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

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

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

asterids-rbcLmatK

Sequence alignment of concatenated plastid rbcL and matK genes for 62 asterid taxa plus 3 outgroup

asterids-cpmtnuc

Sequence alignment of 76 plastid genes, six mitochondrial genes, and three nuclear repeat regions for 62 asterid taxa plus 3 outgroup

rosids-matK

Sequence alignment of the plastid matK gene for 42 rosid taxa plus 3 outgroup

rosids-rbcL

Sequence alignment of the plastid rbcL gene for 42 rosid taxa plus 3 outgroup

rosids-cpmtnuc

Sequence alignment of 73 plastid genes, nine mitochondrial genes, and three nuclear repeat regions for 42 rosid taxa plus 3 outgroup

asterids-rbcL

Sequence alignment of the plastid rbcL gene for 62 asterid taxa plus 3 outgroup

rosids-matKrbcL

Sequence alignment of concatenated plastid matK and rbcL genes for 42 rosid taxa plus 3 outgroup