Biodiversity assessment among two Nebraska prairies: A comparison between traditional and phylogenetic diversity indices

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

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

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.

Original languageEnglish (US)
Article numbere5403
JournalBiodiversity Data Journal
Volume3
Issue number1
DOIs
StatePublished - Jul 17 2015

Fingerprint

diversity index
prairies
prairie
biodiversity
phylogenetics
phylogeny
comparison
ecosystem
rarity
ecosystems
angiosperm
organisms
ecologists
species richness
grassland
Angiospermae
DNA
grasslands
nucleotides
gene

Keywords

  • Asterids
  • Community ecology
  • Conservation
  • Grasslands
  • Next-generation sequencing
  • Phylogenetic diversity

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Ecology

Cite this

Biodiversity assessment among two Nebraska prairies : A comparison between traditional and phylogenetic diversity indices. / Aust, Shelly K.; Ahrendsen, Dakota L.; Kellar, P. Roxanne.

In: Biodiversity Data Journal, Vol. 3, No. 1, e5403, 17.07.2015.

Research output: Contribution to journalArticle

@article{6fcefb182e1d42f49ee13927edae5879,
title = "Biodiversity assessment among two Nebraska prairies: A comparison between traditional and phylogenetic diversity indices",
abstract = "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.",
keywords = "Asterids, Community ecology, Conservation, Grasslands, Next-generation sequencing, Phylogenetic diversity",
author = "Aust, {Shelly K.} and Ahrendsen, {Dakota L.} and Kellar, {P. Roxanne}",
year = "2015",
month = "7",
day = "17",
doi = "10.3897/BDJ.3.e5403",
language = "English (US)",
volume = "3",
journal = "Biodiversity Data Journal",
issn = "1314-2828",
publisher = "Pensoft Publishers",
number = "1",

}

TY - JOUR

T1 - Biodiversity assessment among two Nebraska prairies

T2 - A comparison between traditional and phylogenetic diversity indices

AU - Aust, Shelly K.

AU - Ahrendsen, Dakota L.

AU - Kellar, P. Roxanne

PY - 2015/7/17

Y1 - 2015/7/17

N2 - 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.

AB - 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.

KW - Asterids

KW - Community ecology

KW - Conservation

KW - Grasslands

KW - Next-generation sequencing

KW - Phylogenetic diversity

UR - http://www.scopus.com/inward/record.url?scp=85018193610&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85018193610&partnerID=8YFLogxK

U2 - 10.3897/BDJ.3.e5403

DO - 10.3897/BDJ.3.e5403

M3 - Article

C2 - 26312052

AN - SCOPUS:85018193610

VL - 3

JO - Biodiversity Data Journal

JF - Biodiversity Data Journal

SN - 1314-2828

IS - 1

M1 - e5403

ER -