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opencc-zeroJul 2024View details →

Elk food habits using DNA metabarcoding for plant identification

North American elk (Cervus canadensis) inhabited portions of the Eastern United States until extirpation in the mid-1800s. From 2000 to 2008, 201 elk were reintroduced to the North Cumberland Wildlife Management Area (NCWMA), Tennessee. The stocking source was Elk Island National Park, Alberta Canada where there are two distinct genetic populations isolated from the north and south. This genetic structure has largely persisted in the population after translocation. Food habits were evaluated in the early stages of restoration, but the population has had approximately 20 years to adapt to the landscape, and current food habits are unknown. To assess diet composition using DNA metabarcoding, we collected fecal pellets of elk from 65 openings within the 79,318-ha NCWMA weekly from February to April of 2019. We targeted the ITS2 region of the nuclear ribosomal DNA to amplify vegetation sequences found in the internal portion of the elk feces. DNA metabarcoding of feces was linked to results from an accompanying elk population genetics study to investigate food habits between sexes from the two different genetic groups. The majority (80.298%) of sequences matched plants from 22 genera. The top genera (>5.000%) represented were Vaccinium (15.216%), Festuca (8.446%), Rosa (6.358%), Robinia (5.793%), and Eleagnus (5.186%). Elk heavily used woody plants before and after spring green-up (>50% of diet). However, the quantity of forbs in their diet more than doubled after emergence in the spring. The sex-genetic groups consumed similar vegetation in approximately proportionate amounts. Diversity analyses revealed a significant difference in plant genera sequence detection between males from the two genetic groups, although this finding is likely explained by limited sample size. NCWMA elk used a variety of forage in the winter and DNA metabarcoding analysis allows for a comprehensive analysis of food habits useful for monitoring how elk respond dietarily to habitat management.

Figure 11 in Ethnobotanical investigation of medicinal plants used in Lingchuan county, Shanxi, China

Figure 11. Correlation between use value and relative frequency citation.

Figure 3 in Ethnobotanical investigation of medicinal plants used in Lingchuan county, Shanxi, China

Figure 3. Dominant plant families of the study area.

Figure 2 in Ethnobotanical investigation of medicinal plants used in Lingchuan county, Shanxi, China

Figure 2. Ethnomedicinal data (interviews) and plants collection.

Figure 5 in Ethnobotanical investigation of medicinal plants used in Lingchuan county, Shanxi, China

Figure 5. Collection of plant materials by local inhabitants for medicinal purposes.

opencc-by-4.0Feb 2019View details →

Strong gene activation in plants with genome-wide specificity using a new orthogonal CRISPR/Cas9-based Programmable Transcriptional Activator.

This data set correspond to the supporting data generated in the manuscript:  Strong gene activation in plants with genome-wide specificity using a new orthogonal CRISPR/Cas9-based Programmable Transcriptional Activator.

opencc-by-4.0Feb 2017View details →

Fig. 1 in Distribution, habitat use and plant associations of Moluchia brevipennis (Saussure, 1864) (Blattodea: Ectobiidae): an endemic cockroach from Chilean Mediterranean Matorral biome

Fig. 1. Registration points and theoretical presence extension of M. brevipennis.

opencc-by-4.0Aug 2024View details →

Dataset for plant species richness estimation in a wet grassland field using UAV data features

This dataset supports the estimation of plant species richness in a wet grassland field using features extracted from UAV (Unmanned Aerial Vehicle) data. It includes field and plot shapefiles, pre-processed input data, model performance metrics, spatial predictions (RASTER files).The dataset also contains geospatial imagery in the form of input and scaled GeoTIFF images, as well as two additional CSV files: <code>date.csv</code>, which records the cutting dates relevant to the study, and <code>merged_obs.csv</code>, which consolidates all the features with canopy height information extracted from Digital Elevation Model (DEM) data with field observed plant species richness. <ul> <li> Summary: <ul> <li>BIomass_Samples_Shapefiles: Contains shapefiles for field and plot-level data.</li> <li>Results: <ul> <li>ALLDATA: Pre-processed input data for RF and PLS models.</li> <li>MODELPERF: Performance metrics and variable importance for RF and PLS models.</li> <li>RASTER: Spatially-explicit predictions (maps) for plant species richness estimation.</li> <li>GLCM: Pre-processed Gray Level Co-occurrence Matrix (texture features).</li> <li>VI: Pre-processed Vegetation Indices.</li> </ul> </li> <li>TIF: Input and scaled geotiff images. <ul> <li>rescaled: Rescaled geotiff images.</li> <li>resampled: Resampled geotiff images.</li> </ul> </li> <li>date.csv: Contains cutting dates for the field.</li> <li>merged_obs.csv: Contains DEM and species richness data (number of species).</li> </ul> </li> </ul> This work was supported by the German Federal Ministry of Education and Research (BMBF) through the Digital Agriculture Knowledge and Information System (DAKIS) Project [Grant number 031B0729E].

opencc-by-4.0Jun 2024View details →

Additional files for Horvath et al., 2024. Detection and classification of long terminal repeat sequences in plant LTR-retrotransposons and their analysis using explainable machine learning.

Additional data for Horvath et al., 2024 (source code freeze, models, data, supplementary figures, tables and files(.

opencc-by-4.0Apr 2024View details →

Data and R code used in Hennecke et al. "Plant species richness and the root economics space drive soil fungal communities"

To investigate how plant diversity and root traits relate to soil fungal communities, in 2021 we collected trait data from plots in the Jena Experiment (https://the-jena-experiment.de; funded by the DFG FOR 5000) and characterized fungal communities by sequencing, respiration and lipid fatty acid quantification.

opencc-by-4.0Feb 2021View details →

Fig. 3 in Phylogenomics of the tropical plant family Ochnaceae using targeted enrichment of nuclear genes and 250+ taxa

Fig. 3. Continues. For caption, see next part.

opencc-by-4.0Nov 2024View details →

Computed tomography (CT) was used to study the interaction of NMs with the plant cell tissue in vivo using Zeiss Xradia 510 system on Arabidopsis thaliana leaf. T

This work was supported by the National Research Facility for Lab X-ray CT (NXCT) at the µ-VIS X-ray Imaging Centre, University of Southampton, through EPSRC grant EP/T02593X.

opencc-zeroDec 2017View details →

Data from: Genome-wide search for quantitative trait loci controlling important plant and flower traits in petunia using an interspecific recombinant inbred population of Petunia axillaris and Petunia exserta

A major bottleneck in plant breeding has been the much limited genetic base and much reduced genetic diversity in domesticated, cultivated germplasm. Identification and utilization of favorable gene loci or alleles from wild or progenitor species can serve as an effective approach to increasing genetic diversity and breaking this bottleneck in plant breeding. This study was conducted to identify quantitative trait loci (QTL) in wild or progenitor petunia species that can be used to improve important horticultural traits in garden petunia. An F7 recombinant inbred population derived between Petunia axillaris and P. exserta was phenotyped for plant height, plant spread, plant size, flower counts, flower diameter, flower length, and days to anthesis, in Florida in two consecutive years. Transgressive segregation was observed for all seven traits in both years. The broad-sense heritability estimates for the traits ranged from 0.20 (days to anthesis) to 0.62 (flower length). A genome-wide genetic linkage map consisting 368 single nucleotide polymorphism bins and extending over 277 cM was searched to identify QTL for these traits. Nineteen QTL were identified and localized to five linkage groups. Eleven of the loci were identified consistently in both years; several loci explained up to 34.0% and 24.1% of the phenotypic variance for flower length and flower diameter, respectively. Multiple loci controlling different traits are co-localized in four intervals in four linkage groups. These intervals contain desirable alleles that can be introgressed into commercial petunia germplasm to expand the genetic base and improve plant performance and flower characteristics in petunia.

opencc-zeroJul 2021View details →

Data from: Trophic level and basal resource use of soil animals are hardly affected by local plant associations in abandoned arable land

Stable isotope composition of plants and soil animals in abandoned arable land Dataset provides raw data on stable isotope composition of C and N of plants and soil meso- and macrofauna. Dominating animal groups were collected in arable fallow systems 3 and 14-16 years after abandonment. Animals were sampled from the rhizosphere of three plant species of different functional groups: a legume (Medicaco sativa), a non-legume herb (Taraxacum officinale) and a grass (Bromus sterilis). More information can be found in the associated paper.

opencc-by-4.0Jul 2021View details →

Dataset for: Using plant traits to understand the contribution of biodiversity effects to annual crop community productivity

Dataset for: Using plant traits to understand the contribution of biodiversity effects to annual crop community productivity

opencc-by-4.0Jul 2021View details →

Wild Plants Used as Vegetables by Transhumant People Around the Georgia–Turkey Border in the Western Lesser Caucasus

Recent ethnobotanical studies in the Caucasus, mainly in Georgia, reveal the significant ethnobotanical knowledge of local people related to wild edible plants. However, few studies have been conducted in the Lesser Caucasus, West Georgia, and the Turkish Caucasus. is study aims to represent and evaluate the cultural importance of wild vegetable plants and their patterns of use along the Georgia–Turkey border. During the transhumance period in the summers of 2017 and 2018, 104 participants (65 in Turkey and 39 in Georgia) were interviewed using a semistructured questionnaire. e Cultural Importance Index and Relative Frequency of Citation were used to compare the relative importance of species in each region. e use of 83 wild plant species from 23 plant families as vegetables was documented, with 45 species recorded in Georgia and 72 species in Turkey. One-third of the recorded wild plant species and 52 use instances out of 122 species-use combinations were shared on both sides of the border. Women and men had mentioned almost the same number of species, and there was a nonsignificant correlation between plant knowledge and age. Although there were no significant differences in the plant parts used, the way people used plants as vegetables varied significantly across the border. Considering the floral similarity across the border, the number of species used in common and shared vegetable plant knowledge was quite low. ere is not a significant difference between the two countries in terms of the most frequently cited and culturally important species (Rumex, Urtica, and Polygonum spp.). However, the recognition of some of the most important shared species (Heracleum, Chaerophyllum, Arctium, and Campanula spp.) diverged significantly in different administrative regions.

opencc-zeroAug 2021View details →

Beyond species richness and community composition: Using plant functional diversity to measure restoration success in jarrah forest

Aim: The importance of restoring ecosystem functions to native systems that have been degraded, damaged or destroyed is increasingly recognised. Yet few studies have measured the effect of restoration efforts on ecosystem functioning or the functional diversity (FD) that underpins it. Here we assessed change in FD of restored assemblages one to 25 years after the onset of post-mine restoration. Location: Northern Jarrah (Eucalyptus marginata Donn ex Sm.) Forest bioregion of south-western Australia. Methods: Functional richness, evenness, divergence and dispersion were derived from five plant functional traits relevant to community reassembly. Effects of three explanatory variables (i.e., age, year restoration was initiated, and time since fire) on six response variables (i.e., four FD indices, species richness, and compositional similarity to nearby reference forest) were analysed using linear mixed models for a dataset with repeated measures of plots through time (n= 810 plots), and linear models for a sub-set of one-time measures of different aged assemblages (i.e., space-for-time approach; n= 490 plots). Results: Functional evenness and functional dispersion increased with age, while functional divergence and functional richness decreased with age. Functional dispersion increased with time since fire, while functional richness decreased with time since fire. Species richness decreased with age, but at 25-years, species richness was comparable to that observed in reference forest. In contrast, similarity showed no relationship with age of restored forest, and at 25-years, similarity of restored forest to reference was low compared with similarity of reference forest to itself. Three of four FD indices had not reached those of reference jarrah forest 25-years after restoration had been initiated. Conclusions: Reassembly of FD suggests importance of environmental filtering and high functional redundancy. A longer time frame may be needed to assess FD of restored assemblages, and in the meantime, species richness is not an adequate surrogate of FD.

opencc-zeroJul 2022View details →

Projected impacts of climate and land use changes on the habitat of Atlantic Forest plants in Brazil

Aim: To provide novel evidence on the average impact of climate and land use changes on habitat suitability for tropical plants and to test previous conclusions on the relative importance of these two drivers in shaping future availability of habitat for tropical plant species. Location: Brazil's Atlantic Forest domain. Time period: Plant occurrences recorded between 1960 and 2014. Baseline climate from 1960-2000 and land use from 2015. Projected scenarios of climate for 2041-2060 and land use for 2050. Major taxa studied: Angiosperms. Results: Our results suggest that climate change alone will, surprisingly, have only a modest negative impact on the mean habitat suitability, decreasing it by 2% (median = -5% to -7%, variation associated with scenarios). Land use change alone had a more consistent negative impact on habitat suitability, causing mean and median reductions of 4% to 6%. When the effects of climate and land use are combined, the mean habitat suitability was reduced by 4% (median = -9% to -11%). Main conclusions: The combined impacts of climate and land use changes were substantial, although smaller than expected. Habitat suitability decreased for most species, but it increased substantially for some species, suggesting that the distribution of impacts across species is markedly right skewed. The impacts were typically detrimental to small-ranged species and neutral or beneficial to widespread species. Land use change rather than climate change will likely cause more losses to the habitat of Atlantic Forest plant species within the next several decades.

opencc-zeroSep 2021View details →

An interpolated biogeographic framework for tropical Africa using plant species distributions and the physical environment

Aim: Existing phytogeographic frameworks for tropical Africa lack either spatial completeness, unit definitions smaller than the regional scale, or a quantitative approach. We investigate whether physical environmental variables can be used to interpolate floristically defined vegetation units, presenting an interpolated, hierarchical, quantitative phytogeographic framework for tropical Africa, which is compared to previously defined regions. Location: Tropical mainland Africa 24°N to 24°S. Taxon: 31,046 vascular plant species and infraspecific taxa. Methods: We calculate a betasim dissimilarity matrix from a comprehensive whole-flora database of plant species distributions. We investigate environmental correlates of floristic turnover with local non-metric multidimensional scaling. We derive a hierarchical biogeographic framework by clustering the dissimilarity matrix. The framework is modelled using a classification decision tree method and 12 physical environmental variables to interpolate and downscale the framework across the study region. Results: Floristic turnover is related strongly to water availability and temperature, with smaller contributions from land cover, topographic ruggedness and lithology. Region can be predicted with 90% accuracy by the model. We define 19 regions and 99 districts. We find a novel arrangement of the arid regions. Regional subdivision within the savanna biome is supported with minor variation to borders. Within the forests of west and central Africa, our whole-flora gridded regionalisation supports the divisions identified by a previous analysis of trees only. Main conclusions: Physical environmental variables can be used to predict floristically defined vegetation units with very high accuracy, and the approach could be pursued for other inc ompletely sampled taxa and areas outside of tropical Africa. Geographic coherence is higher than in previous quantitative phytoregional definitions. For most tropical African vascular plant species, we provide predictions of which species will occur within each mapped district and region of tropical Africa. The framework should be useful for future studies in ecology, evolution and conservation.