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A comparative test of phylogenetic diversity indices

  • Community Ecology - Methods Paper
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Abstract

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.

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References

  • 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

  • Bates CR, Saunders GW, Chopin T (2005) An assessment of two taxonomic distinctness indices for detecting seaweed assemblage responses to environmental stress. Bot Mar 48:231–243

    Article  Google Scholar 

  • Clarke KR, Warwick RM (1998) A taxonomic distinctness index and its statistical properties. J Appl Ecol 35:523–531

    Article  Google Scholar 

  • Clarke KR, Warwick RM (2001a) A further biodiversity index applicable to species lists: variation in taxonomic distinctness. Mar Ecol Prog Ser 216:265–278

    Article  Google Scholar 

  • Clarke KR, Warwick RM (2001b) Change in marine communities: an approach to statistical analysis and interpretation. Primer-E, Plymouth

    Google Scholar 

  • Crozier RH (1997) Preserving the information content of species: genetic diversity, phylogeny, and conservation worth. Annu Rev Ecol Syst 28:243–268

    Article  Google Scholar 

  • Diaz S, Cabido M (2001) Vive la difference: plant functional diversity matters to ecosystem processes. Trends Ecol Evol 16:646–655

    Article  Google Scholar 

  • Diniz-Filho JAF (2004) Phylogenetic diversity and conservation priorities under distinct models of phenotypic evolution. Conserv Biol 18:698–704

    Article  Google Scholar 

  • 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 74:1069–1079

    Article  Google Scholar 

  • Faith DP (1992) Conservation evaluation and phylogenetic diversity. Biol Conserv 61:1–10

    Article  Google Scholar 

  • Faith DP (1994) Phylogenetic pattern and the quantification of organismal biodiversity. Philos Trans R Soc B 345:45–58

    Article  CAS  Google Scholar 

  • Farris JS (1969) A successive approximations approach to character weighting. Syst Zool 18:374–385

    Article  Google Scholar 

  • Gittleman JL, Kot M (1990) Adaptation—statistics and a null model for estimating phylogenetic effects. Syst Zool 39:227–241

    Article  Google Scholar 

  • Hacker JE, Cowlishaw G, Williams PH (1998) Patterns of African primate diversity and their evaluation for the selection of conservation areas. Biol Conserv 84:251–262

    Article  Google Scholar 

  • 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 267:613–620

    Article  CAS  Google Scholar 

  • Heino J, Soininen J, Lappalainen J, Virtanen R (2005) The relationship between species richness and taxonomic distinctness in freshwater organisms. Limnol Oceanogr 50:978–986

    Article  Google Scholar 

  • Izsak J, Papp L (1995) Application of the quadratic entropy indices for diversity studies of drosophilid assemblages. Environ Ecol Stat 2:213–224

    Article  Google Scholar 

  • Izsak J, Papp L (2000) A link between ecological diversity indices and measures of biodiversity. Ecol Model 130:151–156

    Article  Google Scholar 

  • 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 8:279–288

    Article  Google Scholar 

  • 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)

  • Krajewski C (1994) Phylogenetic measures of biodiversity—a comparison and critique. Biol Conserv 69:33–39

    Article  Google Scholar 

  • Kühn I, Böhning-Gaese K, Cramer W, Klotz S (2008) Macroecology meets global change research. Global Ecol Biogeogr 17:3–4

    Google Scholar 

  • La Sorte FA, Boecklen WJ (2005) Changes in the diversity structure of avian assemblages in North America. Global Ecol Biogeogr 14:367–378

    Article  Google Scholar 

  • 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 12:474–478

    Article  Google Scholar 

  • 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 9:655–671

    Article  Google Scholar 

  • Mason NWH, MacGillivray K, Steel JB, Wilson JB (2003) An index of functional diversity. J Veg Sci 14:571–578

    Article  Google Scholar 

  • Oksanen J (2006) vegan: community ecology package. R package version 1.8-2. Available at: http://www.r-project.org

  • 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 121:189–206

    Google Scholar 

  • Pavoine S, Ollier S, Dufour AB (2005) Is the originality of a species measurable? Ecol Lett 8:579–586

    Article  Google Scholar 

  • Petchey OL, Gaston KJ (2002) Functional diversity (FD), species richness and community composition. Ecol Lett 5:402–411

    Article  Google Scholar 

  • Petchey OL, Hector A, Gaston KJ (2004) How do different measures of functional diversity perform? Ecology 85:847–857

    Article  Google Scholar 

  • 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

  • Posadas P, Esquivel DRM, Crisci JV (2001) Using phylogenetic diversity measures to set priorities in conservation: an example from southern South America. Conserv Biol 15:1325–1334

    Article  Google Scholar 

  • Poulin R, Mouillot D (2004) The evolution of taxonomic diversity in helminth assemblages of mammalian hosts. Evol Ecol 18:231–247

    Article  Google Scholar 

  • Quinn GP, Keough MJ (2002) Experimental design and data analyses for biologists. Cambridge University Press, Cambridge

    Google Scholar 

  • R Development Core Team (2005) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna

    Google Scholar 

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

    Article  Google Scholar 

  • Ricotta C, Avena GC (2003) An information-theoretical measure of taxonomic diversity. Acta Biotheor 51:35–41

    Article  PubMed  CAS  Google Scholar 

  • Rodrigues ASL, Gaston KJ (2002) Maximising phylogenetic diversity in the selection of networks of conservation areas. Biol Conserv 105:103–111

    Article  Google Scholar 

  • Rogers SI, Clarke KR, Reynolds JD (1999) The taxonomic distinctness of coastal bottom-dwelling fish communities of the North-east Atlantic. J Anim Ecol 68:769–782

    Article  Google Scholar 

  • 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 99:2067–2071

    Article  PubMed  CAS  Google Scholar 

  • 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 14:69–72

    Google Scholar 

  • Smith B, Wilson JB (1996) A consumer’s guide to evenness indices. Oikos 76:70–82

    Article  Google Scholar 

  • Solow AR, Polasky S, Broadus J (1993) On the measurement of biological diversity. J Environ Econ Manage 24:60–68

    Article  Google Scholar 

  • Soutullo A, Dodsworth S, Heard SB, Mooers AO (2005) Distribution and correlates of carnivore phylogenetic diversity across the Americas. Anim Conserv 8:249–258

    Article  Google Scholar 

  • Strauss SY, Webb CO, Salamin N (2006) Exotic taxa less related to native species are more invasive. Proc Natl Acad Sci USA 103:5841–5845

    Article  PubMed  CAS  Google Scholar 

  • ter Braak CJF (1986) Canonical correspondence analysis: a new eigenvector technique for multivariate direct gradient analysis. Ecology 67:1167–1179

    Article  Google Scholar 

  • Tilman D, Knops J, Wedin D, Reich P, Ritchie M, Siemann E (1997) The influence of functional diversity and composition on ecosystem processes. Science 277:1300–1302

    Article  CAS  Google Scholar 

  • Torres NM, Diniz-Filho JAF (2004) Phylogenetic autocorrelation and evolutionary diversity of Carnivora (Mammalia) in conservation units of the New World. Genet Mol Biol 27:511–516

    Google Scholar 

  • Vane-Wright RI, Humphries CJ, Williams PH (1991) What to protect—systematics and the agony of choice. Biol Conserv 55:235–254

    Article  Google Scholar 

  • von Euler F, Svensson S (2001) Taxonomic distinctness and species richness as measures of functional structure in bird assemblages. Oecologia 129:304–311

    Article  Google Scholar 

  • Walsh C, Mac Nally R (2005) hier.part: Hierarchical Partitioning. R package version 1.0–1. Available at: http://www.r-project.org

  • Warwick RM, Clarke KR (1995) New ‘biodiversity’ measures reveal a decrease in taxonomic distinctness with increasing stress. Mar Ecol Prog Ser 129:301–305

    Article  Google Scholar 

  • Warwick RM, Clarke KR (1998) Taxonomic distinctness and environmental assessment. J Appl Ecol 35:532–543

    Article  Google Scholar 

  • Warwick RM, Clarke KR (2001) Practical measures of marine biodiversity based on relatedness of species. Oceanogr Mar Biol 39:207–231

    Google Scholar 

  • Webb CO, Ackerly DD, Mcpeek MA, Donoghue MJ (2002) Phylogenies and community ecology. Annu Rev Ecol Syst 33:475–505

    Article  Google Scholar 

  • Weitzman ML (1992) On diversity. Q J Econ 107:363–405

    Article  Google Scholar 

  • 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 54–76

    Google Scholar 

  • Woodward FI, Cramer W (1996) Plant functional types and climatic changes: introduction. J Veg Sci 7:306–308

    Article  Google Scholar 

Download references

Acknowledgements

We thank Thomas Freina for providing a software for generating artificial phylogenies. This work was made possible by the Virtual Institute for Macroecology, (Kühn et al. 2008; http://www.macroecology.org), funded by the Helmholtz Association of German Research Centres. We further acknowledge the support of European Commission Framework Programme 6 Integrated Project ALARM (Assessing LArge scale environmental Risks with tested Methods; GOCE-CT-2003-506675, see Settele et al. 2005).

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Authors and Affiliations

  1. Department of Community Ecology, UFZ—Helmholtz Centre for Environmental Research, Theodor-Lieser-Street 4, 06210, Halle, Germany

    Oliver Schweiger, Stefan Klotz, Walter Durka & Ingolf Kühn

  2. Virtual Institute for Macroecology, Theodor-Lieser-Street 4, 06120, Halle, Germany

    Oliver Schweiger, Stefan Klotz & Ingolf Kühn

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  1. Oliver Schweiger
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  2. Stefan Klotz
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  3. Walter Durka
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  4. Ingolf Kühn
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Correspondence to Oliver Schweiger.

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Communicated by Wolf Mooij.

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Schweiger, O., Klotz, S., Durka, W. et al. A comparative test of phylogenetic diversity indices. Oecologia 157, 485–495 (2008). https://doi.org/10.1007/s00442-008-1082-2

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