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151 results for “ecological integrity”
Interagency Ecological Program: Integrated Dataset of Phytoplankton Enumeration Data in the San Francisco Estuary, 1992-2024
Phytoplankton community composition is an important driver of zooplankton productivity and food supply for higher trophic levels in the San Francisco Estuary. Various monitoring surveys throughout the region collect phytoplankton enumeration data dating back to the 1990s. These include surveys from the CA Department of Water Resources (CADWR), CA Department of Fish and Wildlife (CDFW), the US Bureau of Reclamation (USBR), and the US Geological Survey (USGS). These surveys collect data via various sampling and laboratory methods which are not always directly comparable. This integrated dataset includes both enumeration counts and well-documented metadata to allow for informed decision-making in the integration of these data. It also standardizes taxonomic names between groups via a key list. Note that, in this dataset, we make conservative decisions about taxonomic resolution to ensure maximum compatibility between groups. For more detailed metadata and higher taxonomic resolution, refer to individual surveys’ publications or reach out to their primary contact.
Interagency Ecological Program: Zooplankton abundance in the Upper San Francisco Estuary from 1972-2021, an integration of 7 long-term monitoring programs
The upper San Francisco Estuary is an inland inverse delta formed by the confluence of 5 major rivers that drain 40% of the land in California (USA). It is a central hub of water delivery in California and home to a number of commercially important and endangered fish, such as Chinook Salmon, Green Sturgeon, and Delta Smelt. To monitor the environmental impacts of water exports from this system, extensive ecological monitoring has been conducted since the 1960s. To track lower trophic levels, zooplankton abundance has been monitored from 1972 to present. Starting with just one survey (the CA Department of Water Resources’ [CDWR] and California Department of Fish and Wildlife’s [CDFW] Environmental Monitoring Program) in 1972, the suite of zooplankton surveys gradually expanded with time. Several surveys traditionally focused on monitoring fish abundance added zooplankton nets to their sampling programs. The CDFW 20-mm larval fish survey added zooplankton sampling in 1995, the CDWR Yolo Bypass Fish Monitoring Program add zooplankton in 1999, the CDFW Summer Townet Survey added zooplankton in 2005, and the Fall Midwater Trawl added zooplankton in 2007. Two new sampling programs, the Fish Restoration Program and Directed Outflow Project, began in 2015 and 2017, respectively. All sampling programs continue today. Each survey samples once or twice monthly at set of fixed or random stations that varies across surveys depending on their objectives. While the Environmental Monitoring Program samples year-round, the other surveys are mostly seasonal, although additional months were sampled in some years. Most surveys target open channels although the Fish Restoration Program samples in or near shallow tidal wetlands. Three size classes of zooplankton are targeted by these sampling programs with different net mesh sizes: micro zooplankton (copepods and rotifers) are targeted with a 43 µm mesh net, meso zooplankton (copepods and cladocerans) are targeted with 150 - 160 µm mesh
FIGURE 18 in Feeding in marine mammals: An integration of evolution and ecology through time
FIGURE 18. Ancestral state reconstruction of prey capture strategies and prey type preference in stem and crown Mysticeti. Topology follows Gatesy et al. (2013) and Fordyce and Marx (2018). Details on the tree can be found in Appendix 1. All data matrices and complete trees with branch lengths can be found in the Supplementary Information (https://doi.org/10.6086/d14671).
FIGURE 3 in Feeding in marine mammals: An integration of evolution and ecology through time
FIGURE 3. Anatomical features associated with suction feeding in walrus (Odobenus rosmarus skull, from Jefferson et al., 2015) and North Sea beaked whale (Mesoplodon bidens skull, authors' work).
FIGURE 11 in Feeding in marine mammals: An integration of evolution and ecology through time
FIGURE 11. Sirenia stem and familial level diversity through time. "Protosirenidae / Prorastomidae" includes all taxa that are not included in the two extant groups. Dashed vertical lines: black, epoch boundaries; gray, age boundaries.
FIGURE 7 in Feeding in marine mammals: An integration of evolution and ecology through time
FIGURE 7. Pinnipedimorpha stem taxa and familial level diversity through time. "Stem-Pinnipedimorpha" includes all stem taxa that are not included in Desmatophocidae and the three extant groups. Dashed vertical lines: black, epoch boundaries; gray, age boundaries.
FIGURE 5 in Feeding in marine mammals: An integration of evolution and ecology through time
FIGURE 5. Anatomical features associated with grazing in African manatee (Trichechus senegalensis skull, from Werth, 2000), Desmostylia (Paleoparadoxia skull, public domain), and aquatic sloth (Thalassocnus sp. skull, modified from de Muizon et al., 2004).
FIGURE 8 in Feeding in marine mammals: An integration of evolution and ecology through time
FIGURE 8. Cetacean stem and Neoceti taxa diversity through time. "Archaeoceti" includes all stem taxa that are not included in the two extant groups. Dashed vertical lines: black, epoch boundaries; gray, age boundaries.
FIGURE 16 in Feeding in marine mammals: An integration of evolution and ecology through time
FIGURE 16. Ancestral state reconstruction of prey capture strategies and tooth pattern and cusp shape in Odobenidae. Topology follows Berta et al. (2018). Details on the tree can be found in Appendix 1. All data matrices and complete trees with branch lengths can be found in the Supplementary Information uploaded to Dryad repository (https:// doi.org/10.6086/d14671).
FIGURE 17 in Feeding in marine mammals: An integration of evolution and ecology through time
FIGURE 17. Ancestral state reconstruction of prey type preference in stem and crown Pinnipedimorpha. Topology follows Rybczynski et al. (2009), Dewaele et al. (2017), and Berta et al. (2018). Details on the tree can be found in Appendix 1. All data matrices and complete trees with branch can be found in the Supplementary Information (https:// doi.org/10.6086/d14671).
FIGURE 19 in Feeding in marine mammals: An integration of evolution and ecology through time
FIGURE 19. Ancestral state reconstruction of prey capture strategies and tooth pattern and cusp shape in stem Odontoceti. Topology follows Gatesy et al. (2013) and Boessenecker et al. (2017). Details on the tree can be found in Appendix 1. All data matrices and complete trees with branch lengths can be found in the Supplementary Information (https://doi.org/10.6086/d14671).
FIGURE 20 in Feeding in marine mammals: An integration of evolution and ecology through time
FIGURE 20. Ancestral state reconstruction of prey capture strategies and tooth pattern and cusp shape in crown Odontoceti. Topology follows McGowen et al. (2009) and Gatesy et al. (2013). Details on the tree can be found in Appendix 1. All data matrices and complete trees with branch lengths can be found in the Supplementary Information (https://doi.org/10.6086/d14671).
FIGURE 1 in Feeding in marine mammals: An integration of evolution and ecology through time
FIGURE 1. Feeding strategies of extant marine mammal predators (from Kienle et al., 2017) with the addition of grazing (sirenians, authors' work).
The ECOLOPES Voxel Model: Multi-domain data integration for ontology-aided generative computational design of ecological building envelopes
<p>The research portrayed in this article is part of the research project ‘ECOlogical building enveLOPES: a game-changing design approach for regenerative ecosystems’ funded by Horizon 2020 Future and Emerging Technologies. The overall research project focuses on developing a multi-domain data-driven computational design framework for the design of ecological building enclosures that addresses humans, plants, animals and microbiota. This article focuses on the development of a key component of the computational workflow in which initial designs are computationally initiated generated and analyzed, namely the ECOLOPES Voxel Model that contains and correlates multi-domain spatialised data for the design process, and its interactions with other components of the ontology-aided generative computational design process for ecological building envelopes.</p> <p>This repository contains all relevant data produced in this paper. Extended technical description is available in the Appendix A to the published paper, containing listing and description of individual voxel data layers. Data were exported from the RDB server (PostgreSQL) in text-based, future-proof format (csv).</p>
Data from: Dispersal in a house sparrow metapopulation: an integrative case study of genetic assignment calibrated with ecological data and pedigree information
<p class="western">Dispersal has a crucial role determining eco-evolutionary dynamics through both gene flow and population size regulation. However, to study dispersal and its consequences, one must distinguish immigrants from residents. Dispersers can be identified using telemetry, capture-mark-recapture (CMR) methods, or genetic assignment methods. All of these methods have disadvantages, such as, high costs and substantial field efforts needed for telemetry and CMR surveys, and adequate genetic distance required in genetic assignment. In this study, we used genome-wide 200K Single Nucleotide Polymorphism data and two different genetic assignment approaches (GSI_SIM, Bayesian framework; BONE, network-based estimation) to identify the dispersers in a house sparrow (<i>Passer domesticus</i>) metapopulation sampled over 16 years. Our results showed higher assignment accuracy with BONE. Hence, we proceeded to diagnose potential sources of errors in the assignment results from the BONE method due to variation in levels of inter-population genetic differentiation, intra-population genetic variation and sample size. We show that assignment accuracy is high even at low levels of genetic differentiation and that it increases with the proportion of a population that has been sampled. Finally, we highlight that dispersal studies integrating both ecological and genetic data provide robust assessments of the dispersal patterns in natural populations.</p>
Data from: Dispersal in a house sparrow metapopulation: an integrative case study of genetic assignment calibrated with ecological data and pedigree information
Open the record for dataset details and reuse information.
Study of the overwintering ecology of the hazelnut pest, Palomena prasina (Hemiptera: Pentatomidae) in a perspective of Integrated Pest Management
<p class="MsoNormal"><em>Palomena prasina</em>, the green shield bug (GSB), is widely distributed in the Eurosiberian region. In the Southwest of France it is considered a serious pest of hazelnuts, its feeding punctures lead to blank hazelnuts and kernel necrosis, causing heavy losses in commercial orchards. To date, no Integrated Pest Management strategy is available to control <em>P. prasina</em>.</p> <p class="MsoNormal">Control strategies often focus on the pests' spring-summer ecology, when they are in the field or in the vicinity of crops. However, the abundance of pest populations in crops is also related to their autumn-winter ecology. The present work focussed on the autumn-winter ecology of <em>P. prasina</em> to identify new opportunities for this pest suppression. We investigate (i) where <em>P. prasina</em> overwinters, (ii) if it aggregates in its overwintering sites, and (iii) if it mates while overwintering. Samples were collected over a two-year period in different ecosystems (forests, hedges, orchards), in human-made structures, and habitats (litter, bushes/trees, dead trees). The reproductive status of GBS individuals was monitored in winter, and in spring when they emerged from overwintering sites.</p> <p class="MsoNormal">Our results show that 97% <em>P. prasina</em> adults overwinter in the leaf litter of orchards and natural ecosystems and that 70% overwinter individually. The abundance of GSB in those sites is negatively correlated with litter temperature and positively correlated with humidity levels. Furthermore, adults only mate after leaving their overwintering site. Finally, there was an important number of overwintering adults hosting endoparasitoids (32%).</p> <p class="MsoNormal">The fact that GSB overwinters alone in the leaf litter means controlling its populations by destroying the overwintering sites is not a solution. All the same, our results do open new perspectives for the control of <em>P. prasina</em>. First, the emergence traps, in particular the cone traps, proved efficient for collecting emerging adults and could be used for monitoring. Moreover, our observations point out the existence of long-range mating signals that could be exploited for trapping. Last but not least, the important number of overwintering parasitised adults is a promising biocontrol avenue.</p>
Integration of genomic and ecologic methods inform management of an undescribed, yet highly exploited, sardine species
<p>Assessing genetic diversity within species is key for conservation strategies in the context of human-induced biotic changes. This is important in marine systems where many species remain undescribed while being overfished, and conflicts between resource-users and conservation agencies are common. Combining niche modelling with population genomics can contribute to resolving those conflicts by identifying management units and understanding how past climatic cycles resulted in current patterns of genetic diversity. We addressed these issues on an undescribed but already overexploited species of sardine of the genus <em>Harengula</em>. We find that the species distribution is determined by salinity and depth, with a continuous distribution along the Brazilian mainland and two disconnected oceanic archipelagos. Genomic data indicates that such biogeographic barriers are associated with two divergent intraspecific lineages. Changes in habitat availability during the last glacial cycle led to different demographic histories among stocks. One coastal population experienced a 3.6-fold expansion, whereas an island-associated population contracted 3-fold, relative to the size of the ancestral population. Our results indicate that the island population should be managed separately from the coastal population, and that a Marine Protected Area covering part of the island population distribution can support the viability of this lineage.</p>
Insight into the ecology of vaginal bacteria through integrative analyses of metagenomic and metatranscriptomic data
<p>Datasets and code used to analyze and and to prepare figures for: "Insight into the ecology of vaginal bacteria through integrative analyses of metagenomic and metatranscriptomic data", France et al 2022.</p>
A quantitative assessment of the patterns of integration in the mandible of bovids and their relationships with trophic ecology, phylogeny, and evolutionary rates
<p>Dataset and R script supporting the findings of the study "A quantitative assessment of the patterns of integration in the mandible of bovids and their relationships with trophic ecology, phylogeny, and evolutionary rates". </p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.