Phylogenetic Methods in Ecology


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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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.

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