Abstract
The amplified fragment length polymorphisms (AFLP) method has become an attractive tool in phylogenetics due to the ease with which large numbers of characters can be generated. In contrast to sequence-based phylogenetic approaches, AFLP data consist of anonymous multilocus markers. However, potential artificial amplifications or amplification failures of fragments contained in the AFLP data set will reduce AFLP reliability especially in phylogenetic inferences. In the present study, we introduce a new automated scoring approach, called “AMARE” (AFLP MAtrix REduction). The approach is based on replicates and makes marker selection dependent on marker reproducibility to control for scoring errors. To demonstrate the effectiveness of our approach we record error rate estimations, resolution scores, PCoA and stemminess calculations. As in general the true tree (i.e. the species phylogeny) is not known, we tested AMARE with empirical, already published AFLP data sets, and compared tree topologies of different AMARE generated character matrices to existing phylogenetic trees and/or other independent sources such as morphological and geographical data. It turns out that the selection of masked character matrices with highest resolution scores gave similar or even better phylogenetic results than the original AFLP data sets.
Highlights
Amplified fragment length polymorphism (AFLP) data consist of sets of anonymous multilocus markers, in contrast to sequence based phylogenetic approaches
This approach does not solve the problem of homology assessment in AFLP data per se, but improves its reproducibility and accuracy, which further increases the reliability of phylogenetic reconstructions based on AFLP markers
To decide between character matrices constructed with different parameter settings of AMARE, we considered the effect of marker selection on mismatch error rate estimations [10,31], principal coordinate analyses (PCoA) [28], stemminess [35] and resolution scores [31]
Summary
Amplified fragment length polymorphism (AFLP) data consist of sets of anonymous multilocus markers, in contrast to sequence based phylogenetic approaches. We address the difficulties in scoring AFLP profiles by measuring marker reproducibility This approach does not solve the problem of homology assessment in AFLP data per se, but improves its reproducibility and accuracy, which further increases the reliability of phylogenetic reconstructions based on AFLP markers. The combination of large numbers of characters and phylogenetic signal in many AFLP data sets [6,7] has led to an increasing use of AFLP markers in phylogenetic analyses as well. In these studies, AFLP markers proved to be valuable characters to resolve phylogenetic relationships among closely related taxa, and at the family-level [3,8]
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