  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.
