Supplementary material for: Phylogenetic biodiversity metrics should account for both accumulation and attrition of evolutionary heritage

Phylogenetic metrics are essential tools used in the study of ecology, evolution and conservation. Phylogenetic diversity (PD) in particular is one of the most prominent measures of biodiversity, and is based on the idea that biological features accumulate along the edges of phylogenetic trees that are summed. We argue that PD and many other phylogenetic biodiversity metrics fail to capture an essential process that we term attrition. Attrition is the gradual loss of features and other sources of variety through causes other than extinction. Here we introduce `EvoHeritage', a generalisation of PD that is founded on the joint processes of accumulation and attrition of features. We argue that whilst PD measures evolutionary history, EvoHeritage is required to capture a more pertinent subset of evolutionary history including only components that have survived attrition. We show that EvoHeritage is not the same as PD on a tree with scaled edges; instead, accumulation and attrition interact ..., Data was reprocessed from published sources as described in the associated manuscript methods section There is no primary data included. Supplementary material and glossary contain mathematical details and proofs rather than any primary data sets., R for use of code, otherwise PDF and CSV readers are needed to access the files., # Title of Dataset *** This dataset contains 1. A glossary 2. Details and mathematical proofs 3. Data plotted in figure 9 ## Description of the data and file structure 1. The glossary is a single PDF file 2. The details and mathematical proofs are a single PDF file 3. Data plotted in figure 9 as a series of 4 .csv files a. Filenames correpond to Jurassic and Cretaceous cases as described in main text b. Column with name result.data.tip.label gives species names c. Columns with names LF.min, LF.lq, LF.median, LF.uq, LF.max give the living-fossil-ness values min, lower quartile, median, upper quartile and max respectively. ## Sharing/Access information Data was derived from the following sources (as described in the associated manuscript methods) * Upham, N. S., J. A. Esselstyn, and W. Jetz. 2019. Inferring the mammal tree: species-level sets of phylogenies for questions in ecology, evolution, and conservation. PLoS Biology 17(12):e3000494. https://datadryad.org/stash/...系统发育度量（phylogenetic metrics）是生态学、进化生物学与保护生物学研究中不可或缺的核心工具。其中，系统发育多样性（Phylogenetic Diversity, PD）是最具影响力的生物多样性衡量指标之一，其核心逻辑基于“生物特征沿系统发育树的分支累积并求和”这一理念。 我们指出，系统发育多样性与诸多其他系统发育生物多样性度量方法，均未能捕捉到我们称之为特征损耗（attrition）的关键演化过程。所谓特征损耗，指的是除物种灭绝以外的其他因素导致的特征与各类多样性来源的逐步丧失。 在此背景下，我们提出演化传承值（EvoHeritage）——这是对系统发育多样性的一般性推广，其构建基础为特征的累积与损耗双重演化过程。我们认为，系统发育多样性仅能衡量整体演化历史，而演化传承值则可捕捉更具生态学相关性的演化历史子集，即仅保留未被特征损耗所淘汰的组分。 我们证明，在分支权重经过缩放的系统发育树上，演化传承值与系统发育多样性并不等价；反之，特征累积与损耗过程存在交互作用…… 本数据集的相关数据均按照关联论文方法部分所述流程，从已发表的数据源重新处理得到，未包含原始实验数据。补充材料与术语表中仅包含数学细节与证明过程，未附带任何原始数据集。如需使用代码，请依托R语言环境；若需查看其余文件，则需配备PDF与CSV阅读器。 # 数据集标题 ## 数据集包含内容 1. 术语表 2. 数学细节与证明材料 3. 图9中绘制的实验数据 ## 数据与文件结构说明 1. 术语表为单个PDF文件 2. 数学细节与证明材料为单个PDF文件 3. 图9对应的绘图数据包含4个CSV格式文件： a. 文件名与正文中所述的侏罗纪、白垩纪案例一一对应 b. 名为`result.data.tip.label`的列存储物种名称 c. 分别名为`LF.min`、`LF.lq`、`LF.median`、`LF.uq`、`LF.max`的列，依次对应“活化石程度”指标的最小值、下四分位数、中位数、上四分位数与最大值。 ## 数据共享与获取说明 本数据集的数据均按照关联论文方法部分所述来源获取： * Upham, N. S., J. A. Esselstyn, and W. Jetz. 2019. 推断哺乳动物系统发育树：面向生态学、进化与保护研究的物种水平系统发育数据集. PLoS Biology 17(12):e3000494. https://datadryad.org/stash/...