Macroecological correlates of Darwinian shortfalls across terrestrial vertebrates

Most described species have not been explicitly included in phylogenetic trees—a problem named the Darwinian shortfall—due to a lack of molecular and/or morphological data, thus hampering the explicit incorporation of evolution into large-scale biodiversity analyses. We investigate potential drivers of the Darwinian shortfall in tetrapods, a group where at least one-third of described species still lack phylogenetic data, thus necessitating the imputation of their evolutionary relationships in fully-sampled phylogenies. We show that the number of preserved specimens in scientific collections is the main driver of phylogenetic knowledge accumulation, highlighting the major role of biological collections in unveiling novel biodiversity data and the importance of continued sampling efforts to reduce knowledge gaps. Additionally, large-bodied and wide-ranged species, as well as terrestrial and aquatic amphibians and reptiles, are phylogenetically better known. Therefore, future efforts shou..., (a)  Phylogenetic assessment and species-level covariates We firstly identified which tetrapod species had their evolutionary relationships imputed in fully-sampled phylogenies available for the group (1–5), thus creating a binary response variable for 33,281 species included in such phylogenies. We excluded 228 marine species (according to the International Union for Conservation of Nature — IUCN), keeping only terrestrial vertebrates (n = 33,053) in subsequent analyses. We then selected eight putative predictors to investigate how species’ biology, geography and biodiversity appeal, and socioeconomic-related factors affect the probability of species being imputed on phylogenies. Many predictors used here comes from the TetrapodTraits, a recent database for the world’s tetrapod including standardised species-level attributes (6). Below, we outline the attributes used as predictors, along with brief explanations of how they were computed. The year of species description was based on th..., , # README: Macroecological correlates of Darwinian shortfalls across terrestrial vertebrates [https://doi.org/10.5061/dryad.wdbrv15ww](https://doi.org/10.5061/dryad.wdbrv15ww) There are five main documents associated with this paper: (*1*) our raw data (**AdditionalVars.csv**); (*2*) marine taxa as per the IUCN (**marine_spp_IUCN.csv**); (*3*) phylogenetic trees for amphibians, birds, mammals, and reptiles stored in a zip file (**phylo_trees.zip**); (*4*) outputs from phylogenetic autocorrelation analyses (**phylocorr_outs.zip**); and (*5*) the R code (**Rcode_DarwinianShortfalls.R**). ## Description of the data and file structure (*1*) **AdditionalVars.csv**; contains 3 columns, each one explained below: * Scientific.Name: scientific name of each species included in the most fully-sampled phylogenies for tetrapods. - sequenced: Informs if there is any genetic data available for each species (data obtained from Smid 2022; DOI: 10.1111/jbi.14491) * GBIF_occ: Total number of pr...目前已被描述的物种中，多数尚未被明确纳入系统发育树（phylogenetic tree），这一问题被称为达尔文缺口（Darwinian shortfall），其成因在于分子数据与/或形态学数据的缺失，进而阻碍了将演化过程明确融入大规模生物多样性分析框架。本研究针对四足动物（tetrapod）类群的达尔文缺口潜在驱动因素展开探究——该类群中至少三分之一的已描述物种仍缺乏系统发育数据，因此需要通过推算（imputation）补充这些物种的演化关系，以构建完整采样的系统发育树。研究结果显示，科研馆藏中的保藏标本数量是系统发育认知积累的核心驱动因素，这凸显了生物标本馆藏在揭示新型生物多样性数据中的关键作用，以及持续开展采样工作以填补认知空白的重要性。此外，体型较大、分布范围较广的物种，以及陆生与水生的两栖类和爬行类，其系统发育认知程度相对更高。因此，未来的研究工作应……（a） 系统发育评估与物种水平协变量 我们首先明确了该类群已发布的完整采样系统发育树（参考文献1–5）中，哪些四足动物物种的演化关系是通过推算得到的，由此为纳入该系统发育树的33281个物种构建了二分类响应变量。我们依据国际自然保护联盟（International Union for Conservation of Nature, IUCN）的分类标准剔除了228个海洋物种，后续分析仅保留陆生脊椎动物（样本量n=33053）。随后我们选取了8个候选预测变量，以探究物种生物学特征、地理分布特征、生物多样性关注度以及社会经济相关因素，如何影响物种的演化关系被推算纳入系统发育树的概率。本研究使用的多数预测变量来自四足动物性状数据库（TetrapodTraits），这是一个面向全球四足动物的新型数据库，包含标准化的物种水平属性信息（参考文献6）。下文将逐一介绍本研究使用的预测变量属性，并简要说明其计算方式。 物种描述年份的相关数据基于…… # 说明文档：陆生脊椎动物达尔文缺口的宏观生态关联因子 [https://doi.org/10.5061/dryad.wdbrv15ww](https://doi.org/10.5061/dryad.wdbrv15ww) 本论文关联的主要文件共5份： 1. 原始数据集（**AdditionalVars.csv**）； 2. IUCN认定的海洋类群物种列表（**marine_spp_IUCN.csv**）； 3. 两栖类、鸟类、哺乳类及爬行类的系统发育树压缩包（**phylo_trees.zip**）； 4. 系统发育自相关分析结果文件（**phylocorr_outs.zip**）； 5. R语言代码文件（**Rcode_DarwinianShortfalls.R**）。 ## 数据与文件结构说明 1. **AdditionalVars.csv**：包含3列数据，各列说明如下： * Scientific.Name：本研究纳入的最全四足动物系统发育树中各物种的学名。 * sequenced：标注各物种是否存在可用的遗传数据（数据来源：Smid 2022; DOI: 10.1111/jbi.14491） * GBIF_occ：全球生物多样性信息设施（Global Biodiversity Information Facility, GBIF）的有效记录总数量（原文此处为pr...）