Phylogenetic patterns of trait and trait plasticity evolution: Insights from amphibian embryos

Environmental variation favors the evolution of phenotypic plasticity. For many species, we understand the costs and benefits of different phenotypes, but we lack a broad understanding of how plastic traits evolve across large clades. Using identical experiments conducted across North America, we examined prey responses to predator cues. We quantified five life‐history traits and the magnitude of their plasticity for 23 amphibian species/populations (spanning three families and five genera) when exposed to no cues, crushed‐egg cues, and predatory crayfish cues. Embryonic responses varied considerably among species and phylogenetic signal was common among the traits, whereas phylogenetic signal was rare for trait plasticities. Among trait‐evolution models, the Ornstein–Uhlenbeck (OU) model provided the best fit or was essentially tied with Brownian motion. Using the best fitting model, evolutionary rates for plasticities were higher than traits for three life‐history traits and lower for two. These data suggest that the evolution of life‐history traits in amphibian embryos is more constrained by a species’ position in the phylogeny than is the evolution of life history plasticities. The fact that an OU model of trait evolution was often a good fit to patterns of trait variation may indicate adaptive optima for traits and their plasticities.     

Environment differentially affects the functional and phylogenetic structures of plant communities in a dry evergreen Afromontane tropical forest

Testing how local environmental conditions influence plant community assembly is important to understand the underlying mechanisms that promote and/or maintain biodiversity. Functional traits are used to find the broad spectrum of resource use strategies that plants use to respond to environmental variation. The patterns and drivers of plant community assembly through the lens of traits and phylogeny; however, remain to be studied in a uniquely biodiversity rich but poorly known fragmented dry Afromontane forest of Ethiopia. Here, we combined trait and community phylogenetic data from thirty sampling plots of 20 × 20 m size to determine the functional and phylogenetic structures and their drivers in a fragmented, human-dominated dry evergreen Afromontane forest. We found phylogenetic and functional clustering of plants in which the effect of environment was found to be trait specific. A weak phylogenetic signal for traits was detected suggesting that species resource use strategies may not be inferred using species phylogenetic distance. Additionally, we found functional traits to be weak in predicting species abundance distribution. Overall, while this study shows a non-random community assembly pattern, it also highlights the importance of deterministic processes being trait specific.     

The ecology of differences: assessing community assembly with trait and evolutionary distances

Species enter and persist in local communities because of their ecological fit to local conditions, and recently, ecologists have moved from measuring diversity as species richness and evenness, to using measures that reflect species ecological differences. There are two principal approaches for quantifying species ecological differences: functional (trait‐based) and phylogenetic pairwise distances between species. Both approaches have produced new ecological insights, yet at the same time methodological issues and assumptions limit them. Traits and phylogeny may provide different, and perhaps complementary, information about species' differences. To adequately test assembly hypotheses, a framework integrating the information provided by traits and phylogenies is required. We propose an intuitive measure for combining functional and phylogenetic pairwise distances, which provides a useful way to assess how functional and phylogenetic distances contribute to understanding patterns of community assembly. Here, we show that both traits and phylogeny inform community assembly patterns in alpine plant communities across an elevation gradient, because they represent complementary information. Differences in historical selection pressures have produced variation in the strength of the trait‐phylogeny correlation, and as such, integrating traits and phylogeny can enhance the ability to detect assembly patterns across habitats or environmental gradients.     

The evolution of male nuptial colour in a sexually dimorphic group of fishes (Percidae: Etheostomatinae)

To test hypotheses explaining variation in elaborate male colouration across closely related species groups, ancestral‐state reconstructions and tests of phylogenetic signal and correlated evolution were used to examine the evolution of male body and fin colouration in a group of sexually dichromatic stream fishes known as darters (Percidae: Etheostomatinae). The presence or absence of red–orange and blue–green male colour traits were scored across six body regions in 99 darter species using a recently estimated amplified fragment length polymorphism (AFLP) phylogeny for comparative analyses. Ancestral‐state reconstructions infer the most recent common ancestor of darters to lack red–orange colour and possess blue–green colour on different body regions, suggesting variation between species is due to independent gains of red–orange and losses of blue–green. Colour traits exhibit substantial phylogenetic signal and are highly correlated across body regions. Comparative analyses were repeated using an alternative phylogenetic hypothesis based on one mitochondrial and two nuclear genes, yielding similar results to analyses based on the AFLP phylogeny. Red–orange colouration in darters appears to be derived; whereas, blue–green appears to be ancestral, which suggests that different selection mechanisms may be acting on these two colour classes in darters.     

phylosignal: an R package to measure,test, and explore the phylogenetic signal

Phylogenetic signal is the tendency for closely related species to display similar trait values as a consequence of their phylogenetic proximity. Ecologists and evolutionary biologists are becoming increasingly interested in studying the phylogenetic signal and the processes which drive patterns of trait values in the phylogeny. Here, we present a new R package, phylosignal which provides a collection of tools to explore the phylogenetic signal for continuous biological traits. These tools are mainly based on the concept of autocorrelation and have been first developed in the field of spatial statistics. To illustrate the use of the package, we analyze the phylogenetic signal in pollution sensitivity for 17 species of diatoms.     

Both traits and phylogenetic history influence community structure in snakes over steep environmental gradients

Assemblages of closely related organisms are generated on axes of deep time diversification, biogeographic processes related to dispersal and habitat filtering, and competition. Using models that account for phylogeny, ecology, and traits, we examine how the interaction among biogeography, habitat filtering, and trait convergence influences community assemblage in Nearctic snakes. With 122 community surveys, environmental niche, trait data including size, diet, parity and habitat preference, and a nearly complete phylogeny of snakes from the United States, we ask 1) do phylogenetic species variability (PSV) and traits change in predictable and correlated ways given ecology and geographic distance, 2) are the measured traits variable within and across communities and how is this related to PSV at local scales, and 3) is there evidence of habitat filtering or trait divergence? Following a general trend of western to eastern North American origin and dispersal of major groups, we similarly show a significant decrease in PSV in this direction but unexpectedly with stable trait variance, showing that traits and phylogenetic variability are disconnected at the community level. We also demonstrate that trait variability and not PSV dominates local communities. Finally, regardless of phylogeny, we show that certain traits, such as reproductive mode (parity) frequency, change within communities in response to steep ecological gradients.     

Spatial patterns of wood traits in China are controlled by phylogeny and the environment

Aim Wood properties are related to tree physiology and mechanical stability and are influenced by both phylogeny and the environment. However, it remains unclear to what extent geographical gradients in wood traits are shaped by either phylogeny or the environment. Here we aimed to disentangle the influences of phylogeny and the environment on spatial trends in wood traits. Location China. Methods We compiled a data set of 11 wood properties for 618 tree species from 98 sampling sites in China to assess their phylogenetic and spatial patterns, and to determine how many of the spatial patterns in wood properties are attributable to the environment after correction for phylogenetic influences. Result All wood traits examined exhibited significant phylogenetic signal. The widest divergence in wood traits was observed between gymnosperms and angiosperms, Rosids and Asterids, Magnoiliids and Eudicots, and in Lamiales. For most wood traits, the majority of trait variation was observed at genus and species levels. The mechanical properties of wood showed correlated evolution with wood density. Most of the mechanical properties of wood exhibited significant latitudinal variation but limited or no altitudinal variation, and were positively correlated with mean annual precipitation based on both Pearson's correlation analysis and the phylogenetic comparative method. Correlations at family level between mean annual temperature and wood density, compression strength, cross‐section hardness, modulus of elasticity and volumetric shrinkage coefficient became significant after correction for phylogenetic influences. Main conclusions Phylogeny interacted with the environment in shaping the spatial patterns of wood traits of trees across China because most wood properties showed strong phylogenetic conservatism and thus affected environmental tolerances and distributions of tree species. Mean annual precipitation was a key environmental factor explaining the spatial patterns of wood traits. Our study provides valuable insights into the geographical patterns in productivity, distribution and ecological strategy of trees linking to wood traits.     

Phylogeny and species traits predict bird detectability

Avian acoustic communication has resulted from evolutionary pressures and ecological constraints. We therefore expect that auditory detectability in birds might be predictable by species traits and phylogenetic relatedness. We evaluated the relationship between phylogeny, species traits, and field‐based estimates of the two processes that determine species detectability (singing rate and detection distance) for 141 bird species breeding in boreal North America. We used phylogenetic mixed models and cross‐validation to compare the relative merits of using trait data only, phylogeny only, or the combination of both to predict detectability. We found a strong phylogenetic signal in both singing rates and detection distances; however the strength of phylogenetic effects was less than expected under Brownian motion evolution. The evolution of behavioural traits that determine singing rates was found to be more labile, leaving more room for species to evolve independently, whereas detection distance was mostly determined by anatomy (i.e. body size) and thus the laws of physics. Our findings can help in disentangling how complex ecological and evolutionary mechanisms have shaped different aspects of detectability in boreal birds. Such information can greatly inform single‐ and multi‐species models but more work is required to better understand how to best correct possible biases in phylogenetic diversity and other community metrics.     

Phylogenetic signal of photobiont switches in the lichen genus <Emphasis Type="Italic">Pseudocyphellaria</Emphasis> s. l. follows a Brownian motion model

Lichen symbioses are defined as a symbiotic relationship between a mycobiont (generally an ascomycete) and one or more photobionts (green algae or/and cyanobacteria). It was proposed that cephalodia emancipation is an evolutionary driver for photobiont switch from chlorophyte to cyanobacteria. In this study we want to test the monophyly of cyanolichens and to measure the phylogenetic signal of the symbiotic relationship between cyanobacteria and a mycobiont partner in the lichen genus Pseudocyphellaria. This genus includes some species that have a chlorophyte as primary photobiont (and Nostoc in internal cephalodia), while others have only cyanobacteria. In a phylogenetic framework we measure the phylogenetic signal (or phylogenetic dispersion) as well as mapped photobiont switches performing stochastic character mapping. Results show that having cyanobacteria as main photobiont has a strong phylogenetic signal that follows a Brownian motion model. Seven clades in the phylogeny had an ancestor with cyanobacteria. Reversal to a green algae photobiont is rare. Several switches were estimated through evolutionary time suggesting that there was some flexibility in these traits along the phylogeny; however, close relatives retained cyanobacteria as main photobiont throughout the cyanolichen’s history. Photobiont switches from green algae to cyanobacteria might enhance ecotypical differentiation. These ecotypes could lead to several speciation events in the new lineage resulting in the phylogenetic signal found in this study. We give insights into the origin of lichen diversity exploring the photobiont switch in a phylogenetic context in Pseudocyphellaria s. l. as a model genus.     

Using phylogeny and functional traits for assessing community assembly along environmental gradients: A deterministic process driven by elevation

Community assembly processes is the primary focus of community ecology. Using phylogenetic‐based and functional trait‐based methods jointly to explore these processes along environmental gradients are useful ways to explain the change of assembly mechanisms under changing world. Our study combined these methods to test assembly processes in wide range gradients of elevation and other habitat environmental factors. We collected our data at 40 plots in Taibai Mountain, China, with more than 2,300 m altitude difference in study area and then measured traits and environmental factors. Variance partitioning was used to distinguish the main environment factors leading to phylogeny and traits change among 40 plots. Principal component analysis (PCA) was applied to colligate other environment factors. Community assembly patterns along environmental gradients based on phylogenetic and functional methods were studied for exploring assembly mechanisms. Phylogenetic signal was calculated for each community along environmental gradients in order to detect the variation of trait performance on phylogeny. Elevation showed a better explanatory power than other environment factors for phylogenetic and most traits’ variance. Phylogenetic and several functional structure clustered at high elevation while some conserved traits overdispersed. Convergent tendency which might be caused by filtering or competition along elevation was detected based on functional traits. Leaf dry matter content (LDMC) and leaf nitrogen content along PCA 1 axis showed conflicting patterns comparing to patterns showed on elevation. LDMC exhibited the strongest phylogenetic signal. Only the phylogenetic signal of maximum plant height showed explicable change along environmental gradients. Synthesis. Elevation is the best environment factors for predicting phylogeny and traits change. Plant's phylogenetic and some functional structures show environmental filtering in alpine region while it shows different assembly processes in middle‐ and low‐altitude region by different trait/phylogeny. The results highlight deterministic processes dominate community assembly in large‐scale environmental gradients. Performance of phylogeny and traits along gradients may be independent with each other. The novel method for calculating functional structure which we used in this study and the focus of phylogenetic signal change along gradients may provide more useful ways to detect community assembly mechanisms.     

Environmental,spatial and phylogenetic determinants of fish life‐history traits and functional composition of Australian rivers

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Is xenodontine snake reproduction shaped by ancestry,more than by ecology?

One of the current challenges of evolutionary ecology is to understand the effects of phylogenetic history (PH) and/or ecological factors (EF) on the life‐history traits of the species. Here, the effects of environment and phylogeny are tested for the first time on the reproductive biology of South American xenodontine snakes. We studied 60% of the tribes of this endemic and most representative clade in a temperate region of South America. A comparative method (canonical phylogenetic ordination—CPO) was used to find the relative contributions of EF and PH upon life‐history aspects of snakes, comparing the reproductive mode, mean fecundity, reproductive potential, and frequency of nearly 1,000 specimens. CPO analysis showed that PH or ancestry explained most of the variation in reproduction, whereas EF explained little of this variation. The reproductive traits under study are suggested to have a strong phylogenetic signal in this clade, the ancestry playing a big role in reproduction. The EF also influenced the reproduction of South American xenodontines, although to a lesser extent. Our finding provides new evidence of how the evolutionary history is embodied in the traits of living species.     

Lack of phylogenetic signal in the variation in anuran microhabitat use in southeastern Brazil

Microhabitat use is an important component of anuran behavior in both the tadpole and the adult stages. It is potentially influenced by phylogeny and extant ecological factors acting as selective pressures, such as predation, competition, or physical habitat properties. We aimed to test whether patterns of microhabitat use vary among species, habitats and sites, and how much of this variation can be explained by phylogenetic relatedness. We collected data on microhabitat use at five different sites, where we obtained a total of 4,230 records of individual tadpoles of 34 species in 15 genera and 7 families, and a total of 1,163 records of adult individuals of 39 species in 16 genera and 8 families. Mantel tests conducted to relate species dissimilarities in microhabitat use and phylogenetic relatedness indicated a weak but significant relationship for adult anurans, and no relationship for tadpoles. Our results suggest that microhabitat use is a plastic and variable trait, overcoming phylogenetic signal in tadpoles. In adult anurans, very little of the variation in microhabitat use can be explained by phylogenetic relatedness. Microhabitat use is not a good predictor of phylogeny, but it may be a very interesting subject to study natural selection and adaptation.     

Phylogenetic effects on functional traits and life history strategies of Australian freshwater fish

Understanding the biogeographic and phylogenetic basis to interspecific differences in species’ functional traits is a central goal of evolutionary biology and community ecology. We quantify the extent of phylogenetic influence on functional traits and life‐history strategies of Australian freshwater fish to highlight intercontinental differences as a result of Australia's unique biogeographic and evolutionary history. We assembled data on life history, morphological and ecological traits from published sources for 194 Australian freshwater species. Interspecific variation among species could be described by a specialist–generalist gradient of variation in life‐history strategies associated with spawning frequency, fecundity and spawning migration. In general, Australian fish showed an affinity for life‐history strategies that maximise fitness in hydrologically unpredictable environments. We also observed differences in trait lability between and within life history, morphological and ecological traits where in general morphological and ecological traits were more labile. Our results showed that life‐history strategies are relatively evolutionarily labile and species have potentially evolved or colonised in freshwaters frequently and independently allowing them to maximise population performance in a range of environments. In addition, reproductive guild membership showed strong phylogenetic constraint indicating that evolutionary history is an important component influencing the range and distribution of reproductive strategies in extant species assemblages. For Australian freshwater fish, biogeographic and phylogenetic history contribute to broad taxonomic differences in species functional traits, while finer scale ecological processes contribute to interspecific differences in smaller taxonomic units. These results suggest that the lability or phylogenetic relatedness of different functional traits affects their suitability for testing hypothesis surrounding community level responses to environmental change.     

Mechanisms driving plant functional trait variation in a tropical forest

Plant functional trait variation in tropical forests results from taxonomic differences in phylogeny and associated genetic differences, as well as, phenotypic plastic responses to the environment. Accounting for the underlying mechanisms driving plant functional trait variation is important for understanding the potential rate of change of ecosystems since trait acclimation via phenotypic plasticity is very fast compared to shifts in community composition and genetic adaptation. We here applied a statistical technique to decompose the relative roles of phenotypic plasticity, genetic adaptation, and phylogenetic constraints. We examined typically obtained plant functional traits, such as wood density, plant height, specific leaf area, leaf area, leaf thickness, leaf dry mass content, leaf nitrogen content, and leaf phosphorus content. We assumed that genetic differences in plant functional traits between species and genotypes increase with environmental heterogeneity and geographic distance, whereas trait variation due to plastic acclimation to the local environment is independent of spatial distance between sampling sites. Results suggest that most of the observed trait variation could not be explained by the measured environmental variables, thus indicating a limited potential to predict individual plant traits from commonly assessed parameters. However, we found a difference in the response of plant functional traits, such that leaf traits varied in response to canopy‐light regime and nutrient availability, whereas wood traits were related to topoedaphic factors and water availability. Our analysis furthermore revealed differences in the functional response of coexisting neotropical tree species, which suggests that endemic species with conservative ecological strategies might be especially prone to competitive exclusion under projected climate change.     

Phylogenetic signal in bone microstructure of sauropsids

In spite of the fact that the potential usefulness of bone histology in systematics has been discussed for over one and a half centuries, the presence of a phylogenetic signal in the variation of histological characters has rarely been assessed. A quantitative assessment of phylogenetic signal in bone histological characters could provide a justification for performing optimizations of these traits onto independently generated phylogenetic trees (as has been done in recent years). Here we present an investigation on the quantification of the phylogenetic signal in the following bone histological, microanatomical, and morphological traits in a sample of femora of 35 species of sauropsids: vascular density, vascular orientation, index of Haversian remodeling, cortical thickness, and cross-sectional area (bone size). For this purpose, we use two methods, regressions on distance matrices tested for significance using permutations (a Mantel test) and random tree length distribution. Within sauropsids, these bone microstructural traits have an optimal systematic value in archosaurs. In this taxon, a Mantel test shows that the phylogeny explains 81.8% of the variation of bone size and 86.2% of the variation of cortical thickness. In contrast, a Mantel test suggests that the phylogenetic signal in histological traits is weak: although the phylogeny explains 18.7% of the variation of vascular density in archosaurs, the phylogenetic signal is not significant either for vascular orientation or for the index of Haversian remodeling. However, Mantel tests seem to underestimate the proportion of variance of the dependent character explained by the phylogeny, as suggested by a PVR (phylogenetic eigenvector) analysis. We also deal with some complementary questions. First, we evaluate the functional dependence of bone vascular density on bone size by using phylogenetically independent contrasts. Second, we perform a variation partitioning analysis and show that the phylogenetic signal in bone vascular density is not a by-product of phylogentic signal in bone size. Finally, we analyze the evolution of cortical thickness in diapsids by using an optimization by squared change parsimony and discuss the functional significance of this character in terms of decreased buoyancy in crocodiles and mass saving in birds. These results are placed in the framework of the constructional morphology model, according to which the variation of a character in a clade has a historical (phylogenetic) component, a functional (adaptive) component, and a structural (architectural) component.     

A PHYLOGENETIC APPROACH TO THE ESTIMATION OF PHYTOPLANKTON TRAITS1

The quantitative characterization of the ecology of individual phytoplankton taxa is essential for model resolution of many aspects of aquatic ecosystems. Existing literature cannot directly parameterize all phytoplankton taxa of interest, as many traits and taxa have not been sampled. However, valuable clues on the value of traits are found in the evolutionary history of species and in common correlations between traits. These two resources were exploited with an existing, statistically consistent method built upon evolutionary concepts. From a new data set with >700 observations on freshwater phytoplankton traits and a qualitative phytoplankton phylogeny, estimates were derived for the size, growth rate, phosphate affinity, and susceptibility to predation of 277 phytoplankton types, from evolutionary ancestors to present‐day species. These estimates account simultaneously for phylogenetic relationships between types, as imposed by the phylogeny, and approximate power‐law relationships (e.g., allometric scaling laws) between traits, as reconstructed from the data set. Results suggest that most phytoplankton traits are to some extent conserved in evolution: cross‐validation demonstrated that the use of phylogenetic information significantly improves trait value estimates. By providing trait value estimates as well as uncertainties, these results could benefit most quantitative studies involving phytoplankton.     

Using genetic networks and homology to understand the evolution of phenotypic traits

Homology can have different meanings for different kinds of biologists. A phylogenetic view holds that homology, defined by common ancestry, is rigorously identified through phylogenetic analysis. Such homologies are taxic homologies (=synapomorphies). A second interpretation, "biological homology" emphasizes common ancestry through the continuity of genetic information underlying phenotypic traits, and is favored by some developmental geneticists. A third kind of homology, deep homology, was recently defined as "the sharing of the genetic regulatory apparatus used to build morphologically and phylogenetically disparate features." Here we explain the commonality among these three versions of homology. We argue that biological homology, as evidenced by a conserved gene regulatory network giving a trait its "essential identity" (a Character Identity Network or "ChIN") must also be a taxic homology. In cases where a phenotypic trait has been modified over the course of evolution such that homology (taxic) is obscured (e.g. jaws are modified gill arches), a shared underlying ChIN provides evidence of this transformation. Deep homologies, where molecular and cellular components of a phenotypic trait precede the trait itself (are phylogenetically deep relative to the trait), are also taxic homologies, undisguised. Deep homologies inspire particular interest for understanding the evolutionary assembly of phenotypic traits. Mapping these deeply homologous building blocks on a phylogeny reveals the sequential steps leading to the origin of phenotypic novelties. Finally, we discuss how new genomic technologies will revolutionize the comparative genomic study of non-model organisms in a phylogenetic context, necessary to understand the evolution of phenotypic traits.     

Experimental evidence that evolutionary relatedness does not affect the ecological mechanisms of coexistence in freshwater green algae

The coexistence of competing species depends on the balance between their fitness differences, which determine their competitive inequalities, and their niche differences, which stabilise their competitive interactions. Darwin proposed that evolution causes species' niches to diverge, but the influence of evolution on relative fitness differences, and the importance of both niche and fitness differences in determining coexistence have not yet been studied together. We tested whether the phylogenetic distances between species of green freshwater algae determined their abilities to coexist in a microcosm experiment. We found that niche differences were more important in explaining coexistence than relative fitness differences, and that phylogenetic distance had no effect on either coexistence or on the sizes of niche and fitness differences. These results were corroborated by an analysis of the frequency of the co‐occurrence of 325 pairwise combinations of algal taxa in > 1100 lakes across North America. Phylogenetic distance may not explain the coexistence of freshwater green algae.