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opencc-zeroSep 2021View details →

Improving wheat yield prediction using secondary traits and high-density phenotyping under heat stressed environments

A primary selection target for wheat (Triticum aestivum) improvement is grain yield. However, the selection for yield is limited by the extent of field trials, fluctuating environments, and the time needed to obtain multiyear assessments. Secondary traits such as spectral reflectance and canopy temperature (CT), which can be rapidly measured many times throughout the growing season, are frequently correlated with grain yield and could be used for indirect selection in large populations particularly in earlier generations in the breeding cycle prior to replicated yield testing. While proximal sensing data collection is increasingly implemented with high-throughput platforms that provide powerful and affordable information, efficient and effective use of these data is challenging. The objective of this study was to monitor wheat growth and predict grain yield in wheat breeding trials using high-density proximal sensing measurements under extreme terminal heat stress that is common in Bangladesh. Over five growing seasons, we analyzed normalized difference vegetation index (NDVI) and CT measurements collected in elite breeding lines from the International Maize and Wheat Improvement Center at the Regional Agricultural Research Station, Jamalpur, Bangladesh. We explored several variable reduction and regularization techniques followed by using the combined secondary traits to predict grain yield. Across years, grain yield heritability ranged from 0.30 to 0.72, with variable secondary trait heritability (0.0–0.6), while the correlation between grain yield and secondary traits ranged from−0.5 to 0.5. The prediction accuracy was calculated by a cross-fold validation approach as the correlation between observed and predicted grain yield using univariate and multivariate models. We found that the multivariate models resulted in higher prediction accuracies for grain yield than the univariate models. Stepwise regression performed equal to, or better than, other models in predicting grain yield. When incorporating all secondary traits into the models, we obtained high prediction accuracies (0.58–0.68) across the five growing seasons. Our results show that the optimized phenotypic prediction models can leverage secondary traits to deliver accurate predictions of wheat grain yield, allowing breeding programs to make more robust and rapid selections.

opencc-by-4.0Sep 2021View details →

Data from: Effects of artificial light at night on the leaf functional traits of freshwater plants

Leaf traits measured on three species of submerged aquatic plants (Myriophyllum verticillatum L., Potamogeton coloratus Hornem., and Vallisneria spiralis L.) grown under light pollution at night or in the dark. Details about the protocols and the data collection can be found in the article published in Freshwater Biology.

opencc-zeroSep 2021View details →

Data from: Traits mediate niches and co-occurrences of forest beetles in ways that differ among bioclimatic regions

Aim To investigate the role of traits in beetle community assembly and test for consistency in these effects among several bioclimatic regions. We asked (1) whether traits predicted species' responses to environmental gradients (i.e., their niches), (2) whether these same traits could predict co-occurrence patterns, and (3) how consistent were niches and the role of traits among study regions. Location Boreal forests in Norway and Finland, temperate forests in Germany. Methods We complied capture records of 468 wood-living beetle species from the three regions, along with nine morphological and ecological traits. Eight climatic and forest covariates were also collected. We used Bayesian hierarchical joint species distribution models to estimate the influence of traits and phylogeny on species' niches. We also tested for correlations between species associations and trait similarity. Finally, we compared species niches and the effects of traits among study regions. Results Traits explained some of the variability in species' niches, but their effects differed among study regions. However, substantial phylogenetic signal in species niches implies that unmeasured but phylogenetically structured traits have a stronger effect. Degree of trait similarity was correlated with species associations but depended idiosyncratically on the trait and region. Species niches were much more consistent – widespread taxa often responded similarly to an environmental gradient among regions. Main conclusions The inconsistent effects of traits among regions limits their current use in understanding beetle community assembly. Phylogenetic signal in niches, however, implies that better predictive traits can eventually be identified. Consistency of species niches among regions means niches may remain relatively stable under future climate and land use changes; this lends credibility to predictive distribution models based on future climate projections but may imply that species' scope for short-term adaptation is limited.

opencc-by-4.0Jul 2024View details →

Agronomic performance of cultivar mixtures and pure stands of 8 winter wheat varieties, obtained from mixture field trials in Switzerland from 2021 to 2023, together with associated functional traits measurements

This dataset contains agronomic performance data for 8 Swiss winter wheat cultivars, grown in pure stands and in mixtures at 3 locations in Switzerland during 3 growing seasons (2021-2023). The dataset has been used to analyse the effects of cultivar mixtures on agronomic performance and stability, which is published in <a title="Persistent link using digital object identifier" href="https://doi.org/10.1016/j.eja.2024.127504" target="_blank" rel="noreferrer noopener">https://doi.org/10.1016/j.eja.2024.127504</a>.  The dataset contains notably grain yield, protein content, thousand kernel weight, specific weight, and Zeleny sedimentation value, as well as functional traits measured at flowering for each mixture and pure stand plot.  The field trials were performed under the Swiss Extenso (low input) conditions, conducted by Agroscope and DSP.  <h3>Methods </h3>  Field trials  <div>Field trials were set up over the course of three growing seasons – 2020/2021, 2021/2022 and 2022/2023 – in three sites across the Swiss Central Plateau. The experimental sites were located in Changins (46°19′ N 6°14′ E, 455m a.s.l), Delley (46°55′ N 6°58′ E, 494m a.s.l) and Utzenstorf (47°97′ N 7°33′ E, 483m a.s.l.). </div> <div>Experimental communities consisted of pure stand plots, 2-cultivars mixtures, and one plot with the 8 cultivars mixed. We sowed every possible combination of 2-cultivar mixtures, amounting to a total of 28 2-cultivar mixtures treatments, to which we added the 8-cultivar mixture. Each community was grown in a plot of 7.1 m2 (1.5m&lowast;4.7m). We used a complete randomized block design, with 3 replicates, the plots being randomized at each site within each block. Sowing was performed with a small plot drill (Wintersteiger plotseed TC). Density of sowing was 350 viable seeds/m2. For the mixtures, seeds were mixed beforehand at a 2 × 50 % mass ratio for 2-cultivars mixtures and 8 × 12.5 % for the 8-cultivar mixture. We chose this method of mixing as this is what is commonly done by farmers in Switzerland. Plots were sowed mechanically each autumn and fertilized with ammonium nitrate at a rate of 140 N/ha in 3 applications (40 N/ha at tillering stage/BBCH 22–29; 60 N/ha at the beginning of stem elongation/BBCH 30–31; 40 N/ha at booting stage/BBCH 45–47). The trials were grown according to the Swiss Extenso scheme, i.e. without any fungicide, insecticide, and growth regulator. Weeds were regulated twice or thrice per season with the application of herbicides commonly used in Switzerland.</div> <div> </div> <div>Ear density</div> <div> </div> <div>Before harvest, we manually harvested horizontal bands of 1.5 × 0.3 square meters per plot. The location of the band was randomly chosen but we avoided plot edges (i.e. the band was located at more than 0.5 m from the lower and upper edge of each plot). We counted the heads, and obtained ear density from the head counts.</div> <div> </div> <div>Trait measurements </div> <div> </div> <div>At flowering time, we randomly sampled 6 healthy leaves per plot. We immediately wrapped this leaf in moist cotton; this was stored overnight at room temperature in open plastic bags. The following day, we removed excess surface water on the leaf and weighted it to obtain its water saturated weight. This leaf was then scanned with a flatbed scanner (Perfection V39II, Epson), oven-dried in a paper envelope at 80°C for 72 hours, and subsequently weighed again to obtain its dry weight. Leaf Dry Matter Content (LDMC) was calculated as the ratio of leaf dry mass (g) to water saturated leaf mass (g). Using the leaf scans, we measured leaf area with the image processing software ImageJ. Specific Leaf Area (SLA) was calculated as the ratio of leaf area (cm2) to leaf dry mass (g).</div> <div> </div> <div>Phenology and height </div> <div> </div> <div>For each plot, we recorded the heading date as the day of the year, in which 50 % of the ears of the plot had fully emerged from the flag leaf. Plant height was measured in each plot at BBCH 59–75, by taking the average height in centimeters from the ground to the top of five random ears, excluding awns.</div> <div> </div> Harvest and post harvest measurements At maturity, we harvested each plot with a combine harvester (Zürn 150, Schontal-Westernhausen, Switzerland). The harvested grains were dried when needed, weighed a first time, then sorted and cleaned by air and with a sieve cleaner, and subsequently weighted again. We measured hectoliter weight (test weight, HLW, kg/hl) and water content at the plot level using a Dickey-John machine (GAC 2100). Grain yield was subsequently standardized to 15 % of humidity. Protein content (% of dry matter) was measured at the site level with a near-infrared instrument (ProxiMate™, Büchi instruments). Thousand kernel weight (TKW, g) was measured at the plot level with a Marvin seed analyzer (GTA Sensorik, Neubrandenburg, Germany). Zeleny sedimentation value was measured by the laboratory of Delley Seeds and Plants.

opencc-by-4.0Dec 2018View details →

Light limitation increases multidimensional trait evenness in phytoplankton populations

This archive includes the final table used for the analyses and a readme file with some explanations. Our dataset consists of phytoplankton cell density and trait diversity estimates measured using scanning flow cytometry under different light intensity regimes.

opencc-zeroNov 2022View details →

Data from: Which traits optimize plant benefits? Meta-analysis on the effect of partner traits on the outcome of an ant-plant protective mutualism

1. Theoretical models on mutualism dynamics predict that partner traits may influence the outcome of mutualistic interactions. However, most empirical data on this issue is restricted to case studies, limiting our ability to reach a more widespread comprehension of the role of partner traits on the dynamic of mutualisms. 2. We investigated how the outcome of protective mutualisms between ants and plants bearing extrafloral nectaries (EFNs) is influenced by the traits of EFNs and ants feeding on EFNs. We used a meta-analytical approach based on 35 studies investigating the effect of ant attendance on the herbivores and reproductive performance of EFN-bearing plants. We evaluated how variation in the EFN vascularization and location on plants and the ant aggressiveness can modulate the effect of ant attendance on the plants. 3. Both plant and ant traits investigated here drove the outcome of the protective mutualism for EFN-bearing plants. Plants exclusively bearing EFNs near reproductive organs benefited more from ant attendance than plants bearing EFNs on vegetative or vegetative and reproductive organs. Ants had a higher positive impact on the reproductive performance of plants bearing non-vascularized EFNs than plants bearing vascularized EFNs, although their effects on herbivores had been similar in both plant types. Regarding the ant behavior, plants often attended by more aggressive ant species had a higher reproductive performance than plants often attended by less aggressive ones. 4. Synthesis: Our results highlight that the selective pressures and evolutionary routes in ant-plant protective mutualisms may depend on the pool of traits exhibited by partner species. Although some studies have already reported some impact of species traits on the outcome of ant-plant mutualisms, this is the first time that a generalization about the role of species traits on the net balance of ant attendance was proposed. Due to this generalization, it was possible to advance our knowledge about the evolution of facultative mutualisms by showing that the role of species traits on the mutualistic outcome can vary in intricate ways due to a particular trait combination found among partners in communities where the interactions are embedded in.

opencc-zeroNov 2022View details →

Data from: Species-specific traits mediate avian demographic responses under past climate change

Anticipating species' responses to environmental change is a pressing mission in biodiversity conservation. Despite decades of research investigating how climate change may affect population sizes, historical context is lacking and the traits which mediate demographic sensitivity to changing climate remain elusive. We use whole-genome sequence data to reconstruct the demographic histories of 263 bird species over the past million years and identify networks of interacting morphological and life-history traits associated with changes in effective population size (Ne) in response to climate warming and cooling. Our results identify direct and indirect effects of key traits representing survival, reproduction, and dispersal processes on long-term demographic responses to climate change and highlight traits most likely to influence population responses to ongoing climate warming.

opencc-zeroNov 2022View details →

Simulated pollinator decline has similar effects on seed production of female and hermaphrodite Lobelia siphilitica, but different effects on selection on floral traits

PREMISE: Pollinator decline, by reducing seed production, is predicted to strengthen natural selection on floral traits. However, the effect of pollinator decline on gender dimorphic species (such as gynodioecious species, where plants produce female or hermaphrodite flowers) may differ between the sex morphs: if pollinator decline reduces the seed production of females more than hermaphrodites, then it should also have a larger effect on selection on floral traits in females than in hermaphrodites. RESULTS: Experimentally reducing pollination decreased seed production of both females and hermaphrodites by ~21%. Reducing pollination also strengthened selection on floral traits, but this effect was not larger in females than in hermaphrodites. Instead, reducing pollination intensified selection for taller inflorescences in hermaphrodites, but did not intensify selection on any floral trait in females. CONCLUSIONS: Our results suggest that pollinator decline will not have a larger effect on either seed production or selection on floral traits of female plants. As such, any effect of pollinator decline on seed production may be similar for gender dimorphic and monomorphic species. However, the potential for floral traits of females (and thus of gender dimorphic species) to evolve in response to pollinator decline could be limited.

opencc-by-4.0Nov 2022View details →

Genomic data and common garden experiments reveal climate-driven selection on ecophysiological traits in two Mediterranean oaks

This release includes the different genomic datasets used in the article entitled "Genomic data and common garden experiments reveal climate-driven selection on ecophysiological traits in two Mediterranean oaks " by Ramírez-Valiente et al., File description: Samples.xlsx: Description of individual and population codes used in the different analyses and genomic datasets. Quercus_faginea_p12r05m05minMAF001_all_loci.str: Input file used to perform genetic clustering analyses (STRUCTURE and DAPC) for Quercus faginea including all loci. Quercus_faginea_p12r05m05minMAF001_neutral_loci.str: Input file used to perform genetic clustering analyses (STRUCTURE and DAPC) for Quercus faginea excluding outlier loci (i.e., putatively under selection) identified by either BAYESCAN or using the FDIST method in ARLEQUIN. Quercus_lusitanica_p7r05m05minMAF001_all_loci.str: Input file used to perform genetic clustering analyses (STRUCTURE and DAPC) for Quercus lusitanica including all loci. Quercus_ lusitanica_p7r05m05minMAF001_neutral_loci.str: Input file used to perform genetic clustering analyses (STRUCTURE and DAPC) for Quercus lusitanica excluding outlier loci (i.e., putatively under selection) identified by either BAYESCAN or using the FDIST method in ARLEQUIN. Quercus_faginea_p12r05m05minMAF001_BAYESCAN.txt: Input file used to perform BAYESCAN analyses for Quercus faginea. Quercus_lusitanica_p7r05m05minMAF001_BAYESCAN.txt: Input file used to perform BAYESCAN analyses for Quercus lusitanica. Quercus_faginea_p12r05m05minMAF001_ARLEQUIN.arp: Input file used to perform ARLEQUIN analyses for Quercus faginea. Quercus_lusitanica_p7r05m05minMAF001_ARLEQUIN.arp: Input file used to perform ARLEQUIN analyses for Quercus lusitanica. Quercus_faginea_p12r05m05minMAF001_all_loci.vcf: Variant call format (VCF) file for Quercus faginea including all loci. Quercus_faginea_p12r05m05minMAF001_neutral_loci.vcf: Variant call format (VCF) file for Quercus faginea excluding outlier loci (i.e., putatively under selection) identified by either BAYESCAN or using the FDIST method in ARLEQUIN. Quercus_lusitanica_p7r05m05minMAF001_all_loci.vcf: Variant call format (VCF) file for Quercus lusitanica including all loci. Quercus_ lusitanica_p7r05m05minMAF001_neutral_loci.vcf: Variant call format (VCF) file for Quercus lusitanica excluding outlier loci (i.e., putatively under selection) identified by either BAYESCAN or using the FDIST method in ARLEQUIN. Quercus_faginea_Greenhouse_DRIFTSEL.txt: Input file used to run DRIFTSEL and evaluate selection on the different studied traits for Quercus faginea under common garden greenhouse experiments. Quercus_faginea_Outdoor_DRIFTSEL.txt: Input file used to run DRIFTSEL and evaluate selection on the different studied traits for Quercus faginea under common garden outdoor experiments. Quercus_lusitanica_Greenhouse_DRIFTSEL.txt: Input file used to run DRIFTSEL and evaluate selection on the different studied traits for Quercus lusitanica under common garden greenhouse experiments.

opencc-zeroDec 2022View details →

Body size as a magic trait in two plant-feeding insect species

When gene flow accompanies speciation, recombination can decouple divergently selected loci and loci conferring reproductive isolation. This barrier to sympatric divergence disappears when assortative mating and disruptive selection involve the same "magic" trait. Although magic traits could be widespread, the relative importance of different types of magic traits to speciation remains unclear. Because body size frequently contributes to host adaptation and assortative mating in plant-feeding insects, we evaluated several magic trait predictions for this trait in a pair of sympatric Neodiprion sawfly species adapted to different pine hosts. A large morphological dataset revealed that sawfly adults from populations and species that use thicker-needled pines are consistently larger than those that use thinner-needled pines. Fitness data from recombinant backcross females revealed that egg size is under divergent selection between the preferred pines. Lastly, mating assays revealed strong size-assortative mating within and between species in three different crosses, with the strongest prezygotic isolation between populations that have the greatest interspecific size differences. Together, our data support body size as a magic trait in pine sawflies and possibly many other plant-feeding insects. Our work also demonstrates how intraspecific variation in morphology and ecology can cause geographic variation in the strength of prezygotic isolation.

opencc-by-4.0Dec 2022View details →

Optically measured mean leaf traits from a large set of taxa growing in two botanical gardens: in the French Alps and southern Finland

This dataset contains records of the optically measured mean leaf traits (adaxial flavonol & anthocyanin index and chlorophyll index, units are an optical index of leaf/epidermal relative absorbance) from a large set of plant taxa growing at alpine botanical garden at the Joseph Fourier Field Station (Université Grenoble Alps, France; 2100 m a.s.l.; 45°2' 9" N, 6°23' 59" E) and at Kumpula Botanical Garden (LUOMUS, University of Helsinki, Finland; 14 m a.s.l.; 60° 12' 7" N, 24° 57' 26" E;). Optical measurements were made during the summers of 2014 and 2015 with a leaf-clip Dualex Scientific + (Force-A, Paris-Orsay, France) and all detailed information about the methods are published in Hartikainen and Robson, doi: 10.3389/fpls.2022.1058162. This dataset also includes spectrophotometer measurements of absorbance by phenolic compounds in leaf extracts in acidified methanol (abs range 290-400 nm) and mini-PAM measurements of chlorophyll fluorescence from different subsets of taxa at alpine botanical garden. All details concerning these data are given in Hartikainen and Robson (doi: 10.3389/fpls.2022.1058162) and its Supplementary Materials. Sheet with explanation of the different variables is also included.

opencc-by-4.0Dec 2022View details →

COJO ARG variants from "Biobank-scale inference of ancestral recombination graphs enables genealogical analysis of complex traits"

These are COJO ARG variants accompanying the manuscript "Biobank-scale inference of ancestral recombination graphs enables genealogical analysis of complex traits". For more details, view the README.md file and refer to our manuscript.

opencc-zeroDec 2022View details →

Experimental addition of marine-derived nutrients affects wildflower traits in a coastal meta-ecosystem

Organismal movement can bring individuals, resources, and novel interactions across ecosystem boundaries and into recipient habitats, thereby forming meta-ecosystems. For example, Pacific salmon ecosystems receive large marine-derived nitrogen subsidies during annual spawning events, which can have a wide range of effects on aquatic and terrestrial plant species and communities. In this study, we evaluate the effects of cross-ecosystem nutrient subsidies on terrestrial plant growth and reproduction. We conducted a large-scale field experiment with four treatments: (1) addition of a pink salmon (Oncorhynchus gorbuscha) carcass, (2) addition of the drift seaweed rockweed (Fucus distichus), (3) addition of both salmon + rockweed, and (4) a control. We examined treatment effects on leaf nitrogen and fitness-associated floral traits in four common estuarine wildflower species. We found elevated leaf ∂15N in all plant species and all sampling years in treatments with salmon carcass additions but did not observe any differences in leaf percent nitrogen. We also observed larger leaf area in two species, a context-dependent increase in floral display area in two species, and a limited increase in plant seed set in response to both salmon carcass treatments. In sum, our study suggests that marine nutrients can affect terrestrial plant growth and reproduction.

opencc-by-4.0Dec 2022View details →

Changes in community-weighted trait mean, functional diversity, precipitation, temperature and surface area along an elevational gradient in Tenerife, Canary Islands

This dataset comprises community-weighted trait means and functional diversity of leaf traits, precipitation, temperature and surface area of the elevational belt recorded in roadside (disturbed) and interior (less disturbed) plots, along an elevational gradient of 2,300 m in Tenerife, Canary Islands. The leaf traits measured were specific leaf area (SLA), nitrogen, carbon, phosphorous, nitrogen to carbon ratio,  leaf dry matter content (LDMC), sodium, potassium and magnesium. The environmental variables measured are total precipitation of the growing season, mean temperature of the growing season and surface area of the elevation belt. This dataset has been used for the analysis presented in Ratier Backes et al. (in press). Mechanisms behind elevational plant species richness patterns revealed by a trait-based approach. Journal of Vegetation Science.

Fast mvSLOUCH: Model comparison for multivariate Ornstein--Uhlenbeck-based models of trait evolution on large phylogenies

These are the Supplementary Material, R scripts and numerical results accompanying Bartoszek, Fuentes Gonzalez, Mitov, Pienaar, Piwczyński, Puchałka, Spalik and Voje "Model Selection Performance in Phylogenetic Comparative Methods under multivariate Ornstein–Uhlenbeck Models of Trait Evolution". The four data files concern two datasets. Ungulates: measurements of muzzle width, unworn lower third molar crown height, unworn lower third molar crown width and feeding style and their phylogeny; Ferula: measurements of ratio of canals, periderm thickness, wing area, wing thickness, and fruit mass, and their phylogeny.

Phenotypic divergence of traits that mediate antagonistic and mutualistic interactions between island and continental populations of the tropical plant, Tribulus cistoides (Zygophyllaceae)

Premise: Island systems have long served as a model for evolutionary processes due to their unique species interactions. Many studies of the evolution of species interactions on islands have focused on endemic taxa. Fewer studies have focused on how antagonistic and mutualistic interactions shape the phenotypic divergence of widespread non-endemic species living on island populations. Methods: We used the widespread plant Tribulus cistoides (Zygophyllaceae) to test phenotypic divergence in traits that mediate antagonistic interactions with vertebrate granivores (birds) and mutualistic interactions with pollinators and how this is explained by bioclimatic variables. We used both herbarium specimens and field-collected samples to compare phenotypic divergence between continental and island populations. Results: Fruits from island populations were larger than on continents, but the presence of lower spines on mericarps was lower on islands. The presence of spines was largely explained by environmental variation among islands. Petal length was on average 9% smaller on island than continental populations, an effect that was especially accentuated on the Galápagos Islands. Conclusions: Tribulus cistoides exhibits phenotypic divergence between island and continental habitats for antagonistic traits (seed defence) and mutualistic traits (floral traits). Further, the evolution of phenotypic traits that mediate antagonistic and mutualistic interactions depended on the abiotic characteristics of specific islands. This study shows the potential of using a combination of herbarium and field samples for comparative studies on a globally distributed species to test phenotypic divergence on island habitats.

Coordination of hydraulic and morphological traits across dominant grasses in eastern Australia

1. Leaf hydraulic traits characterize plant drought tolerance and responses to climate change. Yet, plant hydraulics are biased towards northern hemisphere woody species. We collected rhizomes of several perennial grass species along a precipitation gradient in eastern Australia and grew them in an experimental garden to investigate potential tradeoffs between drought tolerance and plant morphology. 2. We measured the following leaf hydraulic traits: the leaf water potential (Ψleaf) at 50% and 88% loss of leaf hydraulic conductance (P50Kleaf and P88Kleaf), the Ψleaf at 50% loss of stomatal conductance (P50gs), leaf turgor loss point (TLP), leaf dry matter content (LDMC), leaf modulus of elasticity (ε), and the slope of the relationship between predawn and midday Ψleaf. We also measured basal area, tiller density, seed head density, root collar diameter, plant height, and aboveground biomass of each individual. 3. As expected, grass species varied widely in leaf-level drought tolerance, with loss of 88% hydraulic conductance occurring at a Ψleaf ranging from -1.52 to -4.01 MPa. However, all but one species lost leaf turgor, and most reached P50gs before this critical threshold. Taller more productive grass species tended to have drought vulnerable leaves characterized by low LDMC and less negative P88Kleaf. Species with greater tiller production experienced stomatal closure and lost turgor at more negative Ψleaf. Although our sample size was limited, we found no relationships between these species' traits and their climate of origin. 4. Overall, we identified important hydraulic and morphological tradeoffs in Australian grasses that were surprisingly similar to those observed for woody plants: (1) xylem of taller species was less drought tolerant and (2) turgor loss occurs and stomatal closure begins before significant loss of Kleaf. These data build upon a small yet growing field of grass hydraulics and may be informative of species responses to further drought intensification in Australia.

opencc-by-4.0Jan 2023View details →

Data from: Microgeographic variation in early fitness traits of Pinus sylvestris from contrasting soils

Seedling phenotypic data from two Iberian Pinus sylvestris provenances from contrasting soils (calcareous vs. siliceous) grown in a 3-year greenhouse experiment on both types of natural local substrate. Each line in the file corresponds to a different seedling. Phenotypic variables as described in the original paper published in American Journal of Botany, doi <a href="https://doi.org/10.1002/ajb2.16159">10.1002/ajb2.16159</a>

Data for: Can we ignore trait-dependent colonization and diversification in island biogeography?

The application of state-dependent speciation and extinction (SSE) models to phylogenetic trees has shown an important role for traits in diversification. However, this role remains comparatively unexplored on islands, which can include multiple independent clades resulting from different colonization events. To explore whether assuming no dependence on traits leads to bias in inference on island dynamics, we extend an island biodiversity model, DAISIE (Dynamic Assembly of Islands through Speciation, Immigration and Extinction) to include trait-dependent diversification simulations, and evaluate the robustness of the inference model which ignores this trait-dependence. Our results indicate that when the differences between colonization, extinction and speciation rates between trait states are moderate, the model shows negligible error for a variety of island diversity metrics, suggesting that island diversity dynamics can be accurately estimated without the need to explicitly model trait dependence. We conclude that for many biologically realistic scenarios with trait-dependent diversification and colonization, this simple trait-less inference model is informative and robust to trait effects on colonization, speciation and extinction. Nonetheless, our new simulation model may provide a useful tool for studying patterns of trait variation.

Data for: Combining environmental niche models, multi-grain analyses, and species traits identifies pervasive effects of land use on butterfly biodiversity across Italy

Understanding how species respond to human activities is paramount to ecology and conservation science, one outstanding question being how large-scale patterns in land use affect biodiversity. To facilitate answering this question, we propose a novel analytical framework that combines Environmental Niche Models, multi-grain analyses, and species traits. We illustrate the framework capitalizing on the most extensive dataset compiled to date for the butterflies of Italy (106,514 observations for 288 species), assessing how agriculture and urbanization have affected biodiversity of these taxa from landscape to regional scales (3–48 km grains) across the country while accounting for its steep climatic gradients. Multiple lines of evidence suggest pervasive and scale-dependent effects of land use on butterflies in Italy. While land use explained patterns in species richness primarily at grains ≤ 12 km, idiosyncratic responses in species highlighted "winners" and "losers" across human-dominated regions. Detrimental effects of agriculture and urbanization emerged from landscape (3-km grain) to regional (48-km grain) scales, disproportionally affecting small butterflies and butterflies with a short flight curve. Human activities have therefore reorganized the biogeography of Italian butterflies, filtering out species with poor dispersal capacity and narrow niche breadth not only from local assemblages but also from regional species pools. These results suggest that global conservation efforts neglecting large-scale patterns in land use risk falling short of their goals, even for taxa typically assumed to persist in small natural areas (e.g., invertebrates). Our study also confirms that consideration of spatial scales will be crucial to implementing effective conservation actions in the Post-2020 Global Biodiversity Framework. In this context, applications of the proposed analytical framework have broad potential to identify which mechanisms underlie biodiversity change at different spatial scales. Funding statement: FR is supported by the PROBAE project "Protect butterflies across Europe through climate refugia" funded by the European Commission through Horizon 2020, Marie Skłodowska-Curie Actions (MSCA) individual fellowship, reintegration panel (Grant agreement ID: 101024579). Open Access Funding provided by Universita degli Studi di Torino within the CRUI-CARE Agreement.