Data from: Character Analysis in Morphological Phylogenetics: Problems and Solutions

Many aspects of morphological phylogenetics are controversial in the theoretical systematics literature and yet are often poorly explained and justified in empirical studies. In this paper, I argue that most morphological characters describe variation that is fundamentally quantitative, regardless of whether it is coded qualitatively or quantitatively by systematists. Given this view, three fundamental problems in morphological character analysis (character state definition, delimitation, and ordering) may have a common solution: coding morphological characters as continuous quantitative traits. A new parsimony method (step-matrix gap-weighting, a modification 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 different 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 do contain significant phylogenetic structure, and exhibit levels of homoplasy that are similar to those seen in data that are coded qualitatively.形态系统发育学（morphological phylogenetics）的诸多议题在理论分类学文献中尚存争议，却又常在实证研究中得不到充分阐释与论证。本文主张，绝大多数形态性状（morphological characters）所描述的变异本质上属于数量变异，无论分类学家将其编码为定性还是定量性状。基于这一观点，形态性状分析中的三大核心问题——性状状态定义、界定与排序——或可拥有统一解决方案：将形态性状编码为连续数量性状。本文提出一种全新的简约法：步矩阵间隙加权法（step-matrix gap-weighting，对Thiele方法的改进），该方法可将数量性状作为连续变量开展分析。针对数量性状相对于定性性状（以及彼此之间）的加权或标度问题，本文展开综述并阐述了三种可行解决方案。新编码方法被应用于盾尾蜥科（hoplocercid lizards）的数据集，结果显示系统发育推论对不同标度方法具有敏感性。尽管部分学者反对在系统发育分析中使用连续、重叠的数量性状，但采用新方法编码的盾尾蜥科数量数据确实包含显著的系统发育结构，其同塑性（homoplasy）水平与定性编码的数据相近。