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.
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A Bayesian Model of AFLP Marker Evolution and Phylogenetic Inference
Ruiyan Luo / Andrew L Hipp / Bret Larget
1University of Wisconsin - Madison
1The Morton Arboretum
1University of Wisconsin - Madison
Citation Information: Statistical Applications in Genetics and Molecular Biology. Volume 6, Issue 1, Pages –, ISSN (Online) 1544-6115, DOI: 10.2202/1544-6115.1152, April 2007
Publication History:
- Published Online:
- 2007-04-17
Keywords: amplified fragment length polymorphism; Markov chain Monte Carlo; phylogeny; restriction site; statistical phylogenetics
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