Phylogenetic Methods in Ecology

Abstract

Phylogenetic comparative methods, incorporating patterns of similarity among close relatives, are an important tool in the ecological research. In tests of adaptive hypotheses, examining interspecific correlations between traits and environmental conditions, independent contrasts and related methods address the statistical nonindependence among species due to common ancestry. In community ecology, patterns of co‐occurence among related species provide insights into community assembly processes. In conservation biology, phylogenetic diversity can be an important assessment tool to prioritize species assemblages. Developments in phyloinformatics and improved phylogenies for different groups will promote expanded use of comparative methods in many areas of ecology.

Key concepts

  • Comparative biology focuses on similarities and differences among species to test hypotheses in ecology, evolutionary biology and related fields.

  • Closely related species tend to be ecologically similar, reflecting their descent from a common ancestor. This similarity must be considered in tests of adaptive correlations between organismal traits and environmental conditions, as it can create statistical nonindependence among species.

  • The method of phylogenetic independent contrasts, which compares trait values of related species across a phylogeny, provides a robust method to address the nonindependence of species and is widely used in ecology.

  • A variety of processes influence the assembly of ecological communities. Communities may be composed of species that are ecologically similar, reflecting shared adaptations to the environment (known as environmental filtering), or species that are ecologically distinct, as predicted if biotic interactions such as competition or facilitation play an important role.

  • The study of phylogenetic community structure – the degree of relatedness of co‐occurring species – provides insight into the processes influencing community assembly. Co‐occurrence of close relatives is likely caused by environmental filtering, whereas a variety of processes may lead to co‐occurrence of more distant relatives, including competition, facilitation and convergent evolution.

  • Phylogenetic diversity – which can be measured as the sum of the branch lengths in a phylogeny – provides a valuable tool in conservation biology. Targeting areas with high phylogenetic diversity may be an efficient means to maximize conservation of taxa with high diversity of ecological and economic features.

  • Phylogenetic approaches are an important tool to integrate ecological and evolutionary processes across a range of temporal and spatial scales.

Keywords: community ecology; comparative methods; diversity; phylogeny; adaptive trait

Figure 1.

Conceptual illustration of the method of independent contrasts. (a) A hypothetical phylogeny for 8 species is illustrated with values for two correlated traits for the species at the tips (trait x above, trait y below). Step one in the calculation of contrasts involves calculation of the average trait values at the internal nodes of the phylogeny, proceeding down from the tips (shown in small type at each internal node). Independent contrasts are then calculated as the differences between the trait values at each set of adjacent nodes (bold italic type, in boxes at each node). (b) Scatterplot of the species trait values (N=8, R=0.89). (c) Scatterplot of independent contrasts (N=7, R=0.90, with correlation calculated through the origin). Note that the direction of subtraction at each node is arbitrary, but must be consistent for both traits at each node (here, the left node is subtracted from the right node). In this simplified illustration, branch lengths have not been considered (see Felsenstein, for further details).

Figure 2.

Analysis of interspecific correlations among leaf traits, using independent contrasts. (a) and (b) Scatterplot of species values for leaf lifespan versus leaf size and specific leaf area, respectively. Blue circles are data for flowering plant species, and red squares are for conifers. The strength of the associations is indicated by the correlation coefficients in the lower left corner of each panel. (c) and (d) Corresponding scatterplots of independent contrasts. Blue circles are contrasts between nodes within the flowering plant phylogeny, and squares are contrasts among conifers. The black X represents the contrast at the basal node between the two groups. For convenience, the subtraction at each node is arranged such that the contrast for leaf lifespan is positive, and then the contrast for the other trait is positive or negative, depending on the trait values. Reproduced with permission from Ackerly et al.. Copyright, American Institute of Biological Sciences.

Figure 3.

Illustration of the assembly of oak communities in northern Florida. Oak forests in this area occur in three distinct habitats, on different soil types. Oak species in each of these communities are drawn from distinct clades within the group, a pattern known as phylogenetic overdispersion. The physiological traits adapted to each of these different environments have evolved repeatedly within each of the three clades, a pattern of convergent evolution. Adapted with permission from Agrawal et al. and Cavender‐Bares et al.. Copyright, Ecological Society of America.

Figure 4.

Patterns of taxonomic and phylogenetic diversity in the flora of the Cape region of South Africa. (a) Richness of plant genera, per quarter degree square (colour scale corresponds to 10 quantile intervals). (b) phylogenetic diversity of genera, based on the sum of branch lengths for a phylogeny of genera in each square. (c) Residuals of a regression of phylogenetic diversity on richness, illustrating areas where phylogenetic diversity reveals higher or lower diversity relative to the number of genera. Adapted by permission from Macmillan Publishers Ltd, Forest et al., Copyright 2007.

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References

Ackerly DD (2000) Taxon sampling, correlated evolution and independent contrasts. Evolution 54: 1480–1492.

Ackerly DD (2003) Community assembly, niche conservatism and adaptive evolution in changing environments. International Journal of Plant Sciences 164: S165–S184.

Ackerly DD, Dudley S, Sultan S et al. (2000) The evolution of plant ecophysiological traits: recent advances and future directions. Bioscience 50: 979–995.

Ackerly DD and Reich PB (1999) Convergence and correlations among leaf size and function in seed plants: a comparative test using independent contrasts. American Journal of Botany 86: 1272–1281.

Agrawal AA, Ackerly DD, Adler F et al. (2007) Filling key gaps in population and community ecology. Frontiers in Ecology and the Environment 5: 145–152.

Bhaskar R, Valiente‐Banuet A and Ackerly DD (2007) Evolution of hydraulic traits in closely related species pairs from mediterranean and nonmediterranean environments of North America. New Phytologist 176: 718–726.

Bollback JP (2006) SIMMAP: stochastic character mapping of discrete traits on phylogenies. BMC Bioinformatics 7: 88.

Cavender‐Bares J, Ackerly DD, Baum D and Bazzaz FA (2004a) Phylogenetic overdispersion in Floridian oak communities. American Naturalist 163: 823–843.

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

Cavender‐Bares J, Kitajima K and Bazzaz FA (2004b) Multiple trait associations in relation to habitat differentiation among 17 Floridian oak species. Ecological Monographs 74: 635–662.

Chave J, Muller‐Landau HC, Baker TR et al. (2006) Regional and phylogenetic variation of wood density across 2456 Neotropical tree species. Ecological Applications 16: 2356–2367.

Clutton‐Brock TH and Harvey PH (1977) Primate ecology and social organization. Journal of Zoology 183: 1–39.

Cooper N, Rodríguez J and Purvis A (2008) A common tendency for phylogenetic overdispersion in mammalian assemblages. Proceedings of the the Royal Society of London, Biological Sciences 275: 2031–2037.

Darwin C (1859) On the Origin of Species. London: Murray.

DeSantis TZ, Brodie EL, Moberg JP et al. (2007) High‐density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment. Microbial Ecology 53: 371–383.

Diaz‐Uriarte R and Garland T (1996) Testing hypotheses of correlated evolution using phylogenetically independent contrasts: sensitivity to deviations from Brownian motion. Systematic Biology 45: 27–47.

Donoghue MJ (1989) Phylogenies and the analysis of evolutionary sequences, with examples from the seed plants. Evolution 43: 1137–1156.

Edwards EJ, Still CJ and Donoghue MJ (2007) The relevance of phylogeny to studies of global change. Trends in Ecology & Evolution 22: 243–249.

Faith DP (1994) Phylogenetic diversity: a general framework for the prediction of feature diversity. In: Forey PL, Humphries CJ and Vane‐Wright RI (eds) Systematics and Conservation Education, pp. 251–268. Oxford: Clarendon Press.

Felsenstein J (1985) Phylogenies and the comparative method. American Naturalist 125: 1–15.

Felsenstein J (2004) Inferring Phylogenics. Sunderland, MA: Sinauer.

Forest F, Grenyer R and Rouget M (2007) Preserving the evolutionary potential of floras in biodiversity hotspots. Nature 445: 757–760.

Garland TJ, Harvey PH and Ives AR (1992) Procedures for the analysis of comparative data using phylogenetically independent contrasts. Systematic Biology 41: 18–32.

Givnish TJ (1980) Ecological constraints on the evolution of breeding systems in seed plants: Dioecy and dispersal in gymnosperms. Evolution 34: 959–972.

Gotelli NJ (2000) Null model analysis of species co‐occurrence patterns. Ecology 81: 2606–2621.

Gould S and Lewontin R (1979) The spandrels of San Marco and the Panglossian paradigm: a critique of the adaptationist programme. Proceedings of the Royal Society of London. Series B 205: 581–598.

Grafen A (1989) The phylogenetic regression. Philosophical Transactions of the Royal Society of London. Series B 326: 119–157.

Harvey PH and Pagel M (1991) The Comparative Method in Evolutionary Biology. Oxford: Oxford University Press.

Horner‐Devine MC and Bohannan BJ (2006) Phylogenetic clustering and overdispersion in bacterial communities. Ecology 87: S100–S108.

Kembel SW and Hubbell SP (2006) The phylogenetic structure of a neotropical forest tree community. Ecology 87: S86–S99.

Kraft NJB, Cornwell WK, Webb CO and Ackerly DD (2007) Trait evolution, community assembly and the phylogenetic structure of ecological communities. American Naturalist 170: 271–283.

Maddison WP (1990) A method for testing the correlated evolution of two binary characters: are gains or losses concentrated on certain branches of a phylogenetic tree? Evolution 44: 539–557.

Maddison WP and Maddison DR (1992) MacClade: Analysis of Phylogeny and Character Evolution, Version 3. Sunderland, MA: Sinauer.

Martins EP (1994) Estimating the rate of phenotypic evolution from comparative data. American Naturalist 144: 193–209.

Pagel M (1994) Detecting correlated evolution on phylogenies: a general method for the comparative analysis of discrete characters. Proceedings of the Royal Society of London. Series B 255: 37–45.

Ridley M (1983) The Explanation of Organic Diversity. Oxford: Oxford University Press.

Salisbury EJ (1974) Seed size and mass in relation to environment. Proceedings of the Royal Society of London. Series B 186: 83–88.

Silvertown J, McConway K and Gowing D (2006) Absence of phylogenetic signal in the niche structure of meadow plant communities. Proceedings of the Royal Society of London. Series B 273: 39–44.

Swenson NG, Enquist BJ, Pither J, Thompson J and Zimmerman JK (2006) The problem and promise of scale dependency in community phylogenetics. Ecology 87: 2418–2424.

Valiente‐Banuet A and Verdú M (2007) Facilitation can increase the phylogenetic diversity of plant communities. Ecology Letters 10: 1029–1036.

Webb CO (2000) Exploring the phylogenetic structure of ecological communites: an example for rain forest trees. American Naturalist 156: 145–155.

Webb CO, Ackerly DD and Kembel SW (2008) Phylocom: software for the analysis of phylogenetic community structure and trait evolution. Bioinformatics 24: 2098–2100.

Webb CO, Ackerly DD, McPeek M and Donoghue MJ (2002) Phylogenies and community ecology. Annual Review of Ecology and Systematics 33: 475–505.

Webb CO and Donoghue MJ (2005) Phylomatic: tree assembly for applied phylogenetics. Molecular Ecology Notes 5: 181–183.

Westoby M, Cunningham SA, Fonseca CM, Overton JM and Wright IJ (1998) Phylogeny and variation in light capture area deployed per unit investment in leaves: designs for selecting study species with a view to generalizing. In: Lambers H, Poorter H and Van Vuuren MMI (eds) Inherent Variation in Plant Growth: Physiological Mechanisms and Ecological Consequences, pp. 539–566. Leiden, The Netherlands: Backhuys Publishers.

Westoby M, Leishman M and Lord J (1995) Issues of interpretation after relating comparative datasets to phylogeny. Journal of Ecology 83: 892–893.

Woodward FI and Diament AD (1991) Functional approaches to predicting the ecological effects of global change. Functional Ecology 5: 202–212.

Further Reading

Blomberg SP and Garland TJ (2002) Tempo and mode in evolution: phylogenetic inertia, adaptation and comparative methods. Journal of Evolionary Biology 15: 899–910.

Freckleton RP, Harvey PH and Pagel M (2002) Phylogenetic analysis and comparative data: a test and review of the evidence. American Naturalist 160: 712–726.

Pagel MD (1999) Inferring the historical patterns of biological evolution. Nature 401: 877–884.

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How to Cite close
Ackerly, David D(Mar 2009) Phylogenetic Methods in Ecology. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0021223]