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 α = 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 transformat...

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Testing for phylogenetic signal in comparative data: behavioral traits are more labile.

▪ Abstract As better phylogenetic hypotheses become available for many groups of organisms, studies in community ecology can be informed by knowledge of the evolutionary relationships among coexisting species. We note three primary approaches to integrating phylogenetic information into studies of community organization: 1. examining the phylogenetic structure of community assemblages, 2. exploring the phylogenetic basis of community niche structure, and 3. adding a community context to studies of trait evolution and biogeography. We recognize a common pattern of phylogenetic conservatism in ecological character and highlight the challenges of using phylogenies of partial lineages. We also review phylogenetic approaches to three emergent properties of communities: species diversity, relative abundance distributions, and range sizes. Methodological advances in phylogenetic supertree construction, character reconstruction, null models for community assembly and character evolution, and metrics of community ...

/pdf/phylogenies-and-community-ecology-52euwskuu7.pdf

Phylogenies and Community Ecology

The question is often raised whether it is statistically necessary to control for phylogenetic associations in comparative studies. To investigate this question, we explore the use of a measure of phylogenetic correlation, lambda, introduced by Pagel (1999), that normally varies between 0 (phylogenetic independence) and 1 (species' traits covary in direct proportion to their shared evolutionary history). Simulations show lambda to be a statistically powerful index for measuring whether data exhibit phylogenetic dependence or not and whether it has low rates of Type I error. Moreover, lambda is robust to incomplete phylogenetic information, which demonstrates that even partial information on phylogeny will improve the accuracy of phylogenetic analyses. To assess whether traits generally show phylogenetic associations, we present a quantitative review of 26 published phylogenetic comparative data sets. The data sets include 103 traits and were chosen from the ecological literature in which debate about the need for phylogenetic correction has been most acute. Eighty-eight percent of data sets contained at least one character that displayed significant phylogenetic dependence, and 60% of characters overall (pooled across studies) showed significant evidence of phylogenetic association. In 16% of tests, phylogenetic correlation could be neither supported nor rejected. However, most of these equivocal results were found in small phylogenies and probably reflect a lack of power. We suggest that the parameter lambda be routinely estimated when analyzing comparative data, since it can also be used simultaneously to adjust the phylogenetic correction in a manner that is optimal for the data set, and we present an example of how this may be done.

https://www.jstor.org/stable/10.1086/343873

Phylogenetic analysis and comparative data: a test and review of evidence

We discuss and clarify several aspects of applying Felsenstein&#39;s (1985, Am. Nat. 125: 1n15) procedures to test for correlated evolution of continuous traits. This is one of several available comparative methods that maps data for phenotypic traits onto an existing phylogenetic tree (derived from independent information). Application of Felsenstein&#39;s method does not require an entirely dichotomous topology. It also does not require an assumption of gradual, clocklike character evolution, as might be modeled by Brownian motion. Almost any available information can be used to estimate branch lengths (e.g., genetic distances, divergence times estimated from the fossil record or from molecular clocks, numbers of character changes from a cladistic analysis). However, the adequacy for statistical purposes of any proposed branch lengths must be verified empirically for each phytogeny and for each character. We suggest a simple way of doing this, based on graphical analysis of plots of standardized independent contrasts versus their standard deviations (i.e., the square roots of the sums of their branch lengths). In some cases, the branch lengths and/or the values of traits being studied will require transformation. An example involving the scaling of mammalian home range area is presented. Once adequately standardized, sets of independent contrasts can be analyzed using either linear or nonlinear (multiple) regression. In all cases, however, regressions (or correlations) must be computed through the origin. We also discuss ways of correcting for body size effects and how this relates to making graphical representations of relationships of standardized independent contrasts. We close with a consideration of the types of traits that can be analyzed with independent contrasts procedures and conclude that any (continuous) trait that is inherited from ancestors is appropriate for analysis, regardless of the mechanism of inheritance (e.g., genetic or cultural).

http://www.biology.ucr.edu/people/faculty/Garland/GarlEA92.pdf

Procedures for the Analysis of Comparative Data Using Phylogenetically Independent Contrasts

Neocortex size as a constraint on group size in primates

We have presented a formal model for the quantitative analysis of phylogenetic and specific effects on the distribution of trait values among species. Total trait values are divided into phylogenetic values, inherited from an ancestral species, and specific values, the result of independent evolution. This allows a quantitative assessment of the strength of the phylogenetic inertia, or burden, displayed by a character in a lineage, so that questions concerning the relative importance of phylogenetic constraints in evolution can be answered. The separation of phylogenetic from specific effects proposed here also allows phylogenetic factors to be explicitly included in cross-species comparative analyses of adaptation. This solves a long-standing problem in evolutionary comparative studies. Only species' specific values can provide information concerning the independent evolution of characters in a set of related species. Therefore, only correlations among specific values for traits may be used as evidence for adaptation in cross-species comparative analyses. The phylogenetic autocorrelation model was applied to a comparative analysis of the determinants of sexual dimorphism in weight among 44 primate species. In addition to sexual dimorphism in weight, mating system, habitat, diet, and size (weight itself) were included in the analysis. All of the traits, except diet, were substantially influenced by phylogenetic inertia. The comparative analysis of the determinants of sexual dimorphism in weight indicates that 50% of the variation among primate species is due to phylogeny. Size, or scaling, could account for a total of 36% of the variance, making it almost as important as phylogeny in determining the level of dimorphism displayed by a species. Habitat, mating system, and diet follow, accounting for minor amounts of variation. Thus, in attempting to explain why a particular modern primate species is very dimorphic compared to other primates, we would say first because its ancestor was more dimorphic than average, second because it is a relatively large species, and third because it is terrestrial, polygynous, and folivorous.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1558-5646.1985.tb05699.x

The quantitative assessment of phylogenetic constraints in comparative analyses: sexual dimorphism in body weight among primates.

Among anthropoid primates there are interspecific differences in the degree of sexual dimorphism in both body size and canine size. Within the suborder body size dimorphism and canine size dimorphism are positively correlated,r=0.76. This correlation suggests that the two dimorphisms are equally developed in some species, while in other species there is a differential degree of sexual dimorphism. An analysis of these results and their relation to social organization and other ecological variables reveals: (1) the degree of canine size dimorphism is closely related to the amount of male intrasexual selection in a given mating system; and (2) the degree of body size dimorphism is also related to male intrasexual selection, but may be modified (either enhanced or diminished) by selection pressure from factors such as habitat, diet, foraging behavior, antipredator behavior, locomotory behavior, and female preference.

Relationship of sexual dimorphism in canine size and body size to social, behavioral, and ecological correlates in anthropoid primates

The effects of a series of ecological and size factors on the degree of sexual dimorphism in body weight and canine size were studied among subsets of 70 primate species. Variation in body-weight dimorphism can be almost entirely attributed to body weight (83% of variance R2
 of weight dimorphism). Much smaller amounts of the variation can be attributed to mating system (R2 =6.8%,polygynous species being more dimorphic than monogamous ones) and diet (R2 = 2.5%,frugivorous species being more dimorphic than folivorous ones). Habitat (arboreal vs. terrestrial) and activity rhythm (nocturnal vs. diurnal) have only an indirect effect on weight dimorphism. Variation in canine-size dimorphism can be explained in terms of canine size (R2 =49%),activity rhythm (R2 = 20%,diurnal species being more dimorphic than nocturnal ones), and mating system (R2 = 10%).Habitat and diet do not play a significant role in canine-size dimorphism. The unexpectedly high contribution of size to sexual dimorphism coupled with the observation of increased sexual dimorphism with increased size leads us to formulate a new selection model for the evolution of sexual dimorphism. We suggest that if there is selection for size increase, whatever its cause, directional selection in both males and females will lead to an increase in sexual dimorphism based on differences in genetic variance between the sexes. Sexual selection, resource division between the sexes, or lopsided reproductive selection need not play a role in such a model.

Correlates of sexual dimorphism in primates: Ecological and size variables

RENSCH1,2 showed, more than 20 years ago, that sexual dimorphism in body size tends to increase with increasing body size in various arthropod and avian taxa. Recently, the same positive relationship has been suggested for mammals in general3, and primates in particular4. Based on their findings on primates, Clutton-Brock et al.4 discussed several possible functional explanations for this relationship, but considered none of them wholly satisfactory. In particular, they rejected the hypothesis that positive allometry in sexual dimorphism in weight may be the product of an association of size and polygyny; they did not present statistical data to that effect, however. I argue here that, on the contrary, there is a strong relationship between polygyny and positive allometry for sexual dimorphism in body size. The evidence is based on an analysis of the relationship between the scaling of sexual dimorphism in body weight and the breeding system for 53 primate species, which in most cases coincide with those chosen by Clutton-Brock et al.4 for their study. The findings are incorporated into a multifactorial system on the evolution of sexual dimorphism in body size.

Walter Leutenegger

Papers

The quantitative assessment of phylogenetic constraints in comparative analyses: sexual dimorphism in body weight among primates.

Relationship of sexual dimorphism in canine size and body size to social, behavioral, and ecological correlates in anthropoid primates

Correlates of sexual dimorphism in primates: Ecological and size variables

Scaling of sexual dimorphism in body size and breeding system in primates

Functional aspects of pelvic morphology in simian Primates