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Statistical analysis of amplified fragment length polymorphism data: a toolbox for molecular ecologists and evolutionists
Author(s) -
Bonin A.,
Ehrich D.,
Manel S.
Publication year - 2007
Publication title -
molecular ecology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.619
H-Index - 225
eISSN - 1365-294X
pISSN - 0962-1083
DOI - 10.1111/j.1365-294x.2007.03435.x
Subject(s) - amplified fragment length polymorphism , biology , population , evolutionary biology , genetics , identification (biology) , toolbox , population genetics , computational biology , genetic diversity , ecology , computer science , demography , sociology , programming language
Recently, the amplified fragment length polymorphism (AFLP) technique has gained a lot of popularity, and is now frequently applied to a wide variety of organisms. Technical specificities of the AFLP procedure have been well documented over the years, but there is on the contrary little or scattered information about the statistical analysis of AFLPs. In this review, we describe the various methods available to handle AFLP data, focusing on four research topics at the population or individual level of analysis: (i) assessment of genetic diversity; (ii) identification of population structure; (iii) identification of hybrid individuals; and (iv) detection of markers associated with phenotypes. Two kinds of analysis methods can be distinguished, depending on whether they are based on the direct study of band presences or absences in AFLP profiles (‘band‐based’ methods), or on allelic frequencies estimated at each locus from these profiles (‘allele frequency‐based’ methods). We investigate the characteristics and limitations of these statistical tools; finally, we appeal for a wider adoption of methodologies borrowed from other research fields, like for example those especially designed to deal with binary data.