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 ...

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Phylogenies and Community Ecology

An important aim of plant ecology is to identify leading dimensions of ecological variation among species and to understand the basis for them. Dimensions that can readily be measured would be especially useful, because they might offer a path towards improved worldwide synthesis across the thousands of field experiments and ecophysiological studies that use just a few species each. Four dimensions are reviewed here. The leaf mass per area-leaf lifespan (LMA-LL) dimension expresses slow turnover of plant parts (at high LMA and long LL), long nutrient residence times, and slow response to favorable growth conditions. The seed mass-seed output (SM-SO) dimension is an important predictor of dispersal to establishment opportunities (seed output) and of establishment success in the face of hazards (seed mass). The LMA-LL and SM-SO dimensions are each underpinned by a single, comprehensible tradeoff, and their consequences are fairly well understood. The leaf size-twig size (LS-TS) spectrum has obvious consequences for the texture of canopies, but the costs and benefits of large versus small leaf and twig size are poorly understood. The height dimension has universally been seen as ecologically important and included in ecological strategy schemes. Nevertheless, height includes several tradeoffs and adaptive elements, which ideally should be treated separately. Each of these four dimensions varies at the scales of climate zones and of site types within landscapes. This variation can be interpreted as adaptation to the physical environment. Each dimension also varies widely among coexisting species. Most likely this within-site variation arises because the ecological opportunities for each species depend strongly on which other species are present, in other words, because the set of species at a site is a stable mixture of strategies.

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Plant Ecological Strategies: Some Leading Dimensions of Variation Between Species

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

Fitting a line to a bivariate dataset can be a deceptively complex problem, and there has been much debate on this issue in the literature. In this review, we describe for the practitioner the essential features of line-fitting methods for estimating the relationship between two variables: what methods are commonly used, which method should be used when, and how to make inferences from these lines to answer common research questions. A particularly important point for line-fitting in allometry is that usually, two sources of error are present (which we call measurement and equation error), and these have quite different implications for choice of line-fitting method. As a consequence, the approach in this review and the methods presented have subtle but important differences from previous reviews in the biology literature. Linear regression, major axis and standardised major axis are alternative methods that can be appropriate when there is no measurement error. When there is measurement error, this often needs to be estimated and used to adjust the variance terms in formulae for line-fitting. We also review line-fitting methods for phylogenetic analyses. Methods of inference are described for the line-fitting techniques discussed in this paper. The types of inference considered here are testing if the slope or elevation equals a given value, constructing confidence intervals for the slope or elevation, comparing several slopes or elevations, and testing for shift along the axis amongst several groups. In some cases several methods have been proposed in the literature. These are discussed and compared. In other cases there is little or no previous guidance available in the literature. Simulations were conducted to check whether the methods of inference proposed have the intended coverage probability or Type I error. We identified the methods of inference that perform well and recommend the techniques that should be adopted in future work.

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Bivariate line-fitting methods for allometry.

Seed mass is correlated with a number of other plant traits, including dispersal mode, growth form and specific leaf area. Specific leaf area is the main determinant of potential relative growth rate and an indicator of the site quality to which a species is adapted. The relationships with dispersal mode and growth form have consistent form in five datasets from three continents, and each account for about 20-30% of variation in log seed mass. Thus, there is also very substantial variation within growth form and dispersal categories. Much, but not all, of the 20-30% is associated with shifted family composition between growth forms or dispersal modes. Experiments have shown that seedlings of larger-seeded species are better able to survive hazards including deep shade, drought, physical damage and the presence of competing vegetation. If there is a common mechanism under these different hazards, it seemingly must be a `reserve effect', whereby during deployment and early growth larger-seeded species hold a bigger percentage of seed reserves uncommitted to seedling structure and available to support respiration or repair damage. A reserve effect has not yet been demonstrated directly. It remains possible that different mechanisms operate under different hazards. Under a reserve effect, advantages of larger seed size should be temporary, and temporary advantage has indeed been observed with regard to seedling survival under dense shade. Although larger seed mass confers benefits on seedlings, larger seeds must necessarily be produced in smaller numbers per unit of resource allocated. Seed mass is presumed to have evolved as a compromise between these counterposed pressures. Yet there has proved to be surprisingly little difference in average seed mass between very different vegetation regions, at least in temperate climates. Rather, there is startlingly wide variation in seed mass among species growing interspersed with each other. Recent applications of game theory may be capable of accounting for this wide variation between coexisting species, but at present these models are driven by competition among seedling species (as opposed to between seedlings and adults). It remains unclear whether competition among seedlings is a decisive influence on species composition in most of the world's vegetation types.

Comparative ecology of seed size and dispersal

The last 10 years have seen important advances in methodology for taking phylogeny into account when analysing a comparative dataset. This commentary is about a class of interpretive procedures associated with these new statistical methods. We will call the interpretive logic 'phylogenetic correction' (PC for short), because this phrase summarizes the approach. Our essential message, however, is that a PC procedure is not in fact a 'correction', an adjustment to remove errors. Rather, it is a conceptual decision to give priority to one interpretation over another. Accordingly, it is an error to believe that PC is a methodology that must routinely be applied in all comparative analyses. The present Forum was proposed by the Editor during the review process for a paper about comparative ecology of seed mass (Leishman et al. 1995; see p. 517). Accordingly, examples will be drawn from the literature on seed mass, but the points made would be true of many species attributes. By 'comparative dataset', we mean a table with present-day species as rows, and attributes as columns. Some columns describe phylogenetic relations among the species, and others describe present-day attributes affecting the ecology of each species. Ecological attributes may include both those recording the behaviour of species in the field, such as capacity to establish in small canopy gaps (Kelly & Purvis 1993), and those that would be manifested even in glasshouse or garden, such as seeds per carpel (Hodgson & Mackey 1986). The analyses we are concerned with examine between-species variation in a focal ecological trait (here, seed mass), by investigating its correlation with other columns in the dataset.

On misinterpreting the phylogenetic correction

where grain size refers to the size of the landscape elements present. Dispersion is essentially a scalar phenomenon. To adequately describe the dispersion of fragments in an area, a number of fragment attributes need to be considered. Fragments have many features in common with vegetation patches in terms of both their physical properties and the ways organisms respond to them (e.g., Wiens

https://www.jstor.org/stable/info/2385813

Scale and the Spatial Concept of Fragmentation

Seed size is correlated with a number of other plant attributes, and such correlations are commonly interpreted as adaptations to different life histories. However, seed size is also strongly related to species phylogeny. In the current comparative literature, correlations between trait variation and taxonomic membership are often interpreted as evidence for phylogenetic constraints, and such phylogenetic explanations of variation are presented as alternatives to adaptive explanations. However, phylogenetic patterns of trait variation should not be discussed exclusively in terms of constraints. Neither should phylogenetic and adaptive explanations for variation be automatically presented as alternatives. Another explanation for similarity among related taxa is phylogenetic niche conservatism (PNC). This process is well known to exist-indeed, it is an inevitable consequence of evolution by natural selection-and is explicitly adaptive. Under PNC, radiation within a lineage is shaped by phylogeny, by the env...

https://www.jstor.org/stable/pdfplus/2463112

Seed size and phylogeny in six temperate floras: constraints, niche conservatism, and adaptation

In the following pages we publish responses to the papers in the last issue (83:3) by Westoby et al. and Harvey et al. on the use of 'phylogenetic correction' in comparative ecological studies. It has not been possible for every author to comment upon every contribution; in this issue Westoby et al. reply only to Harvey et al. (83:3), while Harvey et al. have been able to comment on all the opinions expressed. A final contribution from Westoby et al. will conclude this debate in the October issue (83:5).

Janice M. Lord

Papers

Comparative ecology of seed size and dispersal

On misinterpreting the phylogenetic correction

Scale and the Spatial Concept of Fragmentation

Seed size and phylogeny in six temperate floras: constraints, niche conservatism, and adaptation

Further Remarks on Phylogenetic Correction