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openCC (other)Feb 2022View details →

Effects of chronic nutrient enrichment on plant diversity and ecosystem productivity, 2008-2019

Human activities are enriching many of Earth's ecosystems with biologically limiting mineral nutrients such as nitrogen (N) and phosphorus (P). In grasslands, this enrichment generally reduces plant diversity and increases productivity. The widely demonstrated positive effect of diversity on productivity suggests a potential negative feedback, whereby nutrient induced declines in diversity reduce the initial gains in productivity arising from nutrient enrichment. In addition, plant productivity and diversity can be inhibited by accumulations of dead biomass, which may be altered by nutrient enrichment. Over longer timeframes, nutrient addition may increase soil fertility by increasing soil organic matter and nutrient pools. We examined the effects of 5-11 years of nutrient addition at 47 grasslands in twelve countries. Nutrient enrichment increased aboveground live biomass and reduced plant diversity at nearly all sites, and these effects became stronger over time. We did not find evidence that nutrient induced losses of diversity reduced the positive effects of nutrients on biomass, however nutrient effects on live biomass increased more slowly at sites where litter was also increasing, regardless of plant diversity. This work suggests that short-term experiments may underestimate the long term nutrient enrichment effects on global, grassland ecosystems.

openCC (other)Oct 2022View details →

Baltimore Ecosystem Study: Increased diversity of the regional species pool via seeding augments establishment of native species in experimental vacant lot restorations

The harsh geophysical template characterized by the urban environment combined with people’s choices has led ecologists to invoke environmental filtering as the main ecological phenomena explaining urban biodiversity patterns. Yet, dispersal is often overlooked as a driving factor, especially on expanding vacant land. Does overcoming dispersal limitation by seeding native species in urban environments and increasing the functional or phylogenetic diversity of the seeding pool increase native plant species diversity and abundance in urban vacant land? We took an experimental approach to learn how different dimensions of plant biodiversity within an augmented regional species pool, via seed additions, can explain variation in community structure over a 3-year period. Vacant lots were cleared and manipulated with seeding treatments of high or low phylogenetic and functional diversities from a pool of 28 native species. Establishment success, total native cover and native species richness were followed and compared to cleared, unseeded control lots as well as un-manipulated lots. Seeding increased native plant abundance and richness over uncleared plots, as well as cleared and unseeded control plots. Phylogenetically diverse seed mixtures had greater establishment success than mixtures composed of closely related species. Diversifying seed mixtures increased the likelihood of including species that are better able to establish on vacant land. However, there were no differences in varying levels of either functional or phylogenetic diversity. Augmenting the regional species pool via diverse seed mixtures can enhance native plant cover and richness under the harsh environmental conditions conferred by land abandonment.

openCC0Sep 2024View details →

Tree mortality in Forest and Biodiversity 2: a tree diversity experiment to understand the consequences of multiple dimensions of diversity and composition for long-term ecosystem function and resilience

openCC0Mar 2025View details →

FAB2_sapling_volume_2021-2022 in Forest and Biodiversity 2: a tree diversity experiment to understand the consequences of multiple dimensions of diversity and composition for long-term ecosystem function and resilience

openCC0Mar 2025View details →

fab2_allometry_2016-2022 in Forest and Biodiversity 2: a tree diversity experiment to understand the consequences of multiple dimensions of diversity and composition for long-term ecosystem function and resilience

openCC0Jan 2026View details →

Predicting aboveground and belowground processes in diverse forest ecosystems using remote sensing and in-situ measurements

The Forest and Biodiversity (FAB2) experiment uses native tree species in varying levels of species richness, phylogenetic diversity, and functional diversity planted in 100 m2 and 400 m2 plots at 1 m spacing, appropriate for testing long-term ecosystem consequences. FAB2 was designed and established in conjunction with a prior experiment (FAB1) in which the same set of twelve species was planted in 16 m2 plots at 0.5 m spacing. This data package examines the connections between aboveground and belowground processes in FAB2. This data package includes information on tree diversity and community composition, forest structure, forest understories, soil microbes, net nitrogen mineralization, and canopy nitrogen. A wide variety of data types are included, such as data from hyperspectral and LiDAR remote sensing, percent cover analysis, soil microbial analyses, and soil assays including C:N, pH, and net nitrogen mineralization. This data package is included in the submission of the manuscript entitled “Predicting aboveground and belowground processes in diverse forest ecosystems using remote sensing and in-situ measurements.”

openCustomJan 2020View details →

Study of Salt Marsh Consumer Diversity and Ecosystem Function on Sapelo Island, Georgia, from May-December 2011

This dataset contains the results of a field study investigating the effect of salt marsh consumer diversity on ecosystem functioning. Our field studies reveal that a diverse consumer assemblage significantly enhances simultaneous functioning of disparate ecosystem processes (i.e., productivity, decomposition, and infiltration). Extreme functional and phylogenetic differences among consumers underlie this relationship. Each marsh consumer affected at least one different ecosystem function and each individual function was affected by more than two consumers.

zenodo44/100

Accompanying dataset; 'Agroforestry enhances biological activity, diversity and soil-based ecosystem functions in mountain agroecosystems of Latin America: A meta-analysis.'

The database created as part of the meta-analysis is designed to facilitate the comparison of biological activity, diversity (BIAD), and ecosystem functions (EFs) between agroforestry systems (AFS) and other land-use types. It incorporates data extracted from selected studies, each record comprising a mean value, sample size, and a variance measure to compute standard deviation. The database also categorizes data according to 22 explanatory variables, including geographical coordinates, climate classification, soil type, AFS classification, and more, to characterize the sites and management systems involved. This detailed classification enables a nuanced analysis of how different factors might influence the BIAD and EFs in the context of AFS. The database supports the meta-analysis by allowing for the estimation of effect sizes using response ratios, which compare the relative difference in BIAD and EFs between AFS and other land uses. Data extraction from primary studies was meticulous, employing both direct and indirect methods such as graph digitizing software, and missing data were supplemented using reliable sources or direct communication with the original study authors. The comprehensive nature of this database ensures that the analysis can account for a wide range of variables that may affect the outcomes of interest in the meta-analysis. For an in-depth exploration of the study's findings and methodology, refer to the comprehensive meta-analysis available in Global Change Biology (2024), entitled "Agroforestry Enhances Biological Activity, Diversity, and Soil-Based Ecosystem Functions in Mountain Agroecosystems of Latin America: A Meta-Analysis."

opencc-by-4.0Nov 2023View details →

edi44/100

Data from publication: Castillioni, K., & Isbell, F. (2023). Early positive spatial selection effects of beta-diversity on ecosystem functioning. Landscape Ecology, 1-15.

Data from publication: Castillioni, K., & Isbell, F. (2023). Early positive spatial selection effects of beta-diversity on ecosystem functioning. Landscape Ecology, 1-15. Spatial beta-diversity may increase landscape productivity if there are positive spatial selection effects. Alternatively, dominant species in mixtures might not be the most productive species in monoculture leading to negative or neutral spatial selection effects. However, these hypotheses remain untested experimentally. Seedling survival can determine species establishment, influencing productivity later. To address this knowledge gap, we experimentally tested whether transplanted seedlings of dominant species optimally sort among habitat types (grassland dominated by Andropogon gerardii, savanna by Quercus macrocarpa, deciduous forest by Acer rubrum, coniferous forest by Pinus strobus, bog by Larix laricina), creating positive effects of landscape diversity on seedling survival and net biodiversity effects at Cedar Creek Ecosystem Science Reserve (CCESR) in Minnesota, USA. The study is named BetaDIV and consists of 100 plots (20 plots per habitat × 5 habitats). Each of the five habitats includes two true replicate monocultures for each of the five species and two true replicates for each of the five possible mixture compositions of four species (leaving each one out in turn to eventually explore the effect of species identity). Each plot is 1.5 by 1.5 m, with 12 seedlings planted 0.5 m apart in a 4 × 4 square grid, except in the plot corners. In the early June 2022, we tagged and planted all seedlings (i.e., bareroot seedlings for trees and plugs for the grass A. gerardii). Two weeks after the initial transplanting, we started tracking seedling survival (presented here) to investigate how seedlings responded to local habitat conditions. We conducted a seedling census for each of the 1200 tagged seedlings (12 seedlings per plot×100 plots), in early September 2022, which was two months at the end

openCC0Nov 2023View details →

opencc-zeroApr 2024View details →

Scripts and data for: Integrating different facets of diversity into food web models: how adaptation among and within functional groups shape ecosystem functioning

Adaptation of communities to environmental fluctuations can emerge from different facets of biodiversity, which may impact ecosystem functioning differently. Previous work examined how ecosystem functions can be influenced by two sources of adaptive potential: sorting (i.e., changes in community composition due to fitness differences) can occur when multiple species or groups are present (richness), and trait adaptability (i.e., trait adjustments within species or functional groups) can emerge from genetic or phenotypic diversity. However, their effect is typically studied separately, and often in the context of only one trophic level. Therefore, we used a bitrophic trait-based model varying in richness and in the presence of trait adaptability at each trophic level, to investigate how sorting and trait adaptability, at one or two trophic levels, separately or jointly shape ecosystem functions. We found that the adaptive potential emerging from any facet of diversity-induced changes in trophic interactions, in turn, affects biomass distributions within and across trophic levels, dynamical behaviour, and synchrony of biomass dynamics within a trophic level. Particularly, sorting and trait adaptability could contribute to a similar degree and at a similar time to temporal changes in ecosystem functions, but their respective contribution depended on the speed of trait adaptation, the trait range between similar functional groups, and trophic interactions. We thus suggest to consider multiple facets of diversity and their corresponding sources of adaptive potential to deepen our mechanistic understanding of ecosystem functioning, especially in a context of rapid biodiversity change.

opencc-by-4.0Feb 2022View details →

ITS1 metabarcoding revealing Phytophthora diversity in anthropized and natural ecosystems in Sicily, Italy

This dataset on Zenodo contains the raw sequencing data for: <a href="https://doi.org/10.3390/jof8040330">La Spada et al. (2022) DNA Metabarcoding and Isolation by Baiting Complement Each Other in Revealing Phytophthora Diversity in Anthropized and Natural Ecosystems</a>. This a subset of 192 demultiplexed Illumina MiSeq raw sequencing samples run at the James Hutton Institute in January 2020, consisting of two 96-well plates labelled with the Illumina A and D multiplexing kits. There are 61 pairs of raw gzipped compressed FASTQ files (122 files), provided as a 930MB gzipped compressed tar-ball. From the D multiplexing kit, there are 27 Nature Reserve (NR) samples, 16 Botanical Garden (BG) samples, and 6 managed Citrus Orchard (CO) samples containing Phytophthora targeted ITS1 marker sequences, and 6 synthetic controls (prefix GL1D) which should have contained only four known synthetic sequences. Additionally included are the 6 synthetic controls (prefix GL1A) from the A multiplexing kit, which were clean. The filenames start with the sample name, followed by something like DH03_S183_L001_R1_001.fastq.gz where DH03 indicates well H03 on the 96-well plate labelled with the D multiplexing set, S183 is the MiSeq sample number (from 1 to 192), and R1 (or R2) indicate the Illumina forward (or reverse) paired read files.

opencc-by-4.0Apr 2022View details →

Fig. 5 in Factors Affecting Avifaunal Diversity In Selected Agro-Ecosystems Of Himachal Pradesh Agricultural University, Palampur, Himachal Pradesh, India

Fig. 5. The heatmap transformed data shows the contributions of different feeding guilds of bird species for clustering of habitats. Blue colour represents negative contribution while red represents positive contribution.

opencc-zeroJul 2022View details →

Data from: Diversity among rare and common congeneric plant species from the Garry oak and Okanagan shrub-steppe ecosystems in British Columbia: implications for conservation

Using universal non-coding chloroplast DNA markers (cpDNA), we investigated genetic diversity and genetic structure in four rare and common plant species pairs inhabiting threatened ecosystems (Garry Oak and Okanagan shrub-steppe) in British Columbia. The species found in the Garry oak ecosystem are: Sanicula bipinnatifida (purple sanicle; Apiaceae; rare), Sanicula crassicaulis (Pacific sanicle; Apiaceae; common), and Balsamorhiza deltoidea (deltoid balsamroot; Asteraceae; rare). The species found in the Okanagan shrub-steppe ecosystem are: Balsamorhiza sagittata (arrowleaf balsamroot; Asteraceae; common), Orthocarpus barbatus (Grand Coulee owl-clover; Orobanchaceae; rare), Orthocarpus luteus (yellow owl-clover; Orobanchaceae; common), Phacelia ramosissima (branching phacelia; Hydrophyllaceae; rare), and Phacelia linearis (thread-leaved phacelia; Hydrophyllaceae; common). Eight cpDNA regions were sequenced for each study species. Sequences were aligned and concatenated within each species, and single nucleotide polymorphisms (SNPs) were used to analyze patterns of regional genetic diversity and phylogeographic structure within genera and species. Results include: total gene diversity (Ht), nucleotide diversity (π), number of private alleles, haplotype networks, isolation by distance, and analysis of molecular variance.

opencc-zeroSep 2022View details →

Vegetation and vantage point influence visibility across diverse ecosystems: implications for animal ecology

Visual information can influence animal behavior and habitat use in diverse ways. Visibility is the property that relates 3D habitat structure to accessibility of visual information. Despite the importance of visibility in animal ecology, this property remains largely unstudied. Our objective was to assess how habitat structure from diverse environments and animal position within that structure can influence visibility. We gathered terrestrial lidar data (1 cm at 10 m) in four ecosystems (forest, shrub-steppe, prairie, and desert) to characterize viewsheds (i.e., estimates of visibility based on spatially explicit sightlines) from multiple vantage points. Both ecosystem-specific structure and animal position influenced potential viewsheds. Generally, as height of the vantage point above the ground increased, viewshed extent also increased, but the relationships were not linear. In low-structure ecosystems (prairie, shrub-steppe, and desert), variability in viewsheds decreased as vantage points increased to heights above the vegetation canopy. In the forest, however, variation in viewsheds was highest at intermediate heights, and markedly lower at the lowest and highest vantage points. These patterns are likely linked to the amount, heterogeneity, and distribution of vegetation structure occluding sightlines. Our work is the first to apply a new method that can be used to estimate viewshed properties relevant to animals (i.e., viewshed extent and variability). We demonstrate that these properties differ across terrestrial landscapes in complex ways that likely influence many facets of animal ecology and behavior.

openother-openOct 2022View details →

Planktonic functional diversity changes in synchrony with lake ecosystem state

Abstract Managing ecosystems to effectively preserve function and services requires reliable tools that can infer changes in the stability and dynamics of a system. Conceptually, functional diversity (FD) appears a sensitive and viable monitoring metric stemming from suggestions that FD is a universally important measure of biodiversity and has a mechanistic influence on ecological processes. It is however unclear whether changes in FD consistently occur prior to state responses or vice versa, with no current work on the temporal relationship between FD and state to support a transition towards trait-based indicators. There is consequently a knowledge gap regarding when functioning changes relative to biodiversity change and where FD change falls in that sequence. We therefore examine the lagged relationship between planktonic FD and abundance-based metrics of system state (e.g. biomass) across five highly monitored lake communities using both correlation and cutting edge non-linear empirical dynamic modelling approaches. Overall, phytoplankton and zooplankton FD display synchrony with lake state but each lake is idiosyncratic in the strength of relationship. It is therefore unlikely that changes in plankton FD are identifiable before changes in more easily collected abundance metrics. These results highlight the power of empirical dynamic modelling in disentangling time lagged relationships in complex multivariate ecosystems, but suggest that FD cannot be generically viable as an early indicator. Individual lakes therefore require consideration of their specific context and any interpretation of FD across systems requires caution. However, FD still retains value as an alternative state measure or a trait representation of biodiversity when considered at the system level. Dataset The deposited dataset contains scripts used in functional diversity, cross correlation and convergent cross mapping analysis, the generation of figures and the custom functions underpinning the work. Raw plankton data is not provided but links to publicly available data portals and maintainer contact details are provided.

opencc-zeroMay 2024View details →

Mesophotic coral ecosystems of French Polynesia are hotspots of alpha and beta generic diversity for scleractinian assemblages

Revealing how diversity varies across the depth gradient is key to understanding the role of mesophotic coral ecosystems in the functioning of coral reefs. We examined how alpha and beta generic diversity of scleractinian coral assemblages vary across a wide depth gradient for coral reefs. We studied generic diversity patterns of scleractinian corals at sixteen sites in eight islands of three archipelagos in French Polynesia, as derived from the analysis of photo-quadrats, across the seafloor from shallow to lower mesophotic depths (6 to 120 m) and on a wide geographic scale. Our sampling considered quantitative coral cover to explore the patterns of alpha and beta components of diversity across depth and horizontal space. We show that in French Polynesia, mesophotic coral ecosystems host higher alpha and beta generic diversity than shallow reefs despite decreasing coral cover with depth. The variation of coral genus richness across the depth gradient is mainly driven by a mid-domain effect with a peak at 40 m depth. At the same time, we found that the turnover of coral genera across islands (i.e., spatial beta diversity) increased steadily along the depth gradient. Our findings report the first quantitative results of coral cover and diversity from mesophotic coral ecosystems in French Polynesia and also present one of the few existing studies to examine the broad breadth of the mesophotic depth gradient. We demonstrate that mesophotic depths can host unexpectedly high generic richness of scleractinian coral assemblages. At the same time, we showed that increasing depth increases the differences in generic diversity composition across islands, whereas shallow reefs are similar in between. While a single island could conserve shallow regional biodiversity, mesophotic depths containing the richest diversity require site-specific measures, suggesting that considering these mesophotic depths in conservation is necessary to maintain regional diversity.

opencc-by-4.0Dec 1995View details →

Fig. 6 in SPECIFIC AND TROPHIC DIVERSITY OF SOIL NEMATODES IN FOREST ECOSYSTEMS FROM THE ZARAND MOUNTAINS

Fig. 6. - Relative abundance of the nematode FEeding groups in podzolic brown soil of the dmmast oak FOrest FRom BIIrzava (b).

opencc-by-4.0Dec 1995View details →

Fig. 5 in SPECIFIC AND TROPHIC DIVERSITY OF SOIL NEMATODES IN FOREST ECOSYSTEMS FROM THE ZARAND MOUNTAINS

Fig. 5. - Relative abundance of the nematode feeding groups in brown earth soil of the durmast oak forest from Corbe�ti.