Data from: Estimating morphological diversity and tempo with discrete character-taxon matrices: implementation, challenges, progress, and future directions

Discrete character-taxon matrices are increasingly being used in an attempt to understand the pattern and tempo of morphological evolution; however, methodological sophistication and bespoke software implementations have lagged behind. In the present study, an attempt is made to provide a state-of-the-art description of methodologies and introduce a new R package (Claddis) for performing foundational disparity (morphologic diversity) and rate calculations. Simulations using its core functions show that: (1) of the two most commonly used distance metrics (Generalized Euclidean Distance and Gower's Coefficient), the latter tends to carry forward more of the true signal; (2) a novel distance metric may improve signal retention further; (3) this signal retention may come at the cost of pruning incomplete taxa from the data set; and (4) the utility of bivariate plots of ordination spaces are undermined by their frequently extremely low variances. By contrast, challenges to estimating morphologic tempo are presented qualitatively, such as how trees are time-scaled and changes are counted. Both disparity and rates deserve better time series approaches that could unlock new macroevolutionary analyses. However, these challenges need not be fatal, and several potential future solutions and directions are suggested.

Usage Notes
Matrix used for the tutorialtutorial_matrix.nexAges file for the tutorial data settutorial_ages.txtR code for the tutorialtutorial_code.rR code used for the simulationssimulation_code.r

离散字符分类矩阵在试图理解形态演化的模式和节奏方面日益得到应用；然而，方法论的高复杂性以及定制化软件的实现却滞后于这一趋势。在本研究中，我们尝试提供最先进的方法论描述，并介绍一款新的 R 包（Claddis），用于执行基础差异度（形态多样性）和速率的计算。使用其核心功能进行的模拟显示：1）在两种最常用的距离度量方法（广义欧几里得距离和 Gower 系数）中，后者往往能够传递更多的真实信号；2）一种新的距离度量方法可能进一步提高信号保留能力；3）这种信号保留可能以从数据集中剪枝不完整分类群为代价；4）排序空间的双变量图由于它们频繁出现的极低方差而削弱了其效用。相比之下，对形态节奏估计的挑战在定性上进行呈现，例如如何对树进行时间刻度和如何计数变化。差异度和速率都应采用更好的时间序列方法，以开启新的宏观进化分析。然而，这些挑战并非不可逾越，文中还提出了若干潜在的未来解决方案和方向。