Extreme Trait Values Research Articles

A kernel integral method to remove biases in estimating trait turnover

Abstract Trait diversity, including trait turnover, that differentiates the roles of species and communities according to their functions, is a fundamental component of biodiversity. Accurately capturing trait diversity is crucial to better understand and predict community assembly, as well as the consequences of global change on community resilience. Existing methods to compute trait turnover have limitations. Trait space approaches based on minimum convex polygons only consider species with extreme trait values. Tree‐based approaches using dendrograms consider all species but distort trait distance between species. More recent trait space methods using complex polytopes try to harmonise the advantages of both methods, but their current implementation has mathematical flaws. We propose a new kernel integral method (KIM) to compute trait turnover, based on the integration of kernel density estimators (KDEs) rather than using polytopes. We explore how this approach and the computational aspects of the KDE computation can influence the estimates of trait turnover. The novel method is compared with existing ones using justified theoretical expectations for a large number of simulations in which the number of species and the distribution of their traits is controlled for. The practical application of KIM is then demonstrated using data on plant species introduced to the Pacific Islands of French Polynesia. Analyses on simulated data show that KIM generates results better aligned with theoretical expectations than other methods and is less sensitive to the total number of species. Analyses for French Polynesia data also show that different methods can lead to different conclusions about trait turnover and that the choice of method should be carefully considered based on the research question. The mathematical properties of methods for computing trait turnover are crucial to consider because they can have important effects on the results, and therefore lead to different conclusions. The novel KIM method provided here generates values that better reflect the distribution of species in trait space than other methods. We therefore recommend using KIM in studies on trait turnover. In contrast, tree‐based approaches should be kept for phylogenetic diversity, as phylogenetic trees will then reflect the speciation process.

Disentangling direct and indirect effects of landscape structure on urban bird richness and functional diversity.

As fragmented landscapes become increasingly common around the world, managing the spatial arrangement of landscape elements (i.e., landscape configuration) may help to promote the conservation of biodiversity. However, the relative effects of landscape configuration on different dimensions of biodiversity across species assemblages are largely unknown. Thus, a key challenge consists in understanding when it is necessary to focus on landscape configuration, in addition to landscape composition, to achieve multifunctional landscapes. We tested the effects of landscape composition (the percentage of tree cover and built infrastructure) and landscape configuration (degree of fragmentation) on landscape-level species richness and different metrics of functional diversity of urban birds. We collected data on different bird guilds (nectarivores/frugivores, insectivores) from Brisbane, Australia. Using structural equation models, we found that landscape structure (landscape composition and configuration) affected functional diversity via two main pathways: (1) through effects of landscape composition, mediated by landscape configuration (indirect effects), and (2) through direct ("independent") effects of landscape composition and configuration, filtering species with extreme trait values. Our results show that landscape-level species richness declined with the extent of built infrastructure, but patterns of trait diversity did not necessarily correlate with this variable. Landscape configuration had a stronger mediating effect on some metrics of the functional diversity of insectivores than on the functional diversity of frugivores/nectarivores. In addition, fragmentation increased the effects of built infrastructure for some traits (body size and dispersal capacity), but not for others (habitat plasticity and foraging behavior). These results suggest that differential approaches to managing landscape structure are needed depending on whether the focus is on protecting functional diversity or species richness and what the target guild is. Managing landscape fragmentation in areas with high levels of built infrastructure is important if the objective is to protect insectivore species with uncommon traits, even if it is not possible to preserve high levels of species richness. However, if the target is to enhance both functional diversity and species richness of multiple guilds, the focus should be on improving composition through the reduction of negative effects of built infrastructure, rather than promoting specific landscape configurations in growing cities.

Variation in pH gradients and FLO11 expression in mat biofilms from environmental isolates of the yeast Saccharomyces cerevisiae.

Saccharomyces cerevisiae produces a multicellular phenotype, known as a mat, on a semi‐solid medium. This biofilm phenotype was first described in the lab strain Σ1278b and has been analyzed mostly in this same background. Yeast cells form a mat by spreading across the medium and adhering to each other and the surface, in part through the variegated expression of the cell adhesion, FLO11. This process creates a characteristic floral pattern and generates pH and glucose gradients outward from the center of the mat. Mats are encapsulated in a liquid which may aid in surface spreading and diffusion. Here, we examine thirteen environmental isolates that vary visually in the phenotype. We predicted that mat properties were universal and increased morphological complexity would be associated with more extreme trait values. Our results showed that pH varied significantly among strains, but was not correlated to mat complexity. Only two isolates generated significant liquid boundaries and neither produced visually complex mats. In five isolates, we tracked the initiation of FLO11 using green fluorescent protein (GFP) under the control of the endogenous promoter. Strains varied in when and how much GFP was detected, with increased signal associated with increased morphological complexity. Generally, the signal was strongest in the center of the mat and absent at the expanding edge. Our results show that traits discovered in one background vary and exist independently of mat complexity in natural isolates. The environment may favor different sets of traits, which could have implications for how this yeast adapts to its many ecological niches.

The effects of ecological selection on species diversity and trait distribution: predictions and an empirical test.

Ecological selection is a major driver of community assembly. Selection is classified as stabilizing when species with intermediate trait values gain the highest reproductive success, whereas selection is considered directional when fitness is highest for species with extreme trait values. Previous studies have investigated the effects of different selection types on trait distribution, but the effects of selection on species diversity have remained unclear. Here, we propose a framework for inferring the type and strength of selection by studying species diversity and trait distribution together against null expectations. We use a simulation model to confirm our prediction that directional selection should lead to lower species diversity than stabilizing selection despite a similar effect on trait community-weighted variance. We apply the framework to a mesocosm system of annual plants to test whether differences in species diversity between two habitats that vary in productivity are related to differences in selection on seed mass. We show that, in both habitats, species diversity was lower than the null expectation, but that species diversity was lower in the more productive habitat. We attribute this difference to strong directional selection for large-seeded species in the productive habitat as indicated by trait community-weighted mean being higher and community-weighted variance being lower than the null expectations. In the less productive habitat, we found that community-weighted variance was higher than expected by chance, suggesting that seed mass could be a driver of niche partitioning under such conditions. Altogether, our results suggest that viewing species diversity and trait distribution as interrelated patterns driven by the same process, ecological selection, is helpful in understanding community assembly.

Functional diversity of Himalayan bat communities declines at high elevation without the loss of phylogenetic diversity

Species richness exhibits well-known patterns across elevational gradients in various taxa, but represents only one aspect of quantifying biodiversity patterns. Functional and phylogenetic diversity have received much less attention, particularly for vertebrate taxa. There is still a limited understanding of how functional, phylogenetic and taxonomic diversity change in concert across large gradients of elevation. Here, we focused on the Himalaya—representing the largest elevational gradients in the world—to investigate the patterns of taxonomic, functional and phylogenetic diversity in a bat assemblage. Combining field data on species occurrence, relative abundance, and functional traits with measures of phylogenetic diversity, we found that bat species richness and functional diversity declined at high elevation but phylogenetic diversity remained unchanged. At the lowest elevation, we observed low functional dispersion despite high species and functional richness, suggesting a niche packing mechanism. The decline in functional richness, dispersion, and divergence at the highest elevation is consistent with patterns observed due to environmental filtering. These patterns are driven by the absence of rhinolophid bats, four congeners with extreme trait values. Our data, some of the first on mammals from the Himalayan region, suggest that in bat assemblages with relatively high species diversity, phylogenetic diversity may not be a substitute to measure functional diversity.

Crop Domestication, Root Trait Syndromes, and Soil Nutrient Acquisition in Organic Agroecosystems: A Systematic Review

Selecting crops that express certain reproductive, leaf, and root traits has formed detectable, albeit diverse, crop domestication syndromes. However, scientific and informal on-farm research has primarily focused on understanding and managing linkages between only certain domestication traits and yield. There is strong evidence suggesting that functional traits can be used to hypothesize and detect trade-offs, constraints, and synergies among crop yield and other aspects of crop biology and agroecosystem function. Comparisons in the functional traits of crops vs. wild plants has emerged as a critical avenue that has helped inform a better understanding of how plant domestication has reshaped relationships among yield and traits. For instance, recent research has shown domestication has led important economic crops to express extreme functional trait values among plants globally, with potentially major implications for yield stability, nutrient acquisition strategies, and the success of ecological nutrient management. Here, we present an evidence synthesis of domestication effects on crop root functional traits, and their hypothesized impact on nutrient acquisition strategies in organic and low input agroecosystems. Drawing on global trait databases and published datasets, we show detectable shifts in root trait strategies with domestication. Relationships between domestication syndromes in root traits and nutrient acquisition strategies in low input systems underscores the need for a shift in breeding paradigms for organic agriculture. This is increasingly important given efforts to achieve Sustainable Development Goal (SDG) targets of Zero Hunger via resilient agriculture practices such as ecological nutrient management and maintenance of genetic diversity.

Root traits explain plant species distributions along climatic gradients yet challenge the nature of ecological trade-offs.

Ecological theory is built on trade-offs, where trait differences among species evolved as adaptations to different environments. Trade-offs are often assumed to be bidirectional, where opposite ends of a gradient in trait values confer advantages in different environments. However, unidirectional benefits could be widespread if extreme trait values confer advantages at one end of an environmental gradient, whereas a wide range of trait values are equally beneficial at the other end. Here, we show that root traits explain species occurrences along broad gradients of temperature and water availability, but model predictions only resembled trade-offs in two out of 24 models. Forest species with low specific root length and high root tissue density (RTD) were more likely to occur in warm climates but species with high specific root length and low RTD were more likely to occur in cold climates. Unidirectional benefits were more prevalent than trade-offs: for example, species with large-diameter roots and high RTD were more commonly associated with dry climates, but species with the opposite trait values were not associated with wet climates. Directional selection for traits consistently occurred in cold or dry climates, whereas a diversity of root trait values were equally viable in warm or wet climates. Explicit integration of unidirectional benefits into ecological theory is needed to advance our understanding of the consequences of trait variation on species responses to environmental change.

Evolution reverses the effect of network structure on metapopulation persistence.

Global environmental change is challenging species with novel conditions, such that demographic and evolutionary trajectories of populations are often shaped by the exchange of organisms and alleles across landscapes. Current ecological theory predicts that random networks with dispersal shortcuts connecting distant sites can promote persistence when there is no capacity for evolution. Here, we show with an eco‐evolutionary model that dispersal shortcuts across environmental gradients instead hinder persistence for populations that can evolve because long‐distance migrants bring extreme trait values that are often maladaptive, short‐circuiting the adaptive response of populations to directional change. Our results demonstrate that incorporating evolution and environmental heterogeneity fundamentally alters theoretical predictions regarding persistence in ecological networks.

Including intraspecific trait variability to avoid distortion of functional diversity and ecological inference: Lessons from natural assemblages

Abstract Functional diversity assessments are crucial and increasingly used for understanding ecological processes and managing ecosystems. The functional diversity of a community is assessed by sampling traits at one or more scales (individuals, populations and species) and calculating a summary index of the variation in trait values. However, it remains unclear how the scales at which traits are sampled and the indices used to estimate functional diversity may alter the patterns observed and inferences about ecological processes. For 40 plant and 61 ant communities, we assess functional diversity using six methods—spanning various mean‐based and probabilistic methods—that reflect common scenarios where different levels of detail are available in trait data. We test whether including trait variability at different scales (from individuals to species) alters functional diversity values calculated using the volume‐based and dissimilarity‐based indices, Functional Richness (FRic) and Rao, respectively. We further test whether such effects alter functional diversity patterns observed across communities and their relationships with environmental drivers such as abiotic gradients and occurrences of invasive species. Intraspecific trait variability strongly determined FRic and Rao. Methods using only species' mean trait values to calculate FRic (convex hulls) and Rao (Gower‐based dissimilarity) distorted the patterns observed when intraspecific trait variability was considered. These distortions generated Type I and Type II errors for the effects of environmental factors structuring the plant and ant communities. A high sensitivity of FRic to individuals with extreme trait values was revealed in comparisons of different probabilistic methods including among‐individual and among‐population trait variability in functional diversity. In contrast, values of and ecological patterns in Rao were consistent among methods including different scales of intraspecific trait variability. Our results show empirically that decisions about where traits are sampled and how trait variability is included in functional diversity can drastically change the patterns observed and conclusions about ecological processes. We recommend sampling the traits of multiple individuals per species and capturing their intraspecific trait variability using probabilistic methods. We discuss how intraspecific trait variability can be reasonably estimated and included in functional diversity in the common circumstance where only limited trait data are available.

Low spatial congruence between temporal functional β‐diversity and temporal taxonomic and phylogenetic β‐diversity in British avifauna

AbstractAssessing spatial and temporal patterns of biodiversity change is essential to understand how communities vary over time and confront to environmental changes for the resilience of ecosystem functioning. We use data from two bird atlases of Britain collected during the breeding periods 1988–1991 and 2008–2011 to measure temporal β‐diversity of taxonomic, functional and phylogenetic dimensions and examine the relationship and the level of congruence of the three dimensions of temporal β‐diversity and their respective partitioned components (turnover‐nestedness). Temporal β‐diversity, turnover and nestedness patterns were highly congruent for the taxonomic and phylogenetic dimension, although these dimensions were weakly associated with the functional dimension. We found higher levels of temporal changes for the taxonomic (mean Jaccard β‐diversity 0.27) and phylogenetic (mean Jaccard β‐diversity 0.21) dimensions than for the functional dimension (mean Jaccard β‐diversity 0.09), implying that despite the changes in species composition the functional composition of the communities remained less affected. For taxonomic and phylogenetic dimensions, turnover contributed more than nestedness to shaping β‐diversity, while for functional β‐diversity the two components contributed similarly. Communities at higher altitudes were also more functionally similar in 20 years but with more changes in taxonomic and phylogenetic diversity possibly due to environmental filtering. We hypothesize that the low congruence might be due to species with extreme trait values persisting throughout time and retaining the volume of functional space and thus contributing to the low temporal change of functional diversity despite the high levels of change in species composition, perhaps an indication of functional “stability.”

Invasive crayfish alter the long‐term functional biodiversity of lotic macroinvertebrate communities

Abstract Invasive species represent one of the primary threats to global biodiversity. Despite acknowledged implications for taxonomic properties of ecological communities following invasion, functional measures remain poorly understood. We examined the long‐term implications of invasion by a crayfish species, Pacifastacus leniusculus, on functional alpha and beta diversity properties of lotic macroinvertebrate communities in three English regions. The dataset comprised 477 samples collected predominantly between 1990 and 2013. Unlike many invasion studies, we employed before and after invasion comparisons, in association with control rivers not invaded by crayfish. Functional richness and divergence metrics displayed the strongest responses to invasion, highlighting that P. leniusculus may alter the range of functional niches and extreme trait values (likely reflecting resistance and resilience mechanisms) displayed by macroinvertebrate communities. Interestingly, in one region, biodiversity gains seen in control rivers were not mirrored in invaded rivers, potentially suggesting that invasion inhibited ecological improvements. Invasion by signal crayfish resulted in functional compositional changes in two of the three English regions studied, with these rivers yielding greater ecological differences between pre‐ and post‐invasion periods relative to control rivers. This change was primarily driven by higher nestedness values in invaded rivers, with communities containing functional subsets relative to control rivers. The third region demonstrated no functional compositional changes or alterations in functional beta diversity associated with invasion. Our findings indicated that in most instances, the functional properties of macroinvertebrate communities responded to crayfish invasion and may therefore represent a complementary means to monitor the ecological condition of lotic ecosystems. Given their spatial transferability, functional traits could provide a platform to guide regional management practices in the face of biological invasions. A free Plain Language Summary can be found within the Supporting Information of this article.

Rapid generation of ecologically relevant behavioral novelty in experimental cichlid hybrids.

The East African cichlid radiations are characterized by repeated and rapid diversification into many distinct species with different ecological specializations and by a history of hybridization events between nonsister species. Such hybridization might provide important fuel for adaptive radiation. Interspecific hybrids can have extreme trait values or novel trait combinations and such transgressive phenotypes may allow some hybrids to explore ecological niches neither of the parental species could tap into. Here, we investigate the potential of second‐generation (F2) hybrids between two generalist cichlid species from Lake Malawi to exploit a resource neither parental species is specialized on: feeding by sifting sand. Some of the F2 hybrids phenotypically resembled fish of species that are specialized on sand sifting. We combined experimental behavioral and morphometric approaches to test whether the F2 hybrids are transgressive in both morphology and behavior related to sand sifting. We then performed a quantitative trait loci (QTL) analysis using RADseq markers to investigate the genetic architecture of morphological and behavioral traits. We show that transgression is present in several morphological traits, that novel trait combinations occur, and we observe transgressive trait values in sand sifting behavior in some of the F2 hybrids. Moreover, we find QTLs for morphology and for sand sifting behavior, suggesting the existence of some loci with moderate to large effects. We demonstrate that hybridization has the potential to rapidly generate novel and ecologically relevant phenotypes that may be suited to a niche neither of the parental species occupies. Interspecific hybridization may thereby contribute to the rapid generation of ecological diversity in cichlid radiations.

The Fight to Capture Light: Functional Diversity Is Related to Aquatic Plant Community Productivity Likely by Enhancing Light Capture

Functional Diversity (FD) experiments are highly effective for investigating how a community interacts with its environment. However, such experiments using morphological and chemical traits have not been conducted for submerged aquatic plants and their insights would be highly valuable for understanding the ecology of these communities. We conducted a 15-week field experiment in the Baltic Sea where we manipulated the species composition of aquatic plant communities to investigate functional diversity. We constructed artificial triculture communities with different species compositions to change the Community Weighted Means (CWMs) and variability of traits. We measured 9 plant traits and tested how community productivity (CP) was related to FD, trait CWMs and community trait ranges. CP varied by more than four times across treatments and functional richness was significantly related to CP. Functional evenness and functional divergence were not significantly related to CP. Height, leaf area and δ¹³C were significantly related to CP. Leaf δ¹³C trends with CP suggested that the carbon supply is not replete, yet species composition was partly responsible for the relationship. Plant height likely had multifaceted benefits to CP because there was evidence of a competitive height interaction between the tallest and 2nd tallest species, therefore the effects of plant height to CP would have been disproportionally large. The height of the tallest species significantly drove the variability of the community height range, which was significantly related to CP and it had a relatively large influence on the calculation of FD indices. Leaf area, which was strongly correlated to plant height, was also significantly related to community productivity. The significant relationship between functional richness and CP was most likely driven by the presence of taller plants. FD likely enhanced CP, by selecting for extreme trait values which enhanced production (selection effect), while niche complementarity effects were not observed. This study provides experimental evidence and mechanistic insights into the role of FD and specific traits for CP in submerged aquatic plant communities. To conclude, FD was significantly related to CP of temperate aquatic plant communities likely by selecting for traits which enhanced light capture, with consequences for carbon supply.

Similarities between invaders and native species: Moving past Darwin's naturalization conundrum

AbstractDarwin's naturalization conundrum states that successful invaders must be closely related to native species to possess the traits to tolerate that environment, but distantly related enough to possess traits allowing exploitation of underutilized niches, thereby minimizing competition. Although influential, this hypothesis is based on several simplistic assumptions. In particular, the relationship among phylogenetic relatedness, similarity, and competition is more complex than assumed and changes with spatial and phylogenetic scale. Competitive interactions are determined by limiting similarity and trait hierarchies associated with separate traits. Successful invaders thus need to be similar to native species in some respects, but different in others. This combination of similarities and differences is unlikely to be conserved. Further, many invasive species are represented in their novel range by genotypes with extreme trait values or plasticity relative to the species mean. Selection for these genotypes may alter the similarity between invasive and native species, thus obscuring the relationship between competition and phylogenetic relatedness. As environmental filtering and competition often act on different spatial scales, approaches assessing how individual traits relate to invasion at these scales (species pools vs local community) may improve our understanding of the relationship between similarity and invasion.

Functional and phylogenetic consequences of plant invasion for coastal native communities

AbstractQuestionDo invasions by alien plant species with contrasting trait profiles (Arctotheca calendula, Carpobrotus spp., Conyza bonariensis and Opuntia dillenii) change the functional and phylogenetic structure of coastal plant communities?LocationAtlantic coastal habitats in Huelva (Spain).MethodsWe identified species diversity and composition in 220 paired (invaded and non‐invaded) plots along the coast (440 plots in total). We measured nine functional traits for every native and invader species, namely, specific leaf area (SLA), specific root length (SRL), leaf and root dry mass content (LDMC and RDMC) and carbon isotope fraction (δ13C). We calculated, at the plot scale, community means (CMs) for each trait, functional richness, Faith's phylogenetic diversity and functional and phylogenetic mean pairwise dissimilarities.ResultsThree out the four species showed rather extreme trait values compared to the native flora with greater impact on invaded communities. In plots invaded by A. calendula the values of the native communities of SLA and SRL increased, while LDMC, RDMC and δ13C decreased showing CMs more similar to its functional profile. Besides, these plots showed lower functional and phylogenetic diversity in the native component of the community. In plots invaded by Carpobrotus spp. and O. dillenii the CMs values for LDMC and δ13C increased, but have little effect on the functional and phylogenetic structure of the native communities, while no differences were observed for the communities invaded by C. bonariensis (the most functionally similar to the native species).ConclusionsOur study highlights that inferring community assembly rules from the exploration of functional and phylogenetic differences between invaded and non‐invaded plots is not straightforward. By considering invaders with different functional profiles, we have shown that species with different mechanisms of invasion have contrasting impacts on the community. Consequently, the effect of plant invaders differs depending on their functional distinction from the recipient community, rather than their phylogenetic origin.

Generating species assemblages for restoration and experimentation: A new method that can simultaneously converge on average trait values and maximize functional diversity

Abstract Restoring resilient ecosystems in an era of rapid environmental change requires a flexible framework for selecting assemblages of species based on functional traits. However, current trait‐based models have been limited to algorithms that select species assemblages that only converge on specified average trait values, and could not accommodate the common desire among restoration ecologists to generate functionally diverse assemblages. We have solved this problem by applying a nonlinear optimization algorithm to solve for the species relative abundances that maximize Rao's quadratic entropy (Q) subject to other linear constraints. Rao's Q is a closed‐form algebraic expression of functional diversity that is maximized when the most abundant species are functionally dissimilar. Previous models have maximized species evenness subject to the linear constraints by maximizing the entropy function (H’). Maximizing Q alone produces an undesirable species abundance distribution because species that exhibit extreme trait values have the highest abundances. We demonstrate that the maximization of an objective function that additively combines Q and H’ produces a more even relative abundance distribution across the trait dimension. Some ecological restoration projects aim to restore communities that converge on one set of traits while diverging across another. The selectSpecies r function can derive assemblages for any size species pool that maximizes the diversity of any set of traits, while simultaneously converging on average values of any other set of traits. We demonstrate how the function works through examples using uniformly spaced trait distributions and data with a known structure. We also demonstrate the utility of the function using real trait data collected on dozens of species from three separate ecosystems: serpentine grasslands, ponderosa pine forests, and subtropical rainforests. The quantitative selection of species based on their functional traits for ecological restoration and experimentation must be both rigorous and accessible to practitioners. The selectSpecies function provides ecologists with an easy‐to‐use open‐source solution to objectively derive species assemblages based on their functional traits.

Trait-fitness relationships determine how trade-off shapes affect species coexistence.

Trade-offs between functional traits are ubiquitous in nature and can promote species coexistence depending on their shape. Classic theory predicts that convex trade-offs facilitate coexistence of specialized species with extreme trait values (extreme species) while concave trade-offs promote species with intermediate trait values (intermediate species). We show here that this prediction becomes insufficient when the traits translate non-linearly into fitness which frequently occurs in nature, e.g., an increasing length of spines reduces grazing losses only up to a certain threshold resulting in a saturating or sigmoid trait-fitness function. We present a novel, general approach to evaluate the effect of different trade-off shapes on species coexistence. We compare the trade-off curve to the invasion boundary of an intermediate species invading the two extreme species. At this boundary, the invasion fitness is zero. Thus, it separates trait combinations where invasion is or is not possible. The invasion boundary is calculated based on measurable trait-fitness relationships. If at least one of these relationships is not linear, the invasion boundary becomes non-linear, implying that convex and concave trade-offs not necessarily lead to different coexistence patterns. Therefore, we suggest a new ecological classification of trade-offs into extreme-favoring and intermediate-favoring which differs from a purely mathematical description of their shape. We apply our approach to a well-established model of an empirical predator-prey system with competing prey types facing a trade-off between edibility and half-saturation constant for nutrient uptake. We show that the survival of the intermediate prey depends on the convexity of the trade-off. Overall, our approach provides a general tool to make a priori predictions on the outcome of competition among species facing a common trade-off in dependence of the shape of the trade-off and the shape of the trait-fitness relationships.

Reversal of response to artificial selection on body size in a wild passerine.

A general assumption in quantitative genetics is the existence of an intermediate phenotype with higher mean individual fitness in the average environment than more extreme phenotypes. Here, we investigate the evolvability and presence of such a phenotype in wild bird populations from an eleven-year experiment with four years of artificial selection for long and short tarsus length, a proxy for body size. The experiment resulted in strong selection in the imposed directions. However, artificial selection was counteracted by reduced production of recruits in offspring of artificially selected parents. This resulted in weak natural selection against extreme trait values. Significant responses to artificial selection were observed at both the phenotypic and genetic level, followed by a significant return toward preexperimental means. During artificial selection, the annual observed phenotypic response closely followed the predicted response from quantitative genetic theory (ryears = 0.96, rcohorts = 0.56). The rapid return to preexperimental means was induced by three interacting mechanisms: selection for an intermediate phenotype, immigration, and recombination between selected and unselected individuals. The results of this study demonstrates the evolvability of phenotypes and that selection may favor an intermediate phenotype in wild populations.

Invasion and succession change the functional traits of serpentine plant communities1,3

Human impacts, such as invasive species introductions and land use changes, have the potential to alter the functional composition and diversity of plant communities. We can make and test clear predictions of how these processes should affect community-level trait values, yet very few studies have done so. We examined how three invasive species and succession from savanna to woodland because of fire suppression may change functional composition and diversity in the State Line serpentine barrens on the Pennsylvania-Maryland border. We characterized native and invasive plants in eight key functional leaf traits and quantified trait overlap between natives and invasives. We compared plots in two successional stages—savannas and woodlands—in functional composition and diversity. The invasive species Elaeagnus umbellata Thunb. and Microstegium vimineum (Trin.) A. Camus had extreme trait values and low overlaps with native species. Invasive species and plant assemblages including invasive species had traits more characteristic of fast growth, competitiveness, and inefficient resource use. Assemblages with invasive plants had higher functional diversity. The conversion of savannas to woodlands also shifted communities toward more fast-growing, competitive, and inefficient traits as well as decreasing functional diversity. Both invasion and succession appear to reduce the distinctive stress tolerance of plant communities on serpentine soils, with the potential for strong ecosystem-level impacts and positive feedbacks.

Exome QTL-seq maps monogenic locus and QTLs in barley

BackgroundQTL-seq, in combination with bulked segregant analysis and next-generation sequencing (NGS), is used to identify loci in small plant genomes, but is technically challenging to perform in species with large genomes, such as barley. A combination of exome sequencing and QTL-seq (exome QTL-seq) was used to map the mono-factorial Mendelian locus black lemma and pericarp (Blp) and QTLs for resistance to net blotch disease, a common disease of barley caused by the fungus Pyrenophora teres, which segregated in a population of 100 doubled haploid barley lines.MethodsThe provisional exome sequences were prepared by ordering the loci of expressed genes based on the genome information and concatenating genes with intervals of 200-bp spacer "N" for each chromosome. The QTL-seq pipeline was used to analyze short reads from the exome-captured library.ResultsIn this study, short NGS reads of bulked total DNA samples from segregants with extreme trait values were subjected to exome capture, and the resulting exome sequences were aligned to the reference genome. SNP allele frequencies were compared to identify the locations of genes/QTLs responsible for the trait value differences between lines. For both objective traits examined, exome QTL-seq identified the monogenic Mendelian locus and associated QTLs. These findings were validated using conventional mapping approaches.ConclusionsExome QTL-seq broadens the utility of NGS-based gene/QTL mapping in organisms with large genomes.