Nothing Wrong with the Analysis of Clades in Comparative Evolutionary Studies: A Reply to Poe et al

In a recent paper, Poe et al. assert that scientists should abandon clade-based approaches, particularly those using named taxonomic ranks. Poe et al. attempt to demonstrate that clade selection can have effects on the results of evolutionary analyses but unfortunately fall short of making any robust conclusions. Here, we demonstrate that the assertions made by Poe et al. have two important flaws: (i) an erroneous view of modern phylogenetic comparative methods; and (ii) a lack of statistical rigor in their analyses. We repeat Poe et al.’s analysis but using appropriate phylogenetic comparative approaches. We demonstrate that results remain consistent regardless of the clade definition. We go on to discuss the value of taxonomic groupings and how they can provide meaningful units of comparison in evolutionary study. Unlike the disheartening suggestion to abandon the use of clades, scientists can instead continue to use phylogenetic “ corrections” that are already the standard for most comparative evolutionary analyses. [Comparative methods; evolution; phylogeny; taxonomy.]

On the Selection and Analysis of Clades in Comparative Evolutionary Studies

Researchers commonly present results of comparative studies of taxonomic groups. In this review, we criticize the focus on named clades, usually, comparably ranked groups such as families or orders, for comparative evolutionary analyses and question the general practice of using clades as units of analysis. The practice of analyzing sets of named groups persists despite widespread appreciation that the groups we have chosen to name are based on subjective human concerns rather than objective properties of nature. We demonstrate an effect of clade selection on results in one study and present some potential alternatives to selecting named clades for analysis that are relatively objective in clade choice. However, we note that these alternatives are only partial solutions for clade-based studies. The practice of analyzing named clades obviously is biased and problematic, but its issues portend broader problems with the general approach of employing clades as units of analysis. Most clade-based studies do not account for the nonindependence of clades, and the biological insight gained from demonstrating some pattern among a particular arbitrary sample of groups is arguable. [Clades; comparative biology; taxonomic groups.]