PřF:Bi0999 Molecular ecology - Course Information

Bi0999 Molecular ecology

Extent and Intensity

2/0. 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 11:00–12:50 D31/238

Prerequisites (in Czech)

( 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 - podzimní semestr, ideálně 4. ročník) + Mechanismy mikroevoluce (nový předmět - podzimní semestr, ideálně 4. ročník)

Course Enrolment Limitations

The course is offered to students of any study field.

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").

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. xv, 652. ISBN 9780878933082. 2007. info
• FREELAND, Joanna. Molecular ecology. Chichester: John Wiley & Sons. x, 388. ISBN 0470090626. 2005. info
• BEEBEE, Trevor J. C. and Graham ROWE. An introduction to molecular ecology. 1st pub. New York: Oxford University Press. xxii, 346. ISBN 0199248575. 2004. info
• AVISE, John C. Phylogeography : the history and formation of species. Cambridge, Mass.: Harvard University Press. viii, 447. ISBN 0674666380. 2001. info
• HARTL, Daniel L. A primer of population genetics. 3rd ed. Sunderland, Mass.: Sinauer Associates. xvii, 221. ISBN 0878933042. 2000. 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.

• Enrolment Statistics (Spring 2016, recent)
  
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