Review
Almost Forgotten or Latest Practice? AFLP applications, analyses and advances

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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. Technical advances have presented new opportunities for data analysis, and recent studies have addressed specific areas of the AFLP technique, including comparison to other genotyping methods, assessment of errors, homoplasy, phylogenetic signal and appropriate analysis techniques. Here we provide a synthesis of these areas and explore new directions for the AFLP technique in the genomic era, with the aim of providing a review that will be applicable to all AFLP-based studies.

Section snippets

AFLP: an established molecular marker technique

The Amplified Fragment Length Polymorphism (AFLP)* technique has come a long way since its publication in 1995 [1], including many technological advances in generating and analysing AFLP data. AFLP has become the method of choice for many

How do AFLPs compare to other genotyping methods?

The three most common techniques for multilocus genomic fingerprinting are AFLP, random amplified polymorphic DNAs (RAPDs), and inter simple sequence repeats (ISSRs). They are PCR-based techniques that use primers to amplify previously uncharacterized DNA fragments and, therefore, can be used on organisms for which there is no a priori sequence information [26]. These three techniques vary with respect to data quality, genetic variability and discriminatory power 5, 14, 22, 27, 28. All three

Linkage mapping

AFLP data can be linked with other sources of data, including RAPDs, restriction fragment length polymorphisms (RFLPs), and microsatellites to produce linkage maps in established mapping populations (such as potato, barley, rice and Arabidopsis [4]; reviewed in Ref. [30]). AFLP characters that do not deviate from expected 1:1 segregation ratios in a chi-square test are then analysed with specialized software [e.g. MapMaker [34], JoinMap (see http://www.joinmap.nl/)] for linkage analysis. The

Assessment of homoplasy in AFLP data

Homoplasy is a major issue in the analysis and interpretation of AFLP data. It occurs when different accessions are incorrectly scored (Box 3) as having a shared character state as a result of either the co-migration of non-homologous fragments (shared ‘1’ character state), or independent losses of a fragment (shared ‘0’ character state). Consequently, homoplasy results in an underestimation of genetic diversity among samples and a loss of resolution in the analyses 59, 60. However, testing the

Innovative hypothesis testing using AFLP data

So, what does the future hold for the AFLP technique? Novel uses of AFLP data to test evolutionary hypotheses are continually being developed. In an exciting new development for evolutionary studies, the use of AFLPs is moving beyond standard inferences of relationships (e.g. population and phylogenetic) toward assessing, for example, the role of selection in shaping patterns of divergence in wild populations in animals 64, 65 and plants 45, 66, 67. For example, studies using a genomic scan

Will AFLPs be obsolete?

The genomic era has been heralded with massive advances in whole genome sequencing and, although obtaining the first genome for a species can still be challenging, new pyrosequencing techniques [79] have enabled re-sequencing, at least, to become increasingly routine and relatively cost effective. In addition, new large-scale genotyping techniques, such as diversity arrays technology (DArT [80]; see http://www.diversityarrays.com/), have the potential to replace and surpass AFLP and other

Acknowledgements

For performing a literature survey of recent AFLP papers we thank Morore Piripi. For helpful comments on the manuscript we thank Dirk Albach, Jeanne Jacobs, Pete Lockhart, Angela McGaughran, Trish McLenachan, Christian Michel, Mary Morgan-Richards, David Penny, Leon Perrie, Morore Piripi, Kai Stölting, Vaughan Symonds, Steve Trewick, Andrea Weeks, Vincent Woo, and three anonymous referees. For financial support H.M.M. acknowledges the National Science Foundation International Research

Glossary

AFLP genotype
the genetic constitution of an individual inferred from an AFLP fingerprint.
Allele
alternative form of a genetic locus. For a single marker (locus), plus and null alleles, although different, are deemed to be homologous (i.e. possess a common evolutionary origin). When the term ‘allele’ is used across different markers (e.g. to refer to any visualized fragment), it should be clear that these alleles will be derived from different loci, and therefore will be mostly non-homologous.

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