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opencc-zeroJan 2023View details →

Divergent selection on behavioural and chemical traits between reproductively isolated populations of Drosophila melanogaster

Speciation is driven by traits that can act to prevent mating between nascent lineages, including male courtship and female preference for male traits. Mating barriers involving these traits evolve quickly because there is strong selection on males and females to maximize reproductive success, and the tight co-evolution of mating interactions can lead to rapid diversification of sexual behavior. Populations of D. melanogaster show strong asymmetrical reproductive isolation that is correlated with geographic origin. Using strains that capture natural variation in mating traits, we ask two key questions: which specific male traits are females selecting, and are these traits under divergent sexual selection? These questions have proven extremely challenging to answer, because even in closely related lineages males often differ in multiple traits related to mating behavior. We address these questions by estimating selection gradients for male courtship and cuticular hydrocarbons for two different female genotypes. We identify specific behaviors and particular cuticular hydrocarbons that are under divergent sexual selection and could potentially contribute to premating reproductive isolation. Additionally, we report that a subset of these traits are plastic; males adjust these traits based on the identity of the female genotype they interact with. These results suggest that even when male courtship is not fixed between lineages, ongoing selection can act on traits that are important for reproductive isolation.

Dataset related to article: Differential effect of climate of origin and cultivation climate on structural and biochemical plant traits

Exploring patterns and causes of intraspecific trait variation is crucial for a better understanding of the effects of climate change on plant populations and ecosystems. However, our current understanding of the intraspecific trait variation is mainly based on structural (morphological) traits, and we have limited knowledge on patterns and causes of variation in biochemical traits (e.g., leaf pigments), which are also crucial for plant adaptation. As a result, we also do not know how similar the climatic effects on structural versus biochemical traits are. Using plant traits from 110 genotypes representing 11 Festuca rubra populations grown in 4 different climates, we studied trait covariation among structural traits (linked to fitness, resource use, gas exchange, and reproduction) and biochemical traits (linked to photosynthesis, photoprotection, and oxidative stress). We also disentangled the relative role of the climate of origin and the climate of cultivation in the structural versus biochemical traits and tested for adaptive plasticity in the traits. We found that 1) biochemical traits did not covary with structural traits and represent independent 'photoharvesting – photoprotection' strategy dimension of functional variation; 2) interactive effects of climate of origin and cultivation were more pronounced for biochemical than structural traits. 3) Trait plasticity was affected by the climate of origin (precipitation and temperature as well as their interaction); 4) F. rubra showed both adaptive and mal-adaptive plasticity, and adaptiveness depended upon trait type, cultivation climate, and climate of origin. Overall, our results suggest that structural and biochemical plant traits respond differentially to climate and thus the response of one group of traits cannot be predicted from the other. Responses are also strongly determined by interactions between the climate of origin and cultivation. Thus, more studies on variation in biochemical traits, their correspondence to other traits, and their variation with climate are needed.

Functional traits of soil nematodes define their response to nitrogen fertilization

1. Nitrogen (N) fertilization and warming are two crucial global change factors affecting the soil nematode communities. The effects of N fertilization and warming, however, on nematode communities in soils are inconsistent across ecosystems and maybe be even opposite. 2. One key reason is that the commonly used taxonomic diversity is less sensitive to environmental changes than the seldom-used trait-based indicators. To verify this, we performed an eight-year field experiment with four N fertilization levels with and without soil warming and collected an extensive dataset consisting of (i) six traits related to the nematode performance, i.e., body size, maximum body length, maximum body width, stylet length, esophagus length, and intestinal length; (ii) the taxonomic alpha (richness and abundance) and beta-diversity (Bray-Curtis dissimilarities) of the whole nematode community and each nematode functional group, (iii) soil food web resources (the total taxonomic richness and abundance of plant, bacterial and fungal communities), and (iv) soil properties (pH, total, ammonium and nitrate N, microbial N and C, total and available P and soil water content). 3. We found that N fertilization altered plant diversity and soil nitrate levels, which in turn decreased taxonomic alpha diversity of two nematode functional groups (phytophagous nematodes and predators), but taxonomic diversity for the whole nematode community remained stable. The decreased taxonomic alpha diversity of phytophagous nematodes resulted in increased maximum body width, but decreased stylet length and esophageal length. Mild warming (~ 0.7 °C) had no effects on soil properties and soil food web resources, and the taxonomic diversity or nematode traits remained unchanged. 4. Our results reveal that nematode functional traits show strong responses to N fertilization as individual nematode groups adapted quickly to changed soil properties and food web resources. Taxonomic diversity indices, however, were more stable under these changes showing that the functional composition of nematode communities may respond in the short-term despite little effects on species diversity. Thus, the trait-based indicators not only reveal how nematodes respond to N fertilization, but also how nematodes mediate the effects of N fertilization on ecosystem functioning (i.e., soil nutrient cycling).

Data for: Dissecting the genetic architecture of leaf morphology traits in mungbean (Vigna radiata (L.) Wizcek) using genome‐wide association study

Mungbean (Vigna radiata (L) Wizcek) is an important pulse crop, increasingly used as a source of protein, fiber, low fat, carbohydrates, minerals, and bioactive compounds in human diets. Mungbean is a dicot plant with trifoliate leaves. Leaves are central to various plant processes like photosynthesis, light interception, and overall canopy structure. The objectives were to study leaf morphological traits, use image analysis to extract leaf traits from images from the Iowa Mungbean Diversity (IMD) panel, develop a regression model for the prediction of leaflet area, and conduct association mapping for leaf morphological traits. We collected more than 5000 leaf images of the IMD panel consisting of 484 accessions over two years (2020 and 2021) with two replications per experiment. Leaf traits were extracted using image analysis, analyzed, and used for association mapping. Morphological diversity included leaflet type (oval or lobed), leaflet size (small, medium, large), lobed angle (shallow, deep), and vein coloration (green, purple). A regression model was developed to predict each ovate leaflet's area (adjusted R2 = 0.97; residual standard errors of <= 1.10). The candidate genes Vradi01g07560, Vradi05g01240, Vradi02g05730, and Vradi03g00440, are associated with multiple traits (length, width, perimeter, and area) across the leaflets (left, terminal, and right). These are suitable candidate genes for further investigation in their role in leaf development, growth, and function. Future studies will be needed to correlate the observed traits discussed here with yield or important agronomic traits for use as phenotypic or genotypic markers in marker-aided selection methods for mungbean crop improvement.

opencc-by-4.0Feb 2023View details →

Model outputs and species-level data for "Functional traits and climate drive interspecific differences in disturbance-induced tree mortality"

This repository is divided in three sub-directories:  <ul> <li>sensitivity contains the posterior of each parameter estimated by the bayesian mortality model in a rdata file. This file was generated by the script https://github.com/jbarrere3/SalvageModel/tree/withFinland</li> <li>climate contains for each tree species the climatic variables (mean annual temperature, minimum annual temperature and annual precipitation) extracted from CHELSA and the disturbance-related climatic indices (Fire Weather Index, Snow Water Equivalent and Gust Wind Speed)</li> <li>traits contains the traits calculated directly with NFI data (bark thickness, height to dbh ratio, maximum growth), and a text file with the Species and Trait ID to request to TRY database. </li> </ul> The content of this repository can be used to reproduce the analyses of the paper, with the script stored in  in https://github.com/jbarrere3/DisturbancePaper Edit (19/09/2023): A minor coding error was found in the pre-formatted data of the paper, which did not affect the main results but led to minor change in the value of the posterior estimates. An updated version of the posterior estimates of this dataset was made available at https://zenodo.org/record/8358921.

Data for: Carbon-concentrating mechanisms are a key trait in lichen ecology and distribution

Carbon-concentrating mechanisms (CCMs) are a widespread phenomenon in photosynthetic organisms. In vascular plants, the evolution of CCMs (C4 and CAM) is associated with significant shifts, most often to hot, dry and bright or aquatic environments. If and how CCMs drive distributions of other terrestrial photosynthetic organisms, remains little studied. Lichens are ecologically important obligate symbioses between fungi and photosynthetic organisms. The primary photosynthetic partner in these symbioses can include CCM-presenting cyanobacteria (as carboxysomes), CCM-presenting green algae (as pyrenoids) or green algae lacking any CCM. We use an extensive dataset of lichen communities from eastern North America, spanning a wide climatic range, to test the importance of CCMs as predictors of lichen ecology and distribution. We show that presence or absence of CCMs leads to opposite responses to temperature and precipitation in green algal lichens, and with different responses in cyanobacterial lichens. These responses contrast with our understanding of lichen physiology, whereby CCMs mitigate carbon limitation by water saturation at the cost of efficient use of vapor hydration. This study demonstrates that CCM-status is a key functional trait in obligate lichen symbioses, equivalent in importance to its role in vascular plants, and central for studying present and future climate responses.

Data from: Scale-dependent effects of landscape structure on pollinator traits, species interactions and pollination success

Data: Plant-pollinator interactions, pollinator body size (inter-tegular distance, ITD) and plant reproductive success (number of seeds produced). Data collected by Christie J. Webber. Data collected in 14 experimental flowering plant patches during December 2012–February 2013. Patches were located in a 105 hectare sheep farm pasture in Oxford, North Canterbury, New Zealand (43°19'21"S 172°12'25"E). Files: <ul> <li>Data_S1: contains plant-pollinator interactions sampled and pollinator inter-tegular distance (ITD). Data_S1 columns: patch ID where the interaction was recorded, plant species, pollinator ITD (mm), and pollinator family, genus and species.</li> <li>Data_S2: contains the number of seeds produced by each of the five flowers of each plant individual from each plant species on each patch. Data_S2 columns: patch ID where the measurement was taken, plant species, plant number (individual sampled), number of seeds.</li> </ul> Dataset used in "Scale-dependent effects of landscape structure on pollinator traits, species interactions and pollination success" by G. Peralta, C.J. Webber, G.L.W. Perry, D.B. Stouffer, D.P. Vázquez and J.M. Tylianakis.

Altered trait covariances between invasive and native ranges of a global plant invader

Increasing evidence suggests that invasive populations adapt to novel environments rapidly, and the ability to rapidly adapt depends on genetically-based trait variation and covariation. However, few studies have investigated the trait covariance in the native and invasive ranges. Such investigation will give a more comprehensive picture of how historical contingency and adaptation shape invasiveness, contributing to the prediction of future invasion dynamics. Here, we collected seven and nine populations alongside latitudes from invasive and native ranges of a global invasive plant, Spartina alterniflora, and planted them in two common gardens at the southernmost and northernmost sites of the invasive range. We measured plant traits, including the first flowering time, plant height, and seed set, and analyzed how these traits varied with garden sites and populations' origin latitudes and how their covariance changed between ranges. We found that plants flowered later, grew taller, and set more seeds in the high-latitude garden than in the low-latitude one. The growth and expression of genetic variation of traits appeared to be limited by high ambient temperature in the low-latitude garden. In the high-latitude garden, the flowering time of populations showed clinal variation for both invasive and native populations, whereas the plant height and seed set showed clinal variation only for native or invasive populations. From the native to the invasive range, the flowering time and seed set developed negative genetic covariance, and flowering time and plant height changed from negative genetically correlated to uncorrelated. Our results suggested that S. alterniflora has experienced rapid adaptation to clinal and local conditions over the 40-year invasion. Such geographic-scale rapid adaptation appeared to have benefited from previously identified genetic admixture that has released the trait covariance. Our study highlights the importance of integrating full-range geographical surveys with introduction history to understand the potential and mechanisms of trait evolution during invasion.

opencc-by-4.0Feb 2023View details →

Sol Genome Annotations and Quantitative Traits Loci

RDF data graphs

Data from: A real data-driven simulation strategy to select an imputation method for mixed-type trait data

Missing observations in trait datasets pose an obstacle for analyses in myriad biological disciplines. Considering the mixed results of imputation, the wide variety of available methods, and the varied structure of real trait datasets, a framework for selecting a suitable imputation method is advantageous. We invoked a real data-driven simulation strategy to select an imputation method for a given mixed-type (categorical, count, continuous) target dataset. Candidate methods included mean/mode imputation, k-nearest neighbour, random forests, and multivariate imputation by chained equations (MICE). Using a trait dataset of squamates (lizards and amphisbaenians; order: Squamata) as a target dataset, a complete-case dataset consisting of species with nearly completed information was formed for the imputation method selection. Missing data were induced by removing values from this dataset under different missingness mechanisms: missing completely at random (MCAR), missing at random (MAR), and missing not at random (MNAR). For each method, combinations with and without phylogenetic information from single gene (nuclear and mitochondrial) or multigene trees were used to impute the missing values for five numerical and two categorical traits. The performances of the methods were evaluated under each missing mechanism by determining the mean squared error and proportion falsely classified rates for numerical and categorical traits, respectively. A random forest method supplemented with a nuclear-derived phylogeny resulted in the lowest error rates for the majority of traits, and this method was used to impute missing values in the original dataset. Data with imputed values better reflected the characteristics and distributions of the original data compared to complete-case data. However, caution should be taken when imputing trait data as phylogeny did not always improve performance for every trait and in every scenario. Ultimately, these results support the use of a real data-driven simulation strategy for selecting a suitable imputation method for a given mixed-type trait dataset.

Data for: Phylogenetically controlled life history trait meta-analysis in cetaceans reveals unexpected negative brain size and longevity correlation

The identification of patterns in trait evolution is essential to understand the interaction of evolutionary forces, and provides useful information for species management. Cetaceans are a phylogenetically well-resolved infraorder that exhibit distinct trait variation across behavioural, molecular and life history dimensions, yet few researchers have applied a meta-analytic or comparative approach to these traits. To understand cetacean trait evolution, we used a phylogenetic generalised least squares approach to examine the cognitive buffer hypothesis (CBH). A large brain should buffer individuals against environmental challenges through increasing survival rates, and a longer lifespan should buffer individuals against the cost of extended development for larger brains according to the CBH, leading to an expected positive correlation between brain size and lifespan. In contrast to this expectation, previously observed in taxa including primates, we found a negative correlation between brain size and lifespan in cetaceans. This suggests cetaceans experience selective pressures different from most other mammals in these traits but may be more similar to some social mammalian carnivores that display alloparenting. We also provide a comprehensive dataset to explore additional aspects of trait evolution but which would greatly benefit from studies on behavioural ecology across cetaceans and increased focus on data-deficient species.

The data table of eleven invasive species in Hungary and Romania: Invasive species' cover, invasive species' traits, basic characteristics, trait composition, functional diversity indices and soil parameters of recipient plant communities

We studied 11 widespread herbaceous invasive alien species of East-Central Europe and their 16 impact metrics (resident plant communities' ecological characteristics, trait composition, functional diversity, and soil parameters) by sampling invaded and similar, uninvaded sites (space-for-time substitution method). Our aim was to (1) investigate the detailed ecological impacts of invasive plants on native plant communities; (2) explore the type of cover-impact relationships across impact metrics and their consistency across species; (3) study whether the cover-impact relationship depends on functional traits of invasive species. We present the data table with the 11 invasive species: the status of the sites (invaded, uninvaded), the cover of invasive species at plot level, the invasive species traits (lifespan, height, SLA, seed mass, clonal spread, flowering duration), community characteristics (species richness and diversity, native vegetation cover and bare ground cover at plot level), trait composition of native plant communities (native vegetation height, CWM height, CWM SLA, CWM seed mass, CWM clonal spread), functional diversity (functional richness, functional evenness, functional divergence, functional distance, RaoQ) and soil properties (N, P, organic C, pH).

Decoupling pioneering traits from latitudinal patterns in a North American bird experiencing a southward range shift

<ol> <li>Eco-geographic rules describe spatial patterns in biological trait variation and shed light on the drivers of such variation. In animals, a consensus is emerging that 'pioneering' traits may facilitate range shifts via a set of bold, aggressive, and stress-resilient traits. Many of these same traits are associated with more northern latitudes, and most range shifts in the northern hemisphere indicate northward movement. As a consequence, it is unclear whether pioneering traits are simply corollaries of existing latitudinal variation, or whether they override other well-trodden latitudinal patterning as a unique eco-geographic rule of phenotypic variation.</li> <li>The tree swallow (Tachycineta bicolor) is a songbird undergoing a southward range shift in the eastern United States, in direct opposition of the poleward movement seen in most other native species' range shifts. Because this organic range shift countervails the typical direction of movement, this case study provides for unique ecological insights on organisms and their ability to thrive in our changing world.</li> <li>We sampled female birds across seven populations, quantifying behavioral, physiological, and morphological traits. We also used GIS and field data to quantify a core set of ecological factors with strong ties to these traits as well as female performance.</li> <li>Females at more southern expansion sites displayed higher maternal aggression, higher baseline corticosterone, and more pronounced elevation of corticosterone following a standardized stressor, contrary to otherwise largely conserved latitudinal patterning in these traits. Microhabitat variation explained some quantitative phenotypic variation, but the expansion and historic ranges did not differ in openness, distance to water, or breeding density.</li> <li>This countervailing range shift therefore suggests that pioneering traits are not simply corollaries of existing latitudinal variation, but rather, they may override other well-trodden latitudinal patterning as a unique eco-geographic rule of phenotypic variation.</li> </ol>

Root functional traits determine the magnitude of the rhizosphere priming effect among eight tree species

Rhizosphere priming effect can accelerate or decelerate the decomposition of soil organic matter. Using a natural abundance 13C tracer method allowing partitioning of native soil organic carbon (SOC) decomposition and plant rhizosphere respiration, we studied the effects of eight tree species on the strength of the rhizosphere priming. All tree species enhanced the rate of SOC decomposition, by 82% on average. Mean diameter of first-order roots and root exudate-derived respiration were positively correlated with the RPE, together explaining a large part of the observed variation in the RPE (R2 = 0.72), whereas root branching density was negatively associated with the RPE. Path analyses further suggested that mean diameter of first-order roots was the main driver of the RPE owing to its positive direct effect on the RPE and its indirect effects via root exudate-derived respiration and root branching density. These results demonstrate that the magnitude of the RPE is regulated by complementary aspects of root morphology, architecture and physiology, implying that comprehensive approaches are needed to reveal the multiple mechanisms driving plant effects on the RPE.

opencc-by-4.0Oct 2022View details →

Data sources and code for: "Species-specific acclimation capacity of key traits explains global vertical distributions of seagrass species"

Minguito-Frutos_etal_2023_Data1.xlsx contains the data for analyzing the relationship between plant size and seagrass growth reproductive strategy and the species-specific vertical distribution of seagrasses.  Minguito-Frutos_etal_2023_Data2.xlsx contains the data for the meta-analityc approach studying the relationship between the vertical distribution of seagrass species and the plasticity of their traits (physiological, morphological, structural and growth).  Scripts_Minguito_Frutos_etal_2023_GEB_Ref.GEB-2022-0592.R contains the R reproducible code to run all the analyses carried out in this study.

Plant functional traits predict heterogeneous distributional shifts in response to climate change

Climate change is causing the rapid redistribution of vegetation as plant species move to track their climatic optima. Despite a global trend of upward movement in latitude and elevation, there is extensive heterogeneity among species and locations, with few emerging generalizations. Greater generalization may be achieved by considering multidimensional changes in species' distributions as well as incorporating ecologically relevant functional traits into studies of range shifts. To better understand how recent changes in climate are influencing the elevational distribution of plant species and how species' functional traits mediate distributional changes, we resampled a 2,438-meter elevation transect spanning a distance of 16 kilometers which encompasses desert scrub, pinyon-juniper woodland, chaparral, and coniferous forest plant communities. Over the last 42 years, total perennial cover and species' average cover increased at lower elevations and decreased at higher elevations while the average elevational leading-edge increased 116 m and the elevational rear edge decreased 84 m. Notably, these changes were mediated by species' functional traits, where species exhibiting more conservative traits (lower SLA, greater δ13C, larger seed mass) and taller height shifted upward in their leading-edge range limit, average elevation, and trailing edge range limit, while declining in abundance at the median and trailing edge of their range. Species possessing more acquisitive traits (higher SLA, lower δ13C, smaller seed mass) and shorter height shifted downward and increased in abundance at their trailing edge, with increases in their total range size. Our results provide clear evidence that heterogeneous range dynamics under recent climate change can be generalized by considering ecologically relevant plant functional traits, and how they respond to localized climate exposure. Further, by documenting changes across a steep ecological gradient comprising a large aridity gradient, we show divergent patterns for plants occupying contrasting positions along the global spectrum of plant form and function, which provides critical insight into how trait-mediated changes under increasing aridity will impact ecosystem functioning.

Data for: Local adaptation of switchgrass drives trait relations to yield and differential responses to climate and soil environments

Switchgrass, a potential biofuel crop, is a genetically diverse species with phenotypic plasticity enabling it to grow in a range of environments. Two primary divergent ecotypes, uplands and lowlands, exhibit trait combinations representative of acquisitive and conservative growth allocation strategies, respectively. Whether these ecotypes respond differently to various types of environmental drivers remains unclear but is crucial to understanding how switchgrass varieties will respond to climate change. We grew two upland, two lowland, and two intermediate/hybrid cultivars of switchgrass at three sites along a latitudinal gradient in the central United States. Over a 4-year period, we measured plant functional traits and biomass yields and evaluated genotype-by-environment (G´E) interaction effects by analyzing switchgrass responses to soil and climate variables. We found substantial evidence of G´E interactions on biomass yield, primarily due to deviations in the response of the southern lowland cultivar Alamo, which produced more biomass in hotter and drier environments relative to other cultivars. While lowland cultivars had the highest potential for yield, their yields were more variable year-to-year compared to other cultivars, suggesting greater sensitivity to environmental perturbations. Models comparing soil and climate principal components as explanatory variables revealed soil properties, especially nutrients, to be most effective at predicting switchgrass biomass yield. Also, conservative plant traits such as high stem mass and tiller height became increasingly positively associated with biomass yield at lower latitudes where the climate is hotter and drier, regardless of ecotype. Lowland cultivars, however, showed a greater predisposition to exhibit these conservative traits. These results suggest switchgrass trait allocation trade-offs that prioritize aboveground biomass production are more tightly associated in hot, dry environments and that lowland cultivars may exhibit a more specialist life strategy relative to other cultivars. Altogether, this research provides essential knowledge for improving the viability of switchgrass as a biofuel crop.

opencc-zeroMar 2023View details →

Data for: A spatially explicit trait-based approach uncovers changes in assembly processes under warming

The re-assembly of plant communities during climate warming depends on several concurrent processes. Here we present a novel framework that integrates spatially explicit sampling, plant trait information and a warming experiment to quantify shifts in these assembly processes. By accounting for spatial distance between individuals, our framework allows separation of potential signals of environmental filtering from those of different types of competition. When applied to an elevational transplant experiment in the French Alps, we found common signals of environmental filtering and competition in all communities. Signals of environmental filtering were generally stronger in alpine than in subalpine control communities, and warming reduced this filter. Competition signals depended on treatments and traits: Symmetrical competition was dominant in control and warmed alpine communities, while hierarchical competition was present in subalpine communities. Our study highlights how distance dependent frameworks can contribute to a better understanding of transient re-assembly dynamics during environmental change.

opencc-by-4.0Mar 2023View details →

Data from: Effects of tree functional traits on soil respiration in tropical forest plantations

The study covers four plantations stands of Acacia auriculiformis (A), Eucalyptus urophylla (E), Hopea odorata (H), and X. xylocarpa (X) through a sample plot (50 m x 50 m) in each stand from July 2015 until June 2016. Physical and chemical soil properties were collected at two depths (0-15 cm, 15-30 cm) at the beginning of the study (soil_properties_initial.csv). Additional samplings of topsoil pH, bulk density (BD, g cm-3), organic matter (OM, %), total carbon (TC, %), and nitrogen (TN, %) were conducted monthly (mo_yr) at five random locations (soil_properties_month.csv). Soil respiration (SR) was measured at the beginning of each month (mo_yr) at 12 locations (Point) within each species sample plot (Species) for ten hours (h_time) simultaneously with soil temperature (ST, C), air temperature (AT, C), relative humidity (RH), and soil moisture (SM, %) (soil_respiration.csv). The location of each soil respiration measurement point within the sample plots is provided as well (soil_respiration_location.csv). All trees within each sample plot were mapped (X, Y) and their stem basal area (BA_cm2) and height (H) were measured (stand_inventories.csv).