AFLPs do not support deep phylogenetic relationships among darters (Teleostei: Percidae: Etheostomatinae)

摘要

In a recent paper Smith et al. (2011) presented an amplified fragment length polymorphism (AFLP) data set from 20 primer pairs that were scored for 69 darter species to infer phylogenetic relationships. Our primary concern with the conclusions presented in Smith et al. (2011) is an overstatement of the phylogenetic utility of ALFP markers for deep relationships among darters, and support for taxonomic groups inferred from non-phylogenetic assessments of morphology. Despite claims to the contrary, the Bayesian phylogeny presented in Figure 2 of Smith et al. (2011) conclusively demonstrates that AFLP markers do not provide strong support for deep relationships among darters, nor does phylogenetic analysis of this data support a majority of the sampled taxonomic groups. In addition, we present a new analysis that shows AFLP markers have a very low probability of providing strong posterior clade support (>0.95) in Bayesian analysis for the nodes representing the oldest lineages in the darter radiation, whereas a recently published analysis of a modest DNA sequence data set provides substantially greater support for these relationships (Near et al, 2011).