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opencc-by-4.0Sep 2022View details →

Determination of traits responding to iron toxicity stress at different stages and genome-wide association analysis for iron toxicity tolerance in rice (Oryza sativa L.)

This vcf file constitute underlying raw data material for the manuscript "Determination of traits responding to iron toxicity stress at different stages and genome-wide association analysis for iron toxicity tolerance in rice (Oryza sativa L.)".  The SNP genotype data came from a whole-genome resequencing and were called using the Nipponbare IRGSP 1.0 rice reference genome. SNPs with a miss rate greater than 30% and minor allele frequency (MAF) less than 5% were removed. Heterozygous alleles were also excluded. Finally, 160,498 SNPs were selected and used in the GWAS analysis.

opencc-by-4.0Sep 2022View details →

Dataset of pollinator functional traits and interaction networks in neotropical mangroves: effects of patch size and surrounding land use

This is the dataset of the manuscript entitled "Pollinator functional traits and interaction networks in neotropical mangroves: effects of patch size and surrounding land use", which was submitted for publication. The dataset include the functional traits of 162 insect pollinator species and 315 interactions with the mangrove species Avicennia germinans, Conocarpus erectus, Laguncularia racemosa, and Rhizophora mangle. The manuscript evaluates the effects of mangrove patch size and surrounding land use on pollinator functional diversity and plant-pollinator interactions in seven mangrove patches from the Colombian Caribbean region. Data variables are pollinator order, family, species, functional traits (pollinator guilds, body size, feeding preference, sociality, and nesting site) and frequency, interacting mangrove species, mangrove patch name, coordinates and size (ha), surrounding land use areas (urban areas, croplands, conserved dry forest, degraded vegetation areas, beach and water) and landscape diversity (Shannon H').

opencc-zeroSep 2022View details →

Genome-wide association implicates numerous genes underlying ecological trait variation in natural populations of Populus trichocarpa

In order to uncover the genetic basis of phenotypic trait variation, we used 448 unrelated wild accessions of black cottonwood (Populus trichocarpa) from much of its range in western North America. Extensive data from large-scale trait phenotyping (with spatial and temporal replications within a common garden) and genotyping (with a 34 K Populus single nucleotide polymorphism (SNP) array) of all accessions were used for gene discovery in a genome-wide association study (GWAS). We performed GWAS with 40 biomass, ecophysiology and phenology traits and 29 355 filtered SNPs representing 3518 genes. The association analyses were carried out using a Unified Mixed Model accounting for population structure effects among accessions. We uncovered 410 significant SNPs using a Bonferroni-corrected threshold (P < 1.7 × 10−6). Markers were found across 19 chromosomes, explained 1–13% of trait variation, and implicated 275 unique genes in trait associations. Phenology had the largest number of associated genes (240 genes), followed by biomass (53 genes) and ecophysiology traits (25 genes). The GWAS results propose numerous loci for further investigation. Many traits had significant associations with multiple genes, underscoring their genetic complexity. Genes were also identified with multiple trait associations within and/or across trait categories. In some cases, traits were genetically correlated while in others they were not.

opencc-zeroSep 2022View details →

Genome-wide association implicates numerous genes underlying ecological trait variation in natural populations of Populus trichocarpa

opencc-zeroOct 2022View details →

Multilevel selection on social network traits differs between sexes in experimental populations of forked fungus beetles

Both individual and group behavior can influence individual fitness, but multilevel selection is rarely quantified on social behaviors. Social networks provide a unique opportunity to study multilevel selection on social behaviors, as they describe complex social traits and patterns of interaction at both the individual and group levels. In this study, we used contextual analysis to measure the consequences of both individual network position and group network structure on individual fitness in experimental populations of forked fungus beetles (Bolitotherus cornutus) with two different resource distributions. We found that males with high individual connectivity (strength) and centrality (betweenness) had higher mating success. However, group network structure did not influence their mating success. Conversely, we found that individual network position had no effect on female reproductive success but that females in populations with many social interactions experienced lower reproductive success. The strength of individual-level selection in males and group-level selection in females intensified when resources were clumped together, showing that habitat structure influences multilevel selection. Individual and emergent group social behavior both influence variation in components of individual fitness but impact male mating success and female reproductive success differently, setting up intersexual conflicts over patterns of social interactions at multiple levels.

opencc-zeroOct 2022View details →

Data from: Local adaptation in shell shape traits of a brooding chiton with strong population genomic differentiation

Comparing divergence in quantitative traits and neutral molecular markers, such as QST–FST comparisons, provides a means to distinguish between natural selection and genetic drift as causes of population differentiation in complex polygenic traits. Onithochiton neglectus (Rochebrune, 1881) is a morphologically variable chiton endemic to New Zealand, with populations distributed over a broad latitudinal environmental gradient. In this species, the morphological variants cluster into two geographically separated shell shape groups, and the phenotypic variation in shell shape has been hypothesised to be adaptive. Here, we assessed this hypothesis by comparing neutral genomic differentiation between populations (FST) with an index of phenotypic differentiation (PST). We used 7,562 putatively neutral single nucleotide polymorphisms (SNPs) across 15 populations and three clades of O. neglectus throughout New Zealand to infer FST. PST was calculated from 18 shell shape traits and gave highly variable estimates across populations, clades and shape groups. By systematically comparing PST with FST, we identified evidence of local adaptation in a number of the O. neglectus shell shape traits. This supports the hypothesis that shell shape could be an adaptive trait, potentially correlated with the ability to live and raft in kelp holdfasts.

opencc-by-4.0Jun 2021View details →

Data used in the paper: Historical and current environmental selection on functional traits of trees in the Atlantic Forest biodiversity hotspot

This repository contains phylogenetic and functional trait data, raster files, and tables with sampling information and references used in the article "Historical and current environmental selection on functional traits of trees in the Atlantic Forest biodiversity hotspot" by Silva, J.L.A., Souza, A., and Vitória, A.P. Journal of Vegetation Science, <a href="https://doi.org/10.1111/jvs.13049">https://doi.org/10.1111/jvs.13049</a> . Description of files: (1) "Species-level_Trait_Data_Silva_et_al._2021.csv": This file contains species-specific mean trait values and the plant growth form of the 2,122 studied species, whenever available. Trait values were compiled from public sources such as original papers, master and doctoral dissertations, and global trait databases. (2) "Phylogenetic_Tree_Silva_et_al._2021.txt": This file contains the phylogenetic tree of the 2,122 studied species. (3) "CWM_Trait_Maps.zip": This file contains seven rasters of spatially contiguous surfaces produced by Ordinary Kriging Interpolation using Community-Weighted Means (CWM) of each functional trait. (4) "References-abundance-data.csv": This file contains sampling details and the references used to compile species abundance data for each studied site. (5) "References-trait-data.csv": This file contains sampling details and the references used to compile functional trait data.

opencc-by-4.0Apr 2024View details →

Assessment of microphytobenthos communities in the Kinzig catchment using photosynthesis-related traits, digital light microscopy and 18S-V9 amplicon sequencing

This folder contains the datasets used in the article submitted to Frontiers in Ecology and Evolution in which we investigated the functional and compositional responses of microphytobenthos communities to surrounding land uses in the Kinzig River catchment, central Germany. We measured photosynthetic biomass using a Benthotorch, and analysed the diatom community using a newly developed digital light microscopy approach and 18S-V9 amplicon sequencing to characterise the whole protistan assemblages at sampling sites located in rural vs. urban areas. The folder contain the following datasets: kinzig2021_18SV9_filtered.csv  # microphytobenthos 18SV9 amplicon sequencing data kinzig_paper.csv # OMNIDIA output of diatom data from microscopy and diatom subset from 18SV9 amplicon sequencing (including 4 letters OMINIDIA taxa codes for diatoms) kinzig2021_benthotorch.csv # Photosynthetic biomass (BenthoTorch data) Kinzig2021_fieldData.csv # environmental data env_dataKinz2021.csv # environment dataset Kinzig2021_diatDM&18S.R # Rscript used for analysis

FIGURE 4 in Taxon-specific variability of leaf traits in three long-ranging fossil-species of the Paleogene and Neogene: Responses to climate?

FIGURE 4. Site-specific data for lamina length and lamina width plotted for each taxon. 4A: Lamina length for Platanus neptuni. 4B: Lamina width for P. neptuni. 4C: Lamina length for Eotrigonobalanus furcinervis. 4D: Lamina width for E. furcinervis. 4E: Lamina length for Daphnogene cinnamomifolia. 4F: Lamina width for D. cinnamomifolia. The boxes span the 50% interquartile. The horizontal lines within the boxes indicate the median values. The "whiskers" mark the highest and lowest values. Outliers located at a distance of up to 1.5 times the quartile span outside the whiskers are drawn as asterisks, and extreme outliers are drawn as circles. Different minuscule letters indicate statistically significant differences among sites. Colors indicate deposit type. Colors indicate deposit type. Green: fluviatile. Red: volcanic. Blue: marine. Lines delimit age groups. LE: Late Eocene. EO: Early Oligocene. LO: Late Oligocene. EM: Early Miocene. For site numbers and dating see Table 1.

FIGURE 1 in Taxon-specific variability of leaf traits in three long-ranging fossil-species of the Paleogene and Neogene: Responses to climate?

FIGURE 1. Map showing the locations of the considered sites, which are numbered according to Table 1.

FIGURE 3 in Taxon-specific variability of leaf traits in three long-ranging fossil-species of the Paleogene and Neogene: Responses to climate?

FIGURE 3. Site-specific data for lamina area and lamina perimeter plotted for each taxon. 3A: Lamina area for Platanus neptuni. 3B: Lamina perimeter for P. neptuni. 3C: Lamina area for Eotrigonobalanus furcinervis. 3D: Lamina perimeter for E. furcinervis. 3E: Lamina area for Daphnogene cinnamomifolia. 3F: Lamina perimeter for D. cinnamomifolia. The boxes span the 50% interquartile. The horizontal lines within the boxes indicate the median values. The "whiskers" mark the highest and lowest values. Outliers located at a distance of up to 1.5 times the quartile span outside the whiskers are drawn as asterisks, and extreme outliers are drawn as circles. Different minuscule letters indicate statistically significant differences among sites. Colors indicate deposit type. Green: fluviatile. Red: volcanic. Blue: marine. Lines delimit age groups. LE: Late Eocene. EO: Early Oligocene. LO: Late Oligocene. EM: Early Miocene. For site numbers and dating see Table 1.

FIGURE 6 in Taxon-specific variability of leaf traits in three long-ranging fossil-species of the Paleogene and Neogene: Responses to climate?

FIGURE 6. Site-specific data for lamina centroid and leaf length-to-width ratio (LWR) plotted for each taxon. 6A: Lamina centroid for Platanus neptuni. 6B: LWR for P. neptuni. 6C: Lamina centroid for Eotrigonobalanus furcinervis. 6D: LWR for E. furcinervis. 6E: Lamina centroid for Daphnogene cinnamomifolia. 6F: LWR for D. cinnamomifolia. The boxes span the 50% interquartile. The horizontal lines within the boxes indicate the median values. The "whiskers" mark the highest and lowest values. Outliers located at a distance of up to 1.5 times the quartile span outside the whiskers are drawn as asterisks, and extreme outliers are drawn as circles. Different minuscule letters indicate statistically significant differences among sites. Colors indicate deposit type. Colors indicate deposit type. Green: fluviatile. Red: volcanic. Blue: marine. Lines delimit age groups. LE: Late Eocene. EO: Early Oligocene. LO: Late Oligocene. EM: Early Miocene. For site numbers and dating see Table 1.

FIGURE 2 in Taxon-specific variability of leaf traits in three long-ranging fossil-species of the Paleogene and Neogene: Responses to climate?

FIGURE 2. Plasticity index (PI) of various leaf traits, for the considered sites and taxa. 2A: PI for lamina area. 2B: PI for lamina length. 2C: PI for lamina perimeter. 2D: PI for lamina width. 2E: PI for lamina circularity. 2F: PI for lamina centroid. Squares: Platanus neptuni. Circles: Daphnogene cinnamomifolia. Triangles: Eotrigonobalanus furcinervis. Colors indicate deposit type. Green: fluviatile. Red: volcanic. Blue: marine. Lines delimit age groups. LE: Late Eocene. EO: Early Oligocene. LO: Late Oligocene. EM: Early Miocene. For site numbers and dating see Table 1.

FIGURE 5 in Taxon-specific variability of leaf traits in three long-ranging fossil-species of the Paleogene and Neogene: Responses to climate?

FIGURE 5. Site-specific data for lamina circularity and lamina roundness plotted for each taxon. 5A: Lamina circularity for Platanus neptuni. 5B: Lamina roundness for P. neptuni. 5C: Lamina circularity for Eotrigonobalanus furcinervis. 5D: Lamina roundness for E. furcinervis. 5E: Lamina circularity for Daphnogene cinnamomifolia. 5F: Lamina roundness for D. cinnamomifolia. The boxes span the 50% interquartile. The horizontal lines within the boxes indicate the median values. The "whiskers" mark the highest and lowest values. Outliers located at a distance of up to 1.5 times the quartile span outside the whiskers are drawn as asterisks, and extreme outliers are drawn as circles. Different minuscule letters indicate statistically significant differences among sites. Colors indicate deposit type. Colors indicate deposit type. Green: fluviatile. Red: volcanic. Blue: marine. Lines delimit age groups. LE: Late Eocene. EO: Early Oligocene. LO: Late Oligocene. EM: Early Miocene. For site numbers and dating see Table 1.

FIGURE 7. Age-specific discriminant analysis using all morphometric parameters for all sites. 7A in Taxon-specific variability of leaf traits in three long-ranging fossil-species of the Paleogene and Neogene: Responses to climate?

FIGURE 7. Age-specific discriminant analysis using all morphometric parameters for all sites. 7A: Eocene. 7B: Oligocene. Triangles: Platanus neptuni. Squares: Eotrigonobalanus furcinervis. Circles: Daphnogene cinnamomifolia.

FIGURE 8 in Taxon-specific variability of leaf traits in three long-ranging fossil-species of the Paleogene and Neogene: Responses to climate?

FIGURE 8. Circularity plotted against LWR. Blue circles: Platanus neptuni. Red squares: Eotrigonobalanus furcinervis. Yellow diamonds: Daphnogene cinnamomifolia. Black line: Relationship between circularity and length-towidth ratio of an ellipse. Please note that this relationship was calculated by using an approximate equation for the perimeter of an ellipse, which causes the slight deflection of the curve for high circularity values. As approximation, the following equation for the ellipse perimeter (EP) was used: EP = π* [2 * (a2 + b2)1/2].

opencc-by-4.0Apr 2024View details →

Group-level trait and individual performance: the impact of in-nest activity on food recruitment in ants

Dataset, R and Python scripts corresponding to the results displayed in the article "Group-level trait and individual performance: the impact of in-nest activity on food recruitment in ants". R script works in pair with all three .csv files. .txt files are example of output generated by the Python script that analyses a worker's path inside the nest. 3 videos from the experiment are also available. They allow visualization of the setup as well as testing of Python scripts.

opencc-zeroApr 2024View details →

Data from: defining the pyro-thermal niche: do seed traits, ecosystem type and phylogeny influence thermal thresholds in seeds with physical dormancy

Seeds are a key pathway for plant population recovery following disturbance. To prevent germination during unsuitable conditions, most species produce dormant seeds. In fire-prone regions, physical dormancy (PY) enables seeds to germinate after fire. The thermal niche, incorporating seed dormancy and mortality temperature responses, has not been characterised for PY seeds from fire prone environments. We aimed to assess variation in thermal thresholds between species with PY seeds and if the pyro-thermal niche is aligned with seed mass, ecosystem type or phylogenetic relatedness. We collected post heat-shock germination data for 58 Australian species that produce PY seeds. We applied species-specific thermal performance curves to define three critical thresholds (DRT50, dormancy release temperature; Topt, optimum dormancy release temperature and LT50, lethal temperature), defining the pyro-thermal niche. Each species was assigned a mean seed weight and ecosystem type. We constructed a phylogeny to account for species relatedness and calculated phylogenetic signal (h2) for LT50, Topt, and DRT50. Seeds of Pomaderris (Rhamnaceae) had the highest Topt and LT50, and Pomaderris bodalla having the highest DRT50 of 101.3°C. Seeds from species within this family exhibited higher temperature thresholds than those from Fabaceae. Seed mass was only influential in explaining LT50 variation.

opencc-zeroApr 2024View details →

Spectral and trait data for Rapid estimates of leaf litter chemistry using reflectance spectroscopy

Measuring the chemical traits of leaf litter is important for understanding plants' roles in nutrient cycles, including through nutrient resorption and litter decomposition, but conventional leaf trait measurements are often destructive and labor-intensive. Here, we develop and evaluate the performance of partial least-squares regression (PLSR) models that use reflectance spectra of intact or ground leaves to estimate leaf litter traits, including carbon and nitrogen concentration, carbon fractions, and leaf mass per area (LMA). Our analyses included more than 300 samples of senesced foliage from 11 species of temperate trees, including needleleaf and broadleaf species. Across all samples, we could predict each trait with moderate-to-high accuracy from both intact-leaf litter spectra (validation R2 = 0.543-0.941; %RMSE = 7.49-18.5) and ground-leaf litter spectra (validation R2 = 0.491-0.946; %RMSE = 7.00-19.5). Notably, intact-leaf spectra yielded better predictions of LMA. Our results support the feasibility of building models to estimate multiple chemical traits from leaf litter of a range of species. In particular, the success of intact-leaf spectral models allows non-destructive trait estimation in a matter of seconds, which could enable researchers to measure the same leaves over time in studies of nutrient resorption.