Data from: Biodiversity assessment among two Nebraska prairies: a comparison between traditional and phylogenetic diversity indices

Background: Conservation of the evolutionary diversity among organisms should be included in the selection of priority regions for preservation of Earth’s biodiversity. Traditionally, biodiversity has been determined from an assessment of species richness (S), abundance, evenness, rarity, etc. of organisms but not from variation in species’ evolutionary histories. Phylogenetic diversity (PD) measures evolutionary differences between taxa in a community and is gaining acceptance as a biodiversity assessment tool. However, with the increase in the number of ways to calculate PD, end-users and decision-makers are left wondering how metrics compare and what data are needed to calculate various metrics. New information: In this study, we used massively parallel sequencing to generate over 65,000 DNA characters from three cellular compartments for over 60 species in the asterid clade of flowering plants. We estimated asterid phylogenies from character datasets of varying nucleotide quantities, and then assessed the effect of varying character datasets on resulting PD metric values. We also compared multiple PD metrics with traditional diversity indices (including S) among two endangered grassland prairies in Nebraska (U.S.A.). Our results revealed that PD metrics varied based on the quantity of genes used to infer the phylogenies; therefore, when comparing PD metrics between sites, it is vital to use comparable datasets. Additionally, various PD metrics and traditional diversity indices characterize biodiversity differently and should be chosen depending on the research question. Our study provides empirical results that reveal the value of measuring PD when considering sites for conservation, and it highlights the usefulness of using PD metrics in combination with other diversity indices when studying community assembly and ecosystem functioning. Ours is just one example of the types of investigations that need to be conducted across the tree of life and across varying ecosystems in order to build a database of phylogenetic diversity assessments that lead to a pool of results upon which a guide through the plethora of PD metrics may be prepared for use by ecologists and conservation planners.

研究背景：在遴选地球生物多样性保护优先区域时，应当纳入生物类群间进化多样性的保护考量。传统上，生物多样性的评估多基于对物种丰富度（species richness, S）、丰度、均匀度、稀有性等生物类群特征的测算，而非基于不同物种的进化历史差异。系统发育多样性（Phylogenetic Diversity, PD）用于衡量群落内不同类群间的进化差异，目前正逐渐被接纳为生物多样性评估工具。然而，随着PD计算方法的不断增多，终端使用者与决策者往往难以厘清不同度量指标间的差异，也不清楚计算各类指标所需的数据类型。新研究发现：本研究采用大规模并行测序（massively parallel sequencing）技术，从被子植物菊类支系（asterid clade）的60余个物种的3个细胞区室中获取了超过65000个DNA特征位点。研究人员基于核苷酸数量不同的特征数据集构建菊类支系的系统发育树，随后分析了不同特征数据集对最终PD度量值的影响。此外，本研究还对比了美国内布拉斯加州（Nebraska）两处濒危草原（prairie）生境中，多种PD度量指标与传统多样性指数（包括物种丰富度S）的差异。研究结果显示，PD度量值会因用于构建系统发育树的基因数量不同而产生差异；因此，若要在不同样地间对比PD度量结果，使用标准化可比的数据集至关重要。此外，不同PD度量指标与传统多样性指数对生物多样性的表征维度各不相同，需根据具体研究问题选择合适的指标。本研究通过实证结果证实了在遴选保护样地时开展PD评估的重要价值，同时也凸显了在研究群落构建与生态系统功能时，将PD度量指标与其他多样性指数结合使用的必要性。本研究仅是众多相关探索的一例：若要构建系统发育多样性评估数据库，并基于积累的大量研究结果，编制一份可帮助生态学家与保护规划者厘清海量PD度量指标选择路径的指南，就需要在整个生命之树与各类生态系统中开展同类研究。