Character analysis in morphological phylogenetics: problems and solutions

Abstract.—Many aspects of morphological phylogenetics are controversial in the theoretical system-atics literature and yet are often poorly explained and justied in empirical studies. In this paper, I argue that most morphological characters describe variation that is fundamentally quantitative, re-gardless of whether they are coded qualitatively or quantitatively by systematists. Given this view, three fundamental problems in morphological character analysis (denition, delimitation, and order-ing of character states) may have a common solution: coding morphological characters as continuous quantitative traits. A new parsimony method (step-matrix gap-weighting, a modication of Thiele’s approach) is proposed that allows quantitative traits to be analyzed as continuous variables. The problem of scaling or weighting quantitative characters relative to qualitative characters (and to each other) is reviewed, and three possible solutions are described. The new coding method is applied to data from hoplocercid lizards, and the results show the sensitivity of phylogenetic conclusions to dif-ferent scaling methods. Although some authors reject the use of continuous, overlapping, quantitative characters in phylogenetic analysis, quantitative data from hoplocercid lizards that are coded using the new approach contain signicant phylogenetic structure and exhibit levels of homoplasy simi-lar to those seen in data that are coded qualitatively. [Character coding; morphology; phylogenetics; quantitative characters; weighting.] Good science requires clearly explained, repeatable methods. Yet, practitioners of morphological phylogenetics tend not to be explicit about their methodology, specically, how morphological characters are selected, and how states are dened, delimited, coded, and ordered (a process I refer to as “character analysis”). The lack of methodological explanation in published morphological studies has been discussedby several authors (e.g., Pimentel and Riggins