Phylogenetic Eigenvector Regression Research Articles

The evolution of large‐scale body size clines in Plethodon salamanders: evidence of heat‐balance or species‐specific artifact?

A major goal in macroecology is to determine how body size varies geographically, and explain why such patterns exist. Recently, a grid‐cell assemblage analysis found significant body size trends with latitude and temperature in Plethodon salamanders, and support for the heat‐balance hypothesis as a possible explanation for these trends. Here we demonstrate that the heat‐balance hypothesis is unlikely to have generated this pattern, and that there is no overall body size trend with temperature in Plethodon. Using data from 3155 local Plethodon assemblages, we find no support for body size clines with latitude, and no relationship between body size and temperature. We also found that body size did not covary with elevation, in contrast to what was predicted by heat‐balance. We then examined the various scenarios under which body size clines across grid‐cell assemblages could evolve via heat‐balance, and found that none were tenable in light of the existing data. Instead, a single, widely distributed species was responsible for the pattern across grid‐cell assemblages. Finally, we examined why phylogenetic eigenvector regression does not account for phylogenetic non‐independence among taxa, and should not be used to account for shared evolutionary history in assembly‐level analyses. Assemblage‐level patterns are a useful means of assessing biogeographic trends, and are an important complement to within‐species and cross‐species patterns. However, while the use of grid‐cell assemblage approaches from digital databases is expedient, their results must be examined critically, and whenever possible, compared with data obtained from local species assemblages (particularly for ecological mechanisms that operate at the level of individuals). Finally, our results emphasize the importance of using corroborative data to evaluate alternative hypotheses, so that potential mechanisms that explain bioegeographic patterns are properly assigned.

Assessment of the Relative Merits of a Few Methods to Detect Evolutionary Trends

Some of the most basic questions about the history of life concern evolutionary trends. These include determining whether or not metazoans have become more complex over time, whether or not body size tends to increase over time (the Cope-Depéret rule), or whether or not brain size has increased over time in various taxa, such as mammals and birds. Despite the proliferation of studies on such topics, assessment of the reliability of results in this field is hampered by the variability of techniques used and the lack of statistical validation of these methods. To solve this problem, simulations are performed using a variety of evolutionary models (gradual Brownian motion, speciational Brownian motion, and Ornstein-Uhlenbeck), with or without a drift of variable amplitude, with variable variance of tips, and with bounds placed close or far from the starting values and final means of simulated characters. These are used to assess the relative merits (power, Type I error rate, bias, and mean absolute value of error on slope estimate) of several statistical methods that have recently been used to assess the presence of evolutionary trends in comparative data. Results show widely divergent performance of the methods. The simple, nonphylogenetic regression (SR) and variance partitioning using phylogenetic eigenvector regression (PVR) with a broken stick selection procedure have greatly inflated Type I error rate (0.123-0.180 at a 0.05 threshold), which invalidates their use in this context. However, they have the greatest power. Most variants of Felsenstein's independent contrasts (FIC; five of which are presented) have adequate Type I error rate, although two have a slightly inflated Type I error rate with at least one of the two reference trees (0.064-0.090 error rate at a 0.05 threshold). The power of all contrast-based methods is always much lower than that of SR and PVR, except under Brownian motion with a strong trend and distant bounds. Mean absolute value of error on slope of all FIC methods is slightly higher than that of phylogenetic generalized least squares (PGLS), SR, and PVR. PGLS performs well, with low Type I error rate, low error on regression coefficient, and power comparable with some FIC methods. Four variants of skewness analysis are examined, and a new method to assess significance of results is presented. However, all have consistently low power, except in rare combinations of trees, trend strength, and distance between final means and bounds. Globally, the results clearly show that FIC-based methods and PGLS are globally better than nonphylogenetic methods and variance partitioning with PVR. FIC methods and PGLS are sensitive to the model of evolution (and, hence, to branch length errors). Our results suggest that regressing raw character contrasts against raw geological age contrasts yields a good combination of power and Type I error rate. New software to facilitate batch analysis is presented.

The shared influence of phylogeny and ecology on the reproductive patterns of Myrteae (Myrtaceae)

Summary1. Many factors shape plant reproductive patterns including climate, competition or attraction of pollinators and seed dispersers, flower and fruit morphologies and phylogenetic relationships. South American Myrtaceae (Myrteae) were chosen to evaluate hypotheses on how abiotic and biotic factors, morphology and phylogeny influence plant reproductive phenology.2. We examined whether Myrteae reproductive patterns are seasonal and related to climate; whether aggregated or segregated flowering and fruiting occur among species sharing pollinators or seed dispersers; the relationship between phenological and morphological traits, time of reproduction and Myrteae phylogenetic history; and the shared influence of ecological (environmental) and phylogenetic factors on Myrteae reproductive patterns.3. We observed flowering and fruiting of 34 Myrteae species during 30 months in an Atlantic rain forest (south‐eastern Brazil). We employed circular statistics to test for seasonality and multiple regressions to relate climate and phenology. Competition and facilitation hypotheses were tested using null models. We quantified the phylogenetic signal on phenology and morphology of Myrteae species using phylogenetic eigenvector regression (PVR) analyses, and used PVR and partial regressions to quantify the influences of ecology and phylogeny on phenology.4. Myrteae flowered seasonally, whereas fruiting was not seasonal. Environmental factors (day‐length and temperature) and associations with biotic vectors through facilitation hypothesis explained the aggregated blossom. Fruit maturation time affected the species’ flowering sequence. Plants with longer fruit maturation times flowered at the end of the appropriate season, explaining the continuous fruit availability despite the seasonal flowering. The random fruiting pattern explained the regular presence of seed dispersers. Myrteae phenology was phylogenetically structured, even when phenophases were not seasonal, i.e., closer related species fruited under more similar environmental conditions, suggesting that the reproductive phenological niche was inherited along the course of evolution. We detected a shared influence of ecology and phylogeny on Myrteae phenological responses, and the ecological component explained better phenological variation than phylogeny.5. Synthesis. We provided a new perspective on plant phenology based on phylogeny and ecology and demonstrated the importance of considering their shared influence in phenological studies. Our analyses can be employed for the most representative families of highly diverse ecosystems to improve our understanding of evolutionary patterns and general trends in phenology.

Phylogenetic, spatial and environmental components of extinction risk in carnivores

ABSTRACTAim Extinction risk is non‐randomly distributed across phylogeny and space and is influenced by environmental conditions. We quantified the relative contribution of these factors to extinction risk to unveil the underlying macroecological processes and derive predictive models.Location Global.Methods Based on the IUCN global assessments, we divided 192 carnivore species into two dichotomous classes representing different levels of extinction risk. We used spatial proximity, phylogenetic relationship and environmental variables together with phylogenetic eigenvector regression and spatial eigenvector filters to model and predict threat status.Results Our full models explained between 57% and 96% of the variance in extinction risk. Phylogeny and spatial proximity roughly explained between 21% and 70% of the total variation in all analyses, while the explanatory power of environmental conditions was relatively weaker (up to 15%). Phylogeny and spatial proximity contributed equally to the explained variance in the lower threat level, while spatial proximity was the most important factor in the models of the higher threat level. Prediction of threat status achieved 97% correct assignments.Main conclusions Our approach differs fundamentally from current studies of extinction risk because it does not necessarily rely on life‐history information. We clearly show that instead of treating phylogenetic inertia and spatial signal as statistical nuisances, space and phylogeny should be viewed as very useful in explaining a wide range of phenomena in comparative studies.

Phylogenetically structured variance in felid bite force: the role of phylogeny in the evolution of biting performance

A key question in evolution is the degree to which morphofunctional complexes are constrained by phylogeny. We investigated the role of phylogeny in the evolution of biting performance, quantified as bite forces, using phylogenetic eigenvector regression. Results indicate that there are strong phylogenetic signals in both absolute and size-adjusted bite forces, although it is weaker in the latter. This indicates that elimination of size influences reduces the level of phylogenetic inertia and that the majority of the phylogenetic constraint is a result of size. Tracing the evolution of bite force through phylogeny by character optimization also supports this notion, in that relative bite force is randomly distributed across phylogeny whereas absolute bite force diverges according to clade. The nonphylogenetically structured variance in bite force could not be sufficiently explained by species-unique morphology or by ecology. This study demonstrates the difficulties in identifying causes of nonphylogenetically structured variance in morphofunctional character complexes.

Climate history, human impacts and global body size of Carnivora (Mammalia: Eutheria) at multiple evolutionary scales

AbstractAim One of the longest recognized patterns in macroecology, Bergmann’s rule, describes the tendency for homeothermic animals to have larger body sizes in cooler climates than their phylogenetic relatives in warmer climates. Here we provide an integrative process‐based explanation for Bergmann’s rule at the global scale for the mammal order Carnivora.Location Global.Methods Our database comprises the body sizes of 209 species of extant terrestrial Carnivora, which were analysed using phylogenetic autocorrelation and phylogenetic eigenvector regression. The interspecific variation in body size was partitioned into phylogenetic (P) and specific (S) components, and mean P‐ and S‐components across species were correlated with environmental variables and human occupation both globally and for regions glaciated or not during the last Ice Age.Results Three‐quarters of the variation in body size can be explained by phylogenetic relationships among species, and the geographical pattern of mean values of the P‐component is the opposite of the pattern predicted by Bergmann’s rule. Partial regression revealed that at least 43% of global variation in the mean phylogenetic component is explained by current environmental factors. In contrast, the mean S‐component of body size shows large positive deviations from ancestors across the Holarctic, and negative deviations in southern South America, the Sahara Desert, and tropical Asia. There is a moderately strong relationship between the human footprint and body size in glaciated regions, explaining 19% of the variance of the mean P‐component. The relationship with the human footprint and the P‐component is much weaker in the rest of the world, and there is no relationship between human footprint and S‐component in any region.Main conclusions Bergmannian clines are stronger at higher latitudes in the Northern Hemisphere because of the continuous alternation of glacial–interglacial cycles throughout the late Pliocene and Pleistocene, which generated increased species turnover, differential colonization and more intense adaptive processes soon after glaciated areas became exposed. Our analyses provide a unified explanation for an adaptive Bergmann’s rule within species and for an interspecific trend towards larger body sizes in assemblages resulting from historical changes in climate and contemporary human impacts.

Ecological and evolutionary components of body size: geographic variation of venomous snakes at the global scale

Biogeographical patterns of animal body size and the environmental and evolutionary mechanisms that may be driving them have been broadly investigated in macroecology, although just barely in ectotherms. We separately studied two snake clades, Viperidae and Elapidae, and used phylogenetic eigenvector regression and ordinary least squares multiple regression methods to perform a global grid-based analysis of the extent at which the patterns of body size (measured for each species as its log10-transformed maximum body length) of these groups are phylogenetically structured or driven by current environment trends. Phylogenetic relatedness explained 20% of the across-species size variation in Viperidae, and 59% of that of Elapidae, which is a more recent clade. Conversely, when we analysed spatial trends in mean body size values (calculated for each grid-cell as the average size of its extant species), an environmental model including temperature, precipitation, primary productivity (as indicated by the global vegetation index) and topography (range in elevation) explained 37.6% of the variation of Viperidae, but only 4.5% of that of Elapidae. These contrasted responses of body size patterns to current environment gradients are discussed, taking into consideration the dissimilar evolutionary histories of these closely-related groups. Additionally, the results obtained emphasize the importance of the need to start adopting deconstructive approaches in macroecology. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 98, 94-109. ADDITIONAL KEYWORDS: Bergmann's rule - ectotherms - interspecific variation - model selection - niche conservatism - phylogenetic eigenvector regression - snakes.

Geographic body size gradients in tropical regions: water deficit and anuran body size in the Brazilian Cerrado

A recent interspecific study found Bergmann's size clines for Holarctic anurans and proposed an explanation based on heat balance to account for the pattern. However, this analysis was limited to cold temperate regions, and exploring the patterns in warmer tropical climates may reveal other factors that also influence anuran body size variation. We address this using a Cerrado anuran database. We examine the relationship between mean body size in a grid of 1° cells and environmental predictors and test the relative support for four hypotheses using an AIC‐based model selection approach. Also, we considered three different amphibian phylogenies to partition the phylogenetic and specific components of the interspecific variation in body size using a method analogous to phylogenetic eigen vector regression (PVR). To consider the potential effects of spatial autocorrelation we use eigenvector‐based spatial filters. We found the largest species inhabiting high water deficit areas in the northeast and the smallest in the wet southwest. Our results are consistent with the water availability hypothesis which, coupled with previous findings, suggests that the major determinant of interspecific body size variation in anurans switches from energy to water towards the equator. We propose that anuran body size gradients reflect effects of reduced surface to volume ratios in larger species to control both heat and water balance.

Use of paleontological and molecular data in supertrees for comparative studies: the example of lissamphibian femoral microanatomy

A new method to assemble time-calibrated supertrees is able to incorporate paleontological and molecular dates. This method, along with new branch length transformations, is implemented in the Stratigraphic Tools for Mesquite. It was used here to analyse a dataset on bone microanatomy, body size and habitat of 46 species of lissamphibians through a variety of methods (Felsenstein independent contrasts, variance partition with phylogenetic eigenvector regression, discriminant analyses and simple regressions). Our analyses showed that the new methods can produce adequate standardization for several characters on a tree whose branch lengths can represent evolutionary time. The analyses confirmed previous conclusions about the presence of an ecological signal in bone microanatomical data.

Phylogenetic autocorrelation and heritability of geographic range size, shape and position of fiddler crabs, genusUca(Crustacea, Decapoda)

The aim of this study was to evaluate the levels of phylogenetic heritability of the geographical range size, shape and position for 88 species of fiddler crabs of the world, using phylogenetic comparative methods and simulation procedures to evaluate their fit to the neutral model of Brownian motion. The geographical range maps were compiled from literature, and range size was based on the entire length of coastline occupied by each species, and the position of each range was calculated as its latitudinal and longitudinal midpoint. The range shape of each species was based in fractal dimension (box-counting technique). The evolutionary patterns in the geographical range metrics were explored by phylogenetic correlograms using Morans I autocorrelation coefficients, autoregressive method (ARM) and phylogenetic eigenvector regression (PVR). The correlograms were compared with those obtained by simulations of Brownian motion processes across phylogenies. The distribution of geographical range size of fiddler crabs is right-skewed and weak phylogenetic autocorrelation was observed. On the other hand, there was a strong phylogenetic pattern in the position of the range (mainly along longitudinal axis). Indeed, the ARM and PVR evidenced, respectively, that ca. 86% and 91% of the longitudinal midpoint could be explained by phylogenetic relationships among the species. The strong longitudinal phylogenetic pattern may be due to vicariant allopatric speciation and geographically structured cladogenesis in the group. The traits analysed (geographical range size and position) did not follow a Brownian motion process, thus suggesting that both adaptive ecological and evolutionary processes must be invoked to explain their dynamics, not following a simple neutral inheritance in the fiddler-crab evolution.

Modeling body size evolution in Felidae under alternative phylogenetic hypotheses

The use of phylogenetic comparative methods in ecological research has advanced during the last twenty years, mainly due to accurate phylogenetic reconstructions based on molecular data and computational and statistical advances. We used phylogenetic correlograms and phylogenetic eigenvector regression (PVR) to model body size evolution in 35 worldwide Felidae (Mammalia, Carnivora) species using two alternative phylogenies and published body size data. The purpose was not to contrast the phylogenetic hypotheses but to evaluate how analyses of body size evolution patterns can be affected by the phylogeny used for comparative analyses (CA). Both phylogenies produced a strong phylogenetic pattern, with closely related species having similar body sizes and the similarity decreasing with increasing distances in time. The PVR explained 65% to 67% of body size variation and all Moran's I values for the PVR residuals were non-significant, indicating that both these models explained phylogenetic structures in trait variation. Even though our results did not suggest that any phylogeny can be used for CA with the same power, or that “good” phylogenies are unnecessary for the correct interpretation of the evolutionary dynamics of ecological, biogeographical, physiological or behavioral patterns, it does suggest that developments in CA can, and indeed should, proceed without waiting for perfect and fully resolved phylogenies.

Evolution of grasping among anthropoids

The prevailing hypothesis about grasping in primates stipulates an evolution from power towards precision grips in hominids. The evolution of grasping is far more complex, as shown by analysis of new morphometric and behavioural data. The latter concern the modes of food grasping in 11 species (one platyrrhine, nine catarrhines and humans). We show that precision grip and thumb-lateral behaviours are linked to carpus and thumb length, whereas power grasping is linked to second and third digit length. No phylogenetic signal was found in the behavioural characters when using squared-change parsimony and phylogenetic eigenvector regression, but such a signal was found in morphometric characters. Our findings shed new light on previously proposed models of the evolution of grasping. Inference models suggest that Australopithecus, Oreopithecus and Proconsul used a precision grip.

Explanations for bird species range size: ecological correlates and phylogenetic effects in the Canary Islands

AbstractAim To explore the determinants of island occupancy of 48 terrestrial bird species in an oceanic archipelago, accounting for ecological components while controlling for phylogenetic effects.Location The seven main islands of the Canary archipelago.Methods We obtained field data on population density, habitat breadth and landscape distribution in Tenerife, Fuerteventura and La Palma, aiming to sample all available habitats and the gradient of altitudes. In total, 1715 line transects of 0.5 km were carried out during the breeding season. We also reviewed the literature for data on occupancy, the distance between the Canary Islands and the nearest distribution border on the mainland, body size and endemicity of the 48 terrestrial bird species studied. Phylogenetic eigenvector regression was used to quantify (and to control for) the amount of phylogenetic signal.Results The two measurements of occupancy (number of occupied islands or 10 × 10 km UTM squares) were tightly correlated and produced very similar results. The occupancy of the terrestrial birds of the Canary Islands during the breeding season had a very low phylogenetic effect. Species with broader habitat breadth, stronger preferences for urban environments, smaller body size, and a lower degree of endemicity had a broader geographical distribution in the archipelago, occupying a larger number of islands and 10 × 10 UTM squares.Main conclusions The habitat‐generalist species with a tolerance for novel urban environments tend to be present on more islands and to occupy a greater area, whereas large‐sized species that are genetically differentiated within the islands are less widespread. Therefore, some properties of the ranges of these species are explicable from basic biological features. A positive relationship of range size with local abundance, previously shown in continental studies, was not found, probably because it relies on free dispersal on continuous landmasses, which may not be applicable on oceanic islands.

Partitioning phylogenetic and adaptive components of the geographical body‐size pattern of New World birds

ABSTRACTAim To evaluate seasonal body‐size patterns for New World birds in geographical space, to develop environmental models to explain the gradients, and to estimate phylogenetic and adaptive contributions.Location The Western Hemisphere.Methods We used range maps to generate gridded geometric mean body masses. Summer and winter patterns were distinguished based on breeding and non‐breeding ranges. We first generated the geographical gradients, followed by phylogenetic eigenvector regression to generate body sizes predicted by the birds’ positions in a phylogenetic tree, which were used to generate the expected phylogenetic gradient. Subtracting the expected pattern from the observed pattern isolated the adaptive component. Ordinary least squares multiple‐regression models examined factors influencing the phylogenetic, adaptive and combined components of the seasonal body‐size patterns, and non‐spatial and spatial models were compared.Results Birds are larger in the temperate zones than in the tropics. The gradient is quantitatively stronger in winter than in summer. Regression models explained 66.6% of the variance in summer mass and 45.9% of the variance in winter mass. In summer, phylogenetic and adaptive responses of birds contribute equally to the gradient. In winter, the gradient in North America is much stronger than that expected by taxonomic turnover, and responses of species independent of their family membership drive the overall pattern.Main conclusions We confirm Bergmann's rule in New World birds and conclude that winter temperatures ultimately drive the pattern, exerting selection pressures on birds that overwhelm patterns expected by phylogenetic inertia at the family level. However, in summer, the movement of migratory species into the temperate zone weakens the gradient and generates a pattern more congruent with that expected from the taxonomic composition of the fauna. The analytical method we develop here represents a useful tool for partitioning the phylogenetic and non‐phylogenetic components of spatially explicit macroecological data.

Determinants of parasite species richness on small taxonomical and geographical scales: Lamellodiscus monogeneans of northwestern Mediterranean sparid fish.

Determinants of parasite species richness have been investigated in a host-parasite system comprising fish of the family Sparidae and their monogenean gill ectoparasites of the genus Lamellodiscus. This study was carried out on a small geographical scale in the northwestern Mediterranean Sea. Host phylogenetic relationships were taken into account by phylogenetic eigenvector regression which required the reconstruction of a phylogenetic tree for the sparid fish species using mtDNA sequences. Several ecological variables potentially acting on Lamellodiscus species richness were considered. Host body size and host migratory behaviour appeared to be the main determinants of parasite species richness in this system. It is concluded that structuring of monogenean communities is controlled more by ecological than evolutionary factors.

Macroecologia de carnívoros do Novo Mundo (Mammalia): envelopes de restrição e análise de padrões filogenéticos

The relationship between body size and geographic range was analyzed for 70 species of terrestrial Carnivora (fissipeds) of the New World, after the control of phylogenetic patterns in the data using phylogenetic eigenvector regression. The analysis from EcoSim software showed that the variables are related as a triangular envelope. Phylogenetic patterns in data were detected by means of phylogenetic correlograms, and 200 simulations of the phenotypic evolution were also performed over the phylogeny. For body size, the simulations suggested a non-linear relationship for the evolution of this character along the phylogeny. For geographic range size, the correlogram showed no phylogenetic patterns. A phylogenetic eigenvector regression was performed on original data and on data simulated under Ornstein-Uhlenbeck process. Since both characters did not evolve under a simple Brownian motion process, the Type I errors should be around 10%, compatible with other methods to analyze correlated evolution. The significant correlation of the original data (r = 0.38; P < 0.05), as well as the triangular envelope, then indicate ecological and adaptive processes connecting the two variables, such as those proposed in minimum viable population models.

Metabolic and thermal physiology of pigeons and doves.

Pigeons and doves (Columbidae) are an interesting group to examine for physiological adaptations to climate and diet because this cosmopolitan family comprises more than 300 species that are mostly granivores, although some are specialized frugivores. We determined allometric and phylogenetic effects on body temperature (T(b)), basal metabolic rate (BMR; J h(-1)), and wet thermal conductance (C(wet); J h(-1) C(-1)), and we examined mass (M) and phylogenetically corrected residuals for further effects of climate, diet, and landmass size (mainland or island). Independent contrasts, correlograms, autoregression, and phylogenetic eigenvector regression (PVR) were used to examine phylogenetically related effects. We found a small but significant phylogenetic pattern for body mass of columbids. For T(b), there was no significant effect of mass or phylogeny. There was a significant effect of climate on T(b) and no significant effects of diet or landmass without mass or phylogenetic correction, but after mass and phylogenetic correction, there were no effects of climate, diet, or landmass. For BMR, there was a strong allometric effect, and residuals were significantly lower for arid and tropical species but not for temperate species, compared to predictions for nonpasserine birds. There was a nearly significant autoregressive phylogenetic relationship for BMR parl0;r=0.44), and the strong allometry of BMR remained for independent contrasts (slope=0.731), autoregressive residuals (0.698), and PVR (0.705). Residuals, from regression of autoregression and PVR residuals of M and BMR, were significantly associated with climate: arid pigeons had a lower BMR residual than tropical and temperate pigeons. PVR residuals were significantly affected by landmass (island columbids had a smaller residual than mainland columbids), but autoregression residuals were not. There was no association of autoregression or PVR residuals with diet. For C(wet), there was a strong allometric effect, and residuals for columbids were significantly higher compared to other birds. There was no significant relationship for C(wet) of columbids to climate, diet, or landmass. There was no significant autoregressive or PVR relationship for C(wet), and the strong allometry remained after phylogenetic analysis by independent contrasts (slope=0.501), autoregression (0.509), and PVR (0.514). Residuals from autoregression and PVR were not significantly correlated with climate, diet, or landmass (mainland/island).

Phylogenetic comparative methods and the geographic range size – body size relationship in new world terrestrial carnivora

Most recent papers avoid describing macroecological relationships and interpreting then without a previous control of non-independence in data caused by phylogenetic patterns in data. In this paper, we analyzed the geographic range size – body size relationship for 70 species of New World terrestrial Carnivora (‘fissipeds’) using various phylogenetic comparative methods and simulation procedures to assess their statistical performance. Autocorrelation analyses suggested a strong phylogenetic pattern for body size, but not for geographic range size. The correlation between the two traits was estimated using standard Pearson correlation across species (TIPS) and four different comparative methods: Felsenstein's independent contrasts (PIC), autoregressive method (ARM), phylogenetic eigenvector regression (PVR) and phylogenetic generalized least-squares (PGLS). The correlation between the two variables was significant for all methods, except PIC, in such a way that ecological mechanisms (i.e., minimum viable population or environmental heterogeneity- physiological homeostasis), could be valid explanations for the relationship. Simulations using different O-U processes for each trait were run in order to estimate true Type I errors of each method. Type I errors at 5% were similar for all phylogenetic methods (always lower than 8%), but equal to 13.1% for TIPS. PIC usually performs better than all other methods under Brownian motion evolution, but not in this case using a more complex combination of evolutionary models. So, recent claims that using independent contrasts in ecological research can be too conservative are correct but, on the other hand, using simple across-species correlation is too liberal even under the more complex evolutionary models exhibited by the traits analyzed here.

ADAPTIVE CONSTRAINTS AND THE PHYLOGENETIC COMPARATIVE METHOD: A COMPUTER SIMULATION TEST

Abstract Recently, the utility of modern phylogenetic comparative methods (PCMs) has been questioned because of the seemingly restrictive assumptions required by these methods. Although most comparative analyses involve traits thought to be undergoing natural or sexual selection, most PCMs require an assumption that the traits be evolving by less directed random processes, such as Brownian motion (BM). In this study, we use computer simulation to generate data under more realistic evolutionary scenarios and consider the statistical abilities of a variety of PCMs to estimate correlation coefficients from these data. We found that correlations estimated without taking phylogeny into account were often quite poor and never substantially better than those produced by the other tested methods. In contrast, most PCMs performed quite well even when their assumptions were violated. Felsenstein's independent contrasts (FIC) method gave the best performance in many cases, even when weak constraints had been acting throughout phenotypic evolution. When strong constraints acted in opposition to variance-generating (i.e., BM) forces, however, FIC correlation coefficients were biased in the direction of those BM forces. In most cases, all other PCMs tested (phylogenetic generalized least squares, phylogenetic mixed model, spatial autoregression, and phylogenetic eigenvector regression) yielded good statistical performance, regardless of the details of the evolutionary model used to generate the data. Actual parameter estimates given by different PCMs for each dataset, however, were occasionally very different from one another, suggesting that the choice among them should depend on the types of traits and evolutionary processes being considered.

ADAPTIVE CONSTRAINTS AND THE PHYLOGENETIC COMPARATIVE METHOD: A COMPUTER SIMULATION TEST

Recently, the utility of modern phylogenetic comparative methods (PCMs) has been questioned because of the seemingly restrictive assumptions required by these methods. Although most comparative analyses involve traits thought to be undergoing natural or sexual selection, most PCMs require an assumption that the traits be evolving by less directed random processes, such as Brownian motion (BM). In this study, we use computer simulation to generate data under more realistic evolutionary scenarios and consider the statistical abilities of a variety of PCMs to estimate correlation coefficients from these data. We found that correlations estimated without taking phylogeny into account were often quite poor and never substantially better than those produced by the other tested methods. In contrast, most PCMs performed quite well even when their assumptions were violated. Felsenstein's independent contrasts (FIC) method gave the best performance in many cases, even when weak constraints had been acting throughout phenotypic evolution. When strong constraints acted in opposition to variance-generating (i.e., BM) forces, however, FIC correlation coefficients were biased in the direction of those BM forces. In most cases, all other PCMs tested (phylogenetic generalized least squares, phylogenetic mixed model, spatial autoregression, and phylogenetic eigenvector regression) yielded good statistical performance, regardless of the details of the evolutionary model used to generate the data. Actual parameter estimates given by different PCMs for each dataset, however, were occasionally very different from one another, suggesting that the choice among them should depend on the types of traits and evolutionary processes being considered.