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The Allan Wilson Centre AFLP Page is intended as a resource for researchers who are currently using, or considering using, the AFLP technique in their research. Included below are:
The latest version of our lab’s AFLP protocol
Genotyping Utilities Package: scripts for manipulating and analysing GeneMapper & GeneMarker data
Data Sets and Python Scripts for Holland, Clarke & Meudt (2008)
AFLP-based publications from Allan Wilson Centre researchers
Links to useful AFLP and AFLP-related websites
Amplified fragment length polymorphism (AFLP) DNA fingerprinting is a firmly established molecular marker technique, with broad applications in population genetics, shallow phylogenetics, linkage mapping, parentage analyses, and single-locus PCR marker development. Our particular interests are:
- Using AFLPs to reconstruct plant evolutionary relationships:
— especially using phylogenetics,
— when hybridisation is occurring,
— when polyploid taxa are present, and
— for very shallow radiations (e.g., crop plants).
- Improvement/optimisation of the fluorescent AFLP (fAFLP) technique:
— to allow high-throughput capillary electrophoresis of hundreds of samples.
- Research into optimising automated AFLP scoring:
— so that scoring can be performed quickly, and
— to produce data with maximum resolution and minimum error.
- Development of multilocus fingerprinting-derived sequencing markers:
— both from AFLPs and inter simple sequence repeats (ISSRs).
AFLP Protocol
Our lab’s protocol for Amplified Fragment Length Polymorphism (AFLP) fingerprinting. We label all our AFLPs with fluorescent dyes (fluorophores) and electrophorese them on an ABI 3730 Genetic Analyzer.
We have done our best to ensure this protocol is as robust and accurate as possible but it should be treated as a guide only. If you have any queries, or suggestions for improvement, please e-mail Andrew Clarke. We would appreciate your feedback.
If using these protocols, a brief attribution note and a link to our website would be appreciated, e.g., “AFLP method based on a protocol by Andrew Clarke & Heidi Meudt, Allan Wilson Centre for Molecular Ecology and Evolution, New Zealand. http://awcmee.massey.ac.nz/aflp/aflp.html.” |
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Version 5 |
Genotyping Utilities Package
The Genotyping Utility Package contains the following programs:
GenoTyper Rearranger (GTR)
GenoTyper Rearranger (GTR) is a utility that converts the output AFLP data from genotyping programs (currently Applied Biosystems’ GeneMapper® and SoftGenetics’ GeneMarker®) to various formats, allowing easier display and manipulation.
GTR can produce several types of output formats, include NEXUS format, an Octave-compatible height matrix and its own ‘gtr’ format. The ability to output in a format compatible with JoinMap® will be added.
An explanation of the available options can be found here.
AFLP Replicate Difference Calculator
AFLP Replicate Difference Calculator is a utility that calculates the difference of some parameter (peak height, for example) between replicates in a table of AFLP data. This script takes two inputs: the AFLP data and a table that declares which samples are replicates of which other samples.
An explanation of the available options can be found here.
Replicate Error Finder
Replicate Error Finder is a utility that simulates the manual scoring process by locating and removing errors between replicates.
An explanation of the available options can be found here.
Binning Error Visualisation
An explanation of the available options can be found here.
GUP GUI
An explanation of the available options can be found here.
Data Sets and Python Scripts for Holland, Clarke & Meudt (2008)
These NEXUS files and scripts are for analyses described in Holland, Clarke & Meudt (2008):
Holland, B. R., Clarke, A. C., and Meudt, H. M. 2008. Optimizing automated AFLP scoring parameters to improve phylogenetic resolution. Systematic Biology 57: 347–366.
The scripts can be used for:
— calculating error rates (both Euclidean and Jaccard),
— calculating resolution scores,
— calculating normalised resolution scores,
— checking robustness of the tree, and
— checking if replicates have been paired correctly.
NEXUS files and scripts can found be here. Complete instructions for running the scripts are included.
Publications
These publications from Allan Wilson Centre researchers focus on AFLP and related techniques.
A Note on Access: We are currently linking to the PDF on the journal website rather than uploading a copy here. If you cannot access the paper, please e-mail the corresponding author for a copy.
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Holland, B. R., Clarke, A. C., and Meudt, H. M. 2008. Optimizing automated AFLP scoring parameters to improve phylogenetic resolution. Systematic Biology 57: 347–366. |
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Meudt, H. M., and Clarke, A. C. 2007. Almost Forgotten or Latest Practice? AFLP applications, analyses and advances. Trends in Plant Science 12: 106–117. |
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Subscription
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Clarke, A. C., Burtenshaw, M. K., McLenachan, P. A., Erickson, D. L., and Penny, D. 2006. Reconstructing the origins and dispersal of the Polynesian bottle gourd (Lagenaria siceraria). Molecular Biology and Evolution 23: 893–900.
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McLenachan, P. A., Stöckler, K., Winkworth, R. C., McBreen, K., Zauner, S., and Lockhart, P. J. 2000. Markers derived from amplified fragment length polymorphism gels for plant ecology and evolution studies. Molecular Ecology 9: 1899–1903. |
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Subscription
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Useful Links
Links to AFLP websites and websites about new multilocus genotyping techniques.
Amplified Fragment Length Polymorphisms and Microsatellites: A Phylogenetic Perspective
Robinson, J. P., and Harris, S. A. 1999. Amplified fragment length polymorphisms and microsatellites: a phylogenetic perspective. In Gillet, E. M. (Ed.), Which DNA Marker for Which Purpose?, pp. 1–27. Institut für Forstgenetik und Forstpflanzenzüchtung, Universität Göttingen: Göttingen, Germany.
Complexity Reduction of Polymorphic Sequences (CRoPS)
A new technique for polymorphism discovery which combines AFLP with recently-developed pyrosequencing technology.
Diversity Arrays Technology (DArT)
A genotyping technique for isolating polymorphic sequences using microarrays.
Plant DNA C-values Database, Royal Botanic Gardens, Kew
The RBG, Kew’s database of C-values is helpful for predicting the appropriate length of AFLP selective primers.
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