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.
"Modeling substitution and indel processes for AFLP marker evolution and phylogenetic inference." Ann. Appl. Stat. 3 (1) 222 - 248, March 2009. https://doi.org/10.1214/08-AOAS212