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：保护生物体间的进化多样性，应当纳入地球生物多样性优先保护区域的遴选范畴。传统生物多样性评估多基于物种丰富度（S）、丰度、均匀度、稀有性等指标，却未考量物种进化历史的差异。系统发育多样性（Phylogenetic Diversity, PD）可衡量群落内类群间的进化差异，正逐渐被接纳为生物多样性评估工具。然而，随着PD计算方法日益增多，终端用户与决策者往往难以厘清不同度量指标间的差异，以及计算各类指标所需的数据类型。
研究新进展：本研究借助大规模并行测序（massively parallel sequencing）技术，对被子植物菊类分支（asterid clade）的60余个物种的3个细胞区室，生成了超过65000个DNA特征位点。我们基于核苷酸数量各异的特征数据集构建菊类系统发育树，进而评估特征数据集规模对最终PD度量值的影响。此外，我们还对比了美国内布拉斯加州两处濒危草原草甸中，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波动，因此在不同样地间对比PD指标时，使用可比的数据集至关重要。同时，不同PD度量指标与传统多样性指数对生物多样性的表征逻辑存在差异，需根据研究问题选择适配的指标。本研究通过实证结果证实了在遴选保护区域时考量PD的价值，并凸显了将PD度量指标与其他多样性指数结合使用，在研究群落组装与生态系统功能过程中的实用性。本研究仅是针对生命之树各分支与不同生态系统开展同类研究的一例，未来需构建涵盖各类系统发育多样性评估结果的数据库，以形成可指引生态学家与保护规划者应对繁多PD度量指标的参考指南。