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22 results for “Ecosystem assembly”
Data for "Ecosystem size filters life-history strategies to shape community assembly in lakes"
<p>Dataset 1. List of 71 fish species collected from north temperate lakes in Wisconsin USA. Data include critical life-history data used for strategy classifications according to Winemiller and Rose (1992), principal component scores, and strategy classification according to the cluster analysis.</p> <p>Dataset 2. Species occurrence data in all study lakes along with results from the 'soft classification" according to Euclidean distance.</p> <p>Dataset 3. Limnological and fish community characteristics of study lakes including species richness, lake area, estimated lake volume, and convex hull statistics for the overall fish community and each life-history strategy type.</p>
Opposing community assembly patterns for dominant and non-dominant plant species in herbaceous ecosystems globally
<p>Biotic and abiotic factors interact with dominant plants —the locally most frequent or with the largest coverage— and non-dominant plants differently, partially because dominant plants modify the environment where non-dominant plants grow. For instance, if dominant plants compete strongly, they will deplete most resources, forcing non-dominant plants into a narrower niche space. Conversely, if dominant plants are constrained by the environment, they might not exhaust available resources but instead may ameliorate environmental stressors that usually limit non-dominants. Hence, the nature of interactions among non-dominant species could be modified by dominant species. Furthermore, these differences could translate into a disparity in the phylogenetic relatedness among dominants compared to the relatedness among non-dominants. By estimating phylogenetic dispersion in 78 grasslands across five continents, we found that dominant species were clustered (e.g., co-dominant grasses), suggesting dominant species are likely organized by environmental filtering, and that non-dominant species were either randomly assembled or overdispersed. Traits showed similar trends for those sites (<50%) with sufficient trait data. Furthermore, several lineages scattered in the phylogeny had more non-dominant species than expected at random, suggesting that traits common in non-dominants are phylogenetically conserved and have evolved multiple times. We also explored environmental drivers of the dominant/non-dominant disparity. We found different assembly patterns for dominants and non-dominants, consistent with asymmetries in assembly mechanisms. Among the different postulated mechanisms, our results suggest two complementary hypotheses seldom explored: (1) Non-dominant species include lineages adapted to thrive in the environment generated by dominant species. (2) Even when dominant species reduce resources to non-dominant ones, dominant species could have a stronger positive effect on some non-dominants by ameliorating environmental stressors affecting them, than by depleting resources and increasing the environmental stress to those non-dominants. These results show that the dominant/non-dominant asymmetry has ecological and evolutionary consequences fundamental to understand plant communities.</p>
Opposing community assembly patterns for dominant and non-dominant plant species in herbaceous ecosystems globally
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OTU table: Ecosystems and Networks Integrated with Genes and Molecular Assemblies (ENIGMA)
<p>This dataset contains the OTU table and associated metadata from the ENIGMA study which was used in "A Practical Guide to Methods Controlling False Discoveries in Computational Biology" (Korthauer, K. and Kimes, P., et al. 2018; associated github: https://github.com/pkimes/benchmark-fdr/).</p> <p>The original raw data is available on MG-RAST (project mgp8190): https://www.mg-rast.org/mgmain.html?mgpage=project&project=mgp8190</p> <p>These data were processed as described in Korthauer & Kimes et al, 2018. The OTU table was provided by Renmao Tian and generated with the following pipeline: <a href="http://zhoulab5.rccc.ou.edu/pipelines/ASAP_web/pipeline_asap.php">http://zhoulab5.rccc.ou.edu/pipelines/ASAP_web/pipeline_asap.php</a>. </p> <p>More information about the ENIGMA project can be found at http://enigma.lbl.gov/</p>
Resource modification by ecosystem engineers generates hotspots of stream community assembly and ecosystem function
<p>Ecosystem engineers can generate hotspots of ecological structure and function by facilitating the aggregation of both resources and consumers. However, nearly all examples of such engineered hotspots come from long-lived foundation species, such as marine and freshwater mussels, intertidal cordgrasses, and alpine cushion plants, with less attention given to small-bodied, and short-lived taxa. Insects often have rapid life cycles and high population densities and are among the most diverse and ubiquitous animals on earth. Although these taxa have the potential to generate hotspots and heterogeneity comparable to that of foundation species, few studies have examined this possibility. We conducted a mesocosm experiment to examine the degree to which a stream insect ecosystem engineer, the net-spinning caddisfly (Tricoptera:Hydropsychidae), creates hotspots of ecosystem function by facilitating invertebrate community assembly. Our experiment used two treatments: (1) stream benthic habitat with patches of caddisfly engineers present and (2) a control treatment with no caddisflies present. We show that compared to controls, caddisflies increased local resource availability, measured as particulate organic matter (POM) by 43%, ecosystem respiration (ER) by 70%, and invertebrate density, biomass and richness by 96%, 244%, and 72%, respectively. These changes resulted in increased spatial variation of POM by 25%, invertebrate density by 76%, and ER by 29% compared to controls, indicating a strong effect of caddisflies on ecological heterogeneity. We found a positive relationship between invertebrate density and ammonium concentration in the caddisfly treatment, but no such relationship in the control, indicating that either caddisflies themselves or the invertebrate aggregations they create increased nutrient availability. When accounting for the amount of POM, caddisfly treatments increased invertebrate density by 48% and richness by 40% compared to controls, suggesting that caddisflies may also enhance the nutritional quality of resources for the invertebrate assemblage. The caddisfly treatment also increased the rate of ecosystem respiration as a function of increasing POM compared to the control. Our study demonstrates that insect ecosystem engineers can generate heterogeneity by concentrating local resources and consumers, with consequences for carbon and nutrient cycling.</p>
Resource modification by ecosystem engineers generates hotspots of stream community assembly and ecosystem function
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Model outputs and observation data for "Implementation and evaluation of the unified stomatal optimization approach in the Functionally Assembled Terrestrial Ecosystem Simulator (FATES)"
<p>Model outputs and observation data for paper "Implementation and evaluation of the unified stomatal optimization approach in the Functionally Assembled Terrestrial Ecosystem Simulator (FATES)".</p>
Data from: Plant functional traits and environmental conditions shape community assembly and ecosystem functioning during restoration
Recovering biological diversity and ecosystem functioning are primary objectives of ecological restoration, yet these outcomes are often unpredictable. Assessments based on functional traits may help with interpreting variability in both community composition and ecosystem functioning because of their mechanistic and generalizable nature. This promise remains poorly realized, however, because tests linking environmental conditions, functional traits, and ecosystem functioning in restoration are rare. Here, we provide such a test through what is to our knowledge the first empirical application of the 'response–effect trait framework' to restoration. This framework provides a trait-based bridge between community assembly and ecosystem functioning by describing how species respond to environmental conditions based on traits and how the traits of species affect ecosystem functioning. Our study took place across 29 prairies restored from former agricultural fields in southwestern Michigan. We considered how environmental conditions affect ecosystem functioning through and independently of measured functional traits. To do so, we paired field-collected trait data with data on plant community composition and measures of ecosystem functioning and used structural equation modelling to determine relationships between environmental conditions, community-weighted means of functional traits and ecosystem functioning. Environmental conditions were predictive of trait composition. Sites restored directly from tillage (as opposed to those allowed to fallow) supported taller species with larger seeds and higher specific leaf area (SLA). Site age and fire frequency were both negatively related to SLA. We also found a positive relationship between soil moisture and SLA. Both trait composition and environmental conditions predicted ecosystem functioning, but these relationships varied among the measured functions. Pollination mode (animal pollination) increased and fire frequency decreased floral resource availability, seed mass had a negative effect on below-ground biomass production, and vegetative height increased decomposition rate. Soil moisture and fire frequency both increased while site age decreased above-ground biomass production, and site age and soil moisture both increased decomposition rate. Synthesis and applications. Our results suggest that both trait composition and environmental conditions play a role in shaping ecosystem function during restoration, and the importance of each is dependent on the function of interest. Because of this, environmental heterogeneity will be necessary to promote multiple ecosystem functions across restored landscapes. A trait-based approach to restoration can aid interpretation of variable outcomes through insights into community assembly and ecosystem functioning.
Data from: The assembly and importance of a novel ecosystem: the ant community of coffee farms in Puerto Rico
<p>Agricultural ecosystems are, by their very nature novel, and, by definition, the more general biodiversity associated with them must likewise constitute a novel community. Here we examine the community of arboreally foraging ants in the coffee agroecosystem of Puerto Rico. We surveyed 20 coffee plants in 25 farms three times in a period of one year. We also conducted a more spatially explicit sampling in two of the farms and conducted a species interaction study between the two most abundant species, Wasmannia auropunctata and Solenopsis invicta in the laboratory. We find that the majority of the most common species are well-known invasive ants and that there is a highly variable pattern of dominance that varies considerably over the main coffee producing region of Puerto Rico, suggesting an unusual modality of community structure. The distribution pattern of the two most common species, W. auropunctata and S. invicta, suggests strong competitive exclusion. However, they also have opposite relationships with the percent of shade cover, with W. auropunctata showing a positive relationship with shade, while S. invicta has a negative relationship. The spatial distribution of these two dominant species in the two more intensively studied farms suggests that young colonies of S. invicta can displace W. auropunctata. Laboratory experiments confirm this. These results suggest the existence of a spatially explicit intransitive loop that includes these two species and is mediated by a phorid fly parasitoid that attack the larger workers of S. invicta. In addition to the elaboration of the nature and extent of this novel ant community, we speculate on the possibilities of its active inclusion as part of a biological control system dealing with several coffee pests, including one of the ants itself, W. auropunctata.</p>
Data from: Plant functional traits and environmental conditions shape community assembly and ecosystem functioning during restoration
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Data from: The assembly and importance of a novel ecosystem: the ant community of coffee farms in Puerto Rico
Open the record for dataset details and reuse information.
Data from: Initial colonization, community assembly, and ecosystem function: fungal colonist traits and litter biochemistry mediate decay rate
Priority effects are an important ecological force shaping biotic communities and ecosystem processes, in which the establishment of early colonists alters the colonization success of later-arriving organisms via competitive exclusion and habitat modification. However, we do not understand which biotic and abiotic conditions lead to strong priority effects and lasting historical contingencies. Using saprotrophic fungi in a model leaf decomposition system, we investigated whether compositional and functional consequences of initial colonization were dependent on initial colonizer traits, resource availability or a combination thereof. To test these ideas, we factorially manipulated leaf litter biochemistry and initial fungal colonist identity, quantifying subsequent community composition, using neutral genetic markers, and community functional characteristics, including enzyme potential and leaf decay rates. During the first 3 months, initial colonist respiration rate and physiological capacity to degrade plant detritus were significant determinants of fungal community composition and leaf decay, indicating that rapid growth and lignolytic potential of early colonists contributed to altered trajectories of community assembly. Further, initial colonization on oak leaves generated increasingly divergent trajectories of fungal community composition and enzyme potential, indicating stronger initial colonizer effects on energy-poor substrates. Together, these observations provide evidence that initial colonization effects, and subsequent consequences on litter decay, are dependent upon substrate biochemistry and physiological traits within a regional species pool. Because microbial decay of plant detritus is important to global C storage, our results demonstrate that understanding the mechanisms by which initial conditions alter priority effects during community assembly may be key to understanding the drivers of ecosystem-level processes.
Supplementary material 1 from: Eisenhauer N, Bonkowski M, Brose U, Buscot F, Durka W, Ebeling A, Fischer M, Gleixner G, Heintz-Buschart A, Hines J, Jesch A, Lange M, Meyer S, Roscher C, Scheu S, Schielzeth H, Schloter M, Schulz S, Unsicker S, van Dam NM, Weigelt A, Weisser WW, Wirth C, Wolf J, Schmid B (2019) Biotic interactions, community assembly, and eco-evolutionary dynamics as drivers of long-term biodiversity–ecosystem functioning relationships. Research Ideas and Outcomes 5: e47042. https://doi.org/10.3897/rio.5.e47042
Detailed design of the Field Experiment
Supplementary material 2 from: Eisenhauer N, Bonkowski M, Brose U, Buscot F, Durka W, Ebeling A, Fischer M, Gleixner G, Heintz-Buschart A, Hines J, Jesch A, Lange M, Meyer S, Roscher C, Scheu S, Schielzeth H, Schloter M, Schulz S, Unsicker S, van Dam NM, Weigelt A, Weisser WW, Wirth C, Wolf J, Schmid B (2019) Biotic interactions, community assembly, and eco-evolutionary dynamics as drivers of long-term biodiversity–ecosystem functioning relationships. Research Ideas and Outcomes 5: e47042. https://doi.org/10.3897/rio.5.e47042
Brief description of the Field Experiment
Figure 1 from: Eisenhauer N, Bonkowski M, Brose U, Buscot F, Durka W, Ebeling A, Fischer M, Gleixner G, Heintz-Buschart A, Hines J, Jesch A, Lange M, Meyer S, Roscher C, Scheu S, Schielzeth H, Schloter M, Schulz S, Unsicker S, van Dam NM, Weigelt A, Weisser WW, Wirth C, Wolf J, Schmid B (2019) Biotic interactions, community assembly, and eco-evolutionary dynamics as drivers of long-term biodiversity–ecosystem functioning relationships. Research Ideas and Outcomes 5: e47042. https://doi.org/10.3897/rio.5.e47042
Figure 1 A. Conceptual diagram of the mechanistic approach of the planned Research Unit. B. Conceptual scheme of the proposed evolutionary niche shifts in plant monocultures and mixtures. This idea feeds into our understanding of how evolutionary history influences the ecological interactions of species that compete for growth factors, ultimately defining biotope space (gray rectangle; Hutchinson 1978). Graphically depicted, species (ellipses) in mixture will show increasing niche differentiation over time due to competition (niche overlap). Thus, history of selection in diverse communities is expected to result in greater interspecific differences (less overlap of ellipses) and more specialization (smaller ellipses) than a history of isolation (monocultures). In monocultures, species will experience strong selection pressure by accumulating soil-borne pathogens, and species may invest energy in chemical and morphological defense traits (depicted by ellipses shifting towards the same corner of the habitat space). Plants in mixtures together may exploit more available biotope space than single monocultures, causing increasing diversity effects on ecosystem functions over time. However, there is limited support for this assumption for traits related to light (e.g., Lipowsky et al. 2015, Roscher et al. 2015) and resource use (Jesch et al. 2018) so far.
Figure 4 from: Eisenhauer N, Bonkowski M, Brose U, Buscot F, Durka W, Ebeling A, Fischer M, Gleixner G, Heintz-Buschart A, Hines J, Jesch A, Lange M, Meyer S, Roscher C, Scheu S, Schielzeth H, Schloter M, Schulz S, Unsicker S, van Dam NM, Weigelt A, Weisser WW, Wirth C, Wolf J, Schmid B (2019) Biotic interactions, community assembly, and eco-evolutionary dynamics as drivers of long-term biodiversity–ecosystem functioning relationships. Research Ideas and Outcomes 5: e47042. https://doi.org/10.3897/rio.5.e47042
Figure 4 Experimental design and hypotheses of the Ecotron Experiment. Briefly, four treatments will be established based on monoliths from a selection of the 9-year old Trait-Based Experiment (TBE; Ebeling et al. 2014) and from bare ground plots of the Jena Experiment as well as two seed sources: the respective plots and the original seed material that was used for the set-up of the TBE. (1) With plot-specific plant history and with plot-specific soil history; (2) without plot-specific plant history and with plot-specific soil history; (3) with plot-specific plant history and without plot-specific soil history; and (4) without plot-specific plant history and without plot-specific soil history. We expect the biodiversity–ecosystem function relationships to differ among the four treatments (see main text for details).
Figure 3 from: Eisenhauer N, Bonkowski M, Brose U, Buscot F, Durka W, Ebeling A, Fischer M, Gleixner G, Heintz-Buschart A, Hines J, Jesch A, Lange M, Meyer S, Roscher C, Scheu S, Schielzeth H, Schloter M, Schulz S, Unsicker S, van Dam NM, Weigelt A, Weisser WW, Wirth C, Wolf J, Schmid B (2019) Biotic interactions, community assembly, and eco-evolutionary dynamics as drivers of long-term biodiversity–ecosystem functioning relationships. Research Ideas and Outcomes 5: e47042. https://doi.org/10.3897/rio.5.e47042
Figure 3 Hypothesized slope of BEF relationships in the different treatments of the Field Experiment (see main text for details). Note that the 'with plant history, with soil history' only serves as a control in the Field Experiment, and effects of plant history can only be tested in the planned Ecotron Experiment. Redrawn after Vogel et al. (2019). '+', with; '-', without.
Supplementary material 4 from: Eisenhauer N, Bonkowski M, Brose U, Buscot F, Durka W, Ebeling A, Fischer M, Gleixner G, Heintz-Buschart A, Hines J, Jesch A, Lange M, Meyer S, Roscher C, Scheu S, Schielzeth H, Schloter M, Schulz S, Unsicker S, van Dam NM, Weigelt A, Weisser WW, Wirth C, Wolf J, Schmid B (2019) Biotic interactions, community assembly, and eco-evolutionary dynamics as drivers of long-term biodiversity–ecosystem functioning relationships. Research Ideas and Outcomes 5: e47042. https://doi.org/10.3897/rio.5.e47042
Detailed design of the Ecotron Experiment
Supplementary material 5 from: Eisenhauer N, Bonkowski M, Brose U, Buscot F, Durka W, Ebeling A, Fischer M, Gleixner G, Heintz-Buschart A, Hines J, Jesch A, Lange M, Meyer S, Roscher C, Scheu S, Schielzeth H, Schloter M, Schulz S, Unsicker S, van Dam NM, Weigelt A, Weisser WW, Wirth C, Wolf J, Schmid B (2019) Biotic interactions, community assembly, and eco-evolutionary dynamics as drivers of long-term biodiversity–ecosystem functioning relationships. Research Ideas and Outcomes 5: e47042. https://doi.org/10.3897/rio.5.e47042
Brief description of the Ecotron Experiment
Figure 2 from: Eisenhauer N, Bonkowski M, Brose U, Buscot F, Durka W, Ebeling A, Fischer M, Gleixner G, Heintz-Buschart A, Hines J, Jesch A, Lange M, Meyer S, Roscher C, Scheu S, Schielzeth H, Schloter M, Schulz S, Unsicker S, van Dam NM, Weigelt A, Weisser WW, Wirth C, Wolf J, Schmid B (2019) Biotic interactions, community assembly, and eco-evolutionary dynamics as drivers of long-term biodiversity–ecosystem functioning relationships. Research Ideas and Outcomes 5: e47042. https://doi.org/10.3897/rio.5.e47042
Figure 2 Structure of the proposed Research Unit. Three complementary experimental approaches are envisaged to study long-term biodiversity-ecosystem function (BEF) relationships, and how these are influenced by plant history and soil history. BEF patterns are studied in the Field Experiment with long-term plant diversity plots and manipulations of soil-history effects. BEF mechanisms are studied in the Ecotron Experiment and in Microcosm Experiments. In the Ecotron Experiment, plant history and soil history are independently crossed and detailed process measurements are possible. The Microcosm Experiments zoom in on focal interactions. In the Field Experiment and in the Ecotron Experiment, studies are conducted at the community level as well as at the plant individual level (magnifier; see detailed design of studies in the Appendices). Subprojects' (SPs') participation in experiments are illustrated with lines. The SPs of the proposed Research Unit fall into two tightly linked main categories (in gray) with two research areas each that aim at exploring variation in community assembly processes, micro-evolutionary changes, and resulting differences in biotic interactions as determinants of the long-term BEF relationship. Subprojects under "Microbial community assembly" (blue) and "Assembly and functions of animal communities" (red) mostly focus on plant diversity effects on the assembly of communities and their feedback effects on biotic interactions and ecosystem functions, while subprojects under "Mediators of plant-biotic interactions" (orange) and "Intraspecific diversity and micro-evolutionary changes" (green) mostly focus on plant diversity effects on plant trait expression and micro-evolution. PIs with requested personnel are underlined.
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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.