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Originally published as Genetics Published Articles Ahead of Print on May 27, 2008.
Genetics, Vol. 179, 927-939, June 2008, Copyright © 2008
doi:10.1534/genetics.107.084541
An Approximate Bayesian Computation Approach to Overcome Biases That Arise When Using Amplified Fragment Length Polymorphism Markers to Study Population Structure
Matthieu Foll*,1,
Mark A. Beaumont
and
Oscar Gaggiotti*
* Laboratoire d'Ecologie Alpine (LECA), CNRS UMR 5553, 38041 Grenoble Cedex 09, France and School of Biological Sciences, University of Reading, Reading RG6 6BX, United Kingdom
1 Corresponding author: Computational and Molecular Population Genetics Lab, Zoology Institute, Baltzerstrasse 6, 3012 Bern, Switzerland.
E-mail: matthieu.foll{at}zoo.unibe.ch
There is great interest in using amplified fragment length polymorphism (AFLP) markers because they are inexpensive and easy to produce. It is, therefore, possible to generate a large number of markers that have a wide coverage of species genomes. Several statistical methods have been proposed to study the genetic structure using AFLPs but they assume Hardy–Weinberg equilibrium and do not estimate the inbreeding coefficient, FIS. A Bayesian method has been proposed by Holsinger and colleagues that relaxes these simplifying assumptions but we have identified two sources of bias that can influence estimates based on these markers: (i) the use of a uniform prior on ancestral allele frequencies and (ii) the ascertainment bias of AFLP markers. We present a new Bayesian method that avoids these biases by using an implementation based on the approximate Bayesian computation (ABC) algorithm. This new method estimates population-specific FIS and FST values and offers users the possibility of taking into account the criteria for selecting the markers that are used in the analyses. The software is available at our web site (http://www-leca.ujf-grenoble.fr/logiciels.htm). Finally, we provide advice on how to avoid the effects of ascertainment bias.
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