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| Content Provider | Springer Nature Link |
|---|---|
| Author | Gort, Gerrit Koopman, Wim J. M. Stein, Alfred Eeuwijk, Fred A. |
| Copyright Year | 2008 |
| 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. |
| Starting Page | 177 |
| Ending Page | 198 |
| Page Count | 22 |
| File Format | |
| ISSN | 10857117 |
| Journal | Journal of Agricultural, Biological, and Environmental Statistics |
| Volume Number | 13 |
| Issue Number | 2 |
| e-ISSN | 15372693 |
| Language | English |
| Publisher | Springer-Verlag |
| Publisher Date | 2008-01-01 |
| Publisher Place | New York |
| Access Restriction | One Nation One Subscription (ONOS) |
| Subject Keyword | Dice Fragment length distribution Jaccard Occupancy distribution Saddlepoint approximation Size homoplasy Statistics for Life Sciences, Medicine, Health Sciences Agriculture Environmental Monitoring/Analysis Biostatistics |
| Content Type | Text |
| Resource Type | Article |
| Subject | Applied Mathematics Statistics and Probability Environmental Science Agricultural and Biological Sciences Statistics, Probability and Uncertainty |
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