Data from amplified fragment length polymorphism (AFLP) markers show indication of size homoplasy and of a relationship between degree of homoplasy and fragment size

Molecular Ecology
X VekemansI Roldán-Ruiz

Abstract

We investigate the distribution of sizes of fragments obtained from the amplified fragment length polymorphism (AFLP) marker technique. We find that empirical distributions obtained in two plant species, Phaseolus lunatus and Lolium perenne, are consistent with the expected distributions obtained from analytical theory and from numerical simulations. Our results indicate that the size distribution is strongly asymmetrical, with a much higher proportion of small than large fragments, that it is not influenced by the number of selective nucleotides nor by genome size but that it may vary with genome-wide GC-content, with a higher proportion of small fragments in cases of lower GC-content when considering the standard AFLP protocol with the enzyme MseI. Results from population samples of the two plant species show that there is a negative relationship between AFLP fragment size and fragment population frequency. Monte Carlo simulations reveal that size homoplasy, arising from pulling together nonhomologous fragments of the same size, generates patterns similar to those observed in P. lunatus and L. perenne because of the asymmetry of the size distribution. We discuss the implications of these results in the context of estimating g...Continue Reading

References

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Citations

Jun 27, 2006·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Bruno StuderRoland Kölliker
Aug 30, 2007·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·H Adoukonou-SagbadjaW Friedt
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May 8, 2009·Proceedings. Biological Sciences·Satoshi Yamamoto, Teiji Sota
May 30, 2008·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Eric C Anderson
May 2, 2003·Genome Génome / Conseil National De Recherches Canada·Eline van Zijll de JongJohn W Forster
Jan 11, 2007·Genome Génome / Conseil National De Recherches Canada·Lena WilfertPaul Schmid-Hempel
Jul 9, 2010·BMC Evolutionary Biology·Jeffrey A MarkertDiane E Nacci
Feb 12, 2011·BMC Evolutionary Biology·Mirjam M J JacobsBen Vosman

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