA barcoding – advantages and disadvantages, analyses of environmental DNA. 3. Genetic identification of individuals and sex by molecular methods. Application of molecular methods in behavioural ecology: Analysis of relatedness and mating systems. Block 2: Phylogenetics, phylogeography, coalescence, species delimitation, hybridization (Miloš Macholán, Ondřej Mikula) 4. Inferring phylogenies I: Basic phylogenetic principles and methods based on DNA sequences. Principle of parsimony, evolutionary models and their selection, distance-based methods. 5. Inferring phylogenies II: Maximum likelihood, Bayesian methods, program BEAST as an example. Phylogenetic contrasts and comparative methods. 6. Phylogeography: coalescent and its application in the inference of evolutionary parameters and population events in the past, mitochondrial DNA: advantages and problems, its alternatives (Y chromosome), refugia and colonization routes, genetic drift vs. Gene flow, phylogeography and coevolution. 7. Species as units of biological diversity. Statistical delimitation of species boundaries, single- and multi-locus methods. Genealogical distinctiveness of species: gene tree incongruence, deep coalescence and multispecies coalescent model. 8. Hybridization in nature, hybrid zones. Fitting clines, selection against hybrids, differences in introgression across the genome. Block 3: Population genetics in zoology (Adam Konečný) 9. Population genetics: Study of genetic diversity. Consequences of the Hardy-Weinberg principle, changes in allele frequencies (mutation, migration, selection, effective population size, genetic drift). 10. Population genetics: Analysis of population structure. Wahlund principle, F-statistics, AMOVA. 11. Bayesian analysis of population structure (STRUCTURE program). Spatial genetics. Isolation by distance. 12. Invasion Genetics. Population history modeling – ABC approach. Block 4: Conservation genetics, functional variability, adaptations (Josef Bryja) 13. Conservation genetics. Non-invasive genetic methods, probability of identity, bottleneck, consequences of population fragmentation, evolutionary significant units, inbreeding, genetic rescue, local adaptations, inbreeding and outbreeding depression. 14. Genes and their biological function – examples of functional genes and their importance in ecology. Adaptive variability, immunogenetics, detection of selection at molecular and population level. Transcriptomics in ecology, gene ontology.
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 2023.
  • Enrolment Statistics (recent)
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