Use of molecular markers in plant systematics and population biology

for Czech version click here

Term: winter
Hour per week: 3/0 
Credits: 3
Good to know before entering the course: basics of population biology, elementary molecular biology

In 2023/2024 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):

• 1st block (TBA) - basic introduction to the work in DNA lab (DNA extraction, electrophoresis, PCR, PCR-RFLP, dominant markers data evaluation) - protocols and provisional program is here (in Czech!!!)
• 2nd block (TBA) - DNA sequencing, microsatellites, analysis of primary data, microsatellite and sequencing data evaluation (incl. NGS data)... - webpage of the practical course is  here

Examination:
- two small tests (10 multiple-choice questions each)
    - first test: 15.11.2023, 9:45 (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 20.12.2023 (10:00) or 3.1.2024 (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%
- 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)

		*.pdf	Theme	Paper
				population	systematic	presentation
1	4.10.		Molecular markers - characteristics, differences, technique overview
2	11.10.		Molecular markers - overview of possible applications and questions
3	18.10.		Isozymes - electrophoresis, evaluation of codominant data, population genetics
4	25.10.		DNA - structure, PCR techniques, applications, dominant markers (AFLP, RAPD, ISSRs...), data evaluation
5	1.11.		Restriction techniques (RFLP, PCR-RFLP), cpDNA, mtDNA, phylogeography
6	8.11.		Microsatellites - nuclear, chloroplast, development, data evaluation, applications
7	15.11.		Sanger sequencing - chloroplast DNA, genes and non-coding regions sequencing
8	22.11.		Sequencing II - nuclear DNA, rDNA, ITS, low-copy markers
9	29.11.		NGS (next-generation sequencing) - overview and examples, applications
10	6.12.		HybSeq - enrichment methods, genome skimming, phylogenomics, species trees
11	13.12.		RADseq - population genomics
12	3.1.2024		student presentations, exam…

Lecture structure

• introduction to the particular technique, other theory
• examples of the data produced by the particular method, data evaluation
• examples of different applications and solving of various problems (systematics and population biology of plants)
• journal paper(s) - read until next lecture, then its presentation and discussion

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

• FSTAT: http://www2.unil.ch/popgen/softwares/fstat.htm
  population genetic parameters from alelic data (isozymes, microsatellites)
  
• POPGENE: http://www.ualberta.ca/~fyeh/
  population genetic parameters for codominant and dominant data (RAPD, AFLP ...)
• GDA (Genetic Data Analysis): http://lewis.eeb.uconn.edu/lewishome/downloads/gda-1.1.win32.exe
  population genetic parameters
• Arlequin: http://anthro.unige.ch/arlequin
  AMOVA (Analysis of MOlecular VAriance) and many other methods
• R package: http://www.fas.umontreal.ca/BIOL/Casgrain/en/labo/R/v4/index.html
  multidimensional and spatial analysis (PCA, PCoA, Mantel test, correlograms...)
  (Macintosh version only, possible emulation on PC :-)
  
• PAUP (Phylogenetic Analysis Using Parsimony and other methods): http://paup.csit.fsu.edu/index.html
  distance based, parsimony and maximum likelihood methods
  
• TREECON: http://www.psb.rug.ac.be/bioinformatics/psb/Userman/treeconw.html
  tree computation and drawing (sequences, dominant and codominant data)
  
• MICROSAT: http://hpgl.stanford.edu/projects/microsat/programs/msat2.exe
  population genetic parameters for microsatellites
  
• MSA (Microsatellite Analyser): http://i122server.vu-wien.ac.at/MSA/MSA_download.html
  population genetic parameters for microsatellites
  
• MrBayes: http://morphbank.ebc.uu.se/mrbayes/
  Bayesian analysis of phylogenetic data
  
• CERVUS: http://helios.bto.ed.ac.uk/evolgen/cervus/cervus.html
  parentage analysis for codominant data
  
• BAPS (Bayesian Analysis of Population Structure): http://www.rni.helsinki.fi/~jic/bapspage.html
  Bayesian population and individual for codominant and dominant markers
  
• SPAGeDi (Spatial Pattern Analysis of Genetic Diversity): http://www.ulb.ac.be/sciences/ecoevol/spagedi.html
  spatial analysis of genetic structure of populations and individuals (for codominant and dominant markers and for different ploidy levels)
  
• HICKORY: http://darwin.eeb.uconn.edu/hickory/hickory.html
  Bayesian analysis of population genetic data

 Other web resources

database of published microsatellite primers

DNA laboratory of the Department of Botany, Charles University, Prague