Skip to main content
SpringerLink
Log in

In Silico Fingerprinting (ISIF): A User-Friendly In Silico AFLP Program

  • Protocol
  • First Online:
Data Production and Analysis in Population Genomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 888))

Abstract

The Amplified fragment Length Polymorphism (AFLP) is one of the cost-effective and useful fingerprinting techniques to study non-model species. One crucial AFLP step in the AFLP procedure is the choice of restriction enzymes and selective bases providing good-quality AFLP profiles. Here, we present a user-friendly program (ISIF) that allows carrying out in silico AFLPs on species for which whole genome sequences are available. Carrying out in silico analyses as preliminary tests can help to optimize the experimental work by allowing a rapid screening of candidate restriction enzymes and the combinations of selective bases to be used. Furthermore, using in silico AFLPs is of great interest to limit homoplasy and amplification of repetitive elements to target genomic regions of interest or to optimize complex and costly high-throughput genomic experiments.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 139.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  1. Vos P, Hogers R, Bleeker M et al (1995) AFLP – a new technique for DNA-fingerprinting. Nucleic Acids Res 23:4407–4414

    Article  PubMed  CAS  Google Scholar 

  2. Bonin A, Pompanon F, Taberlet P (2005) Use of amplified fragment length polymorphism (AFLP) markers in surveys of vertebrate diversity. Mol Evol 395:145–161

    CAS  Google Scholar 

  3. Paris M, Boyer S, Bonin A et al (2010) Genome scan in the mosquito Aedes rusticus: population structure and detection of positive selection after insecticide treatment. Mol Ecol 19:325–337

    Article  PubMed  Google Scholar 

  4. Pompanon F, Bonin A, Bellemain E, Taberlet P (2005) Genotyping errors: causes, consequences and solutions. Nat Rev Genet 6:847–859

    Article  PubMed  CAS  Google Scholar 

  5. Bonin A, Bellemain E, Eidesen PB et al (2004) How to track and assess genotyping errors in population genetics studies. Mol Ecol 13:3261–3273

    Article  PubMed  CAS  Google Scholar 

  6. Conord C, Lemperiere G, Taberlet P, Despres L (2006) Genetic structure of the forest pest Hylobius abietis on conifer plantations at different spatial scales in Europe. Heredity 97:46–55

    Article  PubMed  CAS  Google Scholar 

  7. Fink S, Fischer MC, Excoffier L, Heckel G (2010) Genomic scans support repetitive continental colonization events during the rapid radiation of voles (Rodentia: Microtus): the utility of AFLPs versus mitochondrial and nuclear sequence markers. Syst Biol 59:548–572

    Article  PubMed  CAS  Google Scholar 

  8. Karrenberg S, Favre A (2008) Genetic and ecological differentiation in the hybridizing campions Silene dioica and S. latifolia. Evolution 62:763–773

    Article  PubMed  Google Scholar 

  9. Meyer CL, Vitalis R, Saumitou-Laprade P, Castric V (2009) Genomic pattern of adaptive divergence in Arabidopsis halleri, a model species for tolerance to heavy metal. Mol Ecol 18:2050–2062

    Article  PubMed  Google Scholar 

  10. Mraz P, Gaudeul M, Rioux D et al (2007) Genetic structure of Hypochaeris uniflora (Asteraceae) suggests vicariance in the Carpathians and rapid post-glacial colonization of the Alps from an eastern Alpine refugium. J Biogeogr 34:2100–2114

    Article  Google Scholar 

  11. Nosil P, Egan SP, Funk DJ (2008) Heterogeneous genomic differentiation between walking-stick ecotypes: “isolation by adaptation” and multiple roles for divergent selection. Evolution 62: 316–336

    Article  PubMed  Google Scholar 

  12. Poncet BN, Herrmann D, Gugerli F et al (2010) Tracking genes of ecological relevance using a genome scan in two independent regional population samples of Arabis alpina. Mol Ecol 19:2896–2907

    Article  PubMed  CAS  Google Scholar 

  13. Puscas M, Choler P, Tribsch A et al (2008) Post-glacial history of the dominant alpine sedge Carex curvula in the European Alpine System inferred from nuclear and chloroplast markers. Mol Ecol 17:2417–2429

    Article  PubMed  CAS  Google Scholar 

  14. Tilquin M, Paris M, Reynaud S et al (2008) Long lasting persistence of Bacillus thuringiensis subsp israelensis (Bti) in mosquito natural habitats. PLoS One 3:10

    Article  Google Scholar 

  15. Arrigo N, Holderegger R, Alvarez N (2012) Automated scoring of AFLPs using RawGeno v 20, a free R CRAN library. In: Bonin A, Pompanon F (eds) Data Production and Analysis in Population Genomics, Methods in Mol Biol Series, Humana Press

    Google Scholar 

  16. Arrigo N, Tuszynski JW, Ehrich D et al (2009) 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 10:33

    Article  PubMed  Google Scholar 

  17. Herrmann D, Poncet BN, Manel S et al (2010) Selection criteria for scoring amplified fragment length polymorphisms (AFLPs) positively affect the reliability of population genetic parameter estimates. Genome 53:302–310

    Article  PubMed  CAS  Google Scholar 

  18. Bonin A, Ehrich D, Manel S (2007) Statistical analysis of amplified fragment length polymorphism data: a toolbox for molecular ecologists and evolutionists. Mol Ecol 16:3737–3758

    Article  PubMed  CAS  Google Scholar 

  19. Foll M, Fischer MC, Heckel G, Excoffier L (2010) Estimating population structure from AFLP amplification intensity. Mol Ecol 19:4638–4647

    Article  PubMed  CAS  Google Scholar 

  20. Caballero A, Quesada H (2010) Homoplasy and distribution of AFLP fragments: an analysis in silico of the genome of different species. Mol Biol Evol 27:1139–1151

    Article  PubMed  CAS  Google Scholar 

  21. Caballero A, Quesada H, Rolan-Alvarez E (2008) Impact of amplified fragment length polymorphism size homoplasy on the estimation of population genetic diversity and the detection of selective loci. Genetics 179:539–554

    Article  PubMed  Google Scholar 

  22. Paris M, Bonnes B, Ficetola GF et al (2010) Amplified fragment length homoplasy: in silico analysis for model and non-model species. BMC Genomics 11:287

    Article  PubMed  Google Scholar 

  23. Vekemans X, Beauwens T, Lemaire M, Roldan-Ruiz I (2002) 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 11: 139–151

    Article  PubMed  CAS  Google Scholar 

  24. Bonin A, Paris M, Despres L et al (2008) A MITE-based genotyping method to reveal hundreds of DNA polymorphisms in an animal genome after a few generations of artificial selection. BMC Genomics 9:459

    Article  PubMed  Google Scholar 

  25. Bonin A, Paris M, Tetreau G et al (2009) Candidate genes revealed by a genome scan for mosquito resistance to a bacterial insecticide: sequence and gene expression variations. BMC Genomics 10:551

    Article  PubMed  Google Scholar 

  26. Paris M, Meyer C, Blassiau C et al (2012) Two methods to easily obtain nucleotide sequences from AFLP loci of interest. In: Bonin A, Pompanon F (eds) Data Production and Analysis in Population Genomics. Methods in Mol Biol Series, Humana Press

    Google Scholar 

  27. Van Orsouw NJ, Hogers RJ, Janssen A et al (2007) Complexity reduction of polymorphic sequences (CRoPS (TM)): a novel approach for large-scale polymorphism discovery in complex genomes. PLoS One 2:11

    Google Scholar 

  28. Baird NA, Etter PD, Atwood TS et al (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One 3:10

    Article  Google Scholar 

  29. Hohenlohe PA, Bassham S, Etter PD et al (2010) Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags. PLoS Genet 6:2

    Article  Google Scholar 

  30. R Development Core Team (2005) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. http://www.R-project.org, ISBN 3-900051-900007-900050

Download references

Acknowledgments

This work was supported by a grant from the French Rhône-Alpes region (grant 501545401) and by the French National Research Agency (project ANR-08-CES-006-01 DIBBECO).

Author information

Authors and Affiliations

  1. Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland

    Margot Paris

  2. Laboratoire d’Ecologie Alpine, UMR CNRS 5553, Université Joseph Fourier, Grenoble, France

    Laurence Després

Authors
  1. Margot Paris
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Laurence Després
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Margot Paris .

Editor information

Editors and Affiliations

  1. , Laboratoire d'Ecologie Alpine, Université Grenoble I, CNRS-UMR5553, rue de la Piscine 2233, Grenoble Cedex 09, 38041, France

    François Pompanon

  2. Laboratoire d'Ecologie Alpine, Université Grenoble 1, Rue de la Piscine 2233, Grenoble, 38041, France

    Aurélie Bonin

Rights and permissions

Reprints and permissions

Copyright information

© 2012 Springer Science+Business Media New York

About this protocol

Cite this protocol

Paris, M., Després, L. (2012). In Silico Fingerprinting (ISIF): A User-Friendly In Silico AFLP Program. In: Pompanon, F., Bonin, A. (eds) Data Production and Analysis in Population Genomics. Methods in Molecular Biology, vol 888. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-870-2_4

Download citation

  • DOI: https://doi.org/10.1007/978-1-61779-870-2_4

  • Published:

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-61779-869-6

  • Online ISBN: 978-1-61779-870-2

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation