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A Simple method for the detection of size homoplasy among amplified fragment length polymorphism fragments

A Simple method for the detection of size homoplasy among amplified fragment length polymorphism... Polymerase chain reaction (PCR)‐based methods that produce multilocus DNA profiles such as random amplified polymorphic DNAs (RAPDs) and amplified fragment length polymorphisms (AFLPs) ( Vos . 1995 ) have become widely adopted tools for systematic and ecological applications ( Mueller & Wolfenbarger 1999 ). With these multilocus techniques, it is not possible to directly distinguish between loci and alleles in DNA profiles. Consequently, comparative studies rely on the assumption that co‐migrating fragments are homologous. However, size homoplasy can result in a false interpretations of genetic similarity ( Peakall . 1998 ). In an analysis of 220 co‐migrating RAPD fragments in a wild sunflower species complex, a combination of southern hybridization and fragment digestion revealed that only 79.1% were homologous ( Rieseberg 1996 ). Thormann . (1994) showed that all of the 15 RAPD fragments tested for homology by southern hybridization within six Brassica and one Raphanus species were homologous but when comparing between species, three of these 15 fragments were not homologous. The techniques employed in these studies have been powerful in detecting size homoplasy and demonstrating its widespread importance, but for many molecular ecology laboratories they are technically demanding and time consuming. Consequently, size homoplasy is rarely http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Molecular Ecology Wiley

A Simple method for the detection of size homoplasy among amplified fragment length polymorphism fragments

O’Hanlon, Peter C.; Peakall, Rod
Molecular Ecology , Volume 9 (6) – Jun 1, 2000
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References (7)

Publisher
Wiley
Copyright
Copyright © 2000 Wiley Subscription Services, Inc., A Wiley Company
ISSN
0962-1083
eISSN
1365-294X
DOI
10.1046/j.1365-294x.2000.00924.x
Publisher site
See Article on Publisher Site

Abstract

Polymerase chain reaction (PCR)‐based methods that produce multilocus DNA profiles such as random amplified polymorphic DNAs (RAPDs) and amplified fragment length polymorphisms (AFLPs) ( Vos . 1995 ) have become widely adopted tools for systematic and ecological applications ( Mueller & Wolfenbarger 1999 ). With these multilocus techniques, it is not possible to directly distinguish between loci and alleles in DNA profiles. Consequently, comparative studies rely on the assumption that co‐migrating fragments are homologous. However, size homoplasy can result in a false interpretations of genetic similarity ( Peakall . 1998 ). In an analysis of 220 co‐migrating RAPD fragments in a wild sunflower species complex, a combination of southern hybridization and fragment digestion revealed that only 79.1% were homologous ( Rieseberg 1996 ). Thormann . (1994) showed that all of the 15 RAPD fragments tested for homology by southern hybridization within six Brassica and one Raphanus species were homologous but when comparing between species, three of these 15 fragments were not homologous. The techniques employed in these studies have been powerful in detecting size homoplasy and demonstrating its widespread importance, but for many molecular ecology laboratories they are technically demanding and time consuming. Consequently, size homoplasy is rarely

Journal

Molecular Ecology – Wiley

Published: Jun 1, 2000

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