Theme
Paper
population
systematic
Use of molecular markers in plant systematics and population biology
Term: winter
Hour per week: 3/0
Credits: 3
Good to know before entering the course: basics of population biology,
elementary molecular biology
Moodle: enroll to the course MB120P44 (need to be logged in with CAS password) using enrollment2024 method (and password provided during the first lesson)
In 2024/2025 the lecture is taught on Wednesday 10:10am in seminarium (Benatska 2, 2nd floor, at the end of the corridor).
Practical courses to the lecture (in DNA lab) is divided to two blocks (weeks):
Examination:
- two small tests (10
multiple-choice questions each)
- first test: 20.11.2024,
9:30 (18-21 points: mark 1, 16-17 points: mark 2, 15 points: mark 3, 0-14 point:
not pass and need to repeat) - 25%
- second
test 18.12.2024
(10:00) or 8.1.2025
(11:00)
or 15.1.2025
(from 9:00) (14-15 points: mark 1, 12-13 points: mark 2, 10-11 points: mark 3, 0-10
point: not pass and need to repeat) - 25%
- four small tasks
(calculations) to be submitted via Moodle
- presentation of a
scientific paper of own choice (but approved...) - 50%
-
presentation schedule and papers for download
is here
Lecture overview
(topics in the grey colour are versions from last
year and not yet updated)
Lecture structure
Literature and internet materials
1. molecular markers - general reviews
Avise J.C. (2004): Molecular
markers, natural history and evolution.
Baker A.J. (2000): Molecular methods in ecology.
Beebee T. & Rowe G. (2004): An introduction to molecular ecology.
Caetano-Anollés G. & Gresshoff P.M. (1998): DNA markers. Protocols,
applications, and overviews.
DeSalle R. & Schierwater (1998): Molecular Approaches to Ecology and
Evolution.
Henry R.J. (2001): Plant genotyping. The DNA fingerprinting of plants.
Karp A. et al. (1998): Molecular tools for screening biodiversity.
Lowe A., Harris S. & Ashton P. (2004): Ecological Genetics: Design,
Analysis, and Application.
Weising K. et al. (2005): DNA fingerprinting in plants. Principles,
methods, and applications. 2nd edition.
Karp A. et al. (1996): Molecular techniques in the assesment of botanical
diversity. Annals of Botany 78:143-149
Ouborg N.J. et al. (1999): Population genetics, molecular markers and the study
of dispersal in plants. J. Ecol. 87:551-568.
Parker G.P. et al. (1998): What molecules can tell us about populations:
Choosing and using a molecular marker. Ecology 79: 361-382
Vekemans X. & Jacquemart A.-L.(1997): Perspectives on the use of molecular
markers in plant population biology. Belg. J. Bot. 129:91-100
2. molecular markers - applications questions
3. isozyme analysis, intro to population genetics
Soltis & Soltis [eds.] (1989): Isozymes in plant biology.
Baker A.J. (2000): Molecular methods in ecology.
Hartl & Clark (1997): Principles of Population Genetics.
Karp A. et al. (1998): Molecular tools for screening biodiversity.
Hamrick, Godt, Murawski & Loveless (1991): Correlations between species
traits and allozyme diversity: Implications for conservation biology. pp.
75-86. In: Falk & Holsinger [eds.]: Genetics and Conservation of Rare Plants
enzyme database: http://www.brenda-enzymes.org/
gel evaluation: http://www.science.siu.edu/plant-biology/PLB420/Index.LabTechniques.html
4. DNA, PCR, dominant markers (RAPD, AFLP...)
Harris S.A. (1999): RAPDs in systematics – a useful methodology ? In:
Hollingsworth & al. [eds.]: Molecular systematics and plant evolution, pp.
211-228
Wolfe A.D. & Liston A. (1998): Contributions of PCR-based methods to plant
systematics and evolutionary biology. In: Soltis D.E. & al. [eds.]:
Molecular systematics of plants. II. DNA sequencing, pp. 43-86
Vos P. et al. (1995): AFLP: a new technique for DNA fingerprinting.
Nucleic Acids Research, 23(21):4407-4414
Mueller U.G., Wolfenbarger L.L. (1999): AFLP genotyping and fingerprinting.
Trends in Ecology & Evolution 14:389-394
Robinson J.P. & Harris S.A. (1999): Amplified Fragment Length
Polymorphisms and Microsatellites: A phylogenetic perspective. In: Gillet E.M.[ed.]:
Which DNA Marker for Which Purpose? (http://webdoc.sub.gwdg.de/ebook/y/1999/whichmarker/index.htm)
5. RFLP, PCR-RFLP, cpDNA, phylogeography
Palmer J.D. (1986): Isolation and structural analysis of chloroplast DNA.
Methods in Enzymology 118:167-186
McCauley D.E. (1995): The use of chloroplast DNA polymorphism in studies of
gene flow in plants. Trends in Ecology & Evolution 10(5): 198-202
Newton A.C. et al. (1999): Molecular phylogeography, intraspecific variation
and the conservation of tree species. Trends in Ecology & Evolution
14(4):140-145
Avise J.C. (1994): Molecular
markers, natural history and evolution. pp. 57-78 (Restriction analyses etc.)
Ennos R.A. et al. (1999): Using organelle markers to elucidate the history,
ecology and evolution of plant populations. In:
Hollingsworth & al. [eds.]: Molecular systematics and plant evolution, pp.
211-228
6. microsatellites (SSRs)
Goldstein D.B. & Schlötterer Ch. (1999): Microsatellites. Evolution and
Applications. Oxford University Press
Hajerr A., Worthington J. & John S. [eds.] (2000): SNP and microsatellite
genotyping. Markers for genetic analysis. Eaton Publishing
Jarne P. & Lagoda P.J.L. (1996): Microsatelites, from molecules to
populations and back. Trends in Ecology & Evolution 11(10):424-429
Provan J. et al. (2001): Chloroplast microsatellites: new tools for studies
in plant ecology and evolution. Trends in Ecology & Evolution
16(3):142-147
Lulkart G. & England P.R. (1999): Statistical analysis of microsatellite
DNA data. Trends in Ecology & Evolution 14(7):253-256
Balloux F. & Lugon-Moulin N. (2002): The estimation of population
differentiation with microsatellite markers. Molecular Ecology 11:155-165
Robinson J.P. & Harris S.A. (1999): Amplified Fragment Length
Polymorphisms and Microsatellites: A phylogenetic perspective. In: Gillet E.M.[ed.]:
Which DNA Marker for Which Purpose? http://webdoc.sub.gwdg.de/ebook/y/1999/whichmarker/index.htm
Zane L. et al. (2002): Strategies for microsatelite isolation: a review.
Molecular Ecology 11: 1-16
Li Y.-Ch. et al. (2002): Microsatellites: genomic distribution, putative
function and mutational mechanisms: a review. Molecular Ecology 11:2453-2465
Jones A.G. & Ardren W.R. (2003): Methods of parentage analysis in natural
populations. Molecular Ecology 12:2511-2523
7. DNA sequencing, organellar DNA
Soltis D.E. & al. [eds.] (1998): Molecular systematics of plants.II. DNA
sequencing.
Hollingsworth & al. [eds.] (1999): Molecular systematics and plant
evolution.
Hall B.G. (2001): Phylogenetic trees made easy.
Felsenstein J. (2004): Inferring phylogenies.
Mount D.W. (2004): Bioinformatics. Sequence and genome analysis.
Salemi M. & Vandamme A.-M. (2003): The phylogenetic handbook. A
practical approach to DNA and protein phylogeny.
Alvarez I. & Wendel J.F. (2003): Ribosomal ITS sequences and plant
phylogenetic inference. Molecular Phylogenetics and Evolution 29: 417–434
8. DNA sequencing, nuclear DNA
9. NGS (next generation sequencing) - overview, applications
Metzker M.L. (2010) Sequencing technologies – the next generation. Nature
Reviews Genetics, 11, 31–46
Bräutigam A. & Gowik U. (2010): What can next generation sequencing do for
you? Next generation sequencing as a valuable tool in plant research. Plant
Biology, 12, 831–841
Ansorge W.J. (2009): Next-generation DNA sequencing techniques. New
Biotechnology, 25, 195–203
Glenn T.C. (2011): Field guide to next-generation DNA sequencers. Molecular
Ecology Resources, 11, 759–769.
10. Hyb-Seq, phylogenomis
11. RADseq, population genomics
databases:
GenBank (NCBI): http://www.ncbi.nlm.nih.gov/
EMBL: http://www.ebi.ac.uk/embl/
Software
Other web resources
database of published microsatellite primers
DNA laboratory of the Department of Botany, Charles University, Prague