Evaluating the impact of scoring parameters on the structure of intra-specific genetic variation using RawGeno, an R package for automating AFLP scoring

BMC Bioinformatics

Volumn 10, Issue , 2009, Pages

  Arrigo, Nils ^a   Tuszynski, Jarek W ^b   Ehrich, Dorothee ^c   Gerdes, Tommy ^d   Alvarez, Nadir ^a  

^a UNIVERSITY OF NEUCHÂTEL   (Switzerland)

^b SCIENCE APPLICATIONS INTERNATIONAL CORPORATION   (United States)

^c UNIVERSITY OF TROMSØ   (Norway)

^d University of Copenhagen   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

DESCRIPTIVE STATISTICS; DISCRIMINATORY POWER; EVOLUTIONARY BIOLOGISTS; GENETIC VARIATION; INFORMATION CONTENTS; POPULATION GENETICS; REPLICATED SAMPLES; SCORING ALGORITHMS;

ALGORITHMS; ERRORS; ESTIMATION; GENES;

OPTIMIZATION;

ALGORITHM; AMPLIFIED FRAGMENT LENGTH POLYMORPHISM; ARTICLE; BIOLOGY; COMPUTER PROGRAM; GENETIC VARIABILITY; HETEROZYGOTE; METHODOLOGY;

ALGORITHMS; AMPLIFIED FRAGMENT LENGTH POLYMORPHISM ANALYSIS; COMPUTATIONAL BIOLOGY; GENETIC VARIATION; HETEROZYGOTE; SOFTWARE;

EID: 62849124709     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-33     Document Type: Article

References (26)

1. Avise JC Molecular markers, natural history, and evolution Sunderland: Sinauer 2004
2. Karp A Seberg O Buiatti M Molecular techniques in the assessment of botanical diversity Ann Bot 1996, 78:143-149. 10.1006/anbo.1996.0106
3. Botstein D White RL Skolnick M Davis RW Construction of a genetic-linkage map in man using Restriction Fragment Length Polymorphisms Am J Hum Genet 1980, 32:314-331. 1686077 6247908
4. Williams JGK Kubelik AR Livak KJ Rafalski JA Tingey SV DNA polymorphisms amplified by arbitrary primers are useful as genetic-markers Nucleic Acids Res 1990, 18:6531-6535. 332606 1979162 10.1093/nar/18.22.6531
5. Tautz D Hypervariability of simple sequences as a general source for polymorphic DNA markers Nucleic Acids Res 1989, 17:6463-6471. 318341 2780284 10.1093/nar/17.16.6463
6. Vos P Hogers R Bleeker M Reijans M Vandelee T Hornes M Frijters A Pot J Peleman J Kuiper M Zabeau M AFLP - A new technique for DNA-fingerprinting Nucleic Acids Res 1995, 23:4407-4414. 307397 7501463 10.1093/nar/23.21.4407
7. Vos P Kuiper M AFLP analysis DNA markers: Protocols, Applications and Overviews New-York: J. Wiley & Sons Caetano-Anolles G, Gresshoff PM 1997:115-131.
8. Pompanon F Bonin A Bellemain E Taberlet P Genotyping errors: Causes, consequences and solutions Nat Rev Genet 2005, 6:847-859. 10.1038/ nrg1707 16304600
9. Meudt HM Clarke AC Almost forgotten or latest practice? AFLP applications, analyses and advances Trends Plant Sci 2007, 12:106-117. 10.1016/j.tplants.2007.02.001 17303467
10. Benham J Jeung JU Jasieniuk M Kanazin V Blake T Genographer: A graphical tool for automated AFLP and microsatellite analysis J Agric Genomics 1999, 4:3.
11. Bonin A Bellemain E Bronken Edeisen P Pompanon F Brochmann C Taberlet P How to track and assess genotyping errors in population genetics studies Mol Ecol 2004, 13:3261-3273. 10.1111/j.1365-294X.2004.02346.x 15487987
12. DeHaan LR Antonides R Belina K Ehlke NJ Peakmatcher: Software for semi-automated fluorescence-based AFLP Crop Science 2002, 42:1361-1364.
13. Vekemans X Beauwens T Lemaire M Roldan-Ruiz I Data from amplified fragment length polymorphism (AFLP) markers show indication of size homoplasy and of a relationship between degree of homoplasy and fragment size Mol Ecol 2002, 11:139-151. 10.1046/j.0962-1083.2001.01415.x 11903911
14. Whitlock R Hipperson H Mannarelli M Butlin RK Burke T An objective, rapid and reproducible method for scoring AFLP peak-height data that minimizes genotyping error Mol Ecol Res 2008, 8:725-735. 10.1111/ j.1755-0998.2007.02073.x
15. Holland BR Clarke AC Meudt HM Optimizing automated AFLP scoring parameters to improve phylogenetic resolution Syst Biol 2008, 57:347-366. 10.1080/10635150802044037 18570031
16. Wu BL Liu NJ Zhao HY PSMIX: An R package for population structure inference via maximum likelihood method BMC Bioinformatics 2006, 7:317-325. 1550430 16792813 10.1186/1471-2105-7-317
17. The caMassClass 1.0. Library (Tuszynski 2003) http://cran.r-project.org/ web/packages/
18. Gugerli F Englisch T Niklfeld H Tribsch A Mirek Z Ronikier M Zimmermann NE Holderegger R Taberlet P Relationships among levels of biodiversity and the relevance of intraspecific diversity in conservation - a project synopsis Perspect Plant Ecol 2008, 10:259-281. 10.1016/ j.ppees.2008.07.001
19. Bonin A Ehrich D Manel S Statistical analysis of amplified fragment length polymorphism data: A toolbox for molecular ecologists and evolutionists Mol Ecol 2007, 16:3737-3758. 10.1111/ j.1365-294X.2007.03435.x 17850542
20. Gilder JR Ford S Doom TE Raymer ML Krane DE Systematic differences in electropherogram peak heights reported by different versions of the GeneScan® Software J Forensic Sci 2004, 49:92-95. 10.1520/JFS2003001 14979350
21. Legendre P Legendre L Numerical ecology Amsterdam: Elsevier 2000
22. Vegan: Community ecology package (Oksanen et al. 2008) http://cc.oulu.fi/~jarioksa/softhelp/vegan.html
23. Hadfield JD Richardson DS Burke T Towards unbiased parentage assignment: combining genetic, behavioural and spatial data in a Bayesian framework Mol Ecol 2006, 15:3715-3730. 10.1111/j.1365-294X.2006.03050.x 17032269
24. AFLP-SURV version 1.0. (Vekemans 2002) http://www.ulb.ac.be/sciences/ ecoevol/aflp-surv.html
25. Ehrich D AFLPdat: A collection of R functions for convenient handling of AFLP data Mol Ecol Notes 2006, 6:603-604. 10.1111/ j.1471-8286.2006.01380.x
26. Caballero A Quesada H Rolan-Alvarez E Impact of Amplified Fragment Length Polymorphism size homoplasy on the estimation of population genetic diversity and detection of selective loci Genetics 2008, 179:539-544. 2390631 18493070 10.1534/genetics.107.083246