The outgroup effect on tree topology is   well established for sequence data, but has so far received no attention in   connection with multilocus binary presence–absence data such as those   obtained by AFLP genotyping. However, the elevated potential for homoplasy in   this type of data (Althoff et al., 2007; García-Pereira et al., 2010) implies   that random outgroup effects on AFLP tree topologies are at least as likely   as in analyses of DNA sequences. Despite certain other AFLP-specific   shortcomings, which are associated with low information content, dominance   and phenetics (e.g. García-Pereira et al., 2010), AFLP data nonetheless   harbor potential for improved species tree approximation as the phylogenetic   signal is integrated from numerous loci distributed throughout the genome,   thus reducing the confounding effects of incomplete lineage sorting and   hybridization on phylogenetic inference (Koopman, 2005). Consequently, AFLP   markers are frequently being applied to taxa originating from rapid   radiations (Ogden and Thorpe, 2002; Schliewen and Klee, 2004; Herder et al.,   2006; Fink et al., 2010; Geiger et al., 2010; Koblmüller et al., 2010;   Sturmbauer et al., 2010; Joyce et al., 2011).

对于序列数据，外群效对树拓扑结构的影响已经得到很好的证实，但是到目前为止，对于多位点二元存在-缺失数据还没有引起注意，如通过AFLP基因分型获得的数据。然而，这种类型的数据（Althoff et al., 2007; García-Pereira et al., 2010）中出现内群群同质化的报道在增多，意味着对AFLP树拓扑结构的随机外群效应至少与DNA序列分析中的一样。尽管存在与低信息含量、优势度和酚类（如García-Pereira et al., 2010）相关的其他AFLP特有的缺点，AFLP数据仍然具有改进物种树近似的潜力，因为系统发育信号是从分布在整个基因组中的许多基因座整合而来的，从而减少了不完全谱系分类和杂交对系统发育推断的混杂影响（Koopman, 2005）。因此，AFLP标记经常应用于源自快速辐射的分类群（Ogden and Thorpe, 2002; Schliewen and Klee, 2004; Herder et al.,   2006; Fink et al., 2010; Geiger et al., 2010; Koblmüller et al., 2010;   Sturmbauer et al., 2010; Joyce et al., 2011）。