Find research datasets worth reusing

Adaptation of pathogens to their local plant host, Silphium integrifolium, along a precipitation gradient

All figures and code were generated in RStudio 2022.02.3+492 "Prairie Trillium" Release. All packages needed to run the R code are shown in the RMD’s.   Code to generate figures and statistical analysis:   <ul> <li>DVTindex_help.Rmd <ul> <li>Code to generate figure 3</li> </ul> </li> <li>Figure5_PrairieVSCommonGarden <ul> <li>Code to generate figure 5</li> </ul> </li> <li>PATHOFigs_for_Manu_FEB22.Rmd <ul> <li>Code to generate figures 1, 2, 4</li> </ul> </li> <li>SUPP_Figure3_DimPathoEDIT.Rmd <ul> <li>Code to generate supplementary figure 3 (fig S3)</li> </ul> </li> <li>STATSAnalysis_PathoDim2B.Rmd <ul> <li>Code to generate all tables and statistical analysis in the manuscript</li> </ul> </li> </ul>   Description of data files: <ul> <li>2019and2020Prairie_data.txt <ul> <li>This file contains data collected from the prairie sites in 2019 and 2020</li> </ul> </li> <li>Dim2b_latlon.csv <ul> <li>The latitudinal and longitudinal coordinates for the common garden sites and prairie sites as well as precipitation data</li> </ul> </li> <li>DVTINDEX_from_DVT.csv <ul> <li>A separate file that contains the data that produced fig 3. This data file is sourced from SEPT2019_2020_COMPILED_2b_DATACOLL.txt</li> </ul> </li> <li>SEPT2019_2020_COMPILED_2b_DATACOLL.txt</li> <li>SEPT2019_2020_COMPILED_2b_DATACOLL_plots.txt</li> <li>SEPT2019_2020_COMPILED_2b_DATACOLL_plots_longversion.txt <ul> <li>These 3 data files are different versions of the same raw data that was collected from the common garden sites in 2019 and 2020. The code calls for all 3 at different points to generate plots and run statistical analyses</li> </ul> </li> <li>Summary [ insert unique name here] <ul> <li>Various data frames generated from r mark downs that contain summary statistics of the data. These are used to produce the figures in PATHOFigs_for_Manu_FEB22.Rmd graphs.</li> </ul> </li> </ul>

Data From: Evolution of woody plants to the land‐sea interface: The atypical genomic features of mangroves with atypical phenotypic adaptation

How plants adapt and diverge in extreme environments is a key question of plant evolution and ecology. Mangrove invasion of intertidal environments is facilitated by adaptive phenotypes such as aerial roots, salt-secreting leaf, and viviparity, and genomic mechanisms including whole genome duplication and transposable element number reduction. However, a number of mangroves lack these typical phenotypes. The question we ask is whether these phenotypically atypical mangroves also have distinct genomic features? The sibling mangrove species Lumnitzera littorea and Lumnitzera racemosa provide a model to study this question. We sequenced and assembled their genomes to chromosome level, together with a closely related species Combretum micranthum. While most mangroves have small genomes, the genomes of both Lumnitzera species are large (1443 and 1317 Mb) and carry a high proportion of repeat sequences (~75%). Moreover, Lumnitzera species have not undergone post-gamma whole-genome duplications. Their genome size increased mainly due to the expansion of repeat sequences in their ancestors. However, Lumnitzera genomes have reduced transposable elements by constraining the proliferation of new LTR-RTs. Meanwhile, the two species have more gene families contracted than expanded, and some gene families with reversed size change may underlie their differentiation in root morphology and local distribution. We identified 86 chromosomal inversions, five of which are measured between 6.5 and 12.8 megabases. A number of genes located in these inversions function in pigment biosynthesis, a process likely involved in flower color differentiation between the Lumnitzera species. We conclude that the mangroves with atypical phenotypes also have atypical genomic evolution.

openother-openSep 2021View details →

Supporting data and code for: Host plant and insecticides shape the evolution of genetic and clonal diversity in a major aphid crop pest

This is the first release of the final data and code for the article accepted for publication in Evolutionary Applications journal. It contains the necessary scripts to produce most of the analyses and figures of the manuscript. All the necessary data can be found in the 'data' folder.

opencc-zeroFeb 2023View details →

Area, connectivity and plant life strategy diversity and abundance in temporary ponds of Southeastern Carpathians (Romania, Europe)

We used this dataset to determine whether area and connectivity of temporary ponds can predict plant species diversity, and the diversity and abundance of different plant life histories within the ponds. The studied system is located in the Ciuc Basin of the Southeastern Carpathian Mountains, Romania. We collected data on the macrophyte species diversity of 28 temporary ponds between 2006-2009. Plant species identified in the ponds were assigned into one of the social behaviour types proposed by Borhidi (1995), which describe plant-habitat interactions within a framework extended from Grime's evolutionary life strategies (Grime 1988), as follows: competitors, stress tolerants (generalists or specialists) and ruderals (natural pioneers i.e., plants of habitats disturbed by natural factors, and plants of habitats disturbed by human factors, classified as either: disturbance tolerants, native weeds, naturalised crops, adventitious weeds, ruderal competitors, alien competitors). We expressed species diversity as observed species richness (total number of species) and Shannon diversity index, and abundance as cumulative vegetation cover, calculated for each pond and for each social behaviour type separately. We calculated pond area using the short and long axis of the ellipse that best approximated the pond shape. Pond connectivity with the Olt river was defined as the pond present and respectively past (preceding river regulation) geographic distance from the Olt river, measured between the pond GPS coordinate and the nearest point of the river.

Flower color and flowering phenology mediate plant-pollinator interaction assembly in a diverse co-flowering community

Uncovering the role of competition and facilitation in community assembly is central for developing a predictive understanding of the forces that organize biodiversity. Standard trait-based approaches however rely on detection of only one assembly mechanism (competition or facilitation) along a single trait even though pollinator-mediated plant-plant interactions can be structured along multiple phenotypic, phenological and ecological traits. We evaluated plant species distribution along multiple phenotypic and ecological traits (flower color, flowering time, pollinator sharing) and described an entire co-flowering community as a set of modules with unique patterns of assembly, to test predictions regarding the relative contribution of competition and facilitation to the assembly of a diverse co-flowering community. We show a modular pattern of flower color assembly. Flower color modules differ in their spectral reflectance patterns including color hue and saturation. Within modules, however, species are differentially assembled along phenological and ecological traits (pollinator sharing) depending on the main pollinator group visiting plant species within each module. Results suggest different trait assembly patterns within individual trait-modules in the same co-flowering community and that different trait-patterns can result from the same type of ecological interaction. This study reveals empirical evidence of community assembly along multiple axes of trait differentiation and raises caution when interpreting assembly patterns based on a single trait.

Long-term nitrogen fertilization alters arbuscular mycorrhizal fungi community phylogenetic structure in plant roots across fine spatial scales

Purpose: Nitrogen deposition due to human activities is known to have a substantial impact on arbuscular mycorrhizal fungi (AMF) community in plant roots. However, the influence of elevated nitrogen on the phylogenetic structure of AMF across fine spatial scales, as well as the mechanisms behind such alterations, are remained poorly understood. Results: Nitrogen addition significantly increased the phylogenetic alpha diversity (diversity within a plot) and the 'within-treatment' phylogenetic beta diversity (dissimilarity among replicate plots) of AMF communities, which resulted in an increased 'within-treatment' phylogenetic gamma diversity (overall diversity among all the replicate plots within a treatment). These changes were caused by the relative abundance decline of a dominant genus (Glomus) and an increase in non-dominant genera. Mechanically, nitrogen addition affected phylogenetic alpha diversity mainly by influencing soil properties. Likewise, the increased 'within-treatment' dissimilarity of plant community composition and changes in soil properties caused by nitrogen addition and plot distance contributed to an increase in within-treatment phylogenetic beta diversity. Conclusions: We conclude that deterministic environmental filtering (both abiotic and biotic) and dispersal limitation effect played critical roles in AMF community assembly under global change scenarios. Insightfully, this study provides a mechanistic understanding of the response of AMF to nitrogen addition across fine scales.

Savanna plant and soil carbon data from different burn seasons and histories across Mole National Park, Ghana

Aboveground plant pool and belowground (soil plus root) carbon data for a space-for-time substitution survey of different burn seasons and histories across Mole National Park, Ghana. Carbon data was collected to determine the impact of unintentional late growing season wildfires on carbon storage in a protected area dominated by early growing season prescribed burning land management. The methodology and findings from the study are detailed in the below publication: Awuah J, Smith SW, Speed JDM, Graae BJ. 2022. Can seasonal fire management reduce the risk of carbon loss from wildfires in a protected Guinea savanna? Ecosphere, e4283. https://doi. 88 org/10.1002/ecs2.4283  This data repository contains the following data (and descriptive metadata):  (1) Study_site_coordinates: locations for 28 sites surveyed in 2016 as part of an ecosystem carbon stock assessment (2) Aboveground_carbon: aboveground tree, shrub, herbaceous vegetation, deadwood and litter carbon stocks estimated from either destructive biomass sampling or allometric equations. Aboveground carbon data are presented per site.  (3) LOI_to_carbon_conversion: a subset of soil samples were analysed for both loss on ignition (LOI) and automated dry combustion using an elemental analyser, the latter more accurate for carbon determination and used to correct LOI values.  (4) Belowground_carbon: combined soil and root carbon collected collected to a maximum depth of 17 cm, and split into four soil layers (0-2 cm, 2-7 cm, 7-12 cm and 12-17 cm).  MCD14DL MODIS Active Fire Detections data used to defined different burn seasons and histories for sites has not been uploaded and is freely available from online sources detailed in the journal article.

opencc-by-4.0Dec 2021View details →

Weissflog et al. - Daytime but not plant trichomes provide herbivores with enemy-free space: of plasticine caterpillars, superheroes, and natural enemies.

RAW DATA We use artificial prey to quantify spatial and temporal variation in predation pressure on insect herbivores in two tropical rainforest sites in Panama.  We measured temporal and spatial variation in predation in the understory of the lowland rainforest of Barro Colorado Island in Panama [79°49.79´S, 9°9.48´E; 2600 mm yr-1 rainfall, 3 mo dry season; = island experiment) in February 2020 by comparing diurnal and nocturnal attacks on plasticine caterpillars and hulks placed on glabrous and pubescent plants. We used model prey to measure predation pressure. Caterpillars (50 x 4 mm) and hulks (with a height of 30 mm that equaled the maximum height of the bent caterpillars) were molded from green, (to humans) odorless, non-toxic Newplast (Newclay Products Ltd., Newton Abbot, UK). Caterpillars were shaped and bent to mimic the posture of common geometrid caterpillars. Hulks resembled small (but fearsome) superhero figurines, known from the Marvel comics (Marvel Worldwide Inc.), and were shaped using custom made plastic molds. We used hulks as a control to the more naturally shaped caterpillar models to test whether objects resembling natural prey are indeed recognized as such by potential predators. All objects were modeled and handled using surgical gloves to avoid leaving unwanted cues (i.e., scent or other distracting contaminants) to predators. A hundred caterpillars and a hundred hulks were individually placed on 50 plants per host species. Objects were attached close to the midrib on the upper surface of plant leaves with a small amount of fast-setting glue, 30-80 cm from the ground. For four consecutive days (total of 96 h), the plasticine objects were inspected in 12 hour intervals at dusk and dawn (18:15 and 06:15 hours) to differentiate diurnal from nocturnal predation. Further, we conducted a follow-up experiment in a close-by mainland forest site in Gamboa, Parque Nacional Soberanía (79°43.38 S, 9°8.24 E; = mainland study) in early-March 2021. Following the same procedure as for the island experiment described above, we glued 27 caterpillars, 27 hulks, and 27 small caterpillars (30 x 2 mm) close to the midrib onto the upper side of leaves of tree saplings. In this follow-up experiment, we did however not select specific plant species, but chose saplings that were naturally growing in the field site. All plants were of similar size, with simple, elliptic to ovate, smooth-edged leaves, and without any foliar or stem pubescence. As before, all objects were carefully inspected for attack marks at 12 hour intervals at 18:15 and 06:15 hours for four consecutive days.

Proximate Chemical Analyses of Black Soldier Fly Frass (BSFF), Common House Cricket Frass (CHCF), and NPK 15:15:15 Granulated Slow-Release Fertilizers, Universiti Sains Malaysia Plant House Top Soil, and all Post-harvest Soils of applied Fertilizers.

Proximate Chemical Analyses of Black Soldier Fly Frass (BSFF), Common House Cricket Frass (CHCF), and NPK 15:15:15 Granulated Slow-Release Fertilizers, Universiti Sains Malaysia Plant House Top Soil, and all Post-harvest Soils of applied Fertilizers.

Raw data for the manuscript entitled "Forest age and topographic position jointly shape the species richness and composition of vascular plants in karstic habitats"

Doline surveys from the Mecsek Mountains, Hungary. Transects were established with north to south orientation across each doline, traversing their deepest point. Transects began and ended on doline rims, and consisted of 1 m  × 1 m plots spaced at 2 m intervals (94, 89, 90 and 99 plots in the different forest age classes, respectively; 372 plots in total). We recorded the presence/absence data of shrubs and herbs in each plot. Fieldwork was carried out between 2007 and 2019 from June to August, at the peak of the growing season.

openother-openJul 2022View details →

Data from: Effects of climate change on plant resource allocation and herbivore interactions in a Neotropical rainforest shrub

Data from "Effects of climate change on plant resource allocation and herbivore interactions in a Neotropical rainforest shrub" published in Ecology and Evolution. doi.org/10.1002/ece3.9198

Cryptogam plant community stability: warming weakens influences of species richness but enhances effects of evenness

Community stability is a fundamental factor sustaining ecosystem functioning and is affected by species richness and species evenness. The Arctic is warming more rapidly than other biomes, and cryptogam plant species (specifically lichens and bryophytes in this study) are major contributors to tundra biodiversity and productivity. However, to our knowledge, the impacts of warming on cryptogam community stability and the underlying mechanisms have not been investigated. We conducted a 13-year summer warming experiment in mesic birch hummock tundra vegetation near Daring Lake in the continental interior of low Arctic Canada, and recorded patterns of cryptogam species abundance in several different growing seasons. Warming decreased the stability of total community abundance, had no effects on species richness, but increased species evenness and species synchrony. Structural equation model analyses indicated that higher species richness was the principal factor associated with the stronger community abundance stability in the control plots, and that this effect was driven primarily by a negative correlation with species synchrony. By contrast, higher species evenness was the principal factor associated with the weakened community abundance stability in the warming plots, and this effect was driven primarily by a positive correlation with species synchrony. Our study suggests that climate warming could reduce cryptogam plant community stability in low Arctic tundra, and therefore decrease important ecosystem services including carbon storage and food availability to caribou in northern regions.

The role of tetradecane in the identification of host plants by the pest bugs Apolygus lucorum and Adelphocoris suturalis

Apolygus lucorum and Adelphocoris suturalis are considered serious pests to many cultures in China. Safe alternatives are needed to manage these mirid pests. The current study identified compounds from volatiles of the ethanol extracts of Phaseolus vulgaris pods and the other 10 common hosts. GCMS detection showed that tetradecane, 2-propyl-1-pentanol, and dodecanal were included in these volatiles and tetradecane was present in all the volatiles.

Ineffectiveness of ants in the reproductive success of two sympatric myrmecophilous plants: the success of endophytic beetles

Extrafloral nectaried plants attract ants, which may protect them against herbivory and increase plant fruit set production. In some cases, however, ants are ineffective against herbivores. Such events occur, for instance, when herbivores present adaptations to avoid ant predation. Thus, the outputs of these interactions depend on factors such as ant identity, plant phenology, and herbivore features. Here, we investigated the endophytic florivorous beetles’ impact on the reproductive success of their host plants, two sympatric Banisteriopsis (Malpighiaceae) species, depending on the action of EFNs visiting ants. We experimentally manipulated the presence of ants and herbivores on B. malifolia and B. laevifolia species during their reproductive period. We performed treatments where three similar inflorescences were selected to be (I) control branch, with no manipulations, (II) beetle-free branch, isolated with textile cover, and (III) ant-free branch, isolated at the base with atoxic wax. As a result, we observed (i) that florivorous Anthonomus beetles have a negative impact on Banisteriopsis reproductive success; (ii) ants fail in protecting plants against floral endophytic beetles; and (iii) most of the results were specie-specific. Our results indicate that these systems present very conditional outcomes that depend on THE intrinsic factors of each plant species.

Plant root growth against a mechanical obstacle: The early growth response of a maize root facing an axial resistance is consistent with the Lockhart model

Plant root growth is dramatically reduced in compacted soils, affecting the growth of the whole plant. Through a model experiment coupling force and kinematics measurements, we probed the force-growth relationship of a primary root contacting a stiff resisting obstacle, that mimics the strongest soil impedance variation encountered by a growing root. The growth of maize roots just emerging from a corseting agarose gel and contacting a force sensor (acting as an obstacle) was monitored by time-lapse imaging simultaneously to the force. The evolution of the velocity field along the root was obtained from kinematics analysis of the root texture with a PIV derived-technique. A triangular fit was introduced to retrieve the elemental elongation rate or strain rate. A parameter-free model based on the Lockhart law quantitatively predicts how the force at the obstacle modifies several features of the growth distribution (length of the growth zone, maximal elemental elongation rate, velocity) during the first 10 minutes. These results suggest a strong similarity of the early growth responses elicited either by a directional stress (contact) or by an isotropic perturbation (hyperosmotic bath).

opencc-by-4.0Dec 2021View details →

Plasmid Sequences for Brophy et al., 2022: Synthetic genetic circuits as a means of reprogramming plant roots

Plasmid Sequences for Brophy et. al. 2022: Synthetic genetic circuits as a means of reprogramming plant roots

opencc-zeroAug 2022View details →

Invasive plant species that experience lower herbivory pressure may evolve lower diversities of chemical defence compounds in the exotic range

ABSTRACT PREMISE Invasive plant species often escape from specialist herbivore species and are likely to experience herbivory mostly from generalist herbivore species in the exotic range. Consequently, the Shifting Defence Hypothesis (SDH) predicts that invasive plants will express higher concentrations of qualitative defence compounds to deter dominant generalist herbivores in the exotic range. Here, I additionally propose a Reduced Chemical Diversity Hypothesis (RCDH), which predicts that reduced herbivory pressure will select for invasive plant genotypes that produce lower diversities of defence compounds in the exotic range. METHODS I tested whether: (1) Invasive Brassica nigra populations express a lower diversity and an overall higher concentration of glucosinolate compounds than native-range B. nigra; (2) Brassica nigra individuals that express high diversities and concentrations of glucosinolates are more attractive to specialist and deterrent to generalist herbivores; (3) Tissues of invasive B. nigra are less palatable to two generalist herbivores Theba pisana and Helix aspersa than tissues of native-range B. nigra. RESULTS Invasive B. nigra populations expressed a significantly lower diversity of glucosinolate compounds and a marginally higher concentration of total glucosinolate compounds. Leaf tissues of the invasive B. nigra were significantly less palatable to T. pisana and marginally less so to H. aspersa. Brassica nigra individuals that expressed high concentrations of total glucosinolate compounds were visited by a low diversity of generalist herbivore species in the field. CONCLUSIONS The biogeographical differences in glucosinolate profiles of invasive and native-range populations of B. nigra may be the result of differential herbivore selection pressures in the respective ranges.

opencc-zeroAug 2022View details →

Older populations of the invader Solidago canadensis exhibit stronger positive plant-soil feedbacks and competitive ability in China

PREMISE The enemy release hypothesis predicts that release from natural enemies, including soil-borne pathogens, liberates invasive plants from a negative regulating force. Nevertheless, invasive plants may acquire novel enemies and mutualists in the introduced range, which may cause variable effects on invader growth. However, how soil microorganisms may influence competitive ability of invasive plants along invasion chronosequences has been little explored. METHODS Using the invasive plant Solidago canadensis, we tested whether longer residence times are associated with stronger negative plant-soil feedbacks and thus weaker competitive abilities at the individual level. We grew S. canadensis individuals from 36 populations with different residence times in competition versus no competition and in three different types of soils: (1) conspecific rhizospheric soils, (2) soil from uninvaded patches, and (3) sterilized soil. For our competitor treatments, we constructed synthetic communities of four native species Bidens parviflora, Solanum nigrum, Kalimeris indica, and Mosla scabra, which naturally co-occur with S. canadensis in the field. RESULTS Solidago canadensis populations with longer residence times experienced stronger positive plant-soil feedbacks and had greater competitive responses (i.e., produced greater above-ground biomass and grew taller) in conspecific rhizospheric soils than in sterilized and uninvaded soils. Moreover, S. canadensis from older populations significantly suppressed above-ground biomass of the native communities in rhizospheric and uninvaded soils but not in sterilized soil. CONCLUSIONS The present results suggest that older populations of S. canadensis experience stronger positive plant-soil feedback, which may enhance their competitive ability against native plant communities.

opencc-zeroAug 2022View details →

Floral visitation to alien plants is non-linearly related to their phylogenetic and floral similarity to native plants

Biological invasions are key to understanding ecological processes that determine the formation of novel interactions. Alien species can negatively impact floral visitation to native species, but native species may also facilitate early establishment of closely related alien species by providing a preadapted pollinator community. We tested whether floral visitation to alien species depended on phylogenetic relatedness and floral similarity to native species. In a field experiment, we simulated the early stages of an invasion by adding potted alien plants into co-flowering native communities. We paired each alien plant with a host native plant, and recorded floral visitation to them for 3,068 hours (totalling 84,814 visits). We used 34 alien and 20 native species in 151 species combinations. We tested whether the number of floral visits to alien plants, the proportion of visits to alien plant relative to visits to both alien and native plants, and the similarity in flower visitor compositions of alien and native plants depended on phylogenetic and floral trait distances between alien and native species. Floral visitation to alien species was highest when they had intermediate floral trait distances to native species, and either low or high phylogenetic distances. Alien species received more similar flower-visitor groups to natives when they had low phylogenetic and either low or high floral trait distances to native species. Co-flowering native species may facilitate floral visitation to closely related alien species, and distantly related alien plants seem to avoid competition for flower visitors with native plants. Alien species with similar floral traits to natives compete with them for flower visitors, and alien species with dissimilar floral traits may not share flower visitors with native species. Alien species with intermediate floral trait distances to natives are most likely to receive flower visitors, as they are not too dissimilar and may still share flower visitors with native species, but not too similar to compete for flower visitors with them. The non-linear patterns between floral visitation and similarity of the alien and native species suggest that an interplay of facilitation and competition simultaneously drives the formation of novel plant-pollinator interactions.

Data from: Integrating herbivore assemblages and woody plant cover in an African savanna to reveal how herbivores respond to ecosystem management

African savannas are experiencing anthropogenically-induced stressors that are accelerating the increase of woody vegetation cover. To combat this, land managers frequently implement large-scale clearing of trees, which can have a cascading influence on mammalian herbivores. Studies rarely focus on how differences in woody cover influence the herbivore assemblage, making it difficult to assess how aggressive measures, or the lack of management, to counteract increasing woody cover affect the local composition and biodiversity of herbivores. We address this knowledge gap by applying a model-based clustering approach to field observations from to identify multiple herbivore–vegetation ‘configurations,’ defined as unique sets of herbivore assemblages (i.e., groups of herbivores) associated with differing woody plant covers. Our approach delineated how tree-clearing influences the distribution and abundance of the herbivore community in relation to surrounding savanna areas, which represent a natural mosaic of varying woody cover. Regardless of season, both intensively managed areas cleared of trees and unmanaged areas with high tree cover contained configurations that had depauperate assemblages of herbivores (low species richness, low abundance). By contrast, habitats with intermediate cover of woody vegetation had much higher richness and abundance. These results have substantial implications for managing African savannas in a rapidly changing climate.