Choosing and using diversity indices: insights for ecological applications from the German Biodiversity Exploratories

Morris EK, Caruso T, Buscot F, Fischer M, Hancock C, Maier TS, Meiners T, Müller C, Obermaier E, Prati D, Socher SA, et al. (2014)
Ecology and Evolution 4(18): 3514-3524.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
Download
Es wurden keine Dateien hochgeladen. Nur Publikationsnachweis!
Autor*in
Morris, EK; Caruso, T; Buscot, F; Fischer, M; Hancock, C; Maier, TS; Meiners, T; Müller, CarolineUniBi; Obermaier, E; Prati, D; Socher, SA; Sonnemann, I
Alle
Abstract / Bemerkung
Biodiversity, a multidimensional property of natural systems, is difficult to quantify partly because of the multitude of indices proposed for this purpose. Indices aim to describe general properties of communities that allow us to compare different regions, taxa, and trophic levels. Therefore, they are of fundamental importance for environmental monitoring and conservation, although there is no consensus about which indices are more appropriate and informative. We tested several common diversity indices in a range of simple to complex statistical analyses in order to determine whether some were better suited for certain analyses than others. We used data collected around the focal plant Plantago lanceolata on 60 temperate grassland plots embedded in an agricultural landscape to explore relationships between the common diversity indices of species richness (S), Shannon's diversity (H'), Simpson's diversity (D-1), Simpson's dominance (D-2), Simpson's evenness (E), and Berger-Parker dominance (BP). We calculated each of these indices for herbaceous plants, arbuscular mycorrhizal fungi, aboveground arthropods, belowground insect larvae, and P.lanceolata molecular and chemical diversity. Including these trait-based measures of diversity allowed us to test whether or not they behaved similarly to the better studied species diversity. We used path analysis to determine whether compound indices detected more relationships between diversities of different organisms and traits than more basic indices. In the path models, more paths were significant when using H', even though all models except that with E were equally reliable. This demonstrates that while common diversity indices may appear interchangeable in simple analyses, when considering complex interactions, the choice of index can profoundly alter the interpretation of results. Data mining in order to identify the index producing the most significant results should be avoided, but simultaneously considering analyses using multiple indices can provide greater insight into the interactions in a system.
Stichworte
Arbuscular mycorrhizal fungi; arthropods; Berger-Parker; chemical diversity; Shannon index; Plantago lanceolata; molecular diversity; plant diversity; Simpson's index; Hill's powers
Erscheinungsjahr
2014
Zeitschriftentitel
Ecology and Evolution
Band
4
Ausgabe
18
Seite(n)
3514-3524
ISSN
2045-7758
Page URI
https://pub.uni-bielefeld.de/record/2675339

Zitieren

Morris EK, Caruso T, Buscot F, et al. Choosing and using diversity indices: insights for ecological applications from the German Biodiversity Exploratories. Ecology and Evolution. 2014;4(18):3514-3524.
Morris, E. K., Caruso, T., Buscot, F., Fischer, M., Hancock, C., Maier, T. S., Meiners, T., et al. (2014). Choosing and using diversity indices: insights for ecological applications from the German Biodiversity Exploratories. Ecology and Evolution, 4(18), 3514-3524. doi:10.1002/ece3.1155
Morris, EK, Caruso, T, Buscot, F, Fischer, M, Hancock, C, Maier, TS, Meiners, T, et al. 2014. “Choosing and using diversity indices: insights for ecological applications from the German Biodiversity Exploratories”. Ecology and Evolution 4 (18): 3514-3524.
Morris, E. K., Caruso, T., Buscot, F., Fischer, M., Hancock, C., Maier, T. S., Meiners, T., Müller, C., Obermaier, E., Prati, D., et al. (2014). Choosing and using diversity indices: insights for ecological applications from the German Biodiversity Exploratories. Ecology and Evolution 4, 3514-3524.
Morris, E.K., et al., 2014. Choosing and using diversity indices: insights for ecological applications from the German Biodiversity Exploratories. Ecology and Evolution, 4(18), p 3514-3524.
E.K. Morris, et al., “Choosing and using diversity indices: insights for ecological applications from the German Biodiversity Exploratories”, Ecology and Evolution, vol. 4, 2014, pp. 3514-3524.
Morris, E.K., Caruso, T., Buscot, F., Fischer, M., Hancock, C., Maier, T.S., Meiners, T., Müller, C., Obermaier, E., Prati, D., Socher, S.A., Sonnemann, I., Wäschke, N., Wubet, T., Wurst, S., Rillig, M.C.: Choosing and using diversity indices: insights for ecological applications from the German Biodiversity Exploratories. Ecology and Evolution. 4, 3514-3524 (2014).
Morris, EK, Caruso, T, Buscot, F, Fischer, M, Hancock, C, Maier, TS, Meiners, T, Müller, Caroline, Obermaier, E, Prati, D, Socher, SA, Sonnemann, I, Wäschke, N, Wubet, T, Wurst, S, and Rillig, MC. “Choosing and using diversity indices: insights for ecological applications from the German Biodiversity Exploratories”. Ecology and Evolution 4.18 (2014): 3514-3524.

54 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Re-analysis of archaeobotanical remains from pre- and early agricultural sites provides no evidence for a narrowing of the wild plant food spectrum during the origins of agriculture in southwest Asia.
Wallace M, Jones G, Charles M, Forster E, Stillman E, Bonhomme V, Livarda A, Osborne CP, Rees M, Frenck G, Preece C., Veg Hist Archaeobot 28(4), 2019
PMID: 31231152
Microbiome networks and change-point analysis reveal key community changes associated with cystic fibrosis pulmonary exacerbations.
Layeghifard M, Li H, Wang PW, Donaldson SL, Coburn B, Clark ST, Caballero JD, Zhang Y, Tullis DE, Yau YCW, Waters V, Hwang DM, Guttman DS., NPJ Biofilms Microbiomes 5(), 2019
PMID: 30675371
Fecal Microbiota Analysis in Patients Going through a Depressive Episode during Treatment in a Psychiatric Hospital Setting.
Liśkiewicz P, Pełka-Wysiecka J, Kaczmarczyk M, Łoniewski I, Wroński M, Bąba-Kubiś A, Skonieczna-Żydecka K, Marlicz W, Misiak B, Samochowiec J., J Clin Med 8(2), 2019
PMID: 30717162
Changes in species richness and composition of boreal waterbird communities: a comparison between two time periods 25 years apart.
Pöysä H, Holopainen S, Elmberg J, Gunnarsson G, Nummi P, Sjöberg K., Sci Rep 9(1), 2019
PMID: 30741959
Assessment of the effectiveness of BG-Sentinel traps baited with CO2 and BG-Lure for the surveillance of vector mosquitoes in Miami-Dade County, Florida.
Wilke ABB, Carvajal A, Medina J, Anderson M, Nieves VJ, Ramirez M, Vasquez C, Petrie W, Cardenas G, Beier JC., PLoS One 14(2), 2019
PMID: 30794670
Interpreting mosquito feeding patterns in Australia through an ecological lens: an analysis of blood meal studies.
Stephenson EB, Murphy AK, Jansen CC, Peel AJ, McCallum H., Parasit Vectors 12(1), 2019
PMID: 30944025
Rhizobacterial Community Assembly Patterns Vary Between Crop Species.
Matthews A, Pierce S, Hipperson H, Raymond B., Front Microbiol 10(), 2019
PMID: 31019492
What's Normal? Microbiomes in Human Milk and Infant Feces Are Related to Each Other but Vary Geographically: The INSPIRE Study.
Lackey KA, Williams JE, Meehan CL, Zachek JA, Benda ED, Price WJ, Foster JA, Sellen DW, Kamau-Mbuthia EW, Kamundia EW, Mbugua S, Moore SE, Prentice AM, K DG, Kvist LJ, Otoo GE, García-Carral C, Jiménez E, Ruiz L, Rodríguez JM, Pareja RG, Bode L, McGuire MA, McGuire MK., Front Nutr 6(), 2019
PMID: 31058158
The Combination of 2'-Fucosyllactose with Short-Chain Galacto-Oligosaccharides and Long-Chain Fructo-Oligosaccharides that Enhance Influenza Vaccine Responses Is Associated with Mucosal Immune Regulation in Mice.
Xiao L, Engen PA, Leusink-Muis T, van Ark I, Stahl B, Overbeek SA, Garssen J, Naqib A, Green SJ, Keshavarzian A, Folkerts G, Van't Land B., J Nutr 149(5), 2019
PMID: 31050747
Tire shops in Miami-Dade County, Florida are important producers of vector mosquitoes.
Wilke ABB, Vasquez C, Petrie W, Beier JC., PLoS One 14(5), 2019
PMID: 31107881
Host contact dynamics shapes richness and dominance of pathogen strains.
Pinotti F, Fleury É, Guillemot D, Böelle PY, Poletto C., PLoS Comput Biol 15(5), 2019
PMID: 31112541
Analysis of the Rumen Microbiota of Beef Calves Supplemented During the Suckling Phase.
Lourenco JM, Callaway TR, Kieran TJ, Glenn TC, McCann JC, Stewart RL., Front Microbiol 10(), 2019
PMID: 31191476
Predator-prey interaction reveals local effects of high-altitude insect migration.
Krauel JJ, Brown VA, Westbrook JK, McCracken GF., Oecologia 186(1), 2018
PMID: 29101468
Microbial diversity and activity of an aged soil contaminated by polycyclic aromatic hydrocarbons.
Zhao X, Fan F, Zhou H, Zhang P, Zhao G., Bioprocess Biosyst Eng 41(6), 2018
PMID: 29546466
Microbial Diversity and Toxin Risk in Tropical Freshwater Reservoirs of Cape Verde.
Semedo-Aguiar AP, Pereira-Leal JB, Leite RB., Toxins (Basel) 10(5), 2018
PMID: 29734762
Physicochemical Drivers of Microbial Community Structure in Sediments of Lake Hazen, Nunavut, Canada.
Ruuskanen MO, St Pierre KA, St Louis VL, Aris-Brosou S, Poulain AJ., Front Microbiol 9(), 2018
PMID: 29922252
Diversity and abundance of conspicuous macrocrustaceans on coral reefs differing in level of degradation.
González-Gómez R, Briones-Fourzán P, Álvarez-Filip L, Lozano-Álvarez E., PeerJ 6(), 2018
PMID: 29910975
Staphylococcus aureus infection dynamics.
Pollitt EJG, Szkuta PT, Burns N, Foster SJ., PLoS Pathog 14(6), 2018
PMID: 29902272
Antarctic Cryptoendolithic Fungal Communities Are Highly Adapted and Dominated by Lecanoromycetes and Dothideomycetes.
Coleine C, Stajich JE, Zucconi L, Onofri S, Pombubpa N, Egidi E, Franks A, Buzzini P, Selbmann L., Front Microbiol 9(), 2018
PMID: 30008702
Autoreactive IgG and IgA B Cells Evolve through Distinct Subclass Switch Pathways in the Autoimmune Disease Pemphigus Vulgaris.
Ellebrecht CT, Mukherjee EM, Zheng Q, Choi EJ, Reddy SG, Mao X, Payne AS., Cell Rep 24(9), 2018
PMID: 30157430
Evaluating freshwater macroinvertebrates from eDNA metabarcoding: A river Nalón case study.
Fernández S, Rodríguez S, Martínez JL, Borrell YJ, Ardura A, García-Vázquez E., PLoS One 13(8), 2018
PMID: 30089147
Comparison of microbiomes of cold-water corals Primnoa pacifica and Primnoa resedaeformis, with possible link between microbiome composition and host genotype.
Goldsmith DB, Kellogg CA, Morrison CL, Gray MA, Stone RP, Waller RG, Brooke SD, Ross SW., Sci Rep 8(1), 2018
PMID: 30120375
Effects of water decontamination methods and bedding material on the gut microbiota.
Bidot WA, Ericsson AC, Franklin CL., PLoS One 13(10), 2018
PMID: 30359379
Anti-Inflammatory Activities of Pentaherbs formula and Its Influence on Gut Microbiota in Allergic Asthma.
Tsang MS, Cheng SW, Zhu J, Atli K, Chan BC, Liu D, Chan HY, Sun X, Chu IM, Hon KL, Lam CW, Shaw PC, Leung PC, Wong CK., Molecules 23(11), 2018
PMID: 30373169
SEDE-GPS: socio-economic data enrichment based on GPS information.
Sperlea T, Füser S, Boenigk J, Heider D., BMC Bioinformatics 19(suppl 15), 2018
PMID: 30497363
Citizen science charts two major "stomatotypes" in the oral microbiome of adolescents and reveals links with habits and drinking water composition.
Willis JR, González-Torres P, Pittis AA, Bejarano LA, Cozzuto L, Andreu-Somavilla N, Alloza-Trabado M, Valentín A, Ksiezopolska E, Company C, Onywera H, Montfort M, Hermoso A, Iraola-Guzmán S, Saus E, Labeeuw A, Carolis C, Hecht J, Ponomarenko J, Gabaldón T., Microbiome 6(1), 2018
PMID: 30522523
Construction sites in Miami-Dade County, Florida are highly favorable environments for vector mosquitoes.
Wilke ABB, Vasquez C, Petrie W, Caban-Martinez AJ, Beier JC., PLoS One 13(12), 2018
PMID: 30571764
Characterisation of Early-Life Fecal Microbiota in Susceptible and Healthy Pigs to Post-Weaning Diarrhoea.
Dou S, Gadonna-Widehem P, Rome V, Hamoudi D, Rhazi L, Lakhal L, Larcher T, Bahi-Jaber N, Pinon-Quintana A, Guyonvarch A, Huërou-Luron IL, Abdennebi-Najar L., PLoS One 12(1), 2017
PMID: 28072880
Profiling and validation of individual and patterns of Chlamydia trachomatis-specific antibody responses in trachomatous trichiasis.
Pickering H, Burr SE, Derrick T, Makalo P, Joof H, Hayward RD, Holland MJ., Parasit Vectors 10(1), 2017
PMID: 28288672
Competition and feeding ecology in two sympatric Xenopus species (Anura: Pipidae).
Vogt S, de Villiers FA, Ihlow F, Rödder D, Measey J., PeerJ 5(), 2017
PMID: 28439453
Cyanobacterial Diversity in Microbial Mats from the Hypersaline Lagoon System of Araruama, Brazil: An In-depth Polyphasic Study.
Ramos VMC, Castelo-Branco R, Leão PN, Martins J, Carvalhal-Gomes S, Sobrinho da Silva F, Mendonça Filho JG, Vasconcelos VM., Front Microbiol 8(), 2017
PMID: 28713360
Biogeographical assessment of myxomycete assemblages from Neotropical and Asian Palaeotropical forests
Dagamac NHA, Yuri K. Novozhilov, Steven L. Stephenson, Carlos Lado, Carlos Rojas, Thomas Edison E. dela Cruz, Martin Unterseher, Martin Schnittler., J Biogeogr 44(7), 2017
PMID: IND605874005
Overview of methodologies for T-cell receptor repertoire analysis.
Rosati E, Dowds CM, Liaskou E, Henriksen EKK, Karlsen TH, Franke A., BMC Biotechnol 17(1), 2017
PMID: 28693542
Microbial community structure and soil pH correspond to methane production in Arctic Alaska soils.
Wagner R, Zona D, Oechel W, Lipson D., Environ Microbiol 19(8), 2017
PMID: 28677239
Lentiviral Vector Promoter is Decisive for Aberrant Transcript Formation.
Scholz SJ, Fronza R, Bartholomä CC, Cesana D, Montini E, von Kalle C, Gil-Farina I, Schmidt M., Hum Gene Ther 28(10), 2017
PMID: 28825370
Species traits and connectivity constrain stochastic community re-assembly.
Holt RE, Brown CJ, Schlacher TA, Sheldon F, Balcombe SR, Connolly RM., Sci Rep 7(1), 2017
PMID: 29089543
First-trimester vaginal microbiome diversity: A potential indicator of preterm delivery risk.
Haque MM, Merchant M, Kumar PN, Dutta A, Mande SS., Sci Rep 7(1), 2017
PMID: 29170495
Microbial and Functional Diversity within the Phyllosphere of Espeletia Species in an Andean High-Mountain Ecosystem.
Ruiz-Pérez CA, Restrepo S, Zambrano MM., Appl Environ Microbiol 82(6), 2016
PMID: 26746719
Biliary Microbiota, Gallstone Disease and Infection with Opisthorchis felineus.
Saltykova IV, Petrov VA, Logacheva MD, Ivanova PG, Merzlikin NV, Sazonov AE, Ogorodova LM, Brindley PJ., PLoS Negl Trop Dis 10(7), 2016
PMID: 27447938
Taxa of the Nasal Microbiome Are Associated with Influenza-Specific IgA Response to Live Attenuated Influenza Vaccine.
Salk HM, Simon WL, Lambert ND, Kennedy RB, Grill DE, Kabat BF, Poland GA., PLoS One 11(9), 2016
PMID: 27643883

35 References

Daten bereitgestellt von Europe PubMed Central.

Neighbor species differentially alter resistance phenotypes in Plantago.
Barton KE, Bowers MD., Oecologia 150(3), 2006
PMID: 16944243
Diversity of planktonic foraminifera in deep-sea sediments.
Berger WH, Parker FL., Science 168(3937), 1970
PMID: 17731043
A quantitative index of land-use intensity in grasslands: integrating mowing, grazing and fertilization
Blüthgen N, Dormann CF, Prati D, Klaus VH, Kleinebecker T, Hölzel N., 2012
The Berger-Parker index as an effective tool for monitoring the biodiversity of disturbed soils: a case study on Mediterranean oribatid (Acari: Oribatida) assemblages
Migliorini M., 2007
On the correlations between certain diversity indices
DeBenedictis PA., 1973
Implementing large-scale and long-term functional biodiversity research: the Biodiversity Exploratories
Fischer M, Bossdorf O, Gockel S, Hänsel F, Hemp A, Hessenmöller D., 2010
The effects of arbuscular mycorrhizal fungi on direct and indirect defense metabolites of Plantago lanceolata L.
Fontana A, Reichelt M, Hempel S, Gershenzon J, Unsicker SB., J. Chem. Ecol. 35(7), 2009
PMID: 19568812
Structural equation modeling with the sem package in R
Fox J., 2006

Briscoe DA., 2002
Weak relationships between landscape characteristics and multiple facets of stream macroinvertebrate biodiversity in a boreal drainage basin
Kotanen J., 2008
Diversity and evenness: a unifying notion and its consequences
Hill MO., 1973
Structural equation modelling: guidelines for determining model fit
Mullen MR., 2008
Entropy and diversity
Jost L., 2006

Bos M., 1992
Measuring diversity: the importance of species similarity.
Leinster T, Cobbold CA., Ecology 93(3), 2012
PMID: 22624203

Magurran AE., 2004
Biological diversity in a changing world.
Magurran AE, Dornelas M., Philos. Trans. R. Soc. Lond., B, Biol. Sci. 365(1558), 2010
PMID: 20980308
Patterns of species abundance and diversity
May RM., 1975

Grace JB., 2002
Land use and host neighbor identity effects on arbuscular mycorrhizal fungal community composition
Morris EK, Buscot F, Herbst C, Meiners T, Obermaier E, Wäschke N., 2013
Opposite trends in response for Shannon and Simpson indices of landscape diversity
Nagendra H., 2002

Oksanen J, Blanchet FG, Kindt R, Legendre P, Minchin PR, O’Hara RB., 2012
Getting the measure of biodiversity.
Purvis A, Hector A., Nature 405(6783), 2000
PMID: 10821281

AUTHOR UNKNOWN, 2013
A mathematical theory of communication
Shannon C., 1948
Measurement of diversity
Simpson EH., 1949
A consumer’s guide to evenness indices
Wilson JB., 1996
Evolution and measurement of species diversity
Whittaker RH., 1972
Relationships among indices suggest that richness is an incomplete surrogate for grassland biodiversity
Willig MR., 2005
Root herbivore identity matters in plant-mediated interactions between root and shoot herbivores
van WH., 2007
Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®
Quellen

PMID: 25478144
PubMed | Europe PMC

Suchen in

Google Scholar