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

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Abstract

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.

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Acknowledgments

The authors thank anonymous reviewers and M.W. Cadotte (UT-Scarborough) for many helpful suggestions, C. Kellar and D. Sutherland (UNO) for field and identification assistance, and A. Swift (UNO) for guidance with statistical analyses. We also thank the MU Core Sequencing facility, the UNMC DNA Sequencing Core, the managing institutions (The Nature Conservancy and University of Nebraska Foundation) for access to the two grassland sites, and the following granting institutions: National Science Foundation (NSF) Nebraska Experimental Program to Stimulate Competitive Research (EPSCoR) First Award (Prime Award: EPS1004094; Subaward: 95-3101-0040-217) and the NASA Nebraska Space Grant. DLA also thanks the following for conference travel and research grants: Sigma Xi, UNO-Graduate Research and Creative Activity (GRACA), American Society of Plant Taxonomists (ASPT), Missouri Botanical Garden (MOBOT) Delzie Demaree Travel Award, and the UNO Biology Department.

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  1. Department of Biology, University of Nebraska at Omaha, 6001 Dodge Street, Omaha, NE, 68182, USA

    Dakota L. Ahrendsen, Shelly K. Aust & P. Roxanne Kellar

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  1. Dakota L. Ahrendsen
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Correspondence to P. Roxanne Kellar.

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This study was funded by NSF Nebraska EPSCoR First Award (Prime Award: EPS1004094; Subaward: 95-3101-0040-217) and the NASA Nebraska Space Grant (no number).

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Ahrendsen, D.L., Aust, S.K. & Roxanne Kellar, P. Biodiversity assessment using next-generation sequencing: comparison of phylogenetic and functional diversity between Nebraska grasslands. Plant Syst Evol 302, 89–108 (2016). https://doi.org/10.1007/s00606-015-1246-6

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