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Modeling substitution and indel processes for AFLP marker evolution and phylogenetic inference. (English) Zbl 1160.62091

Summary: The amplified fragment length polymorphism (AFLP) method produces anonymous genetic markers from throughout a genome. We extend the nucleotide substitution model of AFLP evolution to additionally include insertion and deletion processes. The new Sub-ID model relaxes the common assumption that markers are independent and homologous. We build a Markov chain Monte Carlo methodology tailored for the Sub-ID model to implement a Bayesian approach to infer AFLP marker evolution.
The method allows us to infer both the phylogenies and the subset of markers that are possibly homologous. In addition, we can infer the genome-wide relative rate of indels versus substitutions. In a case study with AFLP markers from sedges, a grass-like plant common in North America, we find that accounting for insertion and deletion makes a difference in phylogenetic inference. The inference of topologies is not sensitive to the prior settings and the Jukes-Cantor assumption for nucleotide substitution. The model for insertion and deletion we introduce has potential value in other phylogenetic applications.

MSC:

62P10 Applications of statistics to biology and medical sciences; meta analysis
92D15 Problems related to evolution
62F15 Bayesian inference
60J20 Applications of Markov chains and discrete-time Markov processes on general state spaces (social mobility, learning theory, industrial processes, etc.)
65C40 Numerical analysis or methods applied to Markov chains

Software:

MrBayes; Bali-phy
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Full Text: DOI arXiv

References:

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