, Volume 157, Issue 3, pp 485–495 | Cite as

A comparative test of phylogenetic diversity indices

  • Oliver Schweiger
  • Stefan Klotz
  • Walter Durka
  • Ingolf Kühn
Community Ecology - Methods Paper


Traditional measures of biodiversity, such as species richness, usually treat species as being equal. As this is obviously not the case, measuring diversity in terms of features accumulated over evolutionary history provides additional value to theoretical and applied ecology. Several phylogenetic diversity indices exist, but their behaviour has not yet been tested in a comparative framework. We provide a test of ten commonly used phylogenetic diversity indices based on 40 simulated phylogenies of varying topology. We restrict our analysis to a topological fully resolved tree without information on branch lengths and species lists with presence–absence data. A total of 38,000 artificial communities varying in species richness covering 5–95% of the phylogenies were created by random resampling. The indices were evaluated based on their ability to meet a priori defined requirements. No index meets all requirements, but three indices turned out to be more suitable than others under particular conditions. Average taxonomic distinctness (AvTD) and intensive quadratic entropy (J) are calculated by averaging and are, therefore, unbiased by species richness while reflecting phylogeny per se well. However, averaging leads to the violation of set monotonicity, which requires that species extinction cannot increase the index. Total taxonomic distinctness (TTD) sums up distinctiveness values for particular species across the community. It is therefore strongly linked to species richness and reflects phylogeny per se weakly but satisfies set monotonicity. We suggest that AvTD and J are best applied to studies that compare spatially or temporally rather independent communities that potentially vary strongly in their phylogenetic composition—i.e. where set monotonicity is a more negligible issue, but independence of species richness is desired. In contrast, we suggest that TTD be used in studies that compare rather interdependent communities where changes occur more gradually by species extinction or introduction. Calculating AvTD or TTD, depending on the research question, in addition to species richness is strongly recommended.


Phylogenetic tree Pure diversity Quadratic entropy Taxic weights Taxonomic distinctness 


  1. Bates D, Sarkar D (2006) lme4: linear mixed-effects models using S4 classes. R package version 0.995-2. Available at: http://www.r-project.org
  2. Bates CR, Saunders GW, Chopin T (2005) An assessment of two taxonomic distinctness indices for detecting seaweed assemblage responses to environmental stress. Bot Mar 48:231–243CrossRefGoogle Scholar
  3. Clarke KR, Warwick RM (1998) A taxonomic distinctness index and its statistical properties. J Appl Ecol 35:523–531CrossRefGoogle Scholar
  4. Clarke KR, Warwick RM (2001a) A further biodiversity index applicable to species lists: variation in taxonomic distinctness. Mar Ecol Prog Ser 216:265–278CrossRefGoogle Scholar
  5. Clarke KR, Warwick RM (2001b) Change in marine communities: an approach to statistical analysis and interpretation. Primer-E, PlymouthGoogle Scholar
  6. Crozier RH (1997) Preserving the information content of species: genetic diversity, phylogeny, and conservation worth. Annu Rev Ecol Syst 28:243–268CrossRefGoogle Scholar
  7. Diaz S, Cabido M (2001) Vive la difference: plant functional diversity matters to ecosystem processes. Trends Ecol Evol 16:646–655CrossRefGoogle Scholar
  8. Diniz-Filho JAF (2004) Phylogenetic diversity and conservation priorities under distinct models of phenotypic evolution. Conserv Biol 18:698–704CrossRefGoogle Scholar
  9. Ellingsen KE, Clarke KR, Somerfield PJ, Warwick RM (2005) Taxonomic distinctness as a measure of diversity applied over a large scale: the benthos of the Norwegian continental shelf. J Anim Ecol 74:1069–1079CrossRefGoogle Scholar
  10. Faith DP (1992) Conservation evaluation and phylogenetic diversity. Biol Conserv 61:1–10CrossRefGoogle Scholar
  11. Faith DP (1994) Phylogenetic pattern and the quantification of organismal biodiversity. Philos Trans R Soc B 345:45–58CrossRefGoogle Scholar
  12. Farris JS (1969) A successive approximations approach to character weighting. Syst Zool 18:374–385CrossRefGoogle Scholar
  13. Gittleman JL, Kot M (1990) Adaptation—statistics and a null model for estimating phylogenetic effects. Syst Zool 39:227–241CrossRefGoogle Scholar
  14. Hacker JE, Cowlishaw G, Williams PH (1998) Patterns of African primate diversity and their evaluation for the selection of conservation areas. Biol Conserv 84:251–262CrossRefGoogle Scholar
  15. Heard SB, Mooers AO (2000) Phylogenetically patterned speciation rates and extinction risks change the loss of evolutionary history during extinctions. Proc R Soc B Biol Sci 267:613–620CrossRefGoogle Scholar
  16. Heino J, Soininen J, Lappalainen J, Virtanen R (2005) The relationship between species richness and taxonomic distinctness in freshwater organisms. Limnol Oceanogr 50:978–986CrossRefGoogle Scholar
  17. Izsak J, Papp L (1995) Application of the quadratic entropy indices for diversity studies of drosophilid assemblages. Environ Ecol Stat 2:213–224CrossRefGoogle Scholar
  18. Izsak J, Papp L (2000) A link between ecological diversity indices and measures of biodiversity. Ecol Model 130:151–156CrossRefGoogle Scholar
  19. Keith M, Chimimba CT, Reyers B, van Jaarsveld AS (2005) Taxonomic and phylogenetic distinctiveness in regional conservation assessments: a case study based on extant South African Chiroptera and Carnivora. Anim Conserv 8:279–288CrossRefGoogle Scholar
  20. Knapp S, Kühn I, Schweiger O, Klotz S (2008) Challenging urban species diversity: contrasting phylogenetic patterns across plant functional groups in Germany. Ecol Lett (in press)Google Scholar
  21. Krajewski C (1994) Phylogenetic measures of biodiversity—a comparison and critique. Biol Conserv 69:33–39CrossRefGoogle Scholar
  22. Kühn I, Böhning-Gaese K, Cramer W, Klotz S (2008) Macroecology meets global change research. Global Ecol Biogeogr 17:3–4Google Scholar
  23. La Sorte FA, Boecklen WJ (2005) Changes in the diversity structure of avian assemblages in North America. Global Ecol Biogeogr 14:367–378CrossRefGoogle Scholar
  24. Lavorel S, McIntyre S, Landsberg J, Forbes TDA (1997) Plant functional classifications: from general groups to specific groups based on response to disturbance. Trends Ecol Evol 12:474–478CrossRefGoogle Scholar
  25. Mac Nally R (2000) Regression and model-building in conservation biology, biogeography and ecology: the distinction between—and reconciliation of—‘predictive’ and ‘explanatory’ models. Biodivers Conserv 9:655–671CrossRefGoogle Scholar
  26. Mason NWH, MacGillivray K, Steel JB, Wilson JB (2003) An index of functional diversity. J Veg Sci 14:571–578CrossRefGoogle Scholar
  27. Oksanen J (2006) vegan: community ecology package. R package version 1.8-2. Available at: http://www.r-project.org
  28. Parga IC, Saiz JCM, Humphries CJ, Williams PH (1996) Strengthening the natural and national park system of Iberia to conserve vascular plants. Bot J Linn Soc 121:189–206Google Scholar
  29. Pavoine S, Ollier S, Dufour AB (2005) Is the originality of a species measurable? Ecol Lett 8:579–586CrossRefGoogle Scholar
  30. Petchey OL, Gaston KJ (2002) Functional diversity (FD), species richness and community composition. Ecol Lett 5:402–411CrossRefGoogle Scholar
  31. Petchey OL, Hector A, Gaston KJ (2004) How do different measures of functional diversity perform? Ecology 85:847–857CrossRefGoogle Scholar
  32. Pinheiro J, Bates D (2006) nlme: linear and nonlinear mixed effects models. R package version 3.1-75. Available at: http://www.r-project.org
  33. Posadas P, Esquivel DRM, Crisci JV (2001) Using phylogenetic diversity measures to set priorities in conservation: an example from southern South America. Conserv Biol 15:1325–1334CrossRefGoogle Scholar
  34. Poulin R, Mouillot D (2004) The evolution of taxonomic diversity in helminth assemblages of mammalian hosts. Evol Ecol 18:231–247CrossRefGoogle Scholar
  35. Quinn GP, Keough MJ (2002) Experimental design and data analyses for biologists. Cambridge University Press, CambridgeGoogle Scholar
  36. R Development Core Team (2005) R: a language and environment for statistical computing. R Foundation for Statistical Computing, ViennaGoogle Scholar
  37. Rao CR (1982) Diversity and dissimilarity coefficients—a unified approach. Theor Popul Biol 21:24–43CrossRefGoogle Scholar
  38. Ricotta C, Avena GC (2003) An information-theoretical measure of taxonomic diversity. Acta Biotheor 51:35–41PubMedCrossRefGoogle Scholar
  39. Rodrigues ASL, Gaston KJ (2002) Maximising phylogenetic diversity in the selection of networks of conservation areas. Biol Conserv 105:103–111CrossRefGoogle Scholar
  40. Rogers SI, Clarke KR, Reynolds JD (1999) The taxonomic distinctness of coastal bottom-dwelling fish communities of the North-east Atlantic. J Anim Ecol 68:769–782CrossRefGoogle Scholar
  41. Sechrest W, Brooks TM, da Fonseca GAB, Konstant WR, Mittermeier RA, Purvis A, Rylands AB, Gittleman JL (2002) Hotspots and the conservation of evolutionary history. Proc Natl Acad Sci USA 99:2067–2071PubMedCrossRefGoogle Scholar
  42. Settele J, Hammen V, Hulme P, Karlson U, Klotz S, Kotarac M, Kunin W, Marion G, O’Connor M, Petanidou T, Peterson K, Potts S, Pritchard H, Pysek P, Rounsevell M, Spangenberg J, Steffan-Dewenter I, Sykes M, Vighi M, Zobel M, Kuhn I (2005) ALARM: Assessing LArge-scale environmental Risks for biodiversity with tested Methods. Gaia 14:69–72Google Scholar
  43. Smith B, Wilson JB (1996) A consumer’s guide to evenness indices. Oikos 76:70–82CrossRefGoogle Scholar
  44. Solow AR, Polasky S, Broadus J (1993) On the measurement of biological diversity. J Environ Econ Manage 24:60–68CrossRefGoogle Scholar
  45. Soutullo A, Dodsworth S, Heard SB, Mooers AO (2005) Distribution and correlates of carnivore phylogenetic diversity across the Americas. Anim Conserv 8:249–258CrossRefGoogle Scholar
  46. Strauss SY, Webb CO, Salamin N (2006) Exotic taxa less related to native species are more invasive. Proc Natl Acad Sci USA 103:5841–5845PubMedCrossRefGoogle Scholar
  47. ter Braak CJF (1986) Canonical correspondence analysis: a new eigenvector technique for multivariate direct gradient analysis. Ecology 67:1167–1179CrossRefGoogle Scholar
  48. Tilman D, Knops J, Wedin D, Reich P, Ritchie M, Siemann E (1997) The influence of functional diversity and composition on ecosystem processes. Science 277:1300–1302CrossRefGoogle Scholar
  49. Torres NM, Diniz-Filho JAF (2004) Phylogenetic autocorrelation and evolutionary diversity of Carnivora (Mammalia) in conservation units of the New World. Genet Mol Biol 27:511–516Google Scholar
  50. Vane-Wright RI, Humphries CJ, Williams PH (1991) What to protect—systematics and the agony of choice. Biol Conserv 55:235–254CrossRefGoogle Scholar
  51. von Euler F, Svensson S (2001) Taxonomic distinctness and species richness as measures of functional structure in bird assemblages. Oecologia 129:304–311CrossRefGoogle Scholar
  52. Walsh C, Mac Nally R (2005) hier.part: Hierarchical Partitioning. R package version 1.0–1. Available at: http://www.r-project.org
  53. Warwick RM, Clarke KR (1995) New ‘biodiversity’ measures reveal a decrease in taxonomic distinctness with increasing stress. Mar Ecol Prog Ser 129:301–305CrossRefGoogle Scholar
  54. Warwick RM, Clarke KR (1998) Taxonomic distinctness and environmental assessment. J Appl Ecol 35:532–543CrossRefGoogle Scholar
  55. Warwick RM, Clarke KR (2001) Practical measures of marine biodiversity based on relatedness of species. Oceanogr Mar Biol 39:207–231Google Scholar
  56. Webb CO, Ackerly DD, Mcpeek MA, Donoghue MJ (2002) Phylogenies and community ecology. Annu Rev Ecol Syst 33:475–505CrossRefGoogle Scholar
  57. Weitzman ML (1992) On diversity. Q J Econ 107:363–405CrossRefGoogle Scholar
  58. Williams PH, Humphries CJ (1996) Comparing character diversity among biotas. In: Gaston KJ (ed) Biodiversity: a biology of numbers and differences. Blackwell Science, Oxford, pp 54–76Google Scholar
  59. Woodward FI, Cramer W (1996) Plant functional types and climatic changes: introduction. J Veg Sci 7:306–308CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  • Oliver Schweiger
    • 1
    • 2
  • Stefan Klotz
    • 1
    • 2
  • Walter Durka
    • 1
  • Ingolf Kühn
    • 1
    • 2
  1. 1.Department of Community EcologyUFZ—Helmholtz Centre for Environmental ResearchHalleGermany
  2. 2.Virtual Institute for MacroecologyHalleGermany

Personalised recommendations