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The amplified fragment length polymorphism (AFLP) method produces anonymousgenetic markers from throughout a genome. We extend the nucleotide substitutionmodel of AFLP evolution to additionally include insertion and deletionprocesses. The new Sub-ID model relaxes the common assumption that markers areindependent and homologous. We build a Markov chain Monte Carlo methodologytailored for the Sub-ID model to implement a Bayesian approach to infer AFLPmarker evolution. The method allows us to infer both the phylogenies and thesubset of markers that are possibly homologous. In addition, we can infer thegenome-wide relative rate of indels versus substitutions. In a case study withAFLP markers from sedges, a grass-like plant common in North America, we findthat accounting for insertion and deletion makes a difference in phylogeneticinference. The inference of topologies is not sensitive to the prior settingsand the Jukes--Cantor assumption for nucleotide substitution. The model forinsertion and deletion we introduce has potential value in other phylogeneticapplications.

Modeling substitution and indel processes for AFLP marker evolution and phylogenetic inference