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109 results for “biodiversity patterns”
Data from: The role of climate, water and biotic interactions in shaping biodiversity patterns in arid environments across spatial scales
Aim: Desert ecosystems, with their harsh environmental conditions, hold the key to understanding the responses of biodiversity to climate change. As desert community structure is influenced by processes acting at different spatial scales, studies combining multiple scales are essential for understanding the conservation requirements of desert biota. We investigated the role of environmental variables and biotic interactions in shaping broad and fine-scale patterns of diversity and distribution of bats in arid environments to understand how the expansion of nondesert species can affect the long-term conservation of desert biodiversity. Location: Levant, Eastern Mediterranean. Methods: We combine species distribution modelling and niche overlap statistics with a statistical model selection approach to integrate interspecific interactions into broadscale distribution models and fine-scale analysis of ecological requirements. We focus on competition between desert bats and mesic species that recently expanded their distribution into arid environment following anthropogenic land-use changes. Results: We show that both climate and water availability limit bat distributions and diversity across spatial scales. The broadscale distribution of bats was determined by proximity to water and high temperatures, although the latter did not affect the distribution of mesic species. At the fine-scale, high levels of bat activity and diversity were associated with increased water availability and warmer periods. Desert species were strongly associated with warmer and drier desert types. Range and niche overlap were high among potential competitors, but coexistence was facilitated through fine-scale spatial partitioning of water resources. Main conclusions: Adaptations to drier and warmer conditions allow desert-obligate species to prevail in more arid environments. However, this competitive advantage may disappear as anthropogenic activities encroach further into desert habitats. We conclude that reduced water availability in arid environments under future climate change projections pose a major threat to desert wildlife because it can affect survival and reproductive success and may increase competition over remaining water resources.
Data from: Patterns of biodiverse, understudied groups do not mirror those of the surrogate groups that set conservation priorities: a case study from the Mid-Atlantic Coastal Plain of eastern North America
We conducted biodiversity inventories of lichens, woody plants, and sedges at 32 sites on the Mid-Atlantic Coastal Plain of eastern North America between November 2012 and June 2015. Each site comprised a single, uniform habitat, and sites were classified as: Coastal Plain Floodplain forest, Coastal Plain Flatwood swamp, Coastal Plain Oak-Pine forest, Maritime forest, Mixed Mesic Hardwood forest, or Tidal forest. We compared alpha diversity and community assemblages of each organismal group across the sites, and compared selected minimal reserve sets in order to visualize biodiversity patterns and assess whether specific components of vascular plants (sedges and woody plants) serve as an effective surrogate for lichens. Woody plants provide a direct substrate for lichen growth, but there was no significant correlation between the alpha diversity of these groups. For conserving maximal species richness among the studied groups, lichens outperformed the sedges and woody plants as the better surrogate group for building minimum reserve sets, even though vascular plants are more commonly used as a surrogate. Likewise, sedge alpha diversity was not correlated with lichens, or with woody plants. Although no group was an effective indicator for high alpha diversity sites of other organisms, a significant correlation between the community assemblages of lichens and woody plants suggests that protecting varied types of plant communities might serve as a workable surrogate for protecting lichens. The lack of congruence between species richness patterns across organismal groups suggests that the mechanisms that shape patterns of diversity are not identical, and that identifying and incorporating specific biodiversity indicators for understudied groups into conservation policy is necessary to ensure their protection.
Supplementary material from: Alpine extremophytes in evolutionary turmoil: Complex diversification patterns and demographic responses of a Halophilic grass in a Central Asian biodiversity hotspot
<p>Diversification and demographic responses are key processes shaping species evolutionary history. Yet we still lack a full understanding of ecological mechanisms that shape genetic diversity at different spatial scales upon rapid environmental changes. In this study, we examined genetic differentiation in an extremophilic grass <em>Puccinellia pamirica</em> and factors affecting its population dynamics among the occupied hypersaline alpine wetlands on the arid Pamir Plateau in Central Asia. Using genomic data, we found evidence of fine-scale population structure and gene flow among the localities established across the high-elevation plateau as well as fingerprints of historical demographic expansion. We showed that an increase in the effective population size could coincide with the Last Glacial Period, which was followed by the species demographic decline during the Holocene. Geographic distance plays a vital role in shaping the spatial genetic structure of <em>P. pamirica</em> alongside with isolation-by-environment and habitat fragmentation. Our results highlight a complex history of divergence and gene flow in this species-poor alpine region during the Late Quaternary. We demonstrate that regional climate specificity and a shortage of nonclimate data largely impede predictions of future range changes of the alpine extremophile using ecological niche modeling. This study emphasizes the importance of fine-scale environmental heterogeneity for population dynamics and species distribution shifts.</p>
Predicting time-at-depth weighted biodiversity patterns for sharks of the North Pacific
<p>Depth is a fundamental and universal driver of ocean biogeography, but it is unclear how the biodiversity patterns of larger, more mobile organisms change as a function of depth. Here, we developed a predictive biogeography model to explore how information of mobile species' depth preferences influence biodiversity patterns. We employed a literature review to collate shark biotelemetry studies and used open-access tools to extract 283 total records from 119 studies of 1,133 sharks from 35 species. We then matched field guide reported depth ranges and IUCN habitat associations for each shark species to use as covariates in a hurdle variant of Ensemble Random Forests. We successfully fit this model (R2 = 0.63) to the noisy time-at-depth observations and used it to predict the time budgets of the Northeast Pacific shark regional pool (n = 52). We then assessed how occurrence diversity patterns, informed by minimum and maximum depth of occurrence, compared to time-at-depth weighted diversity patterns. Time-at-depth weighted richness was highest between 0 and 25 m and at the upper part of the mesopelagic zone, 250 – 300 m; resulting in little similarity to common depth or elevational biodiversity patterns while the occurrence-weighted richness pattern was similar to the "low-plateau" pattern. In the phylogenetic and functional dimensions of biodiversity and over three different distance metrics, we found strong but haphazard differences between the occurrence- and time-at-depth weighted biodiversity patterns. The strong influence of time budgets on biodiversity led us to conclude that occurrence data alone is likely insufficient or even misleading in terms of the depth-driven biogeographic patterns in the open ocean. Utilizing the increasing amount of time-at-depth information from biotelemetry studies in predictive biogeographic models may be critical for capturing the preferences of pelagic, mobile species occupying the largest biome on the planet.</p>
Marine biodiversity patterns in coastal Australian waters revealed by a three-year environmental DNA survey
<p><strong>Aim</strong></p> <p>To test the capacity of eDNA to characterise the spatial and seasonal patterns found within a range of zooplankton communities, and investigate links with concurrent abiotic data collected as part of Australia's Integrated Marine Observing System (IMOS) programme.</p> <p><strong>Location</strong></p> <p>Samples were sourced seasonally for three years from nine Pan-Australian marine sites (n=90).</p> <p><strong>Methods</strong></p> <p>Here we apply a multi-assay metabarcoding approach to environmental DNA extracted from a rare long-term collection of bulk plankton samples. Six assays (targeting both the 16SrRNA and COI genes) were used to amplify and sequence the zooplankton diversity found within each sample. The data generated from each assay was filtered and clustered into OTUs prior to analysis. Abiotic IMOS data collected alongside the plankton collection enabled us to explore the physical and chemical drivers of community composition.</p> <p><strong>Results</strong></p> <p>The eDNA metabarcoding generated over 25 million sequences, identified in excess of 500 distinct taxa and detected clear spatial differences in marine metazoan communities. We found that site and sea surface temperature are the most consistent predictors of differences between zooplankton communities. We detected endangered and invasive species such as the bryozoan Membranipora membranace and the mollusc Maoricolpus roseus, and seasonal occurrences of species such as humpback whales (Megaptera novaeangliae). We also estimated the number of samples required to ensure robust marine eDNA metabarcoding biomonitoring programs into the future.</p> <p><strong>Main Conclusion</strong></p> <p>Our results demonstrate the ability of eDNA to capture and map zooplankton community changes in response to seasonal and spatial stressors and provide vital evidence to environmental stakeholders. We confirm that eDNA offers a practical opportunity for an ecosystem-wide approach to the long-term biomonitoring and understanding marine biomes where a morphological approach is not feasible.</p>
Data from: Unravelling large-scale patterns and drivers of biodiversity in dry rivers
<p>We conducted a coordinated experiment and a metabarcoding approach on environmental DNA targeting multiple taxa (i.e. Archaea, Bacteria, Fungi, Algae, Protozoa, Nematoda, Arthropoda, and Streptophyta). Dry sediments were collected from 84 non-perennial rivers across 19 countries on four continents to investigate biodiversity patterns and drivers.</p>
Data from: Surrogate taxa and fossils as reliable proxies of spatial biodiversity patterns in marine benthic communities
Rigorous documentation of spatial heterogeneity (β-diversity) in present-day and preindustrial ecosystems is required to assess how marine communities respond to environmental and anthropogenic drivers. However, the overwhelming majority of contemporary and palaeontological assessments have centred on single higher taxa. To evaluate the validity of single taxa as community surrogates and palaeontological proxies, we compared macrobenthic communities and sympatric death assemblages at 52 localities in Onslow Bay (NC, USA). Compositional heterogeneity did not differ significantly across datasets based on live molluscs, live non-molluscs, and all live organisms. Death assemblages were less heterogeneous spatially, likely reflecting homogenization by time-averaging. Nevertheless, live and dead datasets were greater than 80% congruent in pairwise comparisons to the literature estimates of β-diversity in other marine ecosystems, yielded concordant bathymetric gradients, and produced nearly identical ordinations consistently delineating habitats. Congruent estimates from molluscs and non-molluscs suggest that single groups can serve as reliable community proxies. High spatial fidelity of death assemblages supports the emerging paradigm of Conservation Palaeobiology. Integrated analyses of ecological and palaeontological data based on surrogate taxa can quantify anthropogenic changes in marine ecosystems and advance our understanding of spatial and temporal aspects of biodiversity.
Data from: Effects of sampling effort on biodiversity patterns estimated from environmental DNA metabarcoding surveys
Environmental DNA (eDNA) metabarcoding can greatly enhance our understanding of global biodiversity and our ability to detect rare or cryptic species. However, sampling effort must be considered when interpreting results from these surveys. We explored how sampling effort influenced biodiversity patterns and nonindigenous species (NIS) detection in an eDNA metabarcoding survey of four commercial ports. Overall, we captured sequences from 18 metazoan phyla with minimal differences in taxonomic coverage between 18 S and COI primer sets. While community dissimilarity patterns were consistent across primers and sampling effort, richness patterns were not, suggesting that richness estimates are extremely sensitive to primer choice and sampling effort. The survey detected 64 potential NIS, with COI identifying more known NIS from port checklists but 18 S identifying more operational taxonomic units shared between three or more ports that represent un-recorded potential NIS. Overall, we conclude that eDNA metabarcoding surveys can reveal global similarity patterns among ports across a broad array of taxa and can also detect potential NIS in these key habitats. However, richness estimates and species assignments require caution. Based on results of this study, we make several recommendations for port eDNA sampling design and suggest several areas for future research.
Microevolutionary processes in a foundation tree inform macrosystem patterns of community biodiversity and structure
<p class="MDPI17abstract"><span>Despite an increased focus on multiscale relationships and interdisciplinary integration, few macroecological studies consider the contribution of genetic-based processes to landscape-scale patterns.<strong> </strong>We tested the hypothesis that tree genetics, climate, and geography jointly drive continental-scale patterns of community structure, using genome-wide SNP data from a broadly distributed foundation tree species (<a><em>Populus fremontii</em></a></span><span class="MsoCommentReference"><span> </span></span><span>S. Watson) and two dependent communities (leaf-modifying arthropods and fungal endophytes) spanning southwestern North America. Four key findings emerged: (1) Tree genetic structure was a significant predictor for both communities; however, the strength of influence was both scale- and community-dependent. (2) Tree genetics was the primary driver for endophytes, explaining 17% of variation in continental-scale community structure, whereas (3) climate was the strongest predictor of arthropod structure (24%). (4) Power to detect tree genotype<a><span>—</span></a></span><span>community phenotype associations changed with scale of genetic organization, increasing from individuals to populations to ecotypes, emphasizing the need to consider nonstationarity (i.e., changes in the effects of factors on ecological processes across scales) when inferring macrosystem properties. Our findings highlight the role of foundation tree species as drivers of macroscale community structure and provide macrosystems ecology with a theoretical framework for linking fine- and intermediate-scale genetic processes to landscape-scale patterns. Management of genetic diversity harbored within foundation species is a critical consideration for conserving and sustaining regional biodiversity.</span></p>
Analysing spatio-temporal patterns of non-native fish in a biodiversity hotspot across decades
<p><strong>Aim</strong>: Analysing the spatio-temporal patterns and dynamics of non-native species is essential to understanding the mechanisms underlying successful invasions and developing effective management strategies. Yet, such analyses generally neglect the influence of receiving ecosystem types and non-native species sources (i.e. alien species, non-natives originating outside the concerned region; translocated species, nonnatives introduced to locations outside their historical range within the concerned region). </p> <p><strong>Location</strong>: Yunnan, China.</p> <p><strong>Methods</strong>: We analysed long-term (1950–2022) spatio-temporal patterns and potential underlying dynamics of non-native fishes in a biodiversity hotspot (Yunnan, China), paying special attention to waterbody types receiving non-native species and comparing alien and translocated species. We did this through compiling a highly comprehensive occurrence dataset of native and non-native fishes.</p> <p><strong>Results</strong>: We recorded 783 native species and 94 non-native species (49 alien species and 45 translocated species), which mainly belonged to the order Cypriniformes (52 species) and were introduced via purposes for advancing aquaculture. Most frequently encountered non-native species were either intentionally introduced aquaculture species or small-bodied fish unintentionally introduced via aquaculture activities. The richness and spatial ranges of non-native fishes increased consistently since the 1950s and demonstrated a pronounced change after the 2000s, with densely populated areas and the middle to lower reaches of large rivers being more profoundly affected. The number of records of translocated species exceeded the number of records of alien species after the 2000s. Lakes and reservoirs are hotspots for both alien and translocated species introductions, and watersheds with large areas in Yunnan (e.g. the Jinsha-Yangtze and Lancang-Mekong basins) contained more non-native fish.</p> <p><strong>Main Conclusions</strong>: Our study highlights the need to consider invasion sensitivities of receiving ecosystems and pay special attention to intra-regional species translocations when developing prevention and management strategies against invasions of alien species, particularly in important biodiversity hotspots around the world.</p>
Mind the Gap: Comparing Exploration Effort with Global Biodiversity Patterns and Climate Projections to Determine Ocean Areas with Greatest Exploration Needs- Dive metadata
<p>Meta data for deep submergence dive locations associated with "Mind the Gap: Comparing Exploration Effort with Global Biodiversity Patterns and Climate Projections to Determine Ocean Areas with Greatest Exploration Needs" published in Frontier of Marine Science 2023. </p>
Data from: Invasive fish reshape biodiversity patterns in China’s freshwater lakes
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Aquatic-terrestrial linkages drive contrasting biodiversity patterns in tropical and temperate forests
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Data from: Effects of sampling effort on biodiversity patterns estimated from environmental DNA metabarcoding surveys
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Data from: Patterns of biodiverse, understudied groups do not mirror those of the surrogate groups that set conservation priorities: a case study from the Mid-Atlantic Coastal Plain of eastern North America
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Predicting time-at-depth weighted biodiversity patterns for sharks of the North Pacific
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Analysing spatio-temporal patterns of non-native fish in a biodiversity hotspot across decades
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Marine biodiversity patterns in coastal Australian waters revealed by a three-year environmental DNA survey
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Data from: The role of climate, water and biotic interactions in shaping biodiversity patterns in arid environments across spatial scales
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Data from: Explaining the ocean’s richest biodiversity hotspot and global patterns of fish diversity
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ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.