Skip to main content
SpringerLink
Log in

Community Diversity

  • Chapter
  • First Online:
Numerical Ecology with R

Part of the book series: Use R! ((USE R))

Abstract

In many people’s minds, the words “diversity” or “biodiversity” simply refer to the number of species in a given area, but actually there are far more dimensions to the concept of biodiversity. Species diversity itself can be defined and measured in a variety of ways. Other types of diversity exist at various levels of organization of the living world, ranging from genome to landscape. At the community level, functional diversity, i.e., the diversity of functional traits, has received much attention in recent years, as well as phylogenetic diversity. We will mostly focus here on species and communities and explore first various facets of taxonomic diversity. In this chapter you will get an overview of the concept of diversity in ecology; compute various measures of alpha species diversity; explore the concept of beta diversity; partition beta diversity into its local and species contributions; partition beta diversity into replacement, richness difference and nestedness; and get a brief introduction to the concept of functional diversity.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 79.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 99.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Notes

  1. 1.

    Note that a matrix of richness difference in the Podani family and the Sørensen group would have been fully Euclidean (Legendre 2014, Appendix S1, Table S1.4). Readers could apply this analysis to such a matrix and discover if the R 2 adj is larger. Legendre (2014, Fig. S6.2b) shows an example of PCoA ordination of a RichDiff S matrix.

  2. 2.

    Relating standard CWM matrices based on quantitative traits to environmental variables representing gradients through linear models (correlation, regression or RDA ) has been strongly criticized by Peres-Neto et al. (2017). In particular, when only the traits or only the environmental variables are important in structuring the species distributions, tests of correlations based on this approach have strongly inflated type I error. The authors recommend the fourth-corner approach (Sect. 6.11) instead.

Bibliography

  • Anderson, M.J., Ellingsen, K.E., McArdle, B.H.: Multivariate dispersion as a measure of beta diversity. Ecol. Lett. 9, 683–693 (2006)

    Article  Google Scholar 

  • Anderson, M.J., Crist, T.O., Chase, J.M., Vellend, M., Inouye, B.D., Freestone, A.L., Sanders, N.J., Cornell, H.V., Comita, L.S., Davies, K.F., Harrison, S.P., Kraft, N.J.B., Stegen, J.C., Swenson, N.G.: Navigating the multiple meanings of β diversity: a roadmap for the practicing ecologist. Ecol. Lett. 14, 19–28 (2011)

    Article  Google Scholar 

  • Baselga, A.: Partitioning the turnover and nestedness components of beta diversity. Glob. Ecol. Biogeogr. 19, 134–143 (2010)

    Article  Google Scholar 

  • Baselga, A.: The relationship between species replacement, dissimilarity derived from nestedness, and nestedness. Glob. Ecol. Biogeogr. 21, 1223–1232 (2012)

    Article  Google Scholar 

  • Botta-Dukát, Z.: Rao’s quadratic entropy as a measure of functional diversity based on multiple traits. J. Veg. Sci. 16, 533–540 (2005)

    Article  Google Scholar 

  • Cadotte, M.W., Davies, T.J.: Phylogenies in Ecology: A Guide to Concepts and Methods. Princeton University Press, Princeton (2016)

    Book  Google Scholar 

  • Carvalho, J.C., Cardoso, P., Gomes, P.: Determining the relative roles of species replacement and species richness differences in generating beta-diversity patterns. Glob. Ecol. Biogeogr. 21, 760–771 (2012)

    Article  Google Scholar 

  • de Bello, F., Lavergne, S., Meynard, C., Lepš, J., Thuiller, W.: The partitioning of diversity: showing Theseus a way out of the labyrinth. J. Veg. Sci. 21, 992–1000 (2010)

    Article  Google Scholar 

  • Ellison, A.M.: Partitioning diversity. Ecology. 91, 1962–1963 (2010)

    Article  Google Scholar 

  • Froese, R., Pauly, D. (Eds): FishBase. World Wide Web electronic publication. www.fishbase.org (2017)

  • Greenberg, J.H.: The measurement of linguistic diversity. Language. 32, 109–115 (1956)

    Article  Google Scholar 

  • Harrison, S., Ross, S.J., Lawton, J.H.: Beta-diversity on geographic gradients in Britain. J. Anim. Ecol. 61, 151–158 (1992)

    Article  Google Scholar 

  • Hill, M.O.: Diversity and evenness: a unifying notation and its consequences. Ecology. 54, 427–432 (1973)

    Article  Google Scholar 

  • Hurlbert, S.H.: The non-concept of species diversity: a critique and alternative parameters. Ecology. 52, 577–586 (1971)

    Article  Google Scholar 

  • Jost, L.: Entropy and diversity. Oikos. 113, 363–375 (2006)

    Article  Google Scholar 

  • Jost, L.: Partitioning diversity into independent alpha and beta components. Ecology. 88, 2427–2439 (2007)

    Article  Google Scholar 

  • Kempton, R.A.: Structure of species abundance and measurement of diversity. Biometrics. 35, 307–322 (1979)

    Article  Google Scholar 

  • Laliberté, E., Legendre, P.: A distance-based framework for measuring functional diversity from multiple traits. Ecology. 91, 299–305 (2010)

    Article  Google Scholar 

  • Lande, R.: Statistics and partitioning of species diversity, and similarity among multiple communities. Oikos. 76, 5–13 (1996)

    Article  Google Scholar 

  • Legendre, P.: Interpreting the replacement and richness difference components of beta diversity. Glob. Ecol. Biogeogr. 23, 1324–1334 (2014)

    Article  Google Scholar 

  • Legendre, P., De Cáceres, M.: Beta diversity as the variance of community data: dissimilarity coefficients and partitioning. Ecol. Lett. 16, 951–963 (2013)

    Article  Google Scholar 

  • Legendre, P., Fortin, M.J.: Comparison of the Mantel test and alternative approaches for detecting complex multivariate relationships in the spatial analysis of genetic data. Mol. Ecol. Resour. 10, 831–844 (2010)

    Article  Google Scholar 

  • Legendre, P., Legendre, L.: Numerical Ecology, 3rd English edn. Elsevier, Amsterdam (2012)

    Google Scholar 

  • Legendre, P., Borcard, D., Peres-Neto, P.R.: Analyzing beta diversity: partitioning the spatial variation of community composition data. Ecol. Monogr. 75, 435–450 (2005)

    Article  Google Scholar 

  • Lennon, J.J., Koleff, P., Greenwood, J.J.D., Gaston, K.J.: The geographical structure of British bird distributions: diversity, spatial turnover and scale. J. Anim. Ecol. 70, 966–979 (2001)

    Article  Google Scholar 

  • Loreau, M.: The challenges of biodiversity science. In: Kinne, O. (ed.) Excellence in Ecology, 17. International Ecology Institute, Oldendorf/Luhe (2010)

    Google Scholar 

  • Magurran, A.E.: Measuring Biological Diversity. Wiley-Blackwell, London (2004)

    Google Scholar 

  • Paradis, E.: Analysis of Phylogenetics and Evolution with R Use R! Series, 2nd edn. Springer, New York (2012)

    Book  MATH  Google Scholar 

  • Pélissier, R., Couteron, P., Dray, S., Sabatier, D.: Consistency between ordination techniques and diversity measurements: two strategies for species occurrence data. Ecology. 84, 242–251 (2003)

    Article  Google Scholar 

  • Peres-Neto, P.R., Dray, S., ter Braak, C.J.F.: Linking trait variation to the environment: critical issues with community-weighted mean correlation resolved by the fourth-corner approach. Ecography. 40, 806–816 (2017)

    Article  Google Scholar 

  • Pielou, E.C.: Ecological Diversity. Wiley, New York (1975)

    Google Scholar 

  • Podani, J., Schmera, D.: A new conceptual and methodological framework for exploring and explaining pattern in presence-absence data. Oikos. 120, 1625–1638 (2011)

    Article  Google Scholar 

  • Rao, C.R.: Diversity and dissimilarity coefficients: a unified approach. Theor. Popul. Biol. 21, 24–43 (1982)

    Article  MathSciNet  MATH  Google Scholar 

  • Rényi, A.: On measures of entropy and information. In J. Neyman (ed) Proceedings of the fourth Berkeley Symposium on mathematical statistics and probability. Univerity of California Press, Berkeley (1961)

    Google Scholar 

  • Shannon, C.E.: A mathematical theory of communications. Bell Syst. Tech. J. 27, 379–423 (1948)

    Article  MathSciNet  MATH  Google Scholar 

  • Sheldon. A. L.: Equitability indices: dependence on the species count. Ecology. 50, 466–467 (1969)

    Article  Google Scholar 

  • Simpson, E.H.: Measurement of diversity. Nature (Lond.) 163, 688 (1949)

    Article  MATH  Google Scholar 

  • Southwood, T.R.E.: Habitat, the templet for ecological strategies? J. Anim. Ecol. 46, 337–365 (1977)

    Article  Google Scholar 

  • Villéger, S., Mason, N.W.H., Mouillot, D.: New multidimensional functional diversity indices for a multifaceted framework in functional ecology. Ecology. 89, 2290–2301 (2008)

    Article  Google Scholar 

  • Whittaker, R.H.: Vegetation of the Siskiyou mountains, Oregon and California. Ecol. Monogr. 30, 279–338 (1960)

    Article  Google Scholar 

  • Whittaker, R.H.: Evolution and measurement of species diversity. Taxon. 21, 213–251 (1972)

    Article  Google Scholar 

  • Williams, P.H.: Mapping variations in the strength and breadth of biogeographic transition zones using species turnover. Proc. R. Soc. B Biol. Sci. 263, 579–588 (1996)

    Article  Google Scholar 

  • Pielou, E.C.: The measurement of diversity in different types of biological collections. Theor. Biol. 13, 131–144 (1966)

    Google Scholar 

  • Sanders, H.L.: Marine benthic diversity: a comparative study. American Naturalist 102, 243–282 (1968)

    Google Scholar 

  • Margalef, R. and Gutiérrez, E.: How to introduce connectance in the frame of an expression for diversity. American Naturalist 121, 601–607 (1983)

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Département de sciences biologiques, Université de Montréal, Montréal, Québec, Canada, H3C 3J7

    Daniel Borcard & Pierre Legendre

  2. UMR Chrono-environnement, Université Bourgogne Franche-Comté, Besançon, France

    François Gillet

Authors
  1. Daniel Borcard
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. François Gillet
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Pierre Legendre
    View author publications

    You can also search for this author in PubMed Google Scholar

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer International Publishing AG, part of Springer Nature

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Borcard, D., Gillet, F., Legendre, P. (2018). Community Diversity. In: Numerical Ecology with R. Use R!. Springer, Cham. https://doi.org/10.1007/978-3-319-71404-2_8

Download citation

Publish with us

Policies and ethics

Search

Navigation