A First insight into the in silico evaluation of the accuracy of AFLP markers for phylogenetic reconstruction

Abstract

Using simulated data, we tested whether the AFLP technique can consistently be used to estimate accurate evolutionary trees. We generated DNA sequences with known phylogenies that were used to simulate the AFLP procedure. In silico AFLP fingerprints were used to estimate neighbor-joining AFLP-based trees. The comparison of the true tree to the AFLP trees obtained over a wide range of conditions indicates that AFLPs usually lead to the wrong phylogeny except when DNA sequences are closely related, typically below the taxonomic rank of species. © 2009 Springer Berlin Heidelberg.