Find research datasets worth reusing

openOpenMar 2017View details →

Fungal community structure associated with experimentally outplanted white spruce seedlings and the closest Salix and Betula nana shrubs, Toolik Lake, AK.

This dataset contains characterizations of fungal community structure associated with experimentally outplanted seedlings and adjacent naturally established resprouting shrubs.

openCustomJan 2020View details →

Tree, shrub, and herb data from 10 Hillslope Project sites located in Macon County, North Carolina, within the Upper Little Tennessee River Basin

Vegetation was surveyed on 10 sites in the upper Little Tennessee River watershed in Macon County, North Carolina during the summer of 2012. The sites represent a gradient of development, including forested sites, agricultural sites, and exurban sites. All woody vegetation >2.5 cm diameter at breast height (DBH) was measured and identified within twelve 10 x 10 m plots at each site. Woody shrubs >0.5 m in height and <2.5 cm DBH were counted and identified within a 1x10 m transect in each plot. Herbs and woody plants <0.5m in height were identified and percent cover estimated in 3 1 x 1 m subplots located within each of the larger 10 x 10 m plots.

openOpenAug 2016View details →

Point-Quarter Harvested Plant Weight Measurements to Estimate Shrub ANPP in a Chihuahuan Desert Creosote Shrubland at the Sevilleta National Wildlife Refuge, New Mexico (2007- present)

In an effort to better quantify NPP of Creosotebush in the Five-Points region, it was decided to test the Point-Quarter method against the standard 1-m2 quadrat method that has been in use since 1998. Transects were laid out across the 5 mammal trapping webs as well as across burned and unburned plots of the Mixed Shrub site (MS). Repeat measures of the same bushes are performed seasonally. Whole shrubs of various size classes are collected and sorted and weighed to develop regressions for biomass.

openOpenJan 2020View details →

SGS-LTER Long Term Nitrogen Percentages in Grass, Forb and Shrub Species on the Central Plains Experimental Range, Nunn, Colorado, USA 1983 - 2008, ARS Stusy Number 6

This data package was produced by researchers working on the Shortgrass Steppe Long Term Ecological Research (SGS-LTER) Project, administered at Colorado State University. Long-term datasets and background information (proposals, reports, photographs, etc.) on the SGS-LTER project are contained in a comprehensive project collection within the Digital Collections of Colorado (http://digitool.library.colostate.edu/R/?func=collections&collection_id=3429). The data table and associated metadata document, which is generated in Ecological Metadata Language, may be available through other repositories serving the ecological research community and represent components of the larger SGS-LTER project collection. Additional information and referenced materials can be found: http://hdl.handle.net/10217/83462. Aboveground plant nitrogen dynamics monitoring consists of two separate data sets. a) Long-term peak-crop nitrogen concentrations have been sampled since 1983 annually from sites sampled for ANPP estimates across the CPER. Plots are clipped for ANPP in August each year and include moderately grazed sites in sections 24 and 25, ungrazed treatments at ESA and owl creek, coarse textured soils in owl creek, fine textured soils in section 25, as well as three catena topopositions in section 24. These datasets have been designed for monitoring and so it is advised to consider calcuating average based at the transect level. B) Seasonal dynamics of life-form (dominant grass, forb, shrub species) nitrogen concentrations were obtained from random grab samples of aboveground plant tissue are taken monthly from May-Aug. and in Oct., Dec., Feb., and April from 1983 – 2007 at sites where ANPP has been collected since 1983 (ESA, ridge, mid-slope and swale in section 24). The objectives are to assess annual/seasonal weather and site productivity/management with quantity and quality of forage and/or litter production. Combined, these two data sets also provide an estimate of nitrogen yield

openCustomJul 2012View details →

Photosynthetic capacity and electron transport rate for a chronosequence of shrub thickets on Hog Island, VA , 2012

Photosynthetic capacity and electron transport rate (ETR) was assessed for Morella cerifera shrubs at 4 sites ranging in age from 10 to 50 years on Hog Island, VA during June and July 2012 using a pulse amplitude modulated (PAM) leaf fluorometer.

openCustomFeb 2022View details →

Simulation data of barrier-shrub interactions from the Barrier3D model

Barrier3D (version 1.0) simulation results of shrub expansion and barrier migration behavior and morphology across a range of input conditions. Simulations vary by the presence or absence of shrubs, the characteristic dune growth rate (0.3-0.9 yr-1), relative sea-level rise rate (3-15 mm/yr), the maximum flow reduction coefficient (0.05-0.35), and the width of initial barrier morphology. Each row in the spreadsheet represents a unique model simulation, and each simulation belongs to one of two different experiments: 1) Barrier_evolution, which is designed to assess the ways in which shrubs alter barrier morphology and the rate and style of barrier retreat by running simulations with and without shrubs across broad ranges of relative sea-level rise rates and dune growth rates; and 2) Shrub_expansion, which explores the ways in which barrier morphologic evolution influences the rate and pattern of shrub expansion. To account for storm stochasticity in the model, each unique combination of parameter values was simulated 100 times. Simulations run for 1,000 model years for the Barrier_evolution experiment, and 150 years for the Shrub_expansion experiment, or until the barrier drowns. The location of the initial cluster of shrub establishment is randomly determined in the Barrier_evolution experiment, but is constrained to the first 100 m (2%) alongshore in the Shrub_expansion experiment. Results from the two experiments are contained in two different files: barrier_island_evolution.csv and shrub_expansion.csv. A table of parameter values, definitions, and sources for the shrub module used in the experiments is given in the file: parameter_values_sources.csv

opencc-by-4.0Jun 2020View details →

Vegetation data along alpine pasture-shrub gradients

Columns of dataset: <ul> <li>Species_richness: Number of species per plot</li> <li>Species_evenness: Pielou's eveness of species cover values</li> <li>Heterogeneity: Beta-diversity, average Jaccard distance to the other three plots within cover zone</li> <li>Nutrient_index: Cover-weighted average nutrient indicator value</li> <li>Light_index: Cover-weighted average light indicator value</li> <li>Water_index: Cover-weighted average humidity indicator value</li> <li>Gradients_ID: gradient identifier</li> <li>Dominant_shrub: Dominant shrub species (3 categories)</li> <li>Zonal_cover: Value of zonal cover in percent</li> <li>Plot_cover: Value of plot cover in percent</li> <li>Geology_4level: Substrate of parent material (4 categories)</li> <li>Geology_2level: Substrate of parent material (2 categories)</li> <li>Aspect_3level: Aspect (3 categories)</li> <li>Elevation: Elevation in m above sea level</li> <li>Steepness_perc: Terrain slope in percent</li> <li>Precipitation: Annual precipitation sum in mm</li> <li>Temperature: Mean annual temperature in °C</li> <li>Soil_phosphorus: Soil phosphorus extracted by AA-EDTA in mg/kg</li> <li>Soil_pH: pH of soil-water suspension</li> </ul>

opencc-zeroJul 2020View details →

Data from: Climate synchronises shrub growth across a high-arctic archipelago: contrasting implications of summer and winter warming

Climate change is most pronounced at high latitudes, where plant and animal populations are often strongly influenced by environmental fluctuations related to climate and weather. Environmental conditions can co-fluctuate over large distances and thereby synchronise primary production in space. However, large-scale studies of such spatiotemporal patterns remain rare in the Arctic, where short time-series and poor spatial replication have characterised the data available on both biotic and abiotic parameters. Here, we use dendrochronological tools to measure ring growth of a dominant dwarf shrub, the polar willow (Salix polaris Wahlenb.), previously found to reliably trace community-level vascular plant biomass production. We investigated climate drivers of vegetation growth and their role in the synchronisation of primary production across the rapidly warming archipelago of Svalbard (n = 8 sites, composed of 17 sub-sites, 0.06-293 km apart). We found contrasting effects of summer versus winter weather on ring growth and its spatial synchrony. Although an overall positive effect of summer temperature caused spatially synchronous growth, negative impacts of winter rain-on-snow events occurred only locally, potentially counteracting such synchrony. However, the anticipated increase in both summer temperature and spatial extent of rain-on-snow events, causing basal ice encapsulation of the vegetation, could change the relative importance of seasons for spatiotemporal dynamics of shrub growth. Because these shrub ring growth chronologies reflect annual fluctuations in total vascular plant biomass, fuelling the bottom-up controlled food-web, these results have large implications for our understanding of how climate change shapes tundra ecosystem productivity in time and space.

openother-openAug 2020View details →

Data from - Secondary metabolites in a neotropical shrub: spatiotemporal allocation and role in fruit defense and dispersal

Data from "Secondary metabolites in a neotropical shrub: spatiotemporal allocation and role in fruit defense and dispersal" published in Ecology in 2020. doi.org/10.1002/ecy.3192

opencc-zeroAug 2020View details →

Data from: Plant trait response of tundra shrubs to permafrost and nutrient addition

Plants may alter their strategies, such as growth and resource acquisition, as a result of climate change, especially in areas like the Arctic. These changes might affect in turn ecosystem functions and vegetation-climate interactions. Plant traits reflect both strategies and plant trade-offs in response to environmental conditions. In combination with observational data, experiments mimicking future climate conditions and data involving multiple leaf and stem traits, can contribute to a better mechanistic understanding of feedbacks between shrub growth strategies, permafrost thaw and carbon and energy fluxes. This dataset contains both metadata and plant trait data measured in individuals of four arctic shrub species under experimental conditions. The permafrost thaw and fertilization experiment (Peng et al., 2017) ran for four years (2011-2014) in the nature reserve of Kytalyk, north-eastern Siberia (70°49'N, 147°28'E). The shrub species, dominant at the research site, were the deciduous species Betula nana ssp. exilis (Sukazcev) Hultén and Salix pulchra Cham., and the evergreen species Ledum palustre ssp. decumbens (Aiton) Hultén and Vaccinium vitis-idaea L.

opencc-zeroSep 2020View details →

Data from: The history of tree and shrub taxa on Bol'shoy Lyakhovsky Island (New Siberian Archipelago) since the last interglacial uncovered by sedimentary ancient DNA and pollen data

Ecosystem boundaries, such as the Arctic-Boreal treeline, are strongly coupled with climate and were spatially highly dynamic during past glacial-interglacial cycles. Only a few studies cover vegetation changes since the last interglacial, as most of the former landscapes are inundated and difficult to access. Using pollen analysis and sedimentary ancient DNA (sedaDNA) metabarcoding, we reveal vegetation changes on Bol'shoy Lyakhovsky Island since the last interglacial from permafrost sediments. Last interglacial samples depict high levels of floral diversity with the presence of trees (Larix, Picea, Populus) and shrubs (Alnus, Betula, Ribes, Cornus, Saliceae) on the currently treeless island. After the Last Glacial Maximum, Larix re-colonised the island but disappeared along with most shrub taxa. This was probably caused by Holocene sea-level rise, which led to increased oceanic conditions on the island. Additionally, we applied two newly developed larch-specific chloroplast markers to evaluate their potential for tracking past population dynamics from environmental samples. The novel markers were successfully re-sequenced and exhibited two variants of each marker in last interglacial samples. SedaDNA can track vegetation changes as well as genetic changes across geographic space through time and can improve our understanding of past processes that shape modern patterns.

opencc-zeroDec 2016View details →

Data from: Does warming by open-top chambers induce change in the root-associated fungal community of the arctic dwarf shrub Cassiope tetragona (Ericaceae)?

Climate change may alter mycorrhizal communities, which impact ecosystem characteristics such as carbon sequestration processes. These impacts occur at a greater magnitude in Arctic ecosystems, where the climate is warming faster than in lower latitudes. Cassiope tetragona (L.) D. Don is an Arctic plant species in the Ericaceae family with a circumpolar range. C. tetragona has been reported to form ericoid mycorrhizal (ErM) as well as ectomycorrhizal (ECM) symbioses. In this study, the fungal taxa present within roots of C. tetragona plants collected from Svalbard were investigated using DNA metabarcoding. In light of ongoing climate change in the Arctic, the effects of artificial warming by open-top chambers (OTCs) on the fungal root community of C. tetragona were evaluated. We detected only a weak effect of warming by OTCs on the root-associated fungal communities that was masked by the spatial variation between sampling sites. The root fungal community of C. tetragona was dominated by fungal groups in the Basidiomycota traditionally classified as either saprotrophic or ECM symbionts, including the orders Sebacinales and Agaricales and the genera Clavaria, Cortinarius, and Mycena. Only a minor proportion of the operational taxonomic units (OTUs) could be annotated as ErM-forming fungi. This indicates that C. tetragona may be forming mycorrhizal symbioses with typically ECM-forming fungi, although no characteristic ECM root tips were observed. Previous studies have indicated that some saprophytic fungi may also be involved in biotrophic associations, but whether the saprotrophic fungi in the roots of C. tetragona are involved in biotrophic associations remains unclear. The need for more experimental and microscopy-based studies to reveal the nature of the fungal associations in C. tetragona roots is emphasized.

opencc-zeroDec 2016View details →

Data from: Do impacts of an invasive nitrogen-fixing shrub on Douglas-fir and its ectomycorrhizal mutualism change over time following invasion?

1. Impacts of invasive species may change in magnitude and even direction with invasion age. Impacts could increase as the population increases, individuals grow in size, and ecological changes accumulate. 2. We used a chronosequence approach to characterize the development of soil impacts over time following the invasion of Cytisus scoparius, a widespread nitrogen-fixing shrub thought to limit reforestation success. In a greenhouse experiment, we evaluated how abundance of ectomycorrhizal fungi, Douglas-fir performance, and leaf nitrogen changed across a 3-31 year chronosequence of invasion. Each of the chronosequence sites were clearcuts where reforestation efforts were unsuccessful and where C. scoparius invaded. To estimate the contributions of the invasion separately from contributions of the accompanying disturbance, i.e. deforestation, we included soils from both invaded and uninvaded patches in each site of the chronosequence. In a complementary soil conditioning experiment, we examined the separate effects of host absence and invader presence on the mycorrhizal mutualism, leaf nitrogen, and seedling growth. 3. Ectomycorrhizal colonization was lower in invaded soil, but this effect did not intensify with time. Despite the suppression of the mutualism, Douglas-fir grew larger in invaded soils. This positive response is likely due to nitrogen fertilization, a conclusion supported by higher concentrations of leaf nitrogen of Douglas-fir grown in invaded soils. While leaf N concentration increased with invasion duration, Douglas-fir survival and growth did not. Synthesis. Our findings suggest that soil impacts of an invader can develop rapidly and can be surprisingly stable over time. In such systems, recently invaded areas may be as difficult to restore as long invaded areas, especially where ectomycorrhizal fungi are important drivers of reforestation success. More chronosequence studies or long time series are needed to evaluate whether this is a general pattern.

opencc-zeroDec 2013View details →

Data from: Gene duplication, population genomics and species-level differentiation within a tropical mountain shrub

Gene duplication leads to paralogy, which complicates the de novo assembly of genotyping-by-sequencing (GBS) data. The issue of paralogous genes is exacerbated in plants, because they are particularly prone to gene duplication events. Paralogs are normally filtered from GBS data before undertaking population genomics or phylogenetic analyses. However, gene duplication plays an important role in the functional diversification of genes and it can also lead to the formation of postzygotic barriers. Using populations and closely related species of a tropical mountain shrub, we examine: (1) the genomic differentiation produced by putative orthologs, and (2) the distribution of recent gene duplication among lineages and geography. We find high differentiation among populations from isolated mountain peaks and species-level differentiation within what is morphologically described as a single species. The inferred distribution of paralogs among populations is congruent with taxonomy and shows that GBS could be used to examine recent gene duplication as a source of genomic differentiation of non-model species.

opencc-zeroFeb 2020View details →

Intraspecific variation in surface water uptake in a perennial desert shrub

<ol> <li class="p1">Despite broad recognition that water is a major limiting factor in arid ecosystems, we lack an empirical understanding of how this resource is shared and distributed among neighboring plants. Intraspecific variability can further contribute to this variation via divergent life-history traits, including root architecture. We investigated these questions in the shrub Artemisia tridentata and hypothesized that the ability to access and utilize surface water varies among subspecies and cytotypes.</li> <li class="p1">We used an isotope tracer to quantify belowground zone of influence in A. tridentata, and tested if spatial neighborhood characteristics can alter plant water uptake. We introduced deuterium-enriched water to the soil in plant interspaces in a common-garden experiment and measured deuterium composition of plant stems. We then applied spatially-explicit models to test for differential water uptake by A. tridentata, including intermingled populations of three subspecies and two ploidy levels. </li> <li class="p1">The results suggest that lateral root functioning in A. tridentata is associated with intraspecific identity and ploidy level. Subspecies adapted to habitats with deep soils generally had a smaller horizontal reach, and polyploid cytotypes were associated with greater water uptake compared to their diploid variants. We also found that plant crown volume was a weak predictor of water uptake, and that neighborhood crowding had no discernable effect on water uptake. </li> <li class="p1">Intraspecific variation in lateral root functioning can lead to differential patterns of resource acquisition, an essential process in arid ecosystems in the contexts of changing climate and seasonal patterns of precipitation. Altogether, we found that lateral root development and activity is more strongly related to genetic variability within A. tridentata than to plant size. Our study highlights how intraspecific variation in life strategies is linked to mechanisms of resource acquisition.</li> </ol>

opencc-zeroNov 2019View details →

Trophic rewilding revives biotic resistance to shrub invasion

Trophic rewilding seeks to rehabilitate degraded ecosystems by repopulating them with large animals, thereby reestablishing strong top-down interactions. Yet there are vanishingly few tests of whether such initiatives can restore ecosystem structure and functions, and on what timescales. Here we show that war-induced collapse of large-mammal populations in Mozambique's Gorongosa National Park exacerbated woody encroachment by the invasive shrub Mimosa pigra—one of the world's '100 worst' invasive species—and that one decade of concerted trophic rewilding restored this invasion to pre-war baseline levels. Mimosa occurrence increased between 1972 and 2015, a period encompassing the near-extirpation of large herbivores during the Mozambican Civil War. From 2015–2019, mimosa abundance declined as ungulate biomass recovered. DNA metabarcoding revealed that ruminant herbivores fed heavily on mimosa, and experimental exclosures confirmed the causal role of mammalian herbivory in containing shrub encroachment. Our results provide mechanistic evidence that trophic rewilding has rapidly revived biotic resistance to a notorious woody invader, underscoring the potential for restoring ecosystem structure and functions in degraded African protected areas.

opencc-zeroDec 2016View details →

Data from: Plant-soil feedbacks mediate shrub expansion in declining forests, but only in the right light

1. Contemporary global change, including the widespread mortality of foundation tree species, is altering ecosystems and plant communities at unprecedented rates. Plant-soil interactions drive myriad community dynamics, and we hypothesized such interactions may be an important driver of succession following the loss of foundation tree species. 2. We examined whether plant-soil biota interactions, in the context of a putatively important light gradient associated with foundation tree decline, mediate the expansion of Rhododendron maximum in southeastern US forests where Tsuga canadensis (eastern hemlock), a dominant foundation tree species, is in decline. Using an 11-month, controlled inoculation experiment paired with Illumina sequencing, we tested the following hypotheses: (1) Relative to conspecific (R. maximum-conditioned) soils, R. maximum seedlings have higher performance in soils conditioned by T. canadensis and lower performance in interspace soils (conditioned by neither T. canadensis nor R. maximum) due to variation in soil fungal biota, and (2) seedling performance is greater in high light versus low light environments (matching environments under infested versus uninfested T. canadensis crowns, respectively). 3. In partial support of the first hypothesis, we found that R. maximum seedling performance was highest in T. canadensis-conditioned and R. maximum-conditioned soils and lowest in interspace soils. Mechanistically, soils conditioned by T. canadensis and R. maximum had more ericoid and ectomycorrhizal fungi, less saprotrophic fungi, and were less species-rich than interspace soils, and variation in these community traits predicted substantial variation in R. maximum seedling biomass. However, in support of our second hypothesis, soil effects on plant performance were evident in high light only; in low light, soil inoculation did not affect plant performance and plants performed worse. 4. Synthesis. Our findings suggest interactions with soil biota act synergistically with altered abiotic environments to mediate species responses to widespread foundation tree mortality, providing evidence for a novel mechanism of plant response to large-scale disturbance. Examining plant-soil interactions in the context of relevant abiotic gradients can therefore enhance our understanding, predictions, and management of community development processes following forest disturbance.

opencc-zeroDec 2015View details →

Data from: Ecological and geographic dimensions of diversification in Piper subgenus Ottonia: a lineage of neotropical rainforest shrubs

The Neotropics are home to incomparable plant diversity. To evaluate the potential roles of geography and ecology on speciation in Neotropical plants we selected a small, tractable lineage of shrubby angiosperms, Piper subgenus Ottonia. We reconstructed a molecular phylogeny and provided insights into the species divergence times based on fossil calibration of the molecular clock. We support the monophyly of Piper subg. Ottonia and the two main lineages: Amazonian and Atlantic Forest, the latter containing the non-Atlantic species pair P. darienense‐P. piscatorum. We also propose the origin of Piper subg. Ottonia in the early Eocene and suggest that the diversification of Piper subg. Ottonia was influenced by geo-historical events such as the Paleocene-Eocene Thermal Maximum (PETM) and the uplift of the Andes in the Miocene, as is the case for other angiosperms. Furthermore, we combined our phylogeny with geographic and environmental data in order to evaluate geographical and ecological contexts for speciation. We indicate that neither climatic/edaphic divergence nor geographic isolation appears to be needed to explain speciation in this lineage.

opencc-by-4.0Dec 2023View details →

Data and code for "Shrubs inhibit plant diseases through reducing herbaceous biomass in alpine meadows"

Supplementary Data and code for "Shrubs inhibit plant diseases through reducing herbaceous biomass in alpine meadows"