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 2018/2019 the lecture is taught on Wednesday 9:00am 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):


Lecture overview
(topics in the grey colour are versions from last year and not yet updated)

   

*.pdf

Theme

Paper

population

systematic

presentation
1 10.10.

molecular markers - characteristics, differences, technique overview
2 17.10.

molecular markers - overview of possible applications and questions
3 24.10.

isozymes - electrophoresis, evaluation of codominant data, population genetics

 

 

4 31.10.

DNA - structure, PCR techniques, applications, dominant markers (AFLP, RAPD, ISSRs...), data evaluation

 

 

5 7.11.   restriction techniques (RFLP, PCR-RFLP), cpDNA, phylogeography  
6 14.11.   microsatellites - nuclear, chloroplast, isolation, data evaluation, applications      
7 21.11.   Sanger sequencing - chloroplast DNA, genes and non-coding regions sequencing    
8 28.11.   sequencing II - nuclear DNA, rDNA, ITS, low-copy markers  
9 5.12.   NGS (next-generation sequencing) - overview and examples, applications
10 12.12. HybSeq - enrichment methods, genome skimming, phylogenomics, species trees
11 19.12.  
12 2.1.2019   student presentations, exam…      

 

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. isozyme analysis
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

3. DNA, PCR, RAPD
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
 

4. AFLP
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
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
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. next generation sequencing
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.

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