Bi0999 Molecular ecology

Faculty of Science
Spring 2013
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)
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 9:00–10:50 VS
Prerequisites (in Czech)
Bi1030 Inverteb. phylog. & divers. && Bi2090 Verteb. phylog. & divers. && Bi3060 Basic genetics && Bi4020 Molecular biology && Bi7900 Genetic methods in zoology ||SOUHLAS
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 now 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.
Main objectives can be summarized as follows: The series of lectures should present the main questions and principles of molecular ecology and special attention will be devoted to interpretation of results obtained by genetic methods when answering ecological questions.
Syllabus
  • 1. What is and what is not molecular ecology? (JB)
  • Limits of the discipline, overlap with related subject areas, brief history
  • 2. Genetic variation in natural populations, overview of field and laboratory methods (JB)
  • Collection and storage of samples, methods for detecting genetic polymorphism in wild living organisms, genetic markers
  • 3. Genetic identification - cryptic species and hybridization, individual identification, sex identification by molecular methods. (JB)
  • DNA barcoding, fixed polymorphism, genetic fingerprinting, CHD genes in birds, Y chromosome in mammals
  • 4. Molecular methods in behavioural ecology. Parentage analysis, minimum number of parents of litters or broods, relatedness (JB)
  • Analysis of relatedness and mating systems, exclusion principle, categorical x fractional likelihood, overview of available computer programs. Genetic identification of dispersal and migration, assignment tests.
  • 5. Reconstruction of phylogeny and the use in ecological analyses. (MM)
  • Phylogenetic principles and programs for analysis of DNA sequences. Distance-based methods, maximum parsimony, maximum likelihood, Bayesian principle, coalescent approach. Phylogenetic contrasts, comparative methods. (2 lectures)
  • 6. Population genetics: analysis of population structure, genetic diversity and inbreeding (JB)
  • Hardy-Weinberg equilibrium, factors affecting changes in allelic frequencies (mutation, migration, selection, effective population size, genetic drift), Wahlund effect, F-statistics, isolation-by-distance, AMOVA, examples with using available population genetic programs (2 lectures)
  • 7. Phylogeography: genetic history of species distribution. (MM)
  • Advantages and disadvantages of mitochondrial DNA and its alternatives (Y chromosom), refugia and colonisation routes, genetic drift vs. gene flow, phylogeography and coevolution.
  • 8. Hybridization in nature, hybrid zones (MM)
  • Construction of clines, selection against hybrids, differences in introgression of various parts of genome
  • 9. Conservation genetics (JB)
  • Non-invasive genetic sampling, probability of identity, estimation of effective population size, identification of bottleneck, consequences of population fragmentation, local adaptation, inbreeding and outbreeding depression
  • 10. Genes and their biological functions - example of functional genes and their importance in ecological studies (JB)
  • Adaptive variation, immunogenetics, genes and communication (MHC, MUPs, ABP), analysis of selection on molecular and population level, the use of "-omics" methods in ecology, expressed-sequence-tags (ESTs)
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 2014, Spring 2015, Spring 2016, Spring 2017, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023, Autumn 2024.
  • Enrolment Statistics (Spring 2013, recent)
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