Relationship between host diversity and parasite diversity: flea assemblages on small mammals

Aim We examined the relationship between host species richness and parasite species richness using simultaneously collected data on small mammals (Insectivora, Rodentia and Lagomorpha) and their flea parasites. Location The study used previously published data on small mammals and their fleas from 37 different regions. All the world's main geographical regions other than Australasia and Wallacea were represented in the study, i.e. neotropical, nearctic, palaearctic, oriental and afrotropical realms. Methods We controlled the data for the area sampled and sampling effort and then tested this relationship using both cross‐region conventional analysis and the independent contrasts method (to control for the effects of biogeographic historical relationships among different regions). Brooks parsimony analysis was used to construct a region cladogram based on the presence/absence of a host species and host phylogeny. Results Both cross‐region and independent contrasts analyses showed a positive correlation between host species richness and flea species richness. Conventional cross‐region regression under‐ or overestimated fleas species richness in the majority of regions. Main conclusions When the regression derived by the independent contrasts method was mapped onto the original tip data space, points that deviated significantly from the regression originated from Kenya, Mississippi and southern California (lower than expected flea richness) and Chile, Idaho, south‐western California and Kyrgyzstan (higher than expected flea richness). These deviations can be explained by the environmental mediation of host–flea relationships and by a degree of environmental variety in sampled areas.     

Convergence and correlations among leaf size and function in seed plants: a comparative test using independent contrasts

Prior studies of a broad array of seed plants have reported strong correlations among leaf life span, specific leaf area, nitrogen concentration, and carbon assimilation rates, which have been interpreted as evidence of coordinated leaf physiological strategies. However, it is not known whether these relationships reflect patterns of evolutionary convergence, or whether they are due to contrasting characteristics of major seed plant lineages. We reevaluated a published data set for these seven traits measured in over 100 species, using phylogenetic independent contrasts calculated over a range of alternative seed plant phylogenies derived from recent molecular systematic analyses. In general, pairwise correlations among these seven traits were similar with and without consideration of phylogeny, and results were robust over a range of alternative phylogenies. We also evaluated relationships between these seven traits and lamina area, another important aspect of leaf function, and found moderate correlations with specific leaf area (0.64), mass-based photosynthesis (0.54), area-based nitrogen (−0.56), and leaf life span (−0.42). However, several of these correlations were markedly reduced using independent contrasts; for example, the correlation between leaf life span and lamina area was reduced to close to zero. This change reflects the large differences in both these traits between conifers and angiosperms and the absence of a relationship between the traits within these groups. This analysis illustrates that most interspecific relationships among leaf functional traits, considered across a broad range of seed plant taxa, reflect significant patterns of correlated evolutionary change, lending further support to the adaptive interpretation of these relationships.     

Using the Past to Predict the Present: Confidence Intervals for Regression Equations in Phylogenetic Comparative Methods

Two phylogenetic comparative methods, independent contrasts and generalized least squares models, can be used to determine the statistical relationship between two or more traits. We show that the two approaches are functionally identical and that either can be used to make statistical inferences about values at internal nodes of a phylogenetic tree (hypothetical ancestors), to estimate relationships between characters, and to predict values for unmeasured species. Regression equations derived from independent contrasts can be placed back onto the original data space, including computation of both confidence intervals and prediction intervals for new observations. Predictions for unmeasured species (including extinct forms) can be made increasingly accurate and precise as the specificity of their placement on a phylogenetic tree increases, which can greatly increase statistical power to detect, for example, deviation of a single species from an allometric prediction. We reexamine published data for basal metabolic rates (BMR) of birds and show that conventional and phylogenetic allometric equations differ significantly. In new results, we show that, as compared with nonpasserines, passerines exhibit a lower rate of evolution in both body mass and mass-corrected BMR; passerines also have significantly smaller body masses than their sister clade. These differences may justify separate, clade-specific allometric equations for prediction of avian basal metabolic rates.     

Xylem function of arid-land shrubs from California, USA: an ecological and evolutionary analysis

Xylem traits were examined among 22 arid-land shrub species, including measures of vessel dimensions and pit area. These structural measures were compared with the xylem functional traits of transport efficiency and safety from cavitation. The influence of evolution on trait relationships was examined using phylogenetic independent contrasts (PICs). A trade-off between xylem safety and efficiency was supported by a negative correlation between vessel dimensions and cavitation resistance. Pit area was correlated with cavitation resistance when cross species data were examined, but PICs suggest that these traits have evolved independently of one another. Differences in cavitation resistance that are not explained by pit area may be related to differences in pit membrane properties or the prevalence of tracheids, the latter of which may alter pit area through the addition of vessel-to-tracheid pits or through changes in xylem conduit connectivity. Some trait relationships were robust regardless of species ecology or evolutionary history. These trait relationships are likely to be the most valuable in predictive models that seek to examine anatomical and functional trait relationships among extant and fossil woods and include the relationship among hydraulic conductivity and vessel diameter, between vessel diameter and vessel length, and between hydraulic conductivity and wood density.     

Interspecific abundance–occupancy relationships of British mammals and birds: is it possible to explain the residual variation?

Aim The majority of studies concerning positive interspecific abundance–occupancy relationships have used broad‐scale and microcosm data to test the occurrence and correlates of the relationship to determine which of the proposed mechanisms give rise to it. It has been argued recently that studying the residual variation about abundance–occupancy relationships is a more logical analysis and may yield faster progress in identifying the relative roles of the mechanisms. However, to date this approach has been largely unsuccessful. Here we test if fundamental species traits such as the status (native and introduced), habitat and trophic group of mammal and bird species may explain any of the residual variation about their respective abundance–occupancy relationships. Location The study used British mammal and bird species. Methods We tested if species traits explained any of the variation about abundance–occupancy relationships using linear regression techniques both treating species as independent data points for analysis and controlling for phylogenetic association. Results None of the species traits could explain any residual variation about the positive interspecific abundance–occupancy relationships of British mammals and birds. This applied both when treating species as independent data points and after controlling for phylogenetic association. Conclusions Given the lack of explanatory power of the species traits here and in other studies using this approach it seems that the variation about positive interspecific abundance–occupancy relationships is not explicable in a simple fashion. Predicting the likely influence of traits that are independent of phylogeny is also problematic. Therefore, the general utility of this approach and its future role in understanding the mechanisms causing positive interspecific abundance–occupancy relationships is doubtful.     

Correlated evolution and independent contrasts.

The use of the independent contrast method in comparative tests is studied. It is assumed that: (i) the traits under investigation are subject to natural selection; (ii) closely related species are similar because they share many characteristics of their niche, inherited from a common ancestor; and (iii) the current adaptive significance of the traits is the focus of investigation. The main objection to the use of species values in this case is that third variables which are shared by closely related species confound the relationship between the focal traits. In this paper, I argue that third variables are largely not controlled by the contrast methods, which are designed to estimate correlated evolution. To the extent that third variables also show correlated evolution, the true relationship among the traits of interest will remain obscured. Although the independent contrast method does not resolve the influence of third traits it does, in principle, provide a greater resolution than the use of the species mean values. However, its validity depends on the applicability of an evolutionary model which has a substantial stochastic component. To illustrate the consequences of relaxing this assumption I consider an alternative model of an adaptive radiation, where species come to fill a fixed niche space. Under this model, the expected value for the contrast correlation differs from that for the species correlation. The two correlations differ because contrasts reflect the historical pattern of diversification among species, whereas the species values describe the present-day relationships among the species. If the latter is of interest, I suggest that assessing significance based on the species correlations can be justified, providing that attention is paid to the role of potentially confounding third traits. Often, differences between contrast and species correlations may be biologically informative, reflecting changes in correlations between traits as an adaptive radiation proceeds; contrasts may be particularly useful as a means of investigating past history, rather than current utility of traits.     

The effect of genome size on detailed species traits within closely related species of the same habitat

In spite of the large number of studies on genome size, studies comparing genome size and growth‐related traits across a wider range of species from the same habitat, taking into account species phylogeny, are largely missing. I estimated the relationship between genome size and different seed and seedling traits in perennial herbs occurring in dry calcareous grasslands in northern Bohemia, Czech Republic. There was no relationship between genome size and plant traits in simple regression analyses, but several strong relationships emerged in analyses based on pairwise phylogenetically independent contrasts. There was a significant relationship between monoploid genome size and production of above‐ground biomass, seedling establishment success and seed weight and between holoploid genome size and seed dormancy. Because the results are based on phylogenetically independent contrasts over a range of species from the same type of habitat, they allow me to conclude that these patterns were not because of species group or habitat type, but really show a correlation with genome size. In contrast to previous studies, I found a higher number of relationships with monoploid than with holoploid genome size. This may be because the traits observed in this study are directly related to plant growth and thus to life‐cycle time, which is determined by monoploid genome size. © 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 160 , 290–298.     

The Independent Evolution Method Is Not a Viable Phylogenetic Comparative Method

Phylogenetic comparative methods (PCMs) use data on species traits and phylogenetic relationships to shed light on evolutionary questions. Recently, Smaers and Vinicius suggested a new PCM, Independent Evolution (IE), which purportedly employs a novel model of evolution based on Felsenstein’s Adaptive Peak Model. The authors found that IE improves upon previous PCMs by producing more accurate estimates of ancestral states, as well as separate estimates of evolutionary rates for each branch of a phylogenetic tree. Here, we document substantial theoretical and computational issues with IE. When data are simulated under a simple Brownian motion model of evolution, IE produces severely biased estimates of ancestral states and changes along individual branches. We show that these branch-specific changes are essentially ancestor-descendant or “directional” contrasts, and draw parallels between IE and previous PCMs such as “minimum evolution”. Additionally, while comparisons of branch-specific changes between variables have been interpreted as reflecting the relative strength of selection on those traits, we demonstrate through simulations that regressing IE estimated branch-specific changes against one another gives a biased estimate of the scaling relationship between these variables, and provides no advantages or insights beyond established PCMs such as phylogenetically independent contrasts. In light of our findings, we discuss the results of previous papers that employed IE. We conclude that Independent Evolution is not a viable PCM, and should not be used in comparative analyses.     

Uncertain branch lengths, taxonomic sampling error, and the egg to body size allometry in temperate butterflies (Lepidoptera)

The allometry of egg to body size in temperate butterflies, and the relationships between egg size and larval host structure, taxonomy, voltinism, and duration of the egg stage, are investigated using cross-species analysis and the comparative analysis of independent contrasts. In addition, the effect of two sources of uncertainty that may affect continuous data when treated under a statistical, comparative, framework, is assessed: (1) unknown evolutionary distances, and (2) taxonomic representativity (proportion of species of a given taxon, from which data are available). It is suggested that the effects of taxonomic under-representation could be important in comparative, quantitative studies, but this problem may be tempered by means of weighted regression. Under the assumption that taxonomy represents butterfly phylogeny, egg and adult body size are related by negative allometry (i.e. the slope of the line fitted to the logarithmically transformed data is lower than 1.0). However, the precise slope (0.2-0.9) depends on the method used, branch lengths, and taxonomic sampling. There is evidence for a relationship between a species' voltinism and the number of days it spends in the egg stage, as well as between adult butterfly size and the gross structure of the plants used as larval hosts (woody plants or herbs). Egg size proves to be related to foodplant taxonomy, voltinism, and duration of the egg stage when the data are analysed using species means, but these relationships become non-significant when the comparative method is employed.     

Statistical Power to Detect Genetic (Co)Variance of Complex Traits Using SNP Data in Unrelated Samples

We have recently developed analysis methods (GREML) to estimate the genetic variance of a complex trait/disease and the genetic correlation between two complex traits/diseases using genome-wide single nucleotide polymorphism (SNP) data in unrelated individuals. Here we use analytical derivations and simulations to quantify the sampling variance of the estimate of the proportion of phenotypic variance captured by all SNPs for quantitative traits and case-control studies. We also derive the approximate sampling variance of the estimate of a genetic correlation in a bivariate analysis, when two complex traits are either measured on the same or different individuals. We show that the sampling variance is inversely proportional to the number of pairwise contrasts in the analysis and to the variance in SNP-derived genetic relationships. For bivariate analysis, the sampling variance of the genetic correlation additionally depends on the harmonic mean of the proportion of variance explained by the SNPs for the two traits and the genetic correlation between the traits, and depends on the phenotypic correlation when the traits are measured on the same individuals. We provide an online tool for calculating the power of detecting genetic (co)variation using genome-wide SNP data. The new theory and online tool will be helpful to plan experimental designs to estimate the missing heritability that has not yet been fully revealed through genome-wide association studies, and to estimate the genetic overlap between complex traits (diseases) in particular when the traits (diseases) are not measured on the same samples.     

VISUALIZING MULTIVARIATE SELECTION

Recent developments in quantitative-genetic theory have shown that natural selection can be viewed as the multivariate relationship between fitness and phenotype. This relationship can be described by a multidimensional surface depicting fitness as a function of phenotypic traits. We examine the connection between this surface and the coefficients of phenotypic selection that can be estimated by multiple regression and show how the interpretation of multivariate selection can be facilitated through the use of the method of canonical analysis. The results from this analysis can be used to visualize the surface implied by a set of selection coefficients. Such a visualization provides a compact summary of selection coefficients, can aid in the comparison of selection surfaces, and can help generate testable hypotheses as to the adaptive significance of the traits under study. Further, we discuss traditional definitions of directional, stabilizing, and disruptive selection and conclude that selection may be more usefully classified into two general modes, directional and nonlinear selection, with stabilizing and disruptive selection as special cases of nonlinear selection.     

热带季雨林不同小生境大戟科植物幼树的叶片结构、耐旱性和光合能力之间的相关性

植物的叶片结构和功能性状受到自身、环境和系统发育的影响。该研究选取西双版纳20 hm²热带雨林动态监测大样地内18种分布格局不同的大戟科植物, 测量了幼树叶片的解剖结构、水分关系特征、最大光合能力和暗呼吸, 主要探讨了叶片结构对植物耐旱性和光合能力的影响, 耐旱性和光合能力之间的权衡关系, 以及环境水分条件对植物功能性状相关性的影响。结果表明: 1)生境内植物表现出一定的结构和功能的趋同性, 分布在山脊和山坡的种比沟谷种具有更强的耐失水能力; 2)去除了系统发育的影响后, 一些关键性状(特别是叶片密度和膨压丧失点时的水势、饱和渗透势等)之间存在跨生境尺度上的相关关系, 植物叶片结构同时影响了植物的耐失水能力和光合能力, 植物叶片自身的结构限制导致了植物的耐旱性(高的叶片密度、比叶质量)和光合能力(低的叶片密度、比叶质量)存在反向进化关系; 3)如果研究的植物类群亲缘关系较近, 传统的Pearson相关分析不能很好地揭示其性状间的相关关系, 因而必须采用系统发育独立对照差作相关分析。大戟科植物的结构和功能在水分梯度和光梯度上的生态位分化也从功能性状的角度为热带季雨林能维持高生物多样性, 保持植物物种长期共存提供了一个可能的解释。     

Comparing the preferences of three herbivore species with resistance traits of 15 perennial dicots: the effects of phylogenetic constraints

Differences in palatability between 15 perennial dicotyledonous herbaceous plant species were investigated in a multiple choice test, involving three generalist herbivores. Palatability was compared with two categories of plant traits: defence characteristics and growth properties. On theoretical grounds, we expected a positive relationship between growth rate and palatability, and a negative relationship between palatability and defence traits. The possible effect of phylogeny on the outcome of the comparisons was investigated by analysing the data using phylogenetically independent contrasts. The three herbivores showed remarkably similar preferences, which indicates that the results of the choice experiment are a good representation of leaf palatability. The significant negative correlations found in a direct comparison between herbivore preference and relative growth rate, and between herbivore preference and lignin and dry matter content, did not hold after phylogenetic correction. On the other hand, one relationship emerged only when comparing phylogenetically independent contrasts: contrary to expectation, a negative relation was noted between juvenile growth rate and plant palatability. A possible explanation for the contradictory nature of this result is the uniformly ready availability of resources in our experiment.     

Does investment into ��expensive�� tissue compromise anti-parasitic defence? Testes size, brain size and parasite diversity in rodent hosts

Species richness of parasite assemblages varies among host species. Earlier studies that searched for host-related determinants of parasite diversity mainly considered host traits that affect the probability of host encounter with parasites, whereas host traits related to defensibility against parasites have rarely been investigated. From the latter perspective, evolutionary investment in ??expensive?? tissue or organs (like testes or brain) may trade off against energetically costly anti-parasitic defences. If so, richer parasite assemblages are expected in hosts with larger testes and brains. We studied the relationships between testes and brain size and diversity of parasites (fleas, gamasid mites and helminths) in 55 rodent species using a comparative approach and application of two methods, namely the method of independent contrasts and generalized least-squares (GLS) analysis. Both phylogenetically correct methods produced similar results for flea and helminth species richness. Testes size positively correlated with flea and helminth species richness but not gamasid mite species richness. No correlation between brain size and species richness of any parasite group was found by the method of independent contrasts. However, GLS analysis indicated negative correlation between brain size and mite species richness. Our results cast doubt on the validity of the expensive tissue hypothesis, but suggest instead that larger testes are associated with higher parasite diversity via their effect on mobility and/or testosterone-mediated immunosuppression.     

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.     

Simulating trait evolution for cross-cultural comparison

Cross-cultural anthropologists have increasingly used phylogenetic methods to study cultural variation. Because cultural behaviours can be transmitted horizontally among socially defined groups, however, it is important to assess whether phylogeny-based methods--which were developed to study vertically transmitted traits among biological taxa--are appropriate for studying group-level cultural variation. Here, we describe a spatially explicit simulation model that can be used to generate data with known degrees of horizontal donation. We review previous results from this model showing that horizontal transmission increases the type I error rate of phylogenetically independent contrasts in studies of correlated evolution. These conclusions apply to cases in which two traits are transmitted as a pair, but horizontal transmission may be less problematic when traits are unlinked. We also use the simulation model to investigate whether measures of homology (the consistency index and the retention index) can detect horizontal transmission of cultural traits. Higher rates of evolutionary change have a stronger depressive impact on measures of homology than higher rates of horizontal transmission; thus, low consistency or retention indices are not necessarily indicative of 'ethnogenesis'. Collectively, these studies demonstrate the importance of using simulations to assess the validity of methods in cross-cultural research.     

A trait‐based trade‐off between growth and mortality: evidence from 15 tropical tree species using size‐specific relative growth rates

A life‐history trade‐off between low mortality in the dark and rapid growth in the light is one of the most widely accepted mechanisms underlying plant ecological strategies in tropical forests. Differences in plant functional traits are thought to underlie these distinct ecological strategies; however, very few studies have shown relationships between functional traits and demographic rates within a functional group. We present 8 years of growth and mortality data from saplings of 15 species of Dipterocarpaceae planted into logged‐over forest in Malaysian Borneo, and the relationships between these demographic rates and four key functional traits: wood density, specific leaf area (SLA), seed mass, and leaf C:N ratio. Species‐specific differences in growth rates were separated from seedling size effects by fitting nonlinear mixed‐effects models, to repeated measurements taken on individuals at multiple time points. Mortality data were analyzed using binary logistic regressions in a mixed‐effects models framework. Growth increased and mortality decreased with increasing light availability. Species differed in both their growth and mortality rates, yet there was little evidence for a statistical interaction between species and light for either response. There was a positive relationship between growth rate and the predicted probability of mortality regardless of light environment, suggesting that this relationship may be driven by a general trade‐off between traits that maximize growth and traits that minimize mortality, rather than through differential species responses to light. Our results indicate that wood density is an important trait that indicates both the ability of species to grow and resistance to mortality, but no other trait was correlated with either growth or mortality. Therefore, the growth mortality trade‐off among species of dipterocarp appears to be general in being independent of species crossovers in performance in different light environments.     

The evolution of threshold traits: effects of selection on fecundity and correlated response in wing dimorphism in the sand cricket

The quantitative genetic basis of traits can be determined using a pedigree analysis or a selection experiment. Each approach is valuable and the combined data can contribute more than either method alone. Analysis using both sib analysis and selection is particularly essential when there are likely to be nonlinearities in the functional relationships among traits. A class of traits for which this occurs is that of threshold traits, which are characterized by a dichotomous phenotype that is determined by a threshold of sensitivity and a continuously distributed underlying trait called the liability. In this case, traits that are correlated with the liability may show a nonlinear relationship due to the dichotomy of expression at the phenotypic level. For example, in wing dimorphic insects fecundity of the macropterous (long-winged) females appears in part to be determined by the allocation of resources to the flight muscles, which are almost invariably small or absent in the micropterous (short-winged, flightless) females. Pedigree analysis of the cricket Gryllus firmus has shown that wing morph, fecundity and the trade-off between the two have additive genetic (co)variance. It has also been shown that selection on proportion macroptery produced an asymmetric correlated response of fecundity. The present paper details the results of direct selection on fecundity and the correlated response in proportion macroptery. Selection for increased fecundity resulted in increased fecundity within both wing morphs and a correlated decrease in proportion macroptery. Similarly, selection for decreased fecundity resulted in a decrease within morphs and a correlated increase in the proportion of macropterous females. This provides additional evidence that the trade-off between fecundity and wing morphology has a genetic basis and will thus modulate the evolution of the two traits.