Data from: Biodiversity assessment using next-generation sequencing: comparison of phylogenetic and functional diversity between Nebraska grasslands

Global biodiversity is declining rapidly as a consequence of anthropogenic changes to the environment. Traditional diversity indices such as species richness have been used to assess biodiversity, but recent arguments call for a more comprehensive assessment that includes both phylogenetic and functional diversity (PD and FD, respectively). Many PD metrics have been developed, but few empirical studies have compared metrics across sites with the goal of understanding their application to characterizing biodiversity. In this study, 17 PD metrics, four traditional diversity indices, and one measure of FD were calculated and compared between two Nebraska grasslands. PD metrics were calculated from robust phylogenies estimated from next-generation sequencing data of 45 species. Traditional indices were calculated using species abundance data, and FD was quantified by measuring the phylogenetic signal, K, of specific leaf area (SLA). Results showed that PD metrics and traditional indices were not always correlated, and various PD metrics characterized biodiversity differently. In addition, phylogenies estimated from >80 genes were more robust than single- or dual-gene phylogenies resulting in more reliable PD metrics. K of SLA indicated random trait assembly in all sites. Results suggested that metrics that identify phylogenetic structure and relatedness can provide information to conservation planners about the ability of a community to persist in an unpredictable future. A combination of these results with those of future investigations applying PD and FD metrics to varying communities will support concrete recommendations to conservation planners about how to incorporate these metrics into the selection of priority regions.

受人类活动引发的环境变化影响，全球生物多样性正快速衰退。诸如物种丰富度在内的传统多样性指数长期被用于生物多样性评估，但近年学界呼吁采用更全面的评估框架，涵盖系统发育多样性（phylogenetic diversity, PD）与功能多样性（functional diversity, FD）两类指标。目前已开发出多种PD计算指标，但鲜有实证研究在不同样地间对这些指标进行对比，以明确其在生物多样性表征中的适用场景。本研究针对美国内布拉斯加州的两处草原，计算并对比了17种PD指标、4种传统多样性指数以及1项FD衡量指标。PD指标的计算基于对45个物种的下一代测序（next-generation sequencing）数据构建的稳健系统发育树；传统多样性指数基于物种多度数据计算得到；FD则通过测定比叶面积（specific leaf area, SLA）的系统发育信号K值进行量化。研究结果表明，PD指标与传统多样性指数并非始终相关，且不同PD指标对生物多样性的表征方式存在差异。此外，基于80余个基因构建的系统发育树，其稳健性优于单基因或双基因系统发育树，由此得到的PD指标也更为可靠。比叶面积的K值显示，所有样地内的性状聚集均呈随机模式。研究结果提示，能够反映系统发育结构与亲缘关系的指标，可为保护规划者提供群落在不可预测的未来中存续能力的相关信息。将本研究结果与未来针对不同群落开展的PD、FD指标应用研究相结合，可为保护规划者提供具体建议，指导其如何将此类指标纳入优先保护区域的遴选流程。