Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Record number 372533
Title Collision probabilities for AFLP bands, with an application to simple measures of genetic similarity
Author(s) Gort, G.; Koopman, W.J.M.; Stein, A.; Eeuwijk, F.A. van
Source Journal of Agricultural, Biological, and Environmental Statistics 13 (2008)2. - ISSN 1085-7117 - p. 177 - 198.
DOI https://doi.org/10.1198/108571108X308116
Department(s) Biometris (WU MAT)
PRI Biodiversity and Breeding
PE&RC
Publication type Refereed Article in a scientific journal
Publication year 2008
Keyword(s) fragment length distributions - size homoplasy - markers - lettuce
Abstract AFLP is a frequently used DNA fingerprinting technique that is popular in the plant sciences. A problem encountered in the interpretation and comparison of individual plant profiles, consisting of band presence-absence patterns, is that multiple DNA fragments of the same length can be generated that eventually show up as single bands on a gel. The phenomenon of two or more fragments coinciding in a band within an individual profile is a type of homoplasy, that we call collision. Homoplasy biases estimates of genetic similarity. In this study, we show how to calculate collision probabilities for bands as a function of band length, given the fragment count, the band count, or band lengths. We also determine probabilities of higher order collisions, and estimate the total number of collisions for a profile. Since short fragments occur more often, short bands are more likely to contain collisions. For a typical plant genome and AFLP procedure, the collision probability for the shortest band is 25 times larger than for the longest. In a profile with 100 bands a quarter of the bands may contain collisions, concentrated at the shorter band lengths. All calculations require a careful estimate of the monotonically decreasing fragment length distribution. Modifications of Dice and Jaccard coefficients are proposed. The principles are illustrated on data from a phylogenetic study in lettuce
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