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Phylogenetic Diversity

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Functional and Phylogenetic Ecology in R

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

Abstract

The objectives of this chapter are to first build a background understanding of why ecologists are interested in quantifying phylogenetic diversity (PD) and then to utilize R to quantify a variety of PD metrics that are the most frequently used. As in other chapters, we will focus on breaking down each analysis into its constituent parts to deepen our understanding of what exactly is being calculated and to facilitate your ability to write modifications of the code or novel code to generate PD analyses suited to your particular research objective.

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References

  1. Swenson, N.G. 2011. The role of evolutionary processes in producing biodiversity patterns, and the interrelationships between taxonomic, functional and phylogenetic biodiversity. American Journal of Botany 98: 472–480.

    Article  Google Scholar 

  2. Webb, C.O., D.D. Ackerly, M.A. McPeek, and M.J. Donoghue. 2002. Phylogenies and community ecology. Annual Review of Ecology and Systematics 33: 475–505.

    Article  Google Scholar 

  3. Faith, D.P. 1992. Conservation evaluation and phylogenetic diversity. Biological Conservation 61: 1–10.

    Article  Google Scholar 

  4. Faith, D.P. 1994. Genetic diversity and taxonomic priorities for conservation. Biological Conservation 68: 69–74.

    Article  Google Scholar 

  5. Faith, D.P. 2002. Quantifying biodiversity: A phylogenetic perspective. Conseration Biology 16: 248–252.

    Article  Google Scholar 

  6. Webb, C.O. 2000. Exploring the phylogenetic structure of ecological communities: An example for rainforest trees. The American Naturalist 156: 145–155.

    Article  Google Scholar 

  7. Tofts, R., and J. Silvertown. 2000. A phylogenetic approach to community assembly from a local species pool. Proceedings of the Royal Society B 267: 363–369.

    Article  Google Scholar 

  8. Cavender-Bares, J., D.D. Ackerly, D.A. Baum, and F.A. Bazzaz. 2004. Phylogenetic overdispersion in Floridian oak communities. The American Naturalist 163: 823–843.

    Article  Google Scholar 

  9. Cavender-Bares, J., A. Keen, and B. Miles. 2006. Phylogenetic structure of Floridian plant communities depends on taxonomic and spatial scale. Ecology 87(Supplement): S109–S122.

    Article  Google Scholar 

  10. Swenson, N.G., B.J. Enquist, J. Pither, J. Thompson, and J.K. Zimmerman. 2006. The problem and promise of scale dependency in community phylogenetics. Ecology 87: 2418–2424.

    Article  Google Scholar 

  11. Swenson, N.G., B.J. Enquist, J. Thompson, and J.K. Zimmerman. 2007. The influence of spatial and size scales on phylogenetic relatedness in tropical forest communities. Ecology 88: 1770–1780.

    Article  Google Scholar 

  12. Gillespie, R.G. 2004. Community assembly through adaptive radiation in Hawaiian spiders. Science 303: 356–359.

    Article  Google Scholar 

  13. The evolution of convergent structure in Caribbean Anolis communities. Systematic Biology 41: 403–420.

    Google Scholar 

  14. Verdu, M., and G. Pausas. 2007. Fire drives phylogenetic clustering in Mediterranean Basin woody plant communities. Journal of Ecology 95: 1316–1323.

    Article  Google Scholar 

  15. Cardillo, M., J.L. Gittleman, and A. Purvis. 2008. Global patterns in the phylogenetic structure of island mammal assemblages. Proceedings of the Royal Society B 275: 1549–1556.

    Article  Google Scholar 

  16. Anderson, T.M., M.A. Lachance, and W.T. Starmer. 2004. The relationship of phylogeny to community structure: The cactus yeast community. The American Naturalist 164: 709–721.

    Article  Google Scholar 

  17. MacArthur, R., and R. Levins. 1967. The limiting similarity, convergence, and divergence of coexisting species. The American Naturalist 101: 377–385.

    Article  Google Scholar 

  18. Keddy, P.A. 1992. Assembly and response rules: Two goals for predictive community ecology. Journal of Vegetation Science 3: 157–164.

    Article  Google Scholar 

  19. Hubbell, S.P. 1979. Tree dispersion, abundance, and diversity in a tropical dry forest. Science 203: 1299–1309.

    Article  Google Scholar 

  20. Hubbell, S.P., and R.B. Foster. 1986. Commonness and rarity in a Neotropical forest: Implications for tropical tree conservation. In Conservation biology: The science of scarcity and diversity, ed. M.E. Soule, 205–231. Sunderland, MA: Sinauer.

    Google Scholar 

  21. Hubbell, S.P. 2001. The unified neutral theory of biodiversity and biogeography. Princeton, NJ: Princeton University Press.

    Google Scholar 

  22. Mayfield, M.M., and J.M. Levine. 2010. Opposing effects of competitive exclusion on the phylogenetic structure of communities. Ecology Letters 13: 1085–1093.

    Article  Google Scholar 

  23. Jaccard, P. 1926. Le coefficient generique et le coefficient communaute dans la flore marocaine. Bulletin de la Societe Vaudoise des Sciences Naurelles 2: 385–403.

    Google Scholar 

  24. Jaccard, P. 1940. Coefficient generique reel et coefficient generique probable. Bulletin de la Societe Vaudoise des Sciences Naurelles 61: 117–136.

    Google Scholar 

  25. Maillefer, A. 1928. Les courbes de Willis: Repartition des especes dans les genres de differente etendue. Bulletin de la Societe Vaudoise des Sciences Naurelles 56: 617–631.

    Google Scholar 

  26. Elton, C. 1946. Competition and the structure of ecological communities. Journal of Animal Ecology 15: 54–68.

    Article  Google Scholar 

  27. Simberloff, D.S. 1970. Taxonomic diversity of island biotas. Evolution 24: 23–47.

    Article  Google Scholar 

  28. Grant, P.R., and I. Abbott. 1980. Interspecific competition, island biogeography and null hypotheses. Evolution 34: 332–341.

    Article  Google Scholar 

  29. Harvey, P.H., R.K. Colwell, J.W. Silvertown, and R.M. May. 1983. Null models in ecology. Annual Review of Ecology and Systematics 14: 189–211.

    Article  Google Scholar 

  30. Jarvinen, O. 1982. Species-to-genus ratios in biogeography: A historical note. Journal of Biogeography 9: 363–370.

    Article  Google Scholar 

  31. Wiens, J.J., and C.H. Graham. 2005. Niche conservatism: Integrating evolution, ecology and conservation biology. Annual Review of Ecology and Systematics 36: 519–539.

    Article  Google Scholar 

  32. Peterson, A.T., J. Soberon, and V. Sanchez-Cordero. 1999. Conservatism of ecological niches in evolutionary time. Science 285: 1265–1267.

    Article  Google Scholar 

  33. Wiens, J.J., D.D. Ackerly, A.P. Allen, B.L. Anacker, L.B. Buckley, H.V. Cornell, E.I. Damschen, T.J. Davies, J.A. Grytnes, S.P. Harrison, B.A. Hawkins, R.D. Holt, C.M. McCain, and P.R. Stephens. 2010. Niche conservatism as an emerging principle in ecology and conservation biology. Ecology Letters 13: 1310–1314.

    Article  Google Scholar 

  34. Webb, C.O., and M.J. Donoghue. 2005. Phylomatic: Tree assembly for applied phylogenetics. Molecular Ecology Notes 5: 181–183.

    Article  Google Scholar 

  35. Webb, C.O., C.H. Cannon, and S.J. Davies. 2008. Ecological organization, biogeography, and the phylogenetic structure of tropical forest tree communities. In Tropical forest community ecology, ed. W.P. Carson and S.S.A. Schnitzer, 79–97. Oxford: Blackwell.

    Google Scholar 

  36. Kembel, S.W., P.D. Cowan, M.R. Helmus, W.K. Cornwell, H. Morlon, D.D. Ackerly, S.P. Blomberg, and C.O. Webb. 2010. Picante: R tools for integrating phylogenies and ecology. Bioinformatics 26: 1463–1464.

    Article  Google Scholar 

  37. Vane-Wright, R.I., C.J. Humphries, and P.H. Williams. 1991. What to protect – Systematics and the agony of choice. Biological Conservation 55: 235–254.

    Article  Google Scholar 

  38. Harmon, L.J., J.T. Weir, C.D. Brock, R.E. Glor, and W. Challenger. 2008. GEIGER: Investigating evolutionary radiations. Bioinformatics 24: 129–131.

    Article  Google Scholar 

  39. Mooers, A.O., S.B. Heard, and E. Chrostowski. 2005. Evolutionary heritage as a metric for conservation. In Phylogeny and conservation, ed. A. Purvis, T.L. Brooks, and J.L. Gittleman, 120–138. Oxford: Oxford University Press.

    Google Scholar 

  40. Barker, G.M. 2002. Phylogenetic diversity: A quantitative framework for measurement of priority and achievement in biodiversity conservation. Biological Journal of the Linnean Society 76: 165–194.

    Article  Google Scholar 

  41. Kembel, S.W., and S.P. Hubbell. 2006. The phylogenetic structure of a neotropical forest tree community. Ecology 87(Supplement): S86–S99.

    Article  Google Scholar 

  42. Swenson, N.G., D.L. Erickson, X. Mi, N.A. Bourge, J. Forero-Montana, X. Ge, R. Howe, J.K. Lake, X. Liu, K. Ma, N. Pei, J. Thompson, M. Uriarte, A. Wolf, S.J. Wright, W. Ye, J. Zhang, J.K. Zimmerman, and W.J. Kress. 2012. Phylogenetic and functional alpha and beta diversity in temperate and tropical tree communities. Ecology 93: S112–S125.

    Article  Google Scholar 

  43. Yang, J., X. Ci, G. Zhang, N.G. Swenson, L. Sha, C.C. Baskin, J. Li, M. Cao, J.W.F. Slik, and L. Lin. in press. Functional and phylogenetic assembly in a Chinese tropical tree community across size classes, spatial scales and habitats. Functional Ecology.

    Google Scholar 

  44. Mi, X., N.G. Swenson, R. Valencia, W.J. Kress, D.L. Erickson, A. Perez-Castaneda, H. Ren, S.H. Su, N. Gunatilleke, S. Gunatilleke, Z. Hao, W. Ye, M. Cao, H.S. Suresh, H.S. Dattaraj, R. Sukumar, and K. Ma. 2012. The contribution of rare species to community phylogenetic diversity across a global network of forest plots. The American Naturalist 180: E17–E30.

    Article  Google Scholar 

  45. Webb, C.O., and N.C.A. Pitman. 2002. Phylogenetic balance and ecological evenness. Systematic Biology 51: 898–907.

    Article  Google Scholar 

  46. Rao, C.R. 1982. Diversity and dissimilarity coefficients: A unified approach. Theoretical Population Biology 21: 24–43.

    Article  MATH  MathSciNet  Google Scholar 

  47. Hardy, O.J., and B. Senterre. 2007. Characterizing the phylogenetic structure of communities by additive partitioning of phylogenetic diversity. Journal of Ecology 95: 493–506.

    Article  Google Scholar 

  48. Helmus, M.R., T.J. Bland, C.K. Williams, and A.R. Ives. 2007. Phylogenetic measures of biodiversity. The American Naturalist 169: E68–E83.

    Article  Google Scholar 

  49. Vellend, M., W.K. Cornwell, K. Magnuson-Ford, and A.O. Mooers. 2010. Measuring phylogenetic biodiversity. In Biological diversity: Frontiers in measurement and assessment, ed. A.E. Magurran and B.J. McGill, 193–206. Oxford: Oxford University Press.

    Google Scholar 

  50. Brown, W.L., and E.O. Wilson. 1956. Character displacement. Systematic Zoology 5: 49–65.

    Article  Google Scholar 

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Authors and Affiliations

  1. Michigan State University, East Lansing, MI, USA

    Nathan G. Swenson (Assistant Professor of Plant Biology)

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  1. Nathan G. Swenson
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Swenson, N.G. (2014). Phylogenetic Diversity. In: Functional and Phylogenetic Ecology in R. Use R!. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-9542-0_3

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