AFLPs support deep relationships among darters (Percidae: Etheostomatinae) consistent with morphological hypotheses

Abstract

Recent attention has focused on the efficacy of amplified fragment length polymorphisms (AFLPs) for resolving deep evolutionary relationships. Here we show that AFLPs provide resolution of deep relationships within the family Percidae that are more consistent with previous morphological hypotheses than are relationships proposed by previous molecular analyses. Despite in silico predictions, we were able to resolve relatively ancient divergences, estimated at 425 MA. We show that the most distantly related species share the fewest fragments, but suggest that large data sets and extensive taxon sampling are sufficient to overcome this obstacle of the AFLP technique for deep divergences. We compare genetic distances estimated from mitochondrial DNA with those from AFLPs and contrast traditional PAUP* NeiLi AFLP genetic distances with a recently proposed method utilizing the Dice equation with constraining nucleotides.

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

“…It is a fact that all of the deep clades in the AFLP-inferred phylogeny, with the exception of the most recent common ancestor of all darters, are poorly supported with Bayesian posterior probabilities that are all o0.90, directly contradicting the claims by Smith et al (2011) in the title of their paper, which promises phylogenetic support for deep relationships among darters. Smith et al (2011) also claim that their analyses of AFLP characters support groups that are consistent with morphological hypotheses.…”

“…Smith et al (2011) also claim that their analyses of AFLP characters support groups that are consistent with morphological hypotheses. It is important to note that these hypotheses of darter taxonomic groups were not derived from explicit phylogenetic analyses, but are rather assumptions of relationships based on an assessment of the gestalt of an organisms overall appearance (Page 1974).…”

“…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.…”

“…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 (X0.95) 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).…”

“…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.…”