The seven deadly sins of comparative analysis

Phylogenetic comparative methods are extremely commonly used in evolutionary biology. In this paper, I highlight some of the problems that are frequently encountered in comparative analyses and review how they can be fixed. In broad terms, the problems boil down to a lack of appreciation of the underlying assumptions of comparative methods, as well as problems with implementing methods in a manner akin to more familiar statistical approaches. I highlight that the advent of more flexible computing environments should improve matters and allow researchers greater scope to explore methods and data.     

Effects of sample size and intraspecific variation in phylogenetic comparative studies: a meta‐analytic review

Comparative analyses aim to explain interspecific variation in phenotype among taxa. In this context, phylogenetic approaches are generally applied to control for similarity due to common descent, because such phylogenetic relationships can produce spurious similarity in phenotypes (known as phylogenetic inertia or bias). On the other hand, these analyses largely ignore potential biases due to within‐species variation. Phylogenetic comparative studies inherently assume that species‐specific means from intraspecific samples of modest sample size are biologically meaningful. However, within‐species variation is often significant, because measurement errors, within‐ and between‐individual variation, seasonal fluctuations, and differences among populations can all reduce the repeatability of a trait. Although simulations revealed that low repeatability can increase the type I error in a phylogenetic study, researchers only exercise great care in accounting for similarity in phenotype due to common phylogenetic descent, while problems posed by intraspecific variation are usually neglected. A meta‐analysis of 194 comparative analyses all adjusting for similarity due to common phylogenetic descent revealed that only a few studies reported intraspecific repeatabilities, and hardly any considered or partially dealt with errors arising from intraspecific variation. This is intriguing, because the meta‐analytic data suggest that the effect of heterogeneous sampling can be as important as phylogenetic bias, and thus they should be equally controlled in comparative studies. We provide recommendations about how to handle such effects of heterogeneous sampling.     

Controlling for non-independence in comparative analysis of patterns across populations within species

How do we quantify patterns (such as responses to local selection) sampled across multiple populations within a single species? Key to this question is the extent to which populations within species represent statistically independent data points in our analysis. Comparative analyses across species and higher taxa have long recognized the need to control for the non-independence of species data that arises through patterns of shared common ancestry among them (phylogenetic non-independence), as have quantitative genetic studies of individuals linked by a pedigree. Analyses across populations lacking pedigree information fall in the middle, and not only have to deal with shared common ancestry, but also the impact of exchange of migrants between populations (gene flow). As a result, phenotypes measured in one population are influenced by processes acting on others, and may not be a good guide to either the strength or direction of local selection. Although many studies examine patterns across populations within species, few consider such non-independence. Here, we discuss the sources of non-independence in comparative analysis, and show why the phylogeny-based approaches widely used in cross-species analyses are unlikely to be useful in analyses across populations within species. We outline the approaches (intraspecific contrasts, generalized least squares, generalized linear mixed models and autoregression) that have been used in this context, and explain their specific assumptions. We highlight the power of ‘mixed models’ in many contexts where problems of non-independence arise, and show that these allow incorporation of both shared common ancestry and gene flow. We suggest what can be done when ideal solutions are inaccessible, highlight the need for incorporation of a wider range of population models in intraspecific comparative methods and call for simulation studies of the error rates associated with alternative approaches.     

系统比较方法的原理及应用

物种的大部分性状与其系统进化过程相联系,亲缘关系近的物种,其性状差异通常较小.因此在种间或更高分类单元层次研究性状之间的关系,或性状与环境间关系时需要考虑系统进化的影响,以满足常规统计分析对于样本独立性的要求.自20世纪80年代以来国际上已经陆续推出一系列的系统比较方法,其共同原理是:在推断物种间系统关系的基础上,在种间水平上比较,将原本不符合样本独立性的物种性状或环境变量数据,将其转化为适用于常规统计分析方法的彼此独立的数据,然后运用常规统计方法分析,得到排除了系统进化历史影响的物种性状间或者物种性状与环境变量间的关系.首先简单介绍了运用系统比较方法之前的建立系统关系和数据诊断这两个步骤,在此基础上阐述简单独立对比分析、Felsenstein的独立比较方法和自回归方法这3种常用的系统比较方法的基本原理、各自的特点以及它们在生态学、进化生物学等领域的应用.系统比较方法已经获得广泛的应用和认可,发现了应用常规统计分析所没有能发现的问题和规律,但在构建准确反映系统进化过程的系统关系、进化模型的选择等方面仍具有一定的局限性;而生物信息学、生物系统学的发展,以及各种相关软件的开发为系统比较方法的进一步完善发展和更为广泛的应用创造了条件.     

Evolutionary trends on extant cat skull morphology (Carnivora: Felidae): a three‐dimensional geometrical approach

The skulls of 33 extant cat species were characterized through three‐dimensional geometric morphometrics using 20 landmarks. A principal component analysis (PCA) was performed with Procrustes fitted coordinates, and the PC‐scores were phylogenetically corrected by independent contrasts method. Three PCs allowed for the definition of five cat skull patterns. PC1: ‘snouted/massive‐headed cats’ (genus Panthera) opposing the ‘round‐headed small cats’ (genus Oncifelis, Prionailurus rubiginosus, Prionailurus bengalensis, among other small cats); PC2: ‘tapering‐headed cats’ (Neofelis nebulosa, Herpailurus yagouaroundi, Prionailurus planiceps) opposing the ‘stout‐headed cats’ (Acinonyx jubatus, Uncia uncia, Otocolobus manul, Felis margarita, and Felis nigripes); and PC3: ‘low profiled‐headed cats’ (mostly, Pr. planiceps). A sixth pattern, the ‘generalized skull’, observed in the Caracal lineage, genus Lynx, Leopardus pardalis, and Catopuma temminckii, indicates a morphological convergence among midsized‐cats. The morphological trends ‘snouted/massive’ and ‘round’ clearly denote a co‐evolution between size and shape. The other skull patterns evolved unrelatedly to the size (i.e. their allometric variations are not a size function). Nevertheless, each species comprises an amalgam of these patterns, so the influence of the size permeates, in some extent, the skull morphology along all cat lineages. The felid ecomorphological fit to hypercarnivory is obvious; however, different skull shapes in same‐sized species with similar habits, indicate that the variation in the skull morphology may result from phenotypic fluctuations, whose adaptive value (if indeed there is any) is still obscure. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 103 , 176–190.     

Geometric morphometric analyses provide evidence for the adaptive character of the Tanganyikan cichlid fish radiations

The cichlids of East Africa are renowned as one of the most spectacular examples of adaptive radiation. They provide a unique opportunity to investigate the relationships between ecology, morphological diversity, and phylogeny in producing such remarkable diversity. Nevertheless, the parameters of the adaptive radiations of these fish have not been satisfactorily quantified yet. Lake Tanganyika possesses all of the major lineages of East African cichlid fish, so by using geometric morphometrics and comparative analyses of ecology and morphology, in an explicitly phylogenetic context, we quantify the role of ecology in driving adaptive speciation. We used geometric morphometric methods to describe the body shape of over 1000 specimens of East African cichlid fish, with a focus on the Lake Tanganyika species assemblage, which is composed of more than 200 endemic species. The main differences in shape concern the length of the whole body and the relative sizes of the head and caudal peduncle. We investigated the influence of phylogeny on similarity of shape using both distance-based and variance partitioning methods, finding that phylogenetic inertia exerts little influence on overall body shape. Therefore, we quantified the relative effect of major ecological traits on shape using phylogenetic generalized least squares and disparity analyses. These analyses conclude that body shape is most strongly predicted by feeding preferences (i.e., trophic niches) and the water depths at which species occur. Furthermore, the morphological disparity within tribes indicates that even though the morphological diversification associated with explosive speciation has happened in only a few tribes of the Tanganyikan assemblage, the potential to evolve diverse morphologies exists in all tribes. Quantitative data support the existence of extensive parallelism in several independent adaptive radiations in Lake Tanganyika. Notably, Tanganyikan mouthbrooders belonging to the C-lineage and the substrate spawning Lamprologini have evolved a multitude of different shapes from elongated and Lamprologus-like hypothetical ancestors. Together, these data demonstrate strong support for the adaptive character of East African cichlid radiations.     

A new phylogenetic test for comparing multiple high‐dimensional evolutionary rates suggests interplay of evolutionary rates and modularity in lanternfishes (Myctophiformes; Myctophidae)

The interplay between evolutionary rates and modularity influences the evolution of organismal body plans by both promoting and constraining the magnitude and direction of trait response to ecological conditions. However, few studies have examined whether the best‐fit hypothesis of modularity is the same as the shape subset with the greatest difference in evolutionary rate. Here, we develop a new phylogenetic comparative method for comparing evolutionary rates among high‐dimensional traits, and apply this method to analyze body shape evolution in bioluminescent lanternfishes. We frame the study of evolutionary rates and modularity through analysis of three hypotheses derived from the literature on fish development, biomechanics, and bioluminescent communication. We show that a development‐informed partitioning of shape exhibits the greatest evolutionary rate differences among modules, but that a hydrodynamically informed partitioning is the best‐fit modularity hypothesis. Furthermore, we show that bioluminescent lateral photophores evolve at a similar rate as, and are strongly integrated with, body shape in lanternfishes. These results suggest that overlapping life‐history constraints on development and movement define axes of body shape evolution in lanternfishes, and that the positions of their lateral photophore complexes are likely a passive outcome of the interaction of these ecological pressures.     

A Bayesian extension of phylogenetic generalized least squares: Incorporating uncertainty in the comparative study of trait relationships and evolutionary rates

Phylogenetic comparative methods use tree topology, branch lengths, and models of phenotypic change to take into account nonindependence in statistical analysis. However, these methods normally assume that trees and models are known without error. Approaches relying on evolutionary regimes also assume specific distributions of character states across a tree, which often result from ancestral state reconstructions that are subject to uncertainty. Several methods have been proposed to deal with some of these sources of uncertainty, but approaches accounting for all of them are less common. Here, we show how Bayesian statistics facilitates this task while relaxing the homogeneous rate assumption of the well-known phylogenetic generalized least squares (PGLS) framework. This Bayesian formulation allows uncertainty about phylogeny, evolutionary regimes, or other statistical parameters to be taken into account for studies as simple as testing for coevolution in two traits or as complex as testing whether bursts of phenotypic change are associated with evolutionary shifts in intertrait correlations. A mixture of validation approaches indicates that the approach has good inferential properties and predictive performance. We provide suggestions for implementation and show its usefulness by exploring the coevolution of ankle posture and forefoot proportions in Carnivora.     

A METHOD FOR ASSESSING PHYLOGENETIC LEAST SQUARES MODELS FOR SHAPE AND OTHER HIGH‐DIMENSIONAL MULTIVARIATE DATA

Studies of evolutionary correlations commonly use phylogenetic regression (i.e., independent contrasts and phylogenetic generalized least squares) to assess trait covariation in a phylogenetic context. However, while this approach is appropriate for evaluating trends in one or a few traits, it is incapable of assessing patterns in highly multivariate data, as the large number of variables relative to sample size prohibits parametric test statistics from being computed. This poses serious limitations for comparative biologists, who must either simplify how they quantify phenotypic traits, or alter the biological hypotheses they wish to examine. In this article, I propose a new statistical procedure for performing ANOVA and regression models in a phylogenetic context that can accommodate high‐dimensional datasets. The approach is derived from the statistical equivalency between parametric methods using covariance matrices and methods based on distance matrices. Using simulations under Brownian motion, I show that the method displays appropriate Type I error rates and statistical power, whereas standard parametric procedures have decreasing power as data dimensionality increases. As such, the new procedure provides a useful means of assessing trait covariation across a set of taxa related by a phylogeny, enabling macroevolutionary biologists to test hypotheses of adaptation, and phenotypic change in high‐dimensional datasets.     

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.     

Rapid maximum likelihood ancestral state reconstruction of continuous characters: A rerooting‐free algorithm

Ancestral state reconstruction is a method used to study the evolutionary trajectories of quantitative characters on phylogenies. Although efficient methods for univariate ancestral state reconstruction under a Brownian motion model have been described for at least 25 years, to date no generalization has been described to allow more complex evolutionary models, such as multivariate trait evolution, non‐Brownian models, missing data, and within‐species variation. Furthermore, even for simple univariate Brownian motion models, most phylogenetic comparative R packages compute ancestral states via inefficient tree rerooting and full tree traversals at each tree node, making ancestral state reconstruction extremely time‐consuming for large phylogenies. Here, a computationally efficient method for fast maximum likelihood ancestral state reconstruction of continuous characters is described. The algorithm has linear complexity relative to the number of species and outperforms the fastest existing R implementations by several orders of magnitude. The described algorithm is capable of performing ancestral state reconstruction on a 1,000,000‐species phylogeny in fewer than 2 s using a standard laptop, whereas the next fastest R implementation would take several days to complete. The method is generalizable to more complex evolutionary models, such as phylogenetic regression, within‐species variation, non‐Brownian evolutionary models, and multivariate trait evolution. Because this method enables fast repeated computations on phylogenies of virtually any size, implementation of the described algorithm can drastically alleviate the computational burden of many otherwise prohibitively time‐consuming tasks requiring reconstruction of ancestral states, such as phylogenetic imputation of missing data, bootstrapping procedures, Expectation‐Maximization algorithms, and Bayesian estimation. The described ancestral state reconstruction algorithm is implemented in the Rphylopars functions anc.recon and phylopars.     

Evidence for speciational change in the evolution of ratites (Aves: Palaeognathae)

To perform a comparative analysis of character associations framed in a phylogenetic context (e.g. independent contrasts), a model of character evolution must be assumed. According to phyletic gradualism, morphological change accumulates gradually over time within lineages, and speciation events do not have a major role. Under speciational models, morphological change is assumed to occur during or just after cladogenesis in both daughter species, and the resulting morphologies do not change over long periods of time (stasis), until the next cladogenetic event. A novel method is presented for comparing these models of character evolution that uses permutational multiple phylogenetic regressions. The addition of divergence times to well-corroborated phylogenetic trees and the utilization of the method developed in this paper allows the estimation of relative frequency of gradual change and speciational change from living organisms. This method is applied to a dataset from ratites with the conclusion that, for a range of morphological features, change tends to have been speciational rather than gradual.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society , 2003, 80 , 99–106.     

Evaluating evolutionary pressures and phylogenetic signal in earthworms: a case study – the number of typhlosole lamellae in Hormogastridae (Annelida,Oligochaeta)

Rarely have phylogenetic comparative methods been used to study the correlation between phenotypic traits and environmental variables in invertebrates. With the widespread convergence and conservativeness of the morphological characters used in earthworms, these comparative methods could be useful to improve our understanding of their evolution and systematics. One of the most prominent morphological characters in the family Hormogastridae, endemic to Mediterranean areas, is their multilamellar typhlosole, traditionally thought to be an adaptation to soils poor in nutrients. We tested the correlation of body size and soil characteristics with the number of typhlosole lamellae through a phylogenetic generalized least squares (PGLS) analysis. An ultrametric phylogenetic hypothesis was built with a 2580‐bp DNA sequence from 90 populations, used in combination with three morphological and 11 soil variables. The best‐supported model, based on the Akaike information criterion, was obtained by optimizing the parameters lambda (λ), kappa (κ), and delta (δ). The phylogenetic signal was strong for the number of typhlosole lamellae and average body weight, and was lower for soil variables. Increasing body weight appeared to be the main evolutionary pressure behind the increase in the number of typhlosole lamellae, with soil texture and soil richness having a weaker but significant effect. Information on the evolutionary rate of the number of typhlosole lamellae suggested that the early evolution of this character could have strongly shaped its variability, as is found in an adaptive radiation. This work highlights the importance of implementing the phylogenetic comparative method to test evolutionary hypotheses in invertebrate taxa.     

The influence of size on body shape diversification across Indo‐Pacific shore fishes*

Understanding the causes of body shape variability across the tree of life is one of the central issues surrounding the origins of biodiversity. One potential mechanism driving observed patterns of shape disparity is a strongly conserved relationship between size and shape. Conserved allometry has been shown to account for as much as 80% of shape variation in some vertebrate groups. Here, we quantify the amount of body shape disparity attributable to changes in body size across nearly 800 species of Indo‐Pacific shore fishes using a phylogenetic framework to analyze 17 geometric landmarks positioned to capture general body shape and functionally significant features. In marked contrast to other vertebrate lineages, we find that changes in body size only explain 2.9% of the body shape variation across fishes, ranging from 3% to 50% within our 11 sampled families. We also find a slight but significant trend of decreasing rates of shape evolution with increasing size. Our results suggest that the influence of size on fish shape has largely been overwhelmed by lineage‐specific patterns of diversification that have produced the modern landscape of highly diverse forms that we currently observe in nature.     

Factors shaping the evolution of colour patterns in Australian agamid lizards (Agamidae): a comparative study

Identifying general patterns of adaptive coloration in animals can help to elucidate the evolutionary processes that generate them. We examined the evolution of colour patterns in Australian agamid lizards, a morphologically and ecologically diverse group that relies primarily on visual communication. We tested whether certain types of colour (yellow–reds and black) were likely to be used as sexual signals, as indicated by their association with indices of sexual selection, namely, sexual dichromatism and sexual dimorphism in body size and head shape. We then tested whether sexually dichromatic colours are associated with specific patterns (uniform, mottled, striped, blotched, reticulated) or ecological variables such as habitat openness, arboreality, and substrate type. The presence of yellow–red on lateral and ventral body regions and black on ventral body regions was significantly more common in males than females. Lateral yellow–red in males was associated with the total extent of sexual dichromatism and size dimorphism, whereas ventral yellow–red was associated with sexual dichromatism. Both lateral and ventral yellow–red were associated with uniform patterning, suggesting that sexual signals in male agamid lizards may often comprise uniform patches or flushes of yellow–red. Although ventral black coloration was more prevalent on males (i.e. strongly sexually dichromatic), it was not associated with indices of sexual selection, suggesting that, in agamid lizards, yellow–red coloration is more likely to be sexually selected than black. Sexually dichromatic coloration was not strongly associated with any of the ecological variables measured. We found some associations, however, between female dorsal patterns and ecological variables, suggesting that female patterns are influenced by natural selection. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109 , 101–112.     

Functional morphology of the bovid astragalus in relation to habitat: Controlling phylogenetic signal in ecomorphology

Bovid astragali are one of the most commonly preserved bones in the fossil record. Accordingly, astragali are an important target for studies seeking to predict the habitat preferences of fossil bovids based on bony anatomy. However, previous work has not tested functional hypotheses linking astragalar morphology with habitat while controlling for body size and phylogenetic signal. This article presents a functional framework relating the morphology of the bovid astragalus to habitat‐specific locomotor ecology and tests four hypotheses emanating from this framework. Highly cursorial bovids living in structurally open habitats are hypothesized to differ from their less cursorial closed‐habitat dwelling relatives in having (1) relatively short astragali to maintain rotational speed throughout the camming motion of the rotating astragalus, (2) a greater range of angular excursion at the hock, (3) relatively larger joint surface areas, and (4) a more pronounced “spline‐and‐groove” morphology promoting lateral joint stability. A diverse sample of 181 astragali from 50 extant species was scanned using a Next Engine laser scanner. Species were assigned to one of four habitat categories based on the published ecological literature. A series of 11 linear measurements and three joint surface areas were measured on each astragalus. A geometric mean body size proxy was used to size‐correct the measurement data. Phylogenetic generalized least squares (PGLS) was used to test for differences between habitat categories while controlling for body size differences and phylogenetic signal. Statistically significant PGLS results support Hypotheses 1 and 2 (which are not mutually exclusive) as well as Hypothesis 3. No support was found for Hypothesis 4. These findings confirm that the morphology of the bovid astragalus is related to habitat‐specific locomotor ecology, and that this relationship is statistically significant after controlling for body size and phylogeny. Thus, this study validates the use of this bone as an ecomorphological indicator. J. Morphol. 275:1201–1216, 2014. © 2014 Wiley Periodicals, Inc.     

The shape of the mandibular corpus in large fissiped carnivores: allometry,function and phylogeny

Mandibular corpus shape variability was investigated in seven families of both extant and extinct mammalian carnivores using two‐dimensional landmarks and geometric morphometric methods. The landmark configuration represents the position of the fourth premolar relative to the canine and the lower carnassial, plus related features of the corpus profile. Between families, the corpus manifests differences in shape and allometry. Additionally, families differ in the relationship between the angle α (a carnassial trait proxy for hypo‐hypercarnivory) and mandibular corpus shape. When phylogenetic relatedness is taken into account using five different phylogenies as covariates, interspecific scaling is still present but the relationship between α and corpus shape is no longer significant. This suggests that the allometric relationship reflects the physical constraints of mastication, resulting in relatively increased corpus depth with higher loads. In contrast, the angle α is related to corpus curvature and this relationship is phylogenetically constrained by the reduction of the molar battery in large feliforms early during the carnivore radiation. In summary, large fissiped carnivores show extensive functional convergence in mandibular corpus shape although the evolutionary routes leading to such functional convergence are different. © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society, 2008, 154 , 832–845.     

Relationships between bone growth rate, body mass and resting metabolic rate in growing amniotes: a phylogenetic approach

We explored the factors that explain the variation in resting metabolic rates (RMR) in growing amniotes by using the phylogenetic comparative method. For this, we measured raw RMR (mL O₂ h⁻¹), body mass, body mass growth rate, and periosteal bone growth rate in a sample of 44 growing individuals belonging to 13 species of amniotes. We performed variation partitioning analyses, which showed that phylogeny explains a significant fraction of the variation of mass-specific RMR (mL O₂ h⁻¹ g⁻¹), and that the cost of growth is much higher than the cost of maintenance. Moreover, we tested the hypothesis of the independence of energy allocation, and found that maintenance metabolism and growth rates are not significantly related. Finally, we calculated the statistical parameters of the relationship between geometry-corrected RMR (mL O₂ h⁻¹ g^−0.67) and bone growth rate. This relationship could potentially be used in palaeobiology to infer RMR from bone tissue samples of fossil species by assuming Amprino's rule (according to which bone tissue types reflect bone growth rates). These estimates would be especially interesting for Mesozoic non-avian theropod dinosaurs and Permian and Triassic therapsids to investigate, respectively, the origin of avian and mammalian endothermy.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 92 , 63–76.     

DISENTANGLING EVOLUTIONARY CAUSE‐EFFECT RELATIONSHIPS WITH PHYLOGENETIC CONFIRMATORY PATH ANALYSIS

Confirmatory path analysis is a statistical technique to build models of causal hypotheses among variables and test if the data conform with the causal model. However, classical path analysis techniques ignore the nonindependence of observations due to phylogenetic relatedness among species, possibly leading to spurious results. Here, we present a simple method to perform phylogenetic confirmatory path analysis (PPA). We analyzed simulated datasets with varying amounts of phylogenetic signal in the data and a known underlying causal structure linking the traits to estimate Type I error and power. Results show that Type I error for PPA appeared to be slightly anticonservative (range: 0.047–0.072) but path analysis models ignoring phylogenetic signal resulted in much higher Type I error rates, which were positively related to the amount of phylogenetic signal (range: 0.051 for λ= 0 to 0.916 for λ= 1). Further, the power of the test was not compromised when accounting for phylogeny. As an example of the application of PPA, we revisit a study on the correlates of aggressive broodmate competition across seven avian families. The use of PPA allowed us to gain greater insight into the plausible causal paths linking species traits to aggressive broodmate competition.