TY - JOUR AU - Abouheif, E. PY - 1998 TI - Random trees and the comparative method: A cautionary tale SP - 1197-1204 JF - Evolution VL - 52 IS - 4 Y2 - Aug N1 - ISI:000075753100023 N1 - KW - allometry; comparative method; independent contrasts; phylogeny; random trees; Rensch's rule; sexual size dimorphism Sexual size dimorphism; phylogenetically independent contrasts; correlated evolution; continuous characters; sensitivity; simulation; allometry; phylogeny; biology N2 - One of the toughest problems facing comparative biology is the paucity of robust phylogenetic hypotheses for many taxonomic groups. Martins (1996) proposed a method to analyze comparative data in the absence of a known phylogeny using randomly generated trees. Before applying this method, however, researchers should be aware that (1) parameter estimates derived from this method essentially assume a star phylogeny, and thus, estimate the same evolutionary regression or correlation coefficient as traditional cross-species analyses; and (2) statistical conclusions derived from this method may be so conservative as to mask evolutionary patterns, such as Rensch's rule, and should be interpreted with caution. ID - 32 ER - TY - JOUR AU - Abouheif, E. PY - 1999 TI - A method for testing the assumption of phylogenetic independence in comparative data SP - 895-909 JF - Evolutionary Ecology Research VL - 1 IS - 8 Y2 - Dec N1 - ISI:000084534400001 N1 - N2 - When making a comparison between two or more traits across taxa, the assumption of phylogenetic independence must be tested. Empirically determining the validity of this assumption before and after applying a phylogenetically based comparative method (PCM) can provide researchers with a rigorous methodological approach for analysing comparative data. This approach can help resolve current debates regarding whether it is always appropriate to apply a PCM, and whether PCMs are in fact successful in accounting for all of the historical non-independence in comparative data. To use this methodological approach, however, a generally applicable statistical diagnostic that can test the assumption of phylogenetic independence in comparative data is required. In this context, I present the application of a statistical diagnostic called the 'test for serial independence'. This diagnostic can be applied to almost all currently employed PCMs, including Felsenstein's (1985) independent contrasts. Furthermore, I demonstrate the application of the test for serial independence by analysing three data sets from the literature. The results of these analyses show that this diagnostic can successfully detect different degrees of phylogenetic autocorrelation in small and large phylogenies as well as in different types of phenotypic characters. The challenges and difficulties associated with applying the proposed methodological approach and the test for serial independence are discussed. ID - 12 ER - TY - JOUR AU - Blomberg, S.P. AU - Garland, T. AU - Ives, A.R. PY - 2003 TI - Testing for phylogenetic signal in comparative data: Behavioral traits are more labile SP - 717-745 JF - Evolution VL - 57 IS - 4 Y2 - Apr N1 - ISI:000182815100003 N1 - N2 - The primary rationale for the use of phylogenetically based statistical methods is that phylogenetic signal, the tendency for related species to resemble each other, is ubiquitous. Whether this assertion is true for a given trait in a given lineage is an empirical question, but general tools for detecting and quantifying phylogenetic signal are inadequately developed. We present new methods for continuous-valued characters that can be implemented with either phylogenetically independent contrasts or generalized least-squares models. First, a simple randomization procedure allows one to test the null hypothesis of no pattern of similarity among relatives. The test demonstrates correct Type I error rate at a nominal alpha = 0.05 and good power (0.8) for simulated datasets with 20 or more species. Second, we derive a descriptive statistic, K, which allows valid comparisons of the amount of phylogenetic signal across traits and trees. Third, we provide two biologically motivated branch-length transformations, one based on the Ornstein-Uhlenbeck (OU) model of stabilizing selection, the other based on a new model in which character evolution can accelerate or decelerate (ACDC) in rate (e.g., as may occur during or after an adaptive radiation). Maximum likelihood estimation of the OU (d) and ACDC (g) parameters can serve as tests for phylogenetic signal because an estimate of d or g near zero implies that a phylogeny with little hierarchical structure (a star) offers a good fit to the data. Transformations that improve the fit of a tree to comparative data will increase power to detect phylogenetic signal and may also be preferable for further comparative analyses, such as of correlated character evolution. Application of the methods to data from the literature revealed that, for trees with 20 or more species, 92% of traits exhibited significant phylogenetic signal (randomization test), including behavioral and ecological ones that are thought to be relatively evolutionarily malleable (e.g., highly adaptive) and/or subject to relatively strong environmental (nongenetic) effects or high levels of measurement error. Irrespective of sample size, most traits (but not body size, on average) showed less signal than expected given the topology, branch lengths, and a Brownian motion model of evolution (i.e., K was less than one), which may be attributed to adaptation and/or measurement error in the broad sense (including errors in estimates of phenotypes, branch lengths, and topology). Analysis of variance of log K for all 121 traits (from 35 trees) indicated that behavioral traits exhibit lower signal than body size, morphological, life-history, or physiological traits. In addition, physiological traits (corrected for body size) showed less signal than did body size itself. For trees with 20 or more species, the estimated OU (25% of traits) and/or ACDC (40%) transformation parameter differed significantly from both zero and unity, indicating that a hierarchical tree with less (or occasionally more) structure than the original better fit the data and so could be preferred for comparative analyses. ID - 5 ER - TY - JOUR AU - Butler, M.A. AU - Losos, J.B. PY - 1997 TI - Testing for unequal amounts of evolution in a continuous character on different branches of a phylogenetic tree using linear and squared-change parsimony: An example using lesser antillean Anolis lizards SP - 1623-1635 JF - Evolution VL - 51 IS - 5 Y2 - Oct N1 - ISI:A1997YE98000029 N1 - N2 - Although a large body of work investigating tests of correlated evolution of two continuous characters exists, hypotheses such as character displacement are really tests of whether substantial evolutionary change has occurred on a particular branch or branches of the phylogenetic tree. In this study, we present a methodology for testing such a hypothesis using ancestral character state reconstruction and simulation. Furthermore, we suggest how to investigate the robustness of the hypothesis test by varying the reconstruction methods or simulation parameters. As a case study, we tested a hypothesis of character displacement in body size of Caribbean Anolis lizards. We compared squared-change, weighted squared-change, and linear parsimony reconstruction methods, gradual Brownian motion and speciational models of evolution, and several resolution methods for linear parsimony. We used ancestor reconstruction methods to infer the amount of body size evolution, and tested whether evolutionary change in body size was greater on branches of the phylogenetic tree in which a transition from occupying a single-species island to a two-species island occurred. Simulations were used to generate null distributions of reconstructed body size change. The hypothesis of character displacement was tested using Wilcoxon Rank-Sums. When tested against simulated null distributions, all of the reconstruction methods resulted in more significant P-values than when standard statistical tables were used. These results confirm that P-values for tests using ancestor reconstruction methods should be assessed via simulation rather than from standard statistical tables. Linear parsimony can produce an infinite number of most parsimonious reconstructions in continuous characters. We present an example of assessing the robustness of our statistical test by exploring the sample space of possible resolutions. We compare ACCTRAN and DELTRAN resolutions of ambiguous character reconstructions in linear parsimony to the most and least conservative resolutions for our particular hypothesis. ID - 13 ER - TY - JOUR AU - Butler, M.A. AU - King, A.A. PY - 2004 TI - Phylogenetic comparative analysis: A modeling approach for adaptive evolution SP - 683-695 JF - American Naturalist VL - 164 IS - 6 Y2 - Dec N1 - ISI:000225968000003 N1 - N2 - Biologists employ phylogenetic comparative methods to study adaptive evolution. However, none of the popular methods model selection directly. We explain and develop a method based on the Ornstein-Uhlenbeck (OU) process, first proposed by Hansen. Ornstein-Uhlenbeck models incorporate both selection and drift and are thus qualitatively different from, and more general than, pure drift models based on Brownian motion. Most importantly, OU models possess selective optima that formalize the notion of adaptive zone. In this article, we develop the method for one quantitative character, discuss interpretations of its parameters, and provide code implementing the method. Our approach allows us to translate hypotheses regarding adaptation in different selective regimes into explicit models, to test the models against data using maximum-likelihood-based model selection techniques, and to infer details of the evolutionary process. We illustrate the method using two worked examples. Relative to existing approaches, the direct modeling approach we demonstrate allows one to explore more detailed hypotheses and to utilize more of the information content of comparative data sets than existing methods. Moreover, the use of a model selection framework to simultaneously compare a variety of hypotheses advances our ability to assess alternative evolutionary explanations. ID - 3 ER - TY - JOUR AU - Diaz-Uriarte, R. AU - Garland, T. PY - 1998 TI - Effects of branch length errors on the performance of phylogenetically independent contrasts SP - 654-672 JF - Systematic Biology VL - 47 IS - 4 Y2 - Dec N1 - ISI:000077592700009 N1 - KW - Correlated evolution; continuous characters; phenotypic evolution; computer-simulation; phylogenies; adaptation; regression N2 - We examined Type I error rates of Felsenstein's (1985; Am. Nat. 125:1-15) comparative method of phylogenetically independent contrasts when branch lengths are in error and the model of evolution is not Brownian motion. We used seven evolutionary models, six of which depart strongly from Brownian motion, to simulate the evolution of two continuously valued characters along two different phylogenies (15 and 49 species). First, we examined the performance of independent contrasts when branch lengths are distorted systematically, for example, by taking the square root of each branch segment. These distortions often caused inflated Type I error rates, but performance was almost always restored when branch length transformations were used. Next, we investigated effects of random errors in branch lengths. After the data were simulated, we added errors to the branch lengths and then used the altered phylogenies to estimate character correlations. Errors in the branches could be of two types: fixed, where branch lengths are either shortened or lengthened by a fixed fraction; or variable, where the error is a normal variate with mean zero and the variance is scaled to the length of the branch (so that expected error relative to branch length is constant for the whole tree). Thus, the error added is unrelated to the microevolutionary model. Without branch length checks and transformations, independent contrasts tended to yield extremely inflated and highly variable Type I error rates. Type I error rates were reduced, however, when branch lengths were checked and transformed as proposed by Garland ct al. (1992; Syst. Biol. 41:18-32), and almost never exceeded twice the nominal P-value at alpha = 0.05. Our results also indicate that, if branch length transformations are applied, then the appropriate degrees of freedom for testing the significance of a correlation coefficient should, in general, be reduced to account fur estimation of the best branch length transformation. These results extend those reported in Diaz-Uriarte and Garland (1996; Syst. Biol. 45:27-47), and show that, even with errors in branch lengths and evolutionary models different from Brownian motion, independent contrasts are a robust method for testing hypotheses of correlated evolution. ID - 30 ER - TY - JOUR AU - GarciaBarros, E. AU - Munguira, M.L. PY - 1997 TI - Uncertain branch lengths, taxonomic sampling error, and the egg to body size allometry in temperate butterflies (Lepidoptera) SP - 201-221 JF - Biological Journal of the Linnean Society VL - 61 IS - 2 Y2 - Jun N1 - ISI:A1997XH42200003 N1 - N2 - The allometry of egg to body size in temperate butterflies, and the relationships between egg size and lan al host structure, taxonomy, voltinism, and duration of the egg stage, are investigated using cross-species analysis and the comparative analysis of independent contrasts. In addition, the effect of two sources of uncertainty that may affect continuous data when treated under a statistical, comparative, framework, is assessed: (1) unknown evolutionary distances, and (2) taxonomic representativity (proportion of species of a given taxon, from which data are available). It is suggested that the effects of taxonomic under-representation could be important in comparative, quantitative studies, but this problem may be tempered by means of weighted regression. Under the assumption that taxonomy represents butterfly phylogeny, egg and adult body size are related by negative allometry (i.e. the slope of the line fitted to the logarithmically transformed data is lower than 1.0). However, the precise slope (0.2-0.9) depends on the method used, branch lengths, and taxonomic sampling. There is evidence for a relationship between a species' voltinism and the number of days it spends in the egg stage, as well as between adult butterfly size and the gross structure of the plants used as larval hosts (woody plants or herbs). Egg size proves to be related to foodplant taxonomy, voltinism, and duration of the egg stage when the data are analysed using species means, but these relationships become non-significant when the comparative method is employed. (C) 1997 The Linnean Society of London. ID - 14 ER - TY - JOUR AU - Garland, T. AU - Diaz-Uriarte, R. PY - 1999 TI - Polytomies and phylogenetically independent contrasts: Examination of the bounded degrees of freedom approach SP - 547-558 JF - Systematic Biology VL - 48 IS - 3 Y2 - Sep N1 - ISI:000083037700006 N1 - KW - comparative method; computer simulation; hypothesis testing; polytomies Continuous characters; correlated evolution; simulation; regression; phylogeny; lizards N2 - We examined the effect of soft polytomies on the performance (Type I error rate and bias) of Felsenstein's (1985; Am. Nat. 125:1-15) method of phylogenetically independent contrasts for estimating a bivariate correlation. We specifically tested the adequacy of bounding degrees of freedom, as suggested by Purvis and Garland (1993; Syst. Biol. 42:569-575). We simulated bivariate character evolution under Brownian motion (assumed by independent contrasts) and eight other models on five phylogenetic trees. For non-Brownian motion simulations, the adequacy of branch-length standardization was checked with a simple diagnostic (Garland et al., 1992; Syst. Biol. 41: 18-32), and transformations were applied as indicated. Surprisingly soft polytomies tended to have negligible effects on Type I error rates when models other than Brownian motion were used. Overall, and irrespective of evolutionary model, degrees of freedom were appropriately bounded for hypothesis testing, and unbiased estimates of the correlation coefficient were obtained. Our results, along with those of previous simulation studies, suggest that independent contrasts can reliably be applied to real data, even with phylogenetic uncertainty. ID - 28 ER - TY - JOUR AU - Garland, T. AU - Midford, P.E. AU - Ives, A.R. PY - 1999 TI - An introduction to phylogenetically based statistical methods, with a new method for confidence intervals on ancestral values SP - 374-388 JF - American Zoologist VL - 39 IS - 2 Y2 - Apr N1 - ISI:000080698300019 N1 - KW - Life-history evolution; aerobic capacity model; independent contrasts; correlated evolution; lacertid lizards; continuous characters; computer-simulation; testing hypotheses; metabolic-rate; phylogeny N2 - Interspecific comparisons have played a prominent role in evolutionary biology at least since the time of Charles Darwin. Since 1985, the "comparative method" has been revitalized by new analytical techniques that use phylogenetic information and by increased availability of phylogenies (often from molecular data sets), Because species descend from common ancestors in a hierarchical fashion, related species tend to resemble each other (elephants look like elephants); therefore, cross-species data sets generally do not comprise Independent and identically distributed data points, Phylogenetically based statistical methods attempt to account for this fact, Phylogenetic methods allow traditional topics in comparative and ecological physiology to be addressed with greater rigor, including the form of allometric relationships and whether physiological phenotypes vary predictably in relation to behavior, ecology or environmental characteristics, which provides evidence about adaptation, They can also address new topics, such as whether rates of physiological evolution have differed among lineages (clades), and where and when a phenotype first evolved, We present brief overviews of three phylogenetically based statistical methods: phylogenetically independent contrasts, Monte Carlo computer simulations to obtain null distributions of test statistics, and phylogenetic autocorrelation, In a new result, we show analytically how to use independent contrasts to estimate ancestral values and confidence intervals about them, These confidence intervals often exceed the range of variation observed among extant species, which points out the relatively great uncertainty inherent in such inferences, The use of phylogenies should become as common as the use of body size and scaling relationships in the analysis of physiological diversity. ID - 29 ER - TY - JOUR AU - Garland, T. AU - Ives, A.R. PY - 2000 TI - Using the past to predict the present: Confidence intervals for regression equations in phylogenetic comparative methods SP - 346-364 JF - American Naturalist VL - 155 IS - 3 Y2 - Mar N1 - ISI:000086444100005 N1 - N2 - Two phylogenetic comparative methods, independent contrasts and generalized least squares models, can be used to determine the statistical relationship between two or more traits. We show that the two approaches are functionally identical and that either can be used to make statistical inferences about values at internal nodes of a phylogenetic tree (hypothetical ancestors), to estimate relationships between characters, and to predict values for unmeasured species. Regression equations derived from independent contrasts can be placed back onto the original data space, including computation of both confidence intervals and prediction intervals for new observations. Predictions for unmeasured species (including extinct forms) can be made increasingly accurate and precise as the specificity of their placement on a phylogenetic tree increases, which can greatly increase statistical power to detect, for example, deviation of a single species from an allometric prediction. We reexamine published data for basal metabolic rates (BMR) of birds and show that conventional and phylogenetic allometric equations differ significantly. In new results, we show that, as compared with nonpasserines, passerines exhibit a lower rate of evolution in both body mass and mass-corrected BMR; passerines also have significantly smaller body masses than their sister clade. These differences may justify separate, clade-specific allometric equations for prediction of avian basal metabolic rates. ID - 11 ER - TY - JOUR AU - Hansen, T.F. PY - 1997 TI - Stabilizing selection and the comparative analysis of adaptation SP - 1341-1351 JF - Evolution VL - 51 IS - 5 Y2 - Oct N1 - ISI:A1997YE98000001 N1 - KW - adaptation; comparative method; macroevolution; optimality; phylogenetic constraint; stabilizing selection Bryozoan phenotypic evolution; fossil horses; macroevolutionary patterns; quantitative characters; phylogenetic regression; morphological evolution; eohippus hyracotherium; correlated evolution; natural-selection; cladistic tests N2 - Comparative studies tend to differ from optimality and functionality studies in how they treat adaptation. While the comparative approach focuses on the origin and change of traits, optimality studies assume that adaptations are maintained at an optimum by stabilizing selection. This paper presents a model of adaptive evolution on a macroevolutionary time scale that includes the maintenance of traits at adaptive optima by stabilizing selection as the dominant evolutionary force. Interspecific variation is treated as variation in the position of adaptive optima. The model illustrates how phylogenetic constraints nor only lead to correlations between phylogenetically related species, but also to imperfect adaptations. From this model, a statistical comparative method is derived that can be used to estimate the effect of a selective factor on adaptive optima in a way that would be consistent with an optimality study of adaptation to this factor. The method is illustrated with an analysis of dental evolution in fossil horses. The use of comparative methods to study evolutionary trends is also discussed. ID - 33 ER - TY - JOUR AU - Housworth, E.A. AU - Martins, E.P. AU - Lynch, M. PY - 2004 TI - The phylogenetic mixed model SP - 84-96 JF - American Naturalist VL - 163 IS - 1 Y2 - Jan N1 - ISI:000188954900008 N1 - N2 - The phylogenetic mixed model is an application of the quantitative-genetic mixed model to interspecific data. Although this statistical framework provides a potentially unifying approach to quantitative-genetic and phylogenetic analysis, the model has been applied infrequently because of technical difficulties with parameter estimation. We recommend a reparameterization of the model that eliminates some of these difficulties, and we develop a new estimation algorithm for both the original maximum likelihood and new restricted maximum likelihood estimators. The phylogenetic mixed model is particularly rich in terms of the evolutionary insight that might be drawn from model parameters, so we also illustrate and discuss the interpretation of the model parameters in a specific comparative analysis. ID - 4 ER - TY - JOUR AU - Levitan, D.R. PY - 2000 TI - Optimal egg size in marine invertebrates: theory and phylogenetic analysis of the critical relationship between egg size and development time in echinoids SP - 175-192 JF - American Naturalist VL - 156 IS - 2 Y2 - Aug N1 - ISI:000088212200006 N1 - N2 - Life-history models for marine invertebrate larvae generally predict a dichotomy in egg size in different species: eggs should be either minimal in size or large enough to support development fully without larval feeding. This prediction is contradicted, however, by the empirical observation of wide, continuous variation in egg size between these extremes. The prediction of dichotomy rests on the assumption of a negative linear relationship between egg size and development time. Here, I present a simple model in which development time is inversely proportional to egg size. Incorporating this relationship into an optimality model produces predictions of intermediate rather than extreme egg size. Modeled variations in mortality, food availability, fertilization rates, and temperature all produce continuous shifts in the value of the intermediate optimal size, in direct contrast to those produced by previous models, which predict shifts between two extreme optima. Empirical data on echinoid egg size and development time strongly support the model's assumption of an inverse proportional relationship between egg size and development time. A composite phylogeny is constructed of the 37 species for which egg size, development time, water temperature, and phylogenetic relatedness are known. Independent contrasts are made of the evolutionary changes in egg size and development time. This analysis indicates that evolutionary shifts in development time are correlated with the inversely proportional shifts in egg size assumed in the model. The assumption of a negative linear relationship used in previous models is rejected. This model provides a potential explanation for intraspecific variation in egg size along environmental gradients, sympatric differences in egg size among species, and biogeographic trends in egg size and development mode across taxa. ID - 9 ER - TY - JOUR AU - Linder, C.R. PY - 2000 TI - Adaptive evolution of seed oils in plants: Accounting for the biogeographic distribution of saturated and unsaturated fatty acids in seed oils SP - 442-458 JF - American Naturalist VL - 156 IS - 4 Y2 - Oct N1 - ISI:000089408200009 N1 - N2 - Structural, energetic, biochemical, and ecological information suggests that germination temperature is an important selective agent causing seed oils of higher-latitude plants to have proportionately more unsaturated fatty acids than lower-latitude plants. Germination temperature is predicted to select relative proportions of saturated and unsaturated fatty acids in seed oils that optimize the total energy stores in a seed and the rate of energy production during germination. Saturated fatty acids store more energy per carbon than unsaturated fatty acids; however, unsaturated fatty acids have much lower melting points than saturated fatty acids. Thus, seeds with lower proportions of saturated fatty acids in their oils should be able to germinate earlier and grow more rapidly at low temperatures even though they store less total energy than seeds with a higher proportion of saturated fatty acids. Seeds that germinate earlier and grow more rapidly should have a competitive advantage. At higher germination temperatures, seeds with higher proportions of saturated fatty acids will be selectively favored because their oils will provide more energy, without a penalty in the rate of energy acquisition. Macroevolutionary biogeographical evidence from a broad spectrum of seed plants and the genus Helianthus support the theory, as do microevolutionary biogeography and seed germination performance within species of Helianthus. ID - 8 ER - TY - JOUR AU - Martins, E.P. AU - Garland, T. PY - 1991 TI - Phylogenetic Analyses of the Correlated Evolution of Continuous Characters - a Simulation Study SP - 534-557 JF - Evolution VL - 45 IS - 3 Y2 - May N1 - ISI:A1991FQ98400004 N1 - N2 - We use computer simulation to compare the statistical properties of several methods that have been proposed for estimating the evolutionary correlation between two continuous traits, and define alternative evolutionary correlations that may be of interest. We focus on Felsenstein's (1985) method and some variations of it and on several "minimum evolution" methods (of which the procedure of Huey and Bennett [1987] is a special case), as compared with nonphylogenetic correlation. The last, a simple correlation of trait values across the tips of a phylogeny, virtually always yields inflated Type I error rates, relatively low power, and relatively poor estimates of evolutionary correlations. We therefore cannot recommend its use. In contrast, Felsenstein's (1985) method yields acceptable significance tests, high power, and good estimates of what we term the input correlation and the standardized realized evolutionary correlation, given complete phylogenetic information and knowledge of the rate and mode of character change (e.g., gradual and proportional to time ["Brownian motion"] or punctional, with change only at speciation events). Inaccurate branch length information may affect any method adversely, but only rarely does it cause Felsenstein's (1985) method to perform worse than do the others tested. Other proposed methods generally yield inflated Type I error rates and have lower power. However, certain minimum evolution methods (although not the specific procedure used by Huey and Bennett [1987]) often provide more accurate estimates of what we term the unstandardized realized evolutionary correlation, and their use is recommended when estimation of this correlation is desired. We also demonstrate how correct Type I error rates can be obtained for any method by reference to an empirical null distribution derived from computer simulations, and provide practical suggestions on choosing an analytical method, based both on the evolutionary correlation of interest and on the availability of branch lengths and knowledge of the model of evolutionary change appropriate for the characters being analyzed. Computer programs that implement the various methods and that will simulate (correlated) character evolution along a known phylogeny are available from the authors on request. These programs can be used to test the effectiveness of any new methods that might be proposed, and to check the generality of our conclusions with regard to other phylogenies. ID - 16 ER - TY - JOUR AU - Martins, E.P. PY - 1994 TI - Estimating the Rate of Phenotypic Evolution from Comparative Data SP - 193-209 JF - American Naturalist VL - 144 IS - 2 Y2 - Aug N1 - ISI:A1994PA42100001 N1 - N2 - This study presents a method to estimate rates of evolutionary change in continuous characters from comparative data. The technique is similar to those introduced previously in which between-species divergence is estimated as a function of time since divergence but also takes into account the possible statistical nonindependence of trait values measured from phylogenetically related species in an approach similar to the independent contrasts methods used in interspecific data analysis. The use of Ornstein-Uhlenbeck processes is also proposed to extend the standard Brownian motion model of evolutionary change and to allow for tests of neutral evolution versus evolution under stabilizing selection. Applications of the method to test specific hypotheses of phenotypic evolution (including the adequacy of Brownian motion to describe real data), to compare rates of change of different types of characters or different groups of organisms, and to estimate branch lengths in units of expected variance of change as required by most comparative-method data analysis techniques are discussed. ID - 15 ER - TY - JOUR AU - Martins, E.P. AU - Hansen, T.F. PY - 1997 TI - Phylogenies and the comparative method: A general approach to incorporating phylogenetic information into the analysis of interspecific data SP - 646-667 JF - American Naturalist VL - 149 IS - 4 Y2 - Apr N1 - ISI:A1997WM92100002 N1 - KW - Quantitative characters; morphological evolution; phenotypic evolution; natural-selection; least-squares; rate tests; adaptation; constraints; behavior N2 - This article considers the statistical issues relevant to the comparative method in evolutionary biology. A generalized Linear model (GLM) is presented for the analysis of comparative data, which can be used to address questions regarding the relationship between traits or between traits and environments, the rate of phenotypic evolution, the degree of phylogenetic effect, and the ancestral state of a character. Our approach thus emphasizes the similarity among evolutionary questions asked in comparative studies. We then discuss ways of specifying the sources of error involved in a comparative study (e.g., measurement error, error due to evolution along a phylogeny, error due to misspecification of a phylogeny) and show how the impact of these sources of error can be taken into account in a comparative analysis. In contrast to most existing phylogenetic comparative methods, our procedure offers substantial flexibility in the choice of microevolutionary assumptions underlying the statistical analysis, allowing researchers to choose assumptions that are most appropriate for their particular set of data and evolutionary question. In developing the approach, we also propose novel ways of incorporating within-species variation and/or measurement error into phylogenetic analyses, of estimating ancestral states, and of considering both continuous (quantitative) and categorical (qualitative or ''state'') characters in the same analysis. ID - 36 ER - TY - JOUR AU - Martins, E.P. PY - 2000 TI - Adaptation and the comparative method SP - 296-299 JF - Trends in Ecology & Evolution VL - 15 IS - 7 Y2 - Jul N1 - ISI:000087831100017 N1 - KW - Correlated evolution; independent contrasts; continuous characters; computer-simulation; adaptive radiation; interspecific data; phylogenies; hypotheses; states N2 - Over the past two decades, it has become widely accepted that phylogenies need to be incorporated into statistical analyses of interspecific data. However, recent debate has focused on whether it is appropriate to apply phylogenetic comparative methods (PCMs) to the study of adaptation, Although some of the criticisms are serious, it is premature to stop applying PCMs altogether. New statistical methods designed explicitly for the comparative study of adaptation overcome these criticisms and offer fresh insights into the evolution of phenotypes. ID - 24 ER - TY - CHAP AU - Morand, S. AU - Poulin, R. PY - 2003 BT - Advances in Parasitology, Vol 54 CT - Phylogenies, the comparative method and parasite evolutionary ecology VL - 54 T3 - Advances in Parasitology SP - 281-302 N1 - ISI:000229182300007 N2 - A growing number of comparative analyses in the field of parasite evolution and ecology have used phylogenetically based comparative methods. However, the comparative approach has not been used much by parasitologists. We present the rationale for the use of phylogenetic information in comparative studies, and we illustrate the use of several phylogenetically based comparative methods with case studies in parasite evolutionary ecology. The independent contrasts method is the most popular one, but presents some problems for studying co-adaptation between host and parasite life traits. The eigenvector method has been recently proposed as a new method to estimate and correct for phylogenetic inertia. We illustrate this method with an investigation of patterns of helminth parasite species richness across mammalian host species. This method seems to perform well in situations where host and parasite phylogenies are not perfectly congruent, but one might still want to correct for the effects of both. Finally, we present a method recently proposed for variation partitioning in a phylogenetic context, i.e. the phylogenetically structured environmental variation. VL - 54 ID - 2 ER - TY - JOUR AU - Morse, G.E. AU - Farrell, B.D. PY - 2005 TI - Ecological and evolutionary diversification of the seed beetle genus Stator (Coleoptera : Chrysomelidae : Bruchinae) SP - 1315-1333 JF - Evolution VL - 59 IS - 6 Y2 - Jun N1 - ISI:000230077500015 N1 - N2 - Ehrlich and Raven's (1964) hypothesis on coevolution has stimulated numerous phylogenetic studies that focus on the effects of plant defensive chemistry as the main ecological axis of phytophagous insect diversification. However, other ecological features affect host use and diet breadth and they may have very different consequences for insect evolution. In this paper, we present a phylogenetic study based on DNA sequences from mitochondrial and protein-coding genes of species in the seed beetle genus Stator, which collectively show considerable interspecific variation in host affiliation, diet breadth, and the dispersal stage of the seeds that they attack. We used comparative analyses to examine transitions in these three axes of resource use. We argue that these analyses show that diet breadth evolution is dependent upon colonizing novel hosts that are closely or distantly related to the ancestral host, and that oviposition substrate affects the evolution of host-plant affiliation, the evolution of dietary specialization, and the degree to which host plants are shared between species. The results of this study show that diversification is structured by interactions between different selective pressures and along multiple ecological axes. ID - 1 ER - TY - JOUR AU - Oakley, T.H. AU - Cunningham, C.W. PY - 2000 TI - Independent contrasts succeed where ancestor reconstruction fails in a known bacteriophage phylogeny SP - 397-405 JF - Evolution VL - 54 IS - 2 Y2 - Apr N1 - ISI:000086886500005 N1 - N2 - Methods of ancestor reconstruction are important tools for evolutionary inference that are difficult to test empirically because ancestral states are rarely known with certainty. We evaluated reconstruction methods for continuous phenotypic characters using taxa from an experimentally generated bacteriophage phylogeny. Except for one slowly evolving character, the estimated ancestral states of continuous phenotypic characters were highly inaccurate and biased, even when including a known ancestor at the root. This error was caused by a directional trend in character evolution and by rapid rates of character evolution. Computer simulations confirmed that such factors affect reconstruction of continuous characters in general. We also used phenotypic viral characters to evaluate two methods that attempt to estimate the correlation between characters during evolution. Whereas a nonphylogenetic regression was relatively inaccurate and biased, independent contrasts accurately estimated the correlation between characters with little bias. ID - 10 ER - TY - JOUR AU - Rohlf, F.J. PY - 2001 TI - Comparative methods for the analysis of continuous variables: Geometric interpretations SP - 2143-2160 JF - Evolution VL - 55 IS - 11 Y2 - Nov N1 - ISI:000172947000001 N1 - N2 - This study is concerned with statistical methods used for the analysis of comparative data (in which observations are not expected to be independent because they are sampled across phylogenetic ally related species). The phylogenetically independent contrasts (PIC), phylogenetic generalized least-squares (PGLS), and phylogenetic autocorrelation (PA) methods are compared. Although the independent contrasts are not orthogonal, they are independent if the data conform to the Brownian motion model of evolution on which they are based. It is shown that uncentered correlations and regressions through the origin using the PIC method are identical to those obtained using PGLS with an intercept included in the model. The PIC method is a special case of PGLS. Corrected standard errors are given for estimates of the ancestral states based on the PGLS approach. The treatment of trees with hard polytomies is discussed and is shown to be an algorithmic rather than a statistical problem. Some of the relationships among the methods are shown graphically using the multivariate space in which variables are represented as vectors with respect to OTUs used as coordinate axes. The maximum-likelihood estimate of the autoregressive parameter, rho, has not been computed correctly in previous studies (an appendix with MATLAB code provides a corrected algorithm). The importance of the eigenvalues and eigenvectors of the connection matrix, W, for the distribution of rho is discussed. The PA method is shown to have several problems that limit its usefulness in comparative studies. Although the PA method is a generalized least-squares procedure, it cannot be made equivalent to the PGLS method using a phylogenetic model. ID - 7 ER - TY - JOUR AU - Symonds, M.R.E. PY - 2002 TI - The effects of topological inaccuracy in evolutionary trees on the phylogenetic comparative method of independent contrasts SP - 541-553 JF - Systematic Biology VL - 51 IS - 4 Y2 - Aug N1 - ISI:000177425900001 N1 - N2 - Computer simulations were used. to test the effect of increasing phylogenetic topological inaccuracy on the results obtained from correlation tests of independent contrasts. Predictably, increasing the number of disruptions in the tree increases the likelihood of significant error in the r values produced and in the statistical conclusions drawn from the analysis. However, the position of the disruption in the tree is important: Disruptions closer to the tips of the tree haje a greater effect than do disruptions that are close to the root of the tree. Independent contrasts derived from inaccurate topologies are more likely to lead to erroneous conclusions when there is a true significant relationship between,the variables being tested (i.e., they tend to be conservative). The results also suggest that random phylogenies perform no better than nonphylogenetic analyses and, under certain conditions, may perform even worse than analyses using raw species data. Therefore, the use of random phylogenies is not beneficial in the absence of knowledge of the true phylogeny. ID - 6 ER - TY - JOUR AU - Wolf, C.M. AU - Garland, T. AU - Griffith, B. PY - 1998 TI - Predictors of avian and mammalian translocation success: reanalysis with phylogenetically independent contrasts SP - 243-255 JF - Biological Conservation VL - 86 IS - 2 Y2 - Nov N1 - ISI:000076273000014 N1 - KW - birds; comparative method; mammals; phylogenetically independent contrasts; reintroduction; translocation Correlated evolution; continuous characters; computer-simulation; lacertid lizards; phylogeny; conservation; nonpasserines; strategies; regression; invaders N2 - We use the phylogenetically based statistical method of independent contrasts to reanalyze the Wolf, C.M., Griffith, B., Reed, C., Temple, S.A. (1996. Avian and mammalian translocations: update and reanalysis of 1987 survey data. Conservation Biology 10, 1142-1154). translocation data set for 181 programs involving 17 mammalian and 28 avian species. Although still novel in conservation and wildlife biology, the incorporation of phylogenetic information into analyses of interspecific comparative data is widely accepted and routinely used in several fields. To facilitate application of independent contrasts, we converted the dichotomous (success/failure) dependent variable (Wolf et al., 1996; Griffith, B., Scott, J.M. Carpenter, J.W., Reed, C., 1989. Translocations as a species conservation tool: status and strategy. Science 245, 477-480) into a more descriptive, continuous variable with the incorporation of persistence of the translocated population beyond the last release year, relative to the species' longevity. For comparison, we present three models: nonphylogenetic multiple logistic regression with the dichotomous dependent variable (the method used by Wolf et al. 1996 and Griffith et al. 1989), nonphylogenetic multiple regression with the continuous dependent variable, and multiple regression using phylogenetically independent contrasts with the continuous dependent variable. Results of the phylogenetically based multiple regression analysis indicate statistical significance of three independent variables: habitat quality of the release area, range of the release site relative to the historical distribution of the translocated species, and number of individuals released. Evidence that omnivorous species are more successful than either herbivores or carnivores is also presented. The results of our reanalysis support several of the more important conclusions of the Wolf et al. (1996) and Griffith et al. (1989) studies and increase our confidence that the foregoing variables should be considered carefully when designing a translocation program. However, the phylogenetically based analysis does not support either the Wolf et al. (1996) or Griffth et al. (1989) findings with respect to the statistical significance of taxonomic class (bird vs mammal) and status (game vs threatened, endangered, or sensitive), or the Griffith et al. (1989) findings with respect to the significance of reproductive potential of the species and program length. (C) 1998 Elsevier Science Ltd. All rights reserved. ID - 31 ER -