Phylogenetic signal, evolutionary process, and rate

A recent advance in the phylogenetic comparative analysis of continuous traits has been explicit, model-based measurement of "phylogenetic signal" in data sets composed of observations collected from species related by a phylogenetic tree. Phylogenetic signal is a measure of the statistical dependence among species' trait values due to their phylogenetic relationships. Although phylogenetic signal is a measure of pattern (statistical dependence), there has nonetheless been a widespread propensity in the literature to attribute this pattern to aspects of the evolutionary process or rate. This may be due, in part, to the perception that high evolutionary rate necessarily results in low phylogenetic signal; and, conversely, that low evolutionary rate or stabilizing selection results in high phylogenetic signal (due to the resulting high resemblance between related species). In this study, we use individual-based numerical simulations on stochastic phylogenetic trees to clarify the relationship between phylogenetic signal, rate, and evolutionary process. Under the simplest model for quantitative trait evolution, homogeneous rate genetic drift, there is no relation between evolutionary rate and phylogenetic signal. For other circumstances, such as functional constraint, fluctuating selection, niche conservatism, and evolutionary heterogeneity, the relationship between process, rate, and phylogenetic signal is complex. For these reasons, we recommend against interpretations of evolutionary process or rate based on estimates of phylogenetic signal.     

The degree and pattern of phylogenetic signal in primate long-bone structure

Interspecific scaling is a fundamental tool for comparative studies of primate long-bone structure and adaptation. However, scaling analyses based on conventional statistical methods can lead to false positives regarding adaptive relationships when traits exhibit strong phylogenetic signal. This problem can be addressed through the use of phylogenetic comparative methods (PCMs). To date, PCMs have not been incorporated into comparative studies of primate long-bone structure because it has been assumed that long-bone structure is free of phylogenetic signal once appropriately scaled. To test this assumption, we evaluated the degree of phylogenetic signal in three types of long-bone structural traits (bone length, articular surface areas, and cross-sectional geometric properties) from 17 quadrupedal primate species. We compared the pattern of phylogenetic signal in raw trait values and residual trait values after regression against body mass, bone length, and the product of body mass x bone length. Our results show that significant phylogenetic signal is present in all traits before scaling, due in part to their strong covariance with body mass. After scaling, bone length still exhibits strong phylogenetic signal, but articular surface areas do not, and cross-sectional properties exhibit different levels of signal depending on the variable used to scale the data. These results suggest that PCMs should be incorporated into interspecific studies of bone length and perhaps cross-sectional geometric properties. Our results also demonstrate that tests for phylogenetic signal prior to implementing a PCM should focus on residual variance, not individual traits.     

Tree asymmetry—A sensitive and practical measure for binary topological trees

The topological structure of a binary tree is characterized by a measure called tree asymmetry, defined as the mean value of the asymmetry of its partitions. The statistical properties of this tree-asymmetry measure have been studied using a growth model for binary trees. The tree-asymmetry measure appears to be sensitive for topological differences and the tree-asymmetry expectation for the growth model that we used appears to be almost independent of the size of the trees. These properties and the simple definition make the measure suitable for practical use, for instance for characterizing, comparing and interpreting sets of branching patterns. Examples are given of the analysis of three sets of neuronal branching patterns. It is shown that the variance in tree-asymmetry values for these observed branching patterns corresponds perfectly with the variance predicted by the used growth model.     

Trait similarity, shared ancestry and the structure of neighbourhood interactions in a subtropical wet forest: implications for community assembly

Ecology Letters (2010) 13: 1503-1514 ABSTRACT: The phylogenetic structure and distribution of functional traits in a community can provide insights into community assembly processes. However, these insights are sensitive to the spatial scale of analysis. Here, we use spatially explicit, neighbourhood models of tree growth and survival for 19 tree species, a highly resolved molecular phylogeny and information on eight functional traits to quantify the relative efficacy of functional similarity and shared ancestry in describing the effects of spatial interactions between tree species on demographic rates. We also assess the congruence of these results with observed phylogenetic and functional structure in the neighbourhoods of live and dead trees. We found strong support for models in which the effects of spatial neighbourhood interactions on tree growth and survival were scaled to species-specific mean functional trait values (e.g., wood specific gravity, leaf succulence and maximum height) but not to phylogenetic distance. The weak phylogenetic signal in functional trait data allowed us to independently interpret the static neighbourhood functional and phylogenetic patterns. We observed greater functional trait similarity in the neighbourhoods of live trees relative to those of dead trees suggesting that environmental filtering is the major force structuring this tree community at this scale while competitive interactions play a lesser role.     

Phylogenetic analysis of Themira (Sepsidae: Diptera): sensitivity analysis, alignment, and indel treatment in a multigene study

In this study we use sensitivity analysis sensu Wheeler (1995 ) for a matrix entirely composed of DNA sequences. We propose that not only congruence but also phylogenetic structure, as measured by character resampling, should be used to choose among competing weighting regimes. An extensive analysis of a five‐gene data set for Themira (Sepsidae: Diptera) reveals that even with different ways of partitioning the data, measures of topological congruence, character incongruence, and phylogenetic structure favor similar weighting regimes involving the down‐weighting of transitions. We furthermore use sensitivity analysis for obtaining empirical evidence that allows us to select weights for third positions, deciding between treating indels as fifth character states or missing values, and choosing between manual and computational alignments. For our data, sensitivity analysis favors manual alignment over a Clustal‐generated numerical alignment, the treatment of indels as fifth character states over considering them missing values, and equal weights for all positions in protein‐encoding genes over the down‐weighting of third positions. Among the topological congruence measures compared, symmetric tree distance performed best. Partitioned Bremer Support analysis reveals that COI contributes the largest amount of support for our phylogenetic tree for Themira. © The Willi Hennig Society 2005.     

Phylogenetic uncertainty revisited: Implications for ecological analyses

Ecologists and biogeographers usually rely on a single phylogenetic tree to study evolutionary processes that affect macroecological patterns. This approach ignores the fact that each phylogenetic tree is a hypothesis about the evolutionary history of a clade, and cannot be directly observed in nature. Also, trees often leave out many extant species, or include missing species as polytomies because of a lack of information on the relationship among taxa. Still, researchers usually do not quantify the effects of phylogenetic uncertainty in ecological analyses. We propose here a novel analytical strategy to maximize the use of incomplete phylogenetic information, while simultaneously accounting for several sources of phylogenetic uncertainty that may distort statistical inferences about evolutionary processes. We illustrate the approach using a clade‐wide analysis of the hummingbirds, evaluating how different sources of uncertainty affect several phylogenetic comparative analyses of trait evolution and biogeographic patterns. Although no statistical approximation can fully substitute for a complete and robust phylogeny, the method we describe and illustrate enables researchers to broaden the number of clades for which studies informed by evolutionary relationships are possible, while allowing the estimation and control of statistical error that arises from phylogenetic uncertainty. Software tools to carry out the necessary computations are offered.     

Partitioning within‐species variance in behaviour to within‐ and between‐population components for understanding evolution

Phenotypes vary at multiple hierarchical levels, of which the interspecific variance is the primary focus of phylogenetic comparative studies. However, the evolutionary role of particular within‐species variance components (between‐population, between‐ or within‐individual variances) remains neglected. Here, we partition the variance in an anti‐predator behaviour, flight initiation distance (FID), and assess how its within‐ and between‐population variance are related to life history, distribution, dispersal and habitat ecology. Although the composition of within‐species variance in FID depended on the phylogeny, most variance occurred within populations. When accounting for allometry, density‐dependence, uncertainty in the phylogenetic hypothesis and heterogeneity in data quality, within‐population variance was significantly associated with habitat diversity and population size. Between‐population variance was a significant predictor of natal dispersal, senescence and habitat diversity. Accordingly, not only species‐specific mean values of a behavioural trait, but also its variance within and among populations can shape the evolutionary ecology of species.     

Intraspecific trait variation of woody species reduced in a savanna community,southwest China

Plants deploy various ecological strategies in response to environmental heterogeneity. In many forest ecosystems, plants have been reported to have notable inter- and intra-specific trait variation, as well as clear phylogenetic signals, indicating that these species possess a degree of phenotypic plasticity to cope with habitat variation in the community. Savanna communities, however, grow in an open canopy structure and exhibit little species diversification, likely as a result of strong environmental stress. In this study, we hypothesized that the phylogenetic signals of savanna species would be weak, the intraspecific trait variation (ITV) would be low, and the contribution of intraspecific variation to total trait variance would be reduced, owing to low species richness, multiple stresses and relatively homogenous community structure. To test these hypotheses, we sampled dominant woody species in a dry-hot savanna in southwestern China, focusing on leaf traits related to adaptability of plants to harsh conditions (year-round intense radiation, low soil fertility and seasonal droughts). We found weak phylogenetic signals in leaf traits and low ITV (at both individual and canopy-layer levels). Intraspecific variation (including leaf-, layer- and individual-scales) contributed little to the total trait variance, whereas interspecific variation and variation in leaf phenology explained substantial variance. Our study suggests that intraspecific trait variation is reduced in savanna community. Furthermore, our findings indicate that classifying species by leaf phenology may help better understand how species coexist under similar habitats with strong stresses.     

核糖体RNA二级结构对拓扑结构准确性的影响

探讨了核糖体小亚基二级结构对真菌系统发育分析的影响。对用不同方法构建的系统发育树进行比较,结果表明结合二级结构信息的分析方法较传统方法产生了更为合理的拓扑结构。二级结构信息除用于优化序列比对外,还需整合到核酸替代模型中;恰当的序列比对方法、进化模型和建树运算法则有助于更加准确地揭示类群之间的亲缘关系。     

Phylogenetic ANOVA: Group‐clade aggregation,biological challenges,and a refined permutation procedure

Phylogenetic regression is frequently used in macroevolutionary studies, and its statistical properties have been thoroughly investigated. By contrast, phylogenetic ANOVA has received relatively less attention, and the conditions leading to incorrect statistical and biological inferences when comparing multivariate phenotypes among groups remain underexplored. Here, we propose a refined method of randomizing residuals in a permutation procedure (RRPP) for evaluating phenotypic differences among groups while conditioning the data on the phylogeny. We show that RRPP displays appropriate statistical properties for both phylogenetic ANOVA and regression models, and for univariate and multivariate datasets. For ANOVA, we find that RRPP exhibits higher statistical power than methods utilizing phylogenetic simulation. Additionally, we investigate how group dispersion across the phylogeny affects inferences, and reveal that highly aggregated groups generate strong and significant correlations with the phylogeny, which reduce statistical power and subsequently affect biological interpretations. We discuss the broader implications of this phylogenetic group aggregation, and its relation to challenges encountered with other comparative methods where one or a few transitions in discrete traits are observed on the phylogeny. Finally, we recommend that phylogenetic comparative studies of continuous trait data use RRPP for assessing the significance of indicator variables as sources of trait variation.     

Competitive interactions between forest trees are driven by species' trait hierarchy, not phylogenetic or functional similarity: implications for forest community assembly

The relative importance of competition vs. environmental filtering in the assembly of communities is commonly inferred from their functional and phylogenetic structure, on the grounds that similar species compete most strongly for resources and are therefore less likely to coexist locally. This approach ignores the possibility that competitive effects can be determined by relative positions of species on a hierarchy of competitive ability. Using growth data, we estimated 275 interaction coefficients between tree species in the French mountains. We show that interaction strengths are mainly driven by trait hierarchy and not by functional or phylogenetic similarity. On the basis of this result, we thus propose that functional and phylogenetic convergence in local tree community might be due to competition-sorting species with different competitive abilities and not only environmental filtering as commonly assumed. We then show a functional and phylogenetic convergence of forest structure with increasing plot age, which supports this view.     

Measuring biodiversity to explain community assembly: a unified approach

One of the oldest challenges in ecology is to understand the processes that underpin the composition of communities. Historically, an obvious way in which to describe community compositions has been diversity in terms of the number and abundances of species. However, the failure to reject contradictory models has led to communities now being characterized by trait and phylogenetic diversities. Our objective here is to demonstrate how species, trait and phylogenetic diversity can be combined together from large to local spatial scales to reveal the historical, deterministic and stochastic processes that impact the compositions of local communities. Research in this area has recently been advanced by the development of mathematical measures that incorporate trait dissimilarities and phylogenetic relatedness between species. However, measures of trait diversity have been developed independently of phylogenetic measures and conversely most of the phylogenetic diversity measures have been developed independently of trait diversity measures. This has led to semantic confusions particularly when classical ecological and evolutionary approaches are integrated so closely together. Consequently, we propose a unified semantic framework and demonstrate the importance of the links among species, phylogenetic and trait diversity indices. Furthermore, species, trait and phylogenetic diversity indices differ in the ways they can be used across different spatial scales. The connections between large‐scale, regional and local processes allow the consideration of historical factors in addition to local ecological deterministic or stochastic processes. Phylogenetic and trait diversity have been used in large‐scale analyses to determine how historical and/or environmental factors affect both the formation of species assemblages and patterns in species richness across latitude or elevation gradients. Both phylogenetic and trait diversity have been used at different spatial scales to identify the relative impacts of ecological deterministic processes such as environmental filtering and limiting similarity from alternative processes such as random speciation and extinction, random dispersal and ecological drift. Measures of phylogenetic diversity combine phenotypic and genetic diversity and have the potential to reveal both the ecological and historical factors that impact local communities. Consequently, we demonstrate that, when used in a comparative way, species, trait and phylogenetic structures have the potential to reveal essential details that might act simultaneously in the assembly of species communities. We highlight potential directions for future research. These might include how variation in trait and phylogenetic diversity alters with spatial distances, the role of trait and phylogenetic diversity in global‐scale gradients, the connections between traits and phylogeny, the importance of trait rarity and independent evolutionary history in community assembly, the loss of trait and phylogenetic diversity due to human impacts, and the mathematical developments of biodiversity indices including within‐species variations.     

treespace: Statistical exploration of landscapes of phylogenetic trees

The increasing availability of large genomic data sets as well as the advent of Bayesian phylogenetics facilitates the investigation of phylogenetic incongruence, which can result in the impossibility of representing phylogenetic relationships using a single tree. While sometimes considered as a nuisance, phylogenetic incongruence can also reflect meaningful biological processes as well as relevant statistical uncertainty, both of which can yield valuable insights in evolutionary studies. We introduce a new tool for investigating phylogenetic incongruence through the exploration of phylogenetic tree landscapes. Our approach, implemented in the R package treespace , combines tree metrics and multivariate analysis to provide low‐dimensional representations of the topological variability in a set of trees, which can be used for identifying clusters of similar trees and group‐specific consensus phylogenies. treespace also provides a user‐friendly web interface for interactive data analysis and is integrated alongside existing standards for phylogenetics. It fills a gap in the current phylogenetics toolbox in R and will facilitate the investigation of phylogenetic results.     

Assessing phylogenetic signal with measurement error: a comparison of mantel tests, blomberg et Al.'s k, and phylogenetic distograms

In macroevolutionary studies, different approaches are commonly used to measure phylogenetic signal-the tendency of related taxa to resemble one another-including the K statistic and the Mantel test. The latter was recently criticized for lacking statistical power. Using new simulations, we show that the power of the Mantel test depends on the metrics used to define trait distances and phylogenetic distances between species. Increasing power is obtained by lowering variance and increasing negative skewness in interspecific distances, as obtained using Euclidean trait distances and the complement of Abouheif proximity as a phylogenetic distance. We show realistic situations involving "measurement error" due to intraspecific variability where the Mantel test is more powerful to detect a phylogenetic signal than a permutation test based on the K statistic. We highlight limitations of the K-statistic (univariate measure) and show that its application should take into account measurement errors using repeated measures per species to avoid estimation bias. Finally, we argue that phylogenetic distograms representing Euclidean trait distance as a function of the square root of patristic distance provide an insightful representation of the phylogenetic signal that can be used to assess both the impact of measurement error and the departure from a Brownian evolution model.     

Phylogenetic imputation of plant functional trait databases

Continental‐scale maps of plant functional diversity are a fundamental piece of data of interest to ecosystem modelers and ecologists, yet such maps have been exceedingly hard to generate. The large effort to compile global plant functional trait databases largely for the purpose of mapping and analyzing the spatial distribution of function has resulted in very sparse data matrices thereby limiting progress. Identifying robust methodologies to gap fill or impute trait values in these databases is an important objective. Here I argue that existing statistical tools from phylogenetic comparative methods can be used to rapidly impute values into global plant functional trait databases due to the large amount of phylogenetic signal often in trait data. In particular, statistical models of phylogenetic signal in traits can be generated from existing data and used to predict missing values of closely related species often with a high degree of accuracy thereby facilitating the continental‐scale mapping of plant function. Despite the promise of this approach, I also discuss potential pitfalls and future challenges that will need to be addressed.     

On fractal properties of arterial trees

The question of fractal properties of arterial trees is considered in light of data from the extensive tree structure of the right coronary artery of a human heart. Because of the highly non-uniform structure of this tree, the study focuses on the purely geometrical rather than statistical aspects of fractal properties. The large number of arterial bifurcations comprising the tree were found to have a mixed degree of asymmetry at all levels of the tree, including the depth of the tree where it has been generally supposed that they would be symmetrical. Cross-sectional area ratios of daughter to parent vessels were also found to be highly mixed at all levels, having values both above and below 1.0, rather than consistently above as has been generally supposed in the past. Calculated values of the power law index which describes the theoretical relation between the diameters of the three vessel segments at an arterial bifurcation were found to range far beyond the two values associated with the cube and square laws, and not clearly favoring one or the other. On the whole the tree structure was found to have what we have termed "pseudo-fractal" properties, in the sense that vessels of different calibers displayed the same branching pattern but with a range of values of the branching parameters. The results suggest that a higher degree of fractal character, one in which the branching parameters are constant throughout the tree structure, is unlikely to be attained in non-uniform vascular structures.     

The comparative ecology and biogeography of parasites

Comparative ecology uses interspecific relationships among traits, while accounting for the phylogenetic non-independence of species, to uncover general evolutionary processes. Applied to biogeographic questions, it can be a powerful tool to explain the spatial distribution of organisms. Here, we review how comparative methods can elucidate biogeographic patterns and processes, using analyses of distributional data on parasites (fleas and helminths) as case studies. Methods exist to detect phylogenetic signals, i.e. the degree of phylogenetic dependence of a given character, and either to control for these signals in statistical analyses of interspecific data, or to measure their contribution to variance. Parasite–host interactions present a special case, as a given trait may be a parasite trait, a host trait or a property of the coevolved association rather than of one participant only. For some analyses, it is therefore necessary to correct simultaneously for both parasite phylogeny and host phylogeny, or to evaluate which has the greatest influence on trait expression. Using comparative approaches, we show that two fundamental properties of parasites, their niche breadth, i.e. host specificity, and the nature of their life cycle, can explain interspecific and latitudinal variation in the sizes of their geographical ranges, or rates of distance decay in the similarity of parasite communities. These findings illustrate the ways in which phylogenetically based comparative methods can contribute to biogeographic research.     

Dispersal between shallow and abyssal seas and evolutionary loss and regain of compound eyes in cylindroleberidid ostracods: conflicting conclusions from different comparative methods

Complex organs such as eyes are commonly lost during evolution, but the timescale on which lost phenotypes could be reactivated is a matter of long-standing debate, with important implications for the molecular mechanisms of trait loss. Two phylogenetic approaches have been used to test whether regain of traits has occurred. One way is by comparison of nested, continuous-time Markov models of trait evolution, approaches that we term tree-based tests. A second way to demonstrate statistical support for trait regain is through use of node-based tests that employ explicit estimation of ancestral node states. Here, we estimate new molecular and morphological phylogenies and use them to examine the possibility of eye regain and dispersal between abyssal and shallow seas during the history of cylindroleberidid ostracods, a family of about 200 species, comprising both eyeless and sighted species. First, we confirmed that eye presence/absence is correlated with habitat depth. Parameter estimates from a phylogenetic model indicate that speciation is more rapid in deep-sea eyeless clades compared with shallow-water sighted clades. In addition, we found that tree-based statistical tests usually indicated reversals, including both transitions from deep to shallow seas and regain of eyes. In contrast, node-based statistical tests usually failed to show significant support for reversals. These results also hold for simulated phylogenies, indicating that they are not unique to the current data set. We recommend that both tree-based and node-based tests should be examined before making conclusions about character reversal and that ideally, alternative character histories should be tested using additional data, besides just the phylogenetic distribution of presence/absence of the characters.     

The effects of intraspecific competition and stabilizing selection on a polygenic trait

The equilibrium properties of an additive multilocus model of a quantitative trait under frequency- and density-dependent selection are investigated. Two opposing evolutionary forces are assumed to act: (i) stabilizing selection on the trait, which favors genotypes with an intermediate phenotype, and (ii) intraspecific competition mediated by that trait, which favors genotypes whose effect on the trait deviates most from that of the prevailing genotypes. Accordingly, fitnesses of genotypes have a frequency-independent component describing stabilizing selection and a frequency- and density-dependent component modeling competition. We study how the equilibrium structure, in particular, number, degree of polymorphism, and genetic variance of stable equilibria, is affected by the strength of frequency dependence, and what role the number of loci, the amount of recombination, and the demographic parameters play. To this end, we employ a statistical and numerical approach, complemented by analytical results, and explore how the equilibrium properties averaged over a large number of genetic systems with a given number of loci and average amount of recombination depend on the ecological and demographic parameters. We identify two parameter regions with a transitory region in between, in which the equilibrium properties of genetic systems are distinctively different. These regions depend on the strength of frequency dependence relative to pure stabilizing selection and on the demographic parameters, but not on the number of loci or the amount of recombination. We further study the shape of the fitness function observed at equilibrium and the extent to which the dynamics in this model are adaptive, and we present examples of equilibrium distributions of genotypic values under strong frequency dependence. Consequences for the maintenance of genetic variation, the detection of disruptive selection, and models of sympatric speciation are discussed.     

The Tree versus the Forest: The Fungal Tree of Life and the Topological Diversity within the Yeast Phylome

A recurrent topic in phylogenomics is the combination of various sequence alignments to reconstruct a tree that describes the evolutionary relationships within a group of species. However, such approach has been criticized for not being able to properly represent the topological diversity found among gene trees. To evaluate the representativeness of species trees based on concatenated alignments, we reconstruct several fungal species trees and compare them with the complete collection of phylogenies of genes encoded in the Saccharomyces cerevisiae genome. We found that, despite high levels of among-gene topological variation, the species trees do represent widely supported phylogenetic relationships. Most topological discrepancies between gene and species trees are concentrated in certain conflicting nodes. We propose to map such information on the species tree so that it accounts for the levels of congruence across the genome. We identified the lack of sufficient accuracy of current alignment and phylogenetic methods as an important source for the topological diversity encountered among gene trees. Finally, we discuss the implications of the high levels of topological variation for phylogeny-based orthology prediction strategies.