Find research datasets worth reusing

Fig. 25. I–IV in Review of the fritillary species systematically close to Melitaea lutko Evans, 1932 (Lepidoptera: Nymphalidae) with analysis of their geographic distribution and interrelations with host plants

Fig. 25. I–IV instar caterpillars of Melitaea shahvarica sp. nov. (a = view from above; b = lateral view). A. First instar caterpillar after hatching. B. First instar caterpillar before molting. C. Second instar caterpillar. D. Third instar caterpillar. E. Fourth instar caterpillar.

Fig. 26. V–VI in Review of the fritillary species systematically close to Melitaea lutko Evans, 1932 (Lepidoptera: Nymphalidae) with analysis of their geographic distribution and interrelations with host plants

Fig. 26. V–VI instar caterpillars of Melitaea shahvarica sp. nov. (a = view from above; b = lateral view). A. Fifth instar caterpillar. B. Sixth instar caterpillar. C. Sixth instar caterpillar, head capsule, front view. D. Sixth instar caterpillar, head capsule, lateral view.

Fig. 20 in Review of the fritillary species systematically close to Melitaea lutko Evans, 1932 (Lepidoptera: Nymphalidae) with analysis of their geographic distribution and interrelations with host plants

Fig. 20. Eggs of Melitaea timandra binaludica subsp. nov., Iran, Kuh-e-Binalud Mts. A–C. Lateral view. D–F. View from above. G–I. Micropile area.

Fig. 19. Male genitalia and harpe. A–C in Review of the fritillary species systematically close to Melitaea lutko Evans, 1932 (Lepidoptera: Nymphalidae) with analysis of their geographic distribution and interrelations with host plants

Fig. 19. Male genitalia and harpe. A–C. Melitaea timandra timandra Coutsis & van Oorschot, 2014. D–I. M. timandra binaludica subsp. nov. A–C. Turkmenistan, Sary-Yazy, alt. 300 m. D–F. Iran, Rezavi Khorassan Prov., Kuh-e-Binalud Mts, Dorrud v. vicinity, alt. 2430 m. G. Afghanistan, Bamian Prov., Band-e-Amir, alt. 3200 m. H. Afghanistan, Bamian Prov., Band-e-Amir, Dzhudoi-Kvak Gorge, alt. 3200 m. I. Afghanistan, Band-e-Amir, Hazarajat.

data for "Plant genetic effects on microbial hubs impact host fitness in repeated field trials"

These are data tables required for the analysis of the paper "Plant genetic effects on microbial hubs impact host fitness in repeated field trials".  All scripts are available at https://forgemia.inra.fr/bbrachi/microbiota_paper.git The folder architecture in the zip files is the same as in the repository: https://forgemia.inra.fr/bbrachi/microbiota_paper.git The dataset includes:  - OTU count tables for 16S and ITS - taxonomic assignation - plant seed-set estimates - plant growth data from the B38 experiment.  - Metabolomics datasets

Data from: Ruderals naturalize, competitors invade: varying roles of plant adaptive strategies along the invasion continuum

1. It is increasingly recognized that the factors facilitating plant invasions depend on the stage along the introduction-naturalization-invasion continuum. Adaptative strategies, i.e., combinations of functional traits that represent overall fitness in the face of one or more selection pressures, have shown promise in explaining plant invasions. However, whether adaptive strategy patterns change with the stages of plant invasion is not yet known. 2. Using the Pladias Database of the Czech Flora and Vegetation, we explored how Grime's adaptive strategies (competitors, stress-tolerators, ruderals; CSR) and introduction pathways (deliberate vs. accidental) relate to plant invasion along the introduction-naturalization-invasion continuum. 3. Phylogenetically corrected ANOVAs showed that naturalized species (referring to non-invasive naturalized species in this study) were mostly R-selected, whereas invasive species tended to be C-selected. The results of phylogenetic regression analysis further confirmed that across the deliberately and accidentally introduced species, R- and C-selection were positively related to naturalization and invasion success, respectively. We also found that deliberate introduction was negatively related to naturalization success and grid-cell occupancy of naturalized species, likely due to the different CSR strategies possessed by deliberately and accidentally introduced aliens. 4. Our study provides empirical evidence that different adaptive strategies are associated with species that have reached different invasion stages and confirms the usefulness of the CSR strategy framework for understanding plant invasion. It has implications for predicting and preventing potential high-impact invaders. For example, our results show that naturalized C-selected species have a higher probability of becoming invasive than naturalized R-selected species. Therefore, management actions are essential to prevent further introductions and spread of competitors.

Long-term experimental drought alters floral scent and pollinator visits in a Mediterranean plant community despite overall limited impacts on plant phenotype and reproduction

Pollinators are declining globally, with climate change implicated as an important driver. Climate change can induce phenological shifts and reduce floral resources for pollinators, but little is known about its effects on floral attractiveness and how this might cascade to affect pollinators, pollination functions and plant fitness. We used an in situ long-term drought experiment to investigate multiple impacts of reduced precipitation in a natural Mediterranean shrubland, a habitat where climate change is predicted to increase the frequency and intensity of droughts. Focusing on three insect-pollinated plant species that provide abundant rewards and support a diversity of pollinators (Cistus albidus, Salvia rosmarinus and Thymus vulgaris), we investigated the effects of drought on a suite of floral traits including nectar production and floral scent. We also measured the impact of reduced rainfall on pollinator visits, fruit set and germination in S. rosmarinus and C. albidus. Drought altered floral emissions of all three plant species qualitatively, and reduced nectar production in T. vulgaris only. Apis mellifera and Bombus gr. terrestris visited more flowers in control plots than drought plots, while small wild bees visited more flowers in drought plots than control plots. Pollinator species richness did not differ significantly between treatments. Fruit set and seed set in S. rosmarinus and C. albidus did not differ significantly between control and drought plots, but seeds from drought plots had slower germination for S. rosmarinus and marginally lower germination success in C. albidus. Synthesis. Overall, we found limited but consistent impacts of a moderate experimental drought on floral phenotype, plant reproduction and pollinator visits. Increased aridity under climate change is predicted to be stronger than the level assessed in the present study. Drought impacts will likely be stronger and this could profoundly affect the structure and functioning of plant-pollinator networks in Mediterranean ecosystems.

opencc-by-4.0Mar 2022View details →

Data for: "Dynamic species distribution modeling reveals the pivotal role of human-mediated long-distance dispersal in plant invasion"

All the data needed to reproduce the results and Figures of our article: Botella, C., Bonnet, P., Hui, C., Joly, A., & Richardson, D. M. (2022). Dynamic Species Distribution Modeling Reveals the Pivotal Role of Human-Mediated Long-Distance Dispersal in Plant Invasion. Biology, 11(9), 1293. <a href="https://doi.org/10.3390/biology11091293">https://doi.org/10.3390/biology11091293</a> Please, find the R scripts and guidelines to reproduce our results on the article's Github repository : <a href="https://github.com/ChrisBotella/plectranthus_barbatus/tree/main">https://github.com/ChrisBotella/plectranthus_barbatus/tree/main</a>

Plant‐eating carnivores: Multispecies analysis on factors influencing the frequency of plant occurrence in obligate carnivores

Plant-eating behavior is one of the greatest mysteries in obligate carnivores. Despite unsuitable morphological and physiological traits for plant consumption, the presence of plants in scat or stomach contents has been reported in various carnivorous species. However, researchers' interpretations of this subject are varied, and knowledge about it is scarce, without any multispecies studies. This study assessed the extent of variation in the frequency of plant occurrence in scat and stomach contents, as well as its relationship with various factors in 24 felid species using data from 213 published articles. Since the frequency of plant occurrence has not always been reported, we created two-part models and estimated parameters in a Bayesian framework. We found a significant negative relationship between the frequency of plant occurrence and body mass. This may be because plant-eating behavior reduces the energy loss caused by parasites and increases the efficiency of energy intake, which has a greater importance in smaller animals that have relatively high metabolic rates. This exploratory study highlights the importance of considering plant consumption in dietary studies on carnivorous species to understand the adaptive significance of this behavior and the relationship between obligate carnivores and plants.

Nectar values from: Quantifying nectar production by flowering plants in urban and rural landscapes

Floral resources (nectar and pollen) provide food for insect pollinators but have declined in the countryside due to land use change. Given widespread pollinator loss, it is important that we quantify their food supply to help develop conservation actions. While nectar resources have been measured in rural landscapes, equivalent data are lacking for urban areas, an important knowledge gap as towns and cities often host diverse pollinator populations. We quantified the nectar supply of urban areas, farmland and nature reserves in the UK by combining floral abundance and nectar sugar production data for 536 flowering plant taxa, allowing us to compare landscape types and assess the spatial distribution of nectar sugar among land uses within cities. The magnitude of nectar sugar production did not differ significantly among the three landscapes. In urban areas the nectar supply was more diverse in origin and predominantly delivered by non-native flowering plants. Within cities, urban land uses varied greatly in nectar sugar production. Gardens provided the most nectar sugar per unit area and 85% of all nectar at a city scale, while gardens and allotments produced the most diverse supplies of nectar sugar. Floral abundance, commonly used as a proxy for pollinators' food supply, correlated strongly with nectar resources, but left a substantial proportion of the variation in nectar supply unexplained. Synthesis. We show that urban areas are hotspots of floral resource diversity rather than quantity and their nectar supply is underpinned by the contribution of residential gardens. Individual gardeners have an important role to play in pollinator conservation as ornamental plants, usually non-native in origin, are a key source of nectar in towns and cities.

openFeb 2024View details →

Data from: Historic deforestation and non-native plant invasions determine vegetation trajectories across an oceanic archipelago

This archive contains data produced in a study of the vegetation trajectories of Ogasawara Islands in 77 years related to following article: Ohashi, H., Kato, H., Murao, M., Kato, H., Kawakami, K., Kurokawa, H., Oguro, M., Kimura, F., Niiyama, K., Matsui, T., and Shibata, M. (2024) Historic deforestation and non-native plant invasions determine vegetation trajectories across an oceanic archipelago. Applied Vegetation Science, 27 (1), e12767. <a href="https://doi.org/10.1111/avsc.12767">https://doi.org/10.1111/avsc.12767</a>   Archive contents The archive contents are organized into five parts, each stored as a .zip compressed file. X1_tif_original_vegmap_scan_georeference Scanned and georeferenced original vegetation maps in GeoTiff format, which was drawn in 1935, scanned at 300 dpi. Coordinate reference system was set at WGS84 (ESPG: 4326). This directory includes: kitanoshima_isl_WGS84.tif mukojima_isl_WGS84.tif yomejima_isl_WGS84.tif ototojima_isl_WGS84.tif anijima_isl_WGS84.tif nishijima_isl_WGS84.tif chichijima_isl_WGS84.tif hahajima_isl_WGS84.tif mukohjima_isl_WGS84.tif kitaiwoto_isl_WGS84.tif iwoto_isl_WGS84.tif   X2_shp_vegmap Shapefile of the geospatial polygon data of vegetation map of Ogasawara Islands surveyed in 1935, and stored as a .zip compressed file. Coordinate reference system was set at WGS84 (ESPG: 4326). This directory includes: VegetationMap_OgasaawraIsl_1935_en_UTF8_v0.dbf VegetationMap_OgasaawraIsl_1935_en_UTF8_v0.prj VegetationMap_OgasaawraIsl_1935_en_UTF8_v0.shp VegetationMap_OgasaawraIsl_1935_en_UTF8_v0.shx attribute_ForSect_code_en.csv attribute_Veg_name_en.csv metadata_vegmap_shp_ogasawara1935_en.csv Following files includes Japanese character (which may corrupt in non-Japanese environment): attribute_ForSect_jp.csv attribute_Veg_name_jp.csv metadata_vegmap_shp_ogasawara1935_jp.csv   X3_tif_vegmap_converted_from_shp Rasterized data of polygon data of vegetation map for analysis. Coordinate reference system was set at JGD2000 / Japan Plane Rectangular CS XIV (EPSG: 2456) This directory includes: vegmap_1935.zip (compressed “vegmap_1935.tif (0.7GB)”) vegnap_1979.zip (compressed “vegmap_1979.tif (1.5GB)”) vegmap_2011.zip (compressed “vegmap_2011.tif (1.5GB)”) islcode_raster.zip (compressed “vegmap_2011.tif (1.5GB)”) attribute_integratedveg_ecoltype.csv attribute_vegid_1935.csv attribute_vegid_1979.csv attribute_vegid_2011.csv   X4_scanned_image_vegdata Scanned images of original vegetation data in 1935. The directory includes: vegetation_survey_sheet_1.pdf vegetation_survey_sheet_2.pdf vegetation_survey_sheet_3.pdf   X5_digitized_vegdata Digitized vegetation data. The directory includes: plot_species_abundance_matrix_v0.csv plotinfo_v0.csv attribute_Species_en_v0.csv Following file includes Japanese character (which may corrupt in non-Japanese environment) attribute_Species_jp_v0.csv   X6_code_for_analysis Tentative.   このアーカイブには、小笠原諸島の77年間の植生の変遷(1935年、1979年、2012年)に関するデータが含まれています。

opencc-by-4.0Aug 2022View details →

Host developmental stages shape the evolution of a plant RNA virus

Datasets used in the generation of figures 1 and 2 of: Melero, I., González, R., Elena, S.F. 2022. Host developmental stages shape the evolution of a plant RNA Virus. Philos. Trans. R. Soc. B doi: 10.1098/rtsb.2022.0005

opencc-zeroAug 2022View details →

Alpine butterflies want to fly high: Species and communities shift upwards faster than their host plants

Despite sometimes strong co-dependencies of insect herbivores and plants, responses of individual taxa to accelerating climate change are typically studied in isolation. Thereby, biotic interactions that potentially limit species in tracking their preferred climatic niches are ignored. Here, we chose butterflies as a prominent representative of herbivorous insects to investigate the impacts of temperature changes and their larval host plant distributions along a 1.4 km elevational gradient in the German Alps. Following a sampling protocol of 2009, we re-visited 33 grassland plots in 2019 over an entire growing season. We quantified changes in butterfly abundance and richness by repeated transect walks on each plot and disentangled the direct and indirect effects of locally assessed temperature, site management, and larval and adult food resource availability on these patterns. Additionally, we determined elevational range shifts of butterflies and host plants at both the community and species level. Comparing the two sampled years (2009, 2019), we found a severe decline in butterfly abundance and a clear upward shift of butterflies along the elevational gradient. We detected shifts in the peak of species richness, community composition and at the species level, whereby mountainous species shifted particularly strongly. In contrast, host plants showed barely any change, neither concerning species richness, nor individual species shifts. Further, temperature and host plant richness were the main drivers of butterfly richness, with change in temperature explaining best the change of richness over time. We conclude that host plants are not yet hindering butterfly species and communities from shifting upwards. However, the mismatch between butterfly and host plant shifts might become a problem for this very close plant-herbivore relationship, especially towards higher elevations, if butterflies fail to adapt to new host plants. Further, our results support the value of conserving traditional extensive pasture use as a promoter of host plants and thereby butterfly richness.

opencc-zeroAug 2022View details →

Novel host plant unmasks heritable variation in plant preference within an insect population

Introductions of novel plant species can disturb the historical resource environment of herbivorous insects, resulting in strong selection to either adopt or exclude the novel host. However, an adaptive response depends on heritable genetic variation for preference or performance within the targeted herbivore population, and it is unclear how heritability of host-use preference may differ between novel and historical hosts. Pieris macdunnoughii butterflies in the Rocky Mountains lay eggs on the nonnative mustard Thlaspi arvense, which is lethal to their offspring. Heritability analyses revealed considerable sex-linked additive genetic variation in host preference within a population of this butterfly. This was contrary to general predictions about the genetic basis of preference variation, which are hypothesized to be sex-linked between populations but autosomal within populations. Evidence of sex-linkage disappeared when butterflies were tested on methanol-based chemical extracts, suggesting these chemicals in isolation may not be the primary driver of female choice among available host plants. Although unexpected, evidence for within-population sex-linked genetic variation in preference for T. arvense over native hosts indicates that persistent maladaptive oviposition on this lethal plant must be maintained by alternative evolutionary dynamics such as migration- or drift-selection balance or pleiotropic constraints.

opencc-by-4.0Aug 2022View details →

High nucleotide similarity of three Copia lineage LTR retrotransposons among plant genomes

Transposable elements (TEs) are mobile genetic elements found in the majority of eukaryotic genomes. TEs deeply impact the structure and evolution of chromosomes and can induce mutations affecting coding genes. In plants, the major group of TEs is Long Terminal Repeats retrotransposons (LTR-RT). They are classified into superfamilies (Gypsy, Copia) and sub-classified into lineages. Horizontal transfer (HT), defined as the nonsexual transmission of genetic material between species, is a process allowing LTR-RTs to invade a new genome. Although this phenomenon was considered rare, recent studies demonstrate numerous transfers of LTR-RTs, suggesting that HT may be more frequent than initially estimated. This study aims to determine which LTR-RT lineages are shared with high similarity among 69 reference plant genomes. We identified and classified 88,450 LTR-RTs and determined 143 cases (involving 94 elements) of high similarities between pairs of genomes. Most of them involved three Copia lineages (Oryco/Ivana, Retrofit/Ale and Tork/Tar/Ikeros). A detailed analysis of three cases of high similarities involving Tork/Tar/Ikeros group shows a patchy distribution of the elements and phylogenetic incongruities, indicating they originated from potential HTs. Overall, our results suggest that Copia LTR-RTs share outstanding similarity between very distant species and may probably be more involved in HT mechanisms.

opencc-by-4.0Sep 2022View details →

Complex plant quality - microbiota - population interactions modulate the response of a specialist herbivore to the defense of its host plant.

1. Many specialist herbivores have evolved strategies to cope with plant defenses, with gut microbiota potentially participating to such adaptations. 2. In this study we assessed whether the history of plant use (population origin) and microbiota may interact with plant defense adaptation. 3. We tested whether microbiota enhance the performance of Melitaea cinxia larvae on their host plant, Plantago lanceolata and increase their ability to cope the defensive compounds, iridoid glycosides (IGs). 3. The gut microbiota was significantly affected by both larval population origin and host plant IG level. Contrary to our prediction, impoverishing the microbiota with antibiotic treatment did not reduce larval performance. 5. As expected for this specialized insect herbivore, sequestration of one of IGs was higher in larvae fed with plants producing higher concentration of IGs. These larvae also showed metabolic signature of intoxication (i.e. decrease in Lysine levels). However, intoxication on highly defended plants was only observed when larvae with history of poorly defended plants were simultaneously treated with antibiotics. 6. Our results suggest that both adaptation and microbiota contribute to the metabolic response of herbivores to plant defense though complex interactions.

opencc-by-4.0Nov 2021View details →

BeeDNA: microfluidic environmental DNA metabarcoding as a tool for connecting plant and pollinator communities

Data repository accompanying the paper 'BeeDNA: microfluidic environmental DNA metabarcoding as a tool for connecting plant and pollinator communities' by Harper et al. (2021). 1_Raw_Data.zip This zipped folder contains the raw sequence data (sorted by primer set and demultiplexed) for both sequencing runs (2019-10-24 and 2019-11-11). To decompress each file, run:  <pre><code>tar -xvf filename.bz2</code></pre> This will create a folder for each primer set containing the raw reads for each sample/control. 2_Anacapa_Bioinformatic_Processing.zip This zipped folder contains all files needed to perform bioinformatic processing with Anacapa. Please process sequence data belonging to each primer set individually (i.e. do not process sequence data belonging to different primer sets together). 3_metaBEAT_Bioinformatic_Processing.zip  This zipped folder contains the scripts and files needed to perform bioinformatic processing with metaBEAT. Before running the scripts, move the raw reads for each sample belonging to each primer set into the dedicated folder within metaBEAT_Bioinformatic_Processing, e.g. all .fastq files in Raw_Data > BF1_BR1 should be moved to metaBEAT_Bioinformatic_Processing > BF1-BR1 > raw_reads. To run metaBEAT, you will have to install Docker on your computer. Docker is compatible with all major operating systems, but see the Docker documentation for details. On Ubuntu, installing Docker should be as easy as: <pre><code>sudo apt-get install docker.io</code></pre> Once Docker is installed, you can enter the environment by typing: <pre><code>sudo docker run -i -t --net=host --name metaBEAT -v $(pwd):/home/working chrishah/metabeat /bin/bash</code></pre> This will download the metaBEAT image (if not yet present on your computer) and enter the 'container', i.e. the self contained environment (NB: sudo may be necessary in some cases). With the above command, the container's directory /home/working will be mounted to your current working directory (as instructed by $(pwd)). In other words, anything you do in the container's /home/working directory will be synced with your current working directory on your local machine. Please process sequence data belonging to each primer set individually (i.e. do not process sequence data belonging to different primer sets together). An example of expected outputs can be seen in the Jupyter Notebook for the BF1/BR1 primer set from the 2019-11-11 sequencing run. 4_Illinois_Invert_Reference_Database.zip This zipped folder contains all files that were used to generate the custom COI and 16S reference databases for invertebrates that occur in Illinois, U.S. You will need to have metaBEAT installed (see above) before you try to run any Jupyter Notebooks (.ipynb files). 5_ecoPCR.zip This zipped folder contains all files used to perform ecoPCR for each primer set evaluated for microfluidic eDNA metabarcoding. You will need to <a href="https://git.metabarcoding.org/obitools/ecopcr/wikis/home">install ecoPCR</a> before running any shell scripts. 6_Tidied_Data.zip This zipped folder contains the taxonomically assigned data for both sequencing runs produced by metaBEAT and Anacapa. These were copied over from the folders 2_Anacapa_Bioinformatic_Processing and 3_metaBEAT_Bioinformatic_Processing and rearranged into a more logical order. These files are used as the input for data analysis using R. 7_Data_Analysis.zip This zipped folder contains all scripts and metadata required to summarise and statistically analyse data in R.   Please contact Dr Lynsey Harper (lynsey.harper2@gmail.com) or Dr Mark Davis (davis63@illinois.edu) if you encounter any issues!

opencc-zeroSep 2022View details →

Data from: Pitcher geometry facilitates extrinsically powered 'springboard trapping' in carnivorous Nepenthes gracilis pitcher plants

<div> Carnivorous pitcher plants capture insects in cup-shaped leaves that function as motionless pitfall traps. Nepenthes gracilis, evolved a unique 'springboard' trapping mechanism that exploits the impact energy of falling raindrops to actuate a fast pivoting motion of the canopy-like pitcher lid. We superimposed multiple computerized micro-tomography images of the same pitcher to reveal distinct deformation patterns in lid-trapping N. gracilis and closely related pitfall-trapping N. rafflesiana. We found prominent differences between downward and upward lid displacement in N. gracilis only. Downward displacement was characterised by bending in two distinct deformation zones while upward displacement was accomplished by evenly distributed straightening of the entire upper rear section of the pitcher. This suggests an anisotropic impact response, which may help to maximize initial jerk forces for prey capture, as well as the subsequent damping of the oscillation. Our results point to a key role of pitcher geometry for effective 'springboard' trapping in N. gracilis. </div>

opencc-by-4.0Sep 2022View details →

CINWA: Database of Cultivated plants and their names in the indigenous languages of South America

This repository contains source data for CINWA -  Database of Cultivated plants and their names in the indigenous languages of South America If you use these data please cite the database Aguilar Panchi, Evelyn Michelle, Saetbyul Lee, Evgenia Brodetsky, and Matthias Urban (eds.). 2022. CINWA - Database of Cultivated plants and their names in the indigenous languages of South America. Version 0.9. Available online at cinwa.org. If you would like to cite specific data entries, please also acknowledge the original source by consulting the reference that is associated with that entry. For example: Cook, Dorothy M., and Frances L. Gralow. 2001. Diccionario bilingüe koreguaje-español español-koreguaje. Santafé de Bogotá: Editorial Alberto Lleras Camargo. In: Aguilar Panchi, Evelyn Michelle, Saetbyul Lee, Evgenia Brodetsky, and Matthias Urban (eds.). 2022. CINWA - Database of Cultivated plants and their names in the indigenous languages of South America. Version 0.9. Available online at cinwa.org.