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759 results for “plant–plant interaction”
The effects of age on the demography of a perennial plant depend on interactions with size and environment
<p>Age-dependence of the demographic rates survival, fecundity and individual growth is a fundamental aspect of population biological theory. Knowledge about plant ageing can also be important for conservation and agriculture as it will improve the accuracy of population viability assessments and long-term performance assessments in perennial crops. Recent studies show age effects on demographic rates for several plant species, yet much remains to be learned about the patterns and mechanisms of plant ageing, particularly about how age effects interact with the environment and with plant size.</p> <p>We collected age-and-size-based demographic data, as well as individual-based environmental data, for the perennial herb Plantago lanceolata in Denmark over three annual transitions (four years). We combined frequent field monitoring of carefully mapped individuals with the underused technique of root histology to determine age of herbaceous plants. We used generalized linear mixed effects models to assess how age, soil properties, and year influenced survival, growth, and reproduction.</p> <p>Our results show no strong evidence of consistent age declines, rather, we found mostly positive effects of age on vital rates. For all vital rates, i.e. survival, growth, flowering, and reproductive output, age effects also differed significantly among years. Additionally, we detected an interactive effect of age and size in the growth model. Size, and temporal and spatial environmental variation also affected vital rates independently of age.</p> <p>Synthesis: Our study shows that age-dependence of demographic rates can depend both on individual size and environmental variation. These results suggest that a consideration of potential age-interactions may improve the accuracy of comparative studies of ageing and population projections. Moreover, this study shows that much is still unknown about how plant ageing can be affected by the environment, and illustrates how age determination using herb chronology provides an opportunity to increase our knowledge about ageing in herbaceous plants.</p>
Data from: A meta-analysis of plant interaction networks reveals competitive hierarchies as well as facilitation and intransitivity
The extent to which competitive interactions and niche differentiation structure communities has been highly controversial. To quantify evidence for key features of plant community structure, I recharacterized published data from interaction experiments as networks of competitive and facilitative interactions. I measured the network structure of 31 woody and herbaceous communities, including the intensity, distribution, and diversity of interactions at the species-pair and community level to determine the generality of competition, winner-loser relationships, and unequal interaction allocation. I developed novel methodology using meta-analysis to incorporate interaction uncertainty into estimates of structural metrics among independent networks. Plant communities were competitive, but intraspecific interactions were sometimes more intense than interspecific interactions. On the whole, interactions were imbalanced and communities were transitive. However, facilitation, balanced interactions, and intransitivity were common in individual communities. Synthesizing network metrics using meta-analysis is an original approach with which to generalize community structure in a systematic way.
Interactive Web-based Annotation of Plant MicroRNAs with iwa-miRNA
<p>MicroRNAs (miRNAs) are important regulators of gene expression. The large-scale detection and profiling of miRNAs has accelerated with the development of high-throughput small RNA sequencing (sRNA-Seq) techniques and bioinformatics tools. However, generating high-quality comprehensive miRNA annotations remains challenging, due to the intrinsic complexity of sRNA-Seq data and inherent limitations of existing miRNA predictions. Here, we present iwa-miRNA, a Galaxy-based framework that can facilitate miRNA annotation in plant species by combining computational analysis and manual curation. iwa-miRNA is specifically designed to generate a comprehensive list of miRNA candidates, bridging the gap between already annotated miRNAs provided by public miRNA databases and new predictions from sRNA-Seq datasets. It can also assist users to select promising miRNA candidates in an interactive mode through the automated and manual steps, contributing to the accessibility and reproducibility of genome-wide miRNA annotation. iwa-miRNA is user-friendly and can be easily deployed as a web application for researchers without programming experience. With flexible, interactive, and easy-to-use features, iwa-miRNA is a valuable tool for annotation of miRNAs in plant species with reference genomes. We illustrated the application of iwa-miRNA for miRNA annotation of plant species with varying complexity. The sources codes and web server of iwa-miRNA is freely accessible at: <a href="http://iwa-miRNA.omicstudio.cloud">http://iwa-miRNA.omicstudio.cloud</a>/.</p>
Data from: Ecosystem nitrogen retention is regulated by plant community trait interactions with nutrient status in an alpine meadow
1.Biotic nitrogen (N) retention is an important ecosystem function in the context of ongoing land use intensification, N deposition and global warming. However, a paucity of experimental evidence limits understanding of how different plant community components influence N retention in terrestrial ecosystems. 2.In this investigation we conducted a 15N labelling experiment to test how plant community properties, including plant species richness/diversity, dominance and functional traits, influence plant N uptake and retention under different nutrient availabilities. A three-year experiment examined the effects of adding N (10 g N m−2 year−1) and phosphorus (P) (5 g P m−2 year−1) to an alpine meadow on the Qinghai-Tibetan Plateau. 3.Results show that 15N retention increased with the addition of N and P; the addition of P produced the largest increase of 15N retention in plant and soil N pools. Changes in soil nutrient conditions also facilitated different plant community controls on ecosystem N retention. Ecosystem 15N retention was influenced by species richness and root biomass in the control plots; whereas the N addition treatment showed an important effect of community-weighted means (CWM) of specific leaf area (SLA), and plots with additional P recorded lower CWM of root nitrogen content (root N) and larger CWM root:shoot ratios (R/S) as important determinants. 4.Synthesis. Ecosystem N retention was influenced by conservative and exploitative plant species and/or their traits under N deficient and abundant conditions, respectively, whereas species richness and community plant biomass were most influential under control conditions. The discovery of an interaction between plant community traits and nutrient biogeochemistry as a mechanism for ecosystem N retention offers a means to predict how vegetation in alpine meadow ecosystems will respond to expected global change.
Data from: Museum specimens provide novel insights into changing plant-herbivore interactions
Mounting evidence shows that species interactions may mediate how individual species respond to climate change. However, long-term anthropogenic effects on species interactions are poorly characterized due to a lack of data. Insect herbivory is a major ecological process that represents the interaction between insect herbivores and their host plants, but historical data on insect damage to plants is particularly sparse. Here, we suggest that museum collections of insects and plants can fill key gaps in our knowledge on changing trophic interactions, including proximate mechanisms and the net outcomes of multiple global change drivers across diverse insect herbivore-plant associations. We outline theory on how global change may affect herbivores and their host plants and highlight the unique data that could be extracted from museum specimens to explore their shifting interactions. We aim to provide a framework for using museum specimens to explore how some of the most diverse co-evolved relationships are responding to climate and land use change.
Data from: Interaction rewiring and the rapid turnover of plant-pollinator networks
Whether species interactions are static or change over time has wide-reaching ecological and evolutionary consequences. However, species interaction networks are typically constructed from temporally aggregated interaction data, thereby implicitly assuming that interactions are fixed. This approach has advanced our understanding of communities, but it obscures the timescale at which interactions form (or dissolve) and the drivers and consequences of such dynamics. We address this knowledge gap by quantifying the within-season turnover of plant–pollinator interactions from weekly censuses across 3 years in a subalpine ecosystem. Week-to-week turnover of interactions (1) was high, (2) followed a consistent seasonal progression in all years of study and (3) was dominated by interaction rewiring (the reassembly of interactions among species). Simulation models revealed that species' phenologies and relative abundances constrained both total interaction turnover and rewiring. Our findings reveal the diversity of species interactions that may be missed when the temporal dynamics of networks are ignored.
Novel plant-microbe interactions: rapid evolution of a legume-rhizobium mutualism in restored prairies
1. When plants colonize new habitats, the novel interactions they form with new mutualists or enemies can immediately affect plant performance. These novel interactions also may provoke rapid evolutionary responses and can be ideal scenarios for investigating how species interactions influence plant evolution. 2. To explore how mutualists influence the evolution of colonizing plant populations, we capitalized on an experiment in which two former agricultural fields were seeded with identical prairie seed mixes in 2010. Six years later, we compared how populations of the legume Chamaecrista fasciculata from these sites and their original (shared) source population responded to nitrogen-fixing rhizobia from the restoration sites in a greenhouse reciprocal cross-inoculation experiment. 3. We found that the two populations differed both from their original source population and from each other in the benefits they derive from rhizobia, that one population has evolved reduced allocation to rhizobia (i.e., forms fewer rhizobium-housing nodules). 4. Synthesis. Our results suggest that these plant populations have evolved different ways of interacting with rhizobia, potentially in response to differences in rhizobium quality between sites. Our study illustrates how microbial mutualists may shape plant evolution in new environments and highlights how variation in microbial mutualists potentially may select for different evolutionary strategies in plant hosts.
Data from: Consequences of multiple flower-insect interactions for subsequent plant-insect interactions and plant reproduction
Premise of the study. Plants often interact simultaneously with multiple antagonists and mutualists that can alter plant traits at the phenotypic or genetic level, subsequent plant-insect interactions, and reproduction. Although many studies have examined the effects of single floral antagonisms on subsequent pollination and plant reproduction, we know very little about the combined, potentially non-additive effects of multiple flower-insect interactions. Methods. We simulated increased florivory, nectar robbing, and pollination on field-grown Impatiens capensis. This allowed us to determine interactive effects on five subsequent plant-insect interactions and 16 plant traits, including traits related to plant growth, floral attractiveness, floral defenses, and plant reproduction. Key results. All three manipulative treatments had significant non-additive effects on the behavior of subsequent floral visitors, indicating that the effect of floral visitors generally depended on the presence or behavior of others. Pollination increased visitation by both pollinators and nectar larcenists (robbers and thieves), while florivory reduced pollinator and larcenist visits. Surprisingly, supplemental pollination also increased leaf herbivory. Florivores often responded to manipulations in opposite ways than did nectar larcenists and pollinators, suggesting different mechanisms influencing visitors that consume nectar compared to floral tissue. While our treatments did not affect any floral trait measured, they non-additively impacted plant reproduction, with florivory having a larger overall impact than either nectar robbing or pollination. Conclusions. These results emphasize the importance of understanding the context in which flower-insect interactions occur, because the composition of the interacting community can have large and non-additive impacts on subsequent insect behavior and plant reproduction. If you would like your personal information to be removed from the database, please contact the publication office.
Community-level interactions between plants and soil biota during range expansion
1. Plant species that expand their range in response to current climate change will encounter soil communities that may hinder, allow, or even facilitate plant performance. It has been shown repeatedly for plant species originating from other continents that these plants are less hampered by soil communities from the new than from the original range. However, information about the interactions between intra-continental range expanders and soil communities is sparse, especially at community level. 2. Here we used a plant-soil feedback experiment approach to examine if the interactions between range expanders and soil communities change during range expansion. We grew communities of range-expanding and native plant species with soil communities originating from the original and new range of range expanders. We determined the composition of fungi, bacteria and nematodes in these conditioned soils by high-throughput amplicon sequencing of the ITS region and the 16S rRNA gene and using morphological methods, respectively. Then we tested how these soil communities influence the growth of subsequent communities of range expanders and natives. 3. We found that after the conditioning phase soil bacterial, fungal and nematode communities differed by origin and by conditioning plant communities. Despite differences in bacterial, fungal and nematode communities between original and new range, soil origin did not influence the biomass production of plant communities. Both native and range expanding plant communities produced most aboveground biomass in soils that were conditioned by plant communities distantly related to them. 4. Synthesis. We conclude that communities of range-expanding plant species shape specific soil communities in both original and new range soil. Plant-soil interactions of range expanders in communities can be similar to the ones of their closely related native plant species.
Ecological mechanisms explaining interactions within plant-hummingbird networks: morphological matching increases towards lower latitudes
<p><a name="ab4">Interactions between species are influenced by different ecological mechanisms, such as morphological matching, phenological overlap, and species abundances</a>. <a name="Ab1"></a><a name="ab5">How</a> these mechanisms explain interaction frequencies across environmental gradients remains poorly understood. Consequently, we also know little about the mechanisms that drive the geographical patterns in network structure, such as complementary specialization and modularity. Here, we use data on morphologies, phenologies and abundances to explain interaction frequencies between hummingbirds and plants at a large geographic scale. <a name="ab2">For 24 quantitative networks sampled throughout the Americas, we found that</a> the tendency of species to interact with morphologically matching partners contributed to specialized and modular network structures. Morphological matching best explained interaction frequencies in networks found closer to the equator and in areas with low temperature seasonality. When comparing the three ecological mechanisms within networks, we found that both morphological matching and phenological overlap generally outperformed abundances in the explanation of interaction frequencies. Together, these findings provide insights into the ecological mechanisms that underlie geographical patterns in resource specialization. Notably, our results highlight morphological constraints on interactions as a potential explanation for increasing resource specialization towards lower latitudes.</p>
Data from: Direct and higher-order interactions in plant communities under increasing weather persistence
<p>ABSTRACT: Climate change is increasing the weather persistence in the midlatitudes, prolonging both dry and wet spells compared to historic averages. These newly emerging environmental conditions destabilize plant communities, but the role of species interactions in this process is unknown. Here, we tested how direct and higher-order interactions (HOIs) between species may change in synthesized grassland communities along an experimental gradient of increasing persistence in precipitation regimes. Our results indicate that species interactions (including HOIs) are an important determinant of plant performance under increasing weather persistence. Out of the 12 most parsimonious models predicting species productivity, 75 % contained significant direct interactions and 92 % significant HOIs. Inclusion of direct interactions or HOIs respectively tripled or quadrupled the explained variance of target species biomass compared to null models only including the precipitation treatment. Drought dominated the plant responses, with longer droughts increasing direct competition but also HOI-driven facilitation. Despite these counteracting changes, drought intensified net competition. Grasses were generally more involved in competitive interactions whereas legumes had a stronger affinity for facilitative interactions. Under longer drought, species affinity for nutrient rich or wet environments resulted in more negative direct interactions or HOIs, respectively. We conclude that higher-order interactions, crucially depending on species identity, only partially stabilize community dynamics under increasing weather persistence</p>
Data from: Direct and higher-order interactions in plant communities under increasing weather persistence
<p>Climate change is increasing the weather persistence in the mid-latitudes, prolonging both dry and wet spells compared to historic averages. These newly emerging environmental conditions destabilize plant communities, but the role of species interactions in this process is unknown. Here, we tested how direct and higher-order interactions (HOIs) between species may change in synthesized grassland communities along an experimental gradient of increasing persistence in precipitation regimes. Our results indicate that species interactions (including HOIs) are an important determinant of plant performance under increasing weather persistence. Out of the 12 most parsimonious models predicting species productivity, 75 % contained significant direct interactions and 92 % significant HOIs. Inclusion of direct interactions or HOIs respectively tripled or quadrupled the explained variance of target species biomass compared to null models only including the precipitation treatment. Drought was the main driver of plant responses, with longer droughts increasing direct competition but also HOI-driven facilitation. Despite these counteracting changes, drought intensified net competition. Grasses were generally more involved in competitive interactions whereas legumes were more involved in facilitative interactions. Under longer drought, species affinity for nutrient rich or wet environments resulted in more negative direct interactions or HOIs, respectively. We conclude that higher-order interactions, crucially depending on species identity, only partially stabilize community dynamics under increasing weather persistence.</p>
Plant-pollinator interactions in Mediterranean semiarid ecosystems
<p>Pollinators are fundamental for plant reproduction in natural and agricultural ecosystems. However, their populations are declining worldwide, threatening the functioning of the ecosystem service they provide. The factors driving this change are manifold, but land use changes and interspecific transmission of pathogens between managed and wild bees are prominent. In this context, most research efforts have focused on specific taxa and rarely at the community level, limiting our ability to fully understand the effects of global change on the functioning of plant-pollinator interactions in ecosystems.</p> <p>Here, we investigate the impact of human activities (beekeeping and land use intensity) on the spread of an emergent pathogen (<em>Vairimorpha ceranae</em>) in Mediterranean wild bee communities inhabiting landscapes with varying levels of anthropogenic disturbance. Plant-pollinator interactions were sampled in nine one-hectare plots along a gradient of land use (urban structures, croplands and natural vegetation) and beekeeping intensity. We analised the impact of human disturbances on pollination networks and pathogen prevalence and applied a network approach to examine whether total effects of species in networks (i.e. direct plus indirect interactions) explain pathogen spread through bee communities.</p> <p>We found that <em>V. ceranae </em>prevalence in honey bees is not a good predictor of the pathogen spread through bee communities. There seems to be a temporal mismatch between pathogen dynamics in managed and wild bees. Networks with more diversity of interactions and more plants showed less pathogen prevalence, but total effect analyses (i.e. combining direct and indirect interactions) failed to explain pathogen transmission across pollination networks. Croplands increased wild bee density, and interactions and species diversity in networks while shrublands had the opposite effect. Our results highlight the importance of studying pathogen dynamics at the community level and analysing species interaction patterns to improve our understanding of pathogen spread through communities.</p>
Data from: The impact of plant genetic variation, drought, and leaf nitrogen on plant-herbivore interactions
<p>Plant genotype, drought stress, and their interaction are among the factors contributing to the susceptibility of plants to herbivory. The plant's nitrogen concentration, a critical and often limiting nutrient, differs with plant genotype and drought. Still, few studies have investigated the impact of the interaction of genotype and drought on herbivory and plant nitrogen. We established a common garden in Duluth, MN, of tall goldenrod, <em>Solidago altissima,</em> collected from a local Minnesota site to analyze the effects of goldenrod genotype and drought stress on leaf nitrogen and the preference and performance of the chrysanthemum lace bug, <em>Corythucha marmorata</em>. Lace bugs had oviposition, nymph, and adult preferences among host plant genotypes, water treatments, and among genotype and water treatment combinations. Nymph and adult survival and adult mass varied significantly due to plant genotype, water treatment, the interaction of plant and water treatment, and the interaction of treatment with lace bug density. Oviposition preference and offspring performance were significantly positively related. Leaf nitrogen increased with the increasing severity of the water limitation in the absence of lace bugs. However, in the presence of lace bugs, there was no difference in nitrogen among water treatments.</p>
A review of the status of web-based African Plant-Pollinator Interaction data
<p>A protocol was developed to collect and mine data from various web-based sources such as journals, web pages, handbooks, manuals and any other source that is web accessible and has information sought. The intention was to collect as much as possible all data with plant-pollinator interaction from studies carried out in Kenya and other parts of Africa. To assure technical support and homogeinity of thoughts, the activity was carried out in a write-shop set up whereby a team of data miners were brought together for 5 days to collect the data. They were trained on the meaning of plant pollinator interactions, key words that should look for, data coverage area, specific sites that are useful and the reporting. Further, monitoring and review of the data collection was continously done, to ensure the right data was collected appropriately. Various search engines were used to collect the data. The data was then prepared in a Globi data base to enhance its use base on the FAIR data principles. The results show that little data exists in Africa on plant-pollinator interaction based on the FAIR data principles. It further shows that Africa need to adopt FAIR principles to enhance utilization of generated data by scientists and expand the benefits of such data in Africa.</p>
Data for: Shifts in plant-invertebrate interactions between wild and ex-situ conservation populations of a critically endangered tree
<p>Ex-situ conservation is an effective approach to prevent the extinction of endangered species. Biotic interactions (eg herbivory and pollination) are critical to ex-situ conservation success, including plant establishment, survival, and reproduction. However, shifts in biotic interactions between wild and ex-situ populations are still poorly understood. We compared herbivory and pollination characteristics between the only wild population (WP) and three ex-situ populations (LP, local population, nearby WP; NP, north population, ca. 850 km; and SP, south population, ca. 750 km) of a critically endangered tree species (<em>Sinojackia huangmeiensis</em>) to explore the latitudinal changes in plant-invertebrate interactions. Larvae of the Limacodidae family were the dominant herbivores in WP, LP, and NP, while the only herbivore observed in SP was a snail. Compared to WP, the leaf herbivory rate was unchanged in LP but decreased in NP and SP. Leaf defense traits (total phenols, tannins, leaf thickness, and leaf dry matter content) increased or remained unchanged in the three ex-situ populations. A pollinator (<em>Apis cerana</em>) of <em>S. huangmeiensis</em> was present in the four populations. NP and SP lacked some pollinators that were found in both WP and LP, but they shared one pollinator that was not observed in WP and LP. The pollinator visiting frequency increased in SP, while it did not change significantly in LP and NP. Synthesis and applications: Our results suggested that both herbivory and pollination of <em>S. huangmeiensis</em> changed in ex-situ populations, with complete or partial changes in herbivores, leaf herbivory rate, pollinators, pollinator visiting frequency, and fruit set in the two distant ex-situ populations. This work provides a unique empirical study of shifts in both antagonistic and mutualistic biotic interactions between wild and ex-situ populations. We emphasized that it is essential to integrate herbivore and pollinator management in future ex-situ conservation of plant species.</p>
Data from: Plant-soil interactions during the native and exotic range expansion of an annual plant
<p>Range expansions, whether they are biological invasions or climate change-mediated range shifts, may have profound ecological and evolutionary consequences for plant-soil interactions. Range-expanding plants encounter soil biota with which they have a limited coevolutionary history, especially when introduced to a new continent. Past studies have found mixed results on whether plants experience positive or negative soil feedback interactions in their novel range, and these effects often change over time. One important theoretical explanation is that plants locally adapt to the soil pathogens and mutualists in their novel range. We tested this hypothesis in <em>Dittrichia graveolens</em>, an annual plant that is both expanding its European native range, initially coinciding with climate warming, and rapidly invading California, after human introduction. In parallel greenhouse experiments on both continents, we used plant genotypes and soils from five locations at the core and edge of each range to compare plant growth in soil from <em>D. graveolens </em>populations and nearby control microsites as a measure of plant-soil feedback. Plant-soil interactions were highly idiosyncratic across sites in each range. On average, plant-soil feedbacks were more positive in the native range than in the exotic range. In line with the strongly heterogeneous pattern of soil responses along our biogeographic gradients, we found no evidence for evolutionary differentiation between plant genotypes from the core to the edge of either range. Our results suggest that the evolution of plant-soil interactions during range expansion may be more strongly driven by local evolutionary dynamics varying across the range than by large-scale biogeographic shifts.</p>
Sites dominated by common fiddleneck (Amsinckia menziesii var. intermedia) support diverse plant-pollinator interactions
<p>Biodiversity is declining at unprecedented rates worldwide due largely to land use change and abnormal disturbance events. The high species diversity and endemicity found in California's coastal sage scrub (CSS) are especially at risk from urban development and ongoing disturbance. However, several CSS plant species have disturbance adaptations which may allow them to serve as vital resources for insect pollinators when native plant diversity is threatened. Common fiddleneck (<em>Amsinckia menziesii var. intermedia</em>) is one of the first annual forbs to germinate in CSS and as a result, it occurs in high density patches in early spring which temporarily creates a near monoculture. Although fiddleneck is a prominent CSS plant, particularly in areas that have experienced a disturbance event, its larger ecological role is not well explored. Therefore, we monitored ten sites across a disturbance gradient for two spring seasons to assess the composition of plant-pollinator networks in fiddleneck-dominated plots. We found fiddleneck supported a diverse pollinator community with 68% of recorded taxa visiting fiddleneck. The plants most frequently visited included two native annual forbs (common fiddleneck and <em>Phacelia distans</em><em>)</em> and two invasive annual forbs (<em>Erodium cicutarium</em> and<em> </em><em>Brassica tournefortii)</em>. Plant and pollinator abundances increased with increased mean precipitation. Additionally, plant-pollinator networks changed over time; the number of links per species increased throughout the season but did not differ amongst disturbance types. Despite the numerical dominance of fiddleneck, CSS supported a diversity of pollinator taxa and exhibited complex plant-pollinator networks across the disturbance gradient.</p>
Data and code for : 'Interactive effects of temperature, aridity, and plant stoichiometry on insect herbivory: past and present', The American Naturalist
<p>The files are for the manuscript 'Interactive effects of temperature, aridity, and plant stoichiometry on insect herbivory: past and present' consist of the following major parts:</p> <p> </p> <p>1. <strong>FILE “all site summary.xlsx”</strong>: Summary data of all the fossil sites used in the study. This is an MS Excel file and has three sheets, namely:</p> <p>a. <strong>All_sites</strong>: This sheet lists various metadata related to each of the 39 fossil sites used in this study. The name of the site is listed as ‘Flora’, and each site has the following data associated with it: Epoch, Latitude Bin, Region, Geographic location, Lat(itude), Long(itude), Depositional.Environment, Age, Age.error, MAT.C (Mean Annual Temperature in degrees C), MAT.Error, MAP.mm.yr (Mean Annual Precipitation in mm), MAP.error, and No.Leaves (number of leaf specimens).</p> <p>b. <strong>PEB sites list (Bighorn)</strong>: This sheet specifically lists the 8 Paleocene-Eocene boundary (PEB) sites from the Bighorn basin along with relevant metadata. These sites are also present in the All_sites tab.</p> <p>c. <strong>PEB sites list (Hanna)</strong>: This sheet lists the 2 Hanna Basin sites from the PEB with relevant metadata.</p> <p><strong>2. </strong><strong>FOLDER “fossil site herbivory data”: </strong>This folder contains the leaf-level herbivory data from all the fossil sites used in this study (including the PEB sites from Hanna Basin) in .csv format. Each file has the following data structure: the first column lists the morphotaxa name of the leaf and the subsequent columns represent whether a particular DT (Damage Type, represented by individual column names) is present (1) or absent (0/NA) in that leaf.</p> <p><strong>3. </strong><strong>FOLDER “modern site herbivory data”: </strong>This folder contains the leaf-level level herbivory data from all the modern sites used in this study in .txt format. “presab_data_HFmatrix” is the data from the three sites in Harvard Forest, “presab_data_LSmatrix” from three sites in La Selva and “presab_data_SERCmatrix” from the three sites in the Smithsonian Environmental Research Center. The quarry number is the name of the site in each file. The rest of the structure is same as fossil data: the second column lists the taxa name for the leaf and the subsequent columns represent whether a particular DT (Damage Type, represented by individual column names) is present (1) or absent (0/NA) in that leaf.</p> <p><strong>4. </strong><strong>FOLDER “masks for FFGs”: </strong>This folder has two files, namely:</p> <p><strong>a. </strong><strong>“ffgdef_DT.csv”: </strong>This file lists which Functional Feeding Group does each DT belong to. Oviposition =0, Skeletonization=1, Surface feeding =2, Galling=3, Hole Feeding=4, Mining =5, Margin Feeding =6, Piercing and Sucking=7.</p> <p><strong>b. </strong><strong>“mask_DT.csv”: </strong>This file lists whether a given DT is a herbivory damage, a specialized damage, gall or mining damage (T/F).</p> <p><strong>5. </strong><strong>FOLDER “N2_fixing_site_level_taxa”: </strong>This folder contains 8 files in .csv format corresponding to each of the 8 PEB Bighorn Basin sites. Each file has the same structure: the first column corresponds to a specific morphotaxa and the next column indicates whether it is a N2 fixing plant (1) or not (0).</p> <p><strong>6. FILE "Analyais_base.Rmd" </strong>gives base code to replicate all the results.</p>
Data from: Higher-order species interactions cause time-dependent niche and fitness differences: experimental evidence in plant-feeding arthropods
<p><strong>trajectories.csv </strong>(the raw data)</p> <p><strong>id</strong>: replicate identifier<br><strong>variant</strong>: co-existence status ("competition" or "monoculture")<br><strong>day</strong>: day of experiment<br><strong>species</strong>: mite species ("CRM" or "WCM")<br><strong>n</strong>: population density</p> <p> </p> <p><strong>model.R</strong></p> <p>The R script with the GAMM fitted to the trajectory data (the GAMM model is saved as <strong>model.RData</strong>); also produces simulations from this model (saved as <strong>sim.csv</strong>).</p> <p> </p> <p><strong>model.RData</strong></p> <p>The GAMM for growth rates.</p> <p> </p> <p><strong>sim.csv</strong> (simulations from the GAMM)</p> <p><strong>day</strong>: day of experiment<br><strong>spec_var</strong>: combination of co-existence status ("competition" or "monoculture") and species ("CRM" or "WCM")<br><strong>X1:X1000</strong>: population densities simulated from the fitted GAMM (on the log scale)</p> <p> </p> <p><strong>NFD_over_time_monte_carlo_gam.py</strong></p> <p>Python script to compute niche and fitness differences. Takes <strong>sim.csv</strong> (densities over time for different instantiations) and <strong>model.RData</strong> (stores the GAMM from R for the growth rates) as input and generates the file <strong>Data_NFD_monte_carlo_multi_c.csv</strong> which stores the niche and fitness differences computed for these communities.</p> <p> </p> <p><strong>figures.R</strong></p> <p>The R script that produces Figures 2-4.</p> <p> </p> <p><strong>plot_biotic_model.py</strong></p> <p>Python code to generate the figures S3 and S4 showing the simulations of a biotic resource competition model. </p> <p> </p> <p><strong>plot_abiotic_model.py</strong></p> <p>Python code to generate the figures S1 and S2 showing simulations of an abiotic resource competition model. </p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.