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Statistical Applications in Genetics and Molecular Biology

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A Bayesian Model of AFLP Marker Evolution and Phylogenetic Inference

Ruiyan Luo1 / Andrew L Hipp2 / Bret Larget3

1University of Wisconsin - Madison

2The Morton Arboretum

3University of Wisconsin - Madison

Citation Information: Statistical Applications in Genetics and Molecular Biology. Volume 6, Issue 1, ISSN (Online) 1544-6115, ISSN (Print) 2194-6302, DOI: 10.2202/1544-6115.1152, April 2007

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Amplified Fragment Length Polymorphism (AFLP) markers are formed by selective amplification of DNA fragments from digested total genomic DNA. The technique is popular because it is a relatively inexpensive way to produce large numbers of reproducible genetic markers. In this paper, we describe a Bayesian approach to modeling AFLP marker evolution by nucleotide substitution and an MCMC approach to estimate phylogeny from AFLP marker data. We demonstrate the method on species in Carex section Ovales, a group of sedges common in North America. We compare the results of our analysis with a clustering method based on Nei and Li's restriction-site distance and a two-state Bayesian analysis using MrBayes.

Keywords: amplified fragment length polymorphism; Markov chain Monte Carlo; phylogeny; restriction site; statistical phylogenetics

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