I.16 Phylogenetics and Comparative Methods
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I.16 Phylogenetics and Comparative Methods David D. Ackerly OUTLINE 1. The role of phylogenetics in ecology 2. Phylogenies and the analysis of trait correlations 3. Phylogenetic signal: Pattern and significance 4. Phylogenetics and community ecology 5. Prospects for the future The study of ecology frequently draws on comparative observations and experiments that rely on the similarities and differences among species and the correlations among species traits and the environment. In such studies, consideration of the phylogenetic relationships among species provides valuable information for statistical inference and an understanding of evolutionary history underlying presentday ecological patterns. From a statistical perspective, related species do not necessarily provide independent data points for hypothesis tests, due to inheritance of shared characteristics from common ancestors. This similarity can be addressed through a variety of statistical techniques, including the widely used method of phylogenetic independent contrasts. Independent contrasts play a particularly valuable role in the analysis of trait and trait–environment correlations and may point toward alternative interpretations of comparative data. In community ecology, measures of the phylogenetic clustering or spacing of co-occurring species provide a useful tool to test alternative processes underlying community assembly. Co-occurrence of close relatives most likely reflects ecological filtering, in which related species with similar traits share the ability to tolerate local conditions . The reverse pattern of phylogenetic spacing of cooccurring species may reflect a variety of processes, and additional observations of species traits in relation to environment and interacting taxa will be necessary to address underlying processes. Use of comparative methods has increased dramatically with the rapid growth in phylogenetic information and computing power and will continue to play an important role in ecological research. GLOSSARY See figure 1 for illustrations of main terms. branch lengths. These may indicate either the number of inferred character changes or a measure of relative or absolute time along any particular branch connecting two nodes. If the molecular data underlying a phylogeny do not violate a molecular clock, a single rate may be imposed such that branch lengths will represent relative time, and contemporaneous taxa will be placed at the same distance from the root (i.e., the same age). If a molecular clock is violated, rate-smoothing methods have been developed to obtain the best-supported estimate of relative time. Fossils and biogeographic or paleoecological information may then be used to calibrate these branch lengths and convert them to units of absolute time. Rate-smoothing and calibration methods are fraught with difficulty, and branch lengths should be treated with caution. (Note that branch lengths may also be set arbitrarily for convenience when one is drawing trees, in which case they have no intrinsic biological meaning.) character states. Phylogenetic trees are reconstructed based on analysis of a matrix of characters, where each character can take on one of two or more states (binary or multistate, respectively) for each taxon in the group. Phylogenies can be reconstructed from molecular and/or morphological data, although the former are now much more common. Analyses that include morphological data are advantageous as they make it possible to incorporate taxa or fossils for which molecular data are not available. lineage. Thisreferstoasinglelineofancestor–descendant relationship, connecting nodes within a phylogeny. most recent common ancestor (MRCA). The MRCA is the most recent node that is shared by any two taxa in a tree. phylogenetic distance. The phylogenetic distance between two nodes or taxa refers to the sum of branch lengths from one tip (or internal node) down to the MRCA and back up to another tip (or node) of a tree. The phylogenetic distance matrix is an nn matrix (for n taxa) of such distances among all pairs of taxa, with 0s in the diagonal. phylogeny. A phylogeny, or phylogenetic tree, is a branching diagram showing the hierarchy of evolutionary relationships among a group of taxa (extant and/or extinct). Terminal taxa or tips are connected by branches to internal nodes that indicate a hypothesized ancestor. A clade includes all of the taxa (extant and extinct) that descend from a node. Phylogenies can be either rooted or unrooted , where the root represents the hypothesized ancestor of all taxa on the tree. polytomy. This refers to a node with three or more daughter nodes. A soft polytomy indicates uncertainty , where the true bifurcating relationships among the daughters are unknown. A hard polytomy represents a hypothesis of near simultaneous divergence where the sequence of individual speciation events cannot be meaningfully resolved. Most phylogenetic comparative methods treat...