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193 results for “diversity dynamics”
Data from: Contrasting trends in plant diversity and soil carbon mineralization under precipitation-driven vegetation and soil carbon dynamics in the Mongolian plateau
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Data from: Diversity, dynamics and effects of long terminal repeat retrotransposons in the model grass Brachypodium distachyon
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Data set - Island area and historical geomorphological dynamics shape multifaceted diversity of barrier island floras
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Eco-evolutionary dynamics modulate plant responses to global change depending on plant diversity and species identity
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Data from: Temperature variation, bacterial diversity, and fungal infection dynamics in the amphibian skin
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Diversity of response and effect traits provides complementary information about avian community dynamics linked to ecological function
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Strain diversity and spatial distribution are linked to epidemic dynamics in host populations
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Space resource utilization of dominant species integrates abundance- and functional-based processes for better predictions of plant diversity dynamics
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Population dynamics of Amazonian floodplain forest species support spatial variation on genetic diversity but not range expansions through time
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Data from: The effects of cryptic diversity on diversification dynamics analyses in Crocodylia
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Holocene plant diversity dynamics shows a distinct biogeographical pattern in temperate Europe
<p>Data for manuscript "<strong>Holocene plant diversity dynamics shows a distinct biogeographical pattern in temperate Europe</strong>" by Roleček J., Abraham V., Vild O., Svitavská Svobodová H., Jamrichová E., Plesková Z., Pokorný P. & Kuneš P. </p> <p>Data originate from 18 sites in Czech and Slovak Republic. Original data and further metadata are stored in <a href="https://botany.natur.cuni.cz/palycz/">Czech Quaternary Palynological Database</a>. Data presented here were adjusted by following procedure:</p> <p>Pollen counts of trees were adjusted (divided) by <a href="https://doi.pangaea.de/10.1594/PANGAEA.908862">mean pollen productivity for North Hemisphere</a> :</p> <p>Abies 6.88<br> Alnus 7.46<br> Betula 4.4<br> Carpinus betulus 4.52<br> Corylus 1.97<br> Fagus 1.96<br> Fraxinus excelsior-Typ 1.25<br> Juniperus 9.8<br> Picea 2.29<br> Pinus 10.47<br> Quercus 3.33<br> Tilia 1.17<br> Ulmus 7.32</p> <p>and subsequently whole spectra were resampled for the same pollen sum (100 grains) in all depths and time windows (300 years).</p> <p>Resampling was done by function "spectra_to_target_sum" at <a href="https://github.com/vojtechabraham/pollen">https://github.com/vojtechabraham/pollen</a>.</p> <p>See repository <a href="https://github.com/vojtechabraham/HolDivTempEur">https://github.com/vojtechabraham/HolDivTempEur</a> for the analysis presented in the paper.</p>
Data from: Mammal diversity and metacommunity dynamics in urban green spaces: implications for urban wildlife conservation
<p>As urban growth expands and natural environments fragment, it is essential to understand the ecological roles fulfilled by urban green spaces. To evaluate how urban green spaces function as wildlife habitat, we estimated mammal diversity and metacommunity dynamics in city parks, cemeteries, golf courses, and natural areas throughout the greater Chicago, IL, USA region. We found similar a-diversity (with the exception of city parks), but remarkably dissimilar communities in different urban green spaces. Additionally, the type of urban green space greatly influenced species colonization and persistence rates. For example, coyotes (Canis latrans) had the highest, but white-tailed deer (Odocoileus virginianus) the lowest, probability of persistence in golf courses compared to other green space types. Further, most species had a difficult time colonizing city parks even when sites were seemingly available. Our results indicate that urban green spaces contribute different, but collectively important, habitats for maintaining and conserving biodiversity in cities.</p>
Multi-decadal shifts in fish community diversity across a dynamic biogeographic transition zone
<p><b><span>Aim: </span></b><span>A 21-year fisheries-independent monitoring dataset was used to explore fish community diversity across a latitudinal gradient to quantify how diversity has changed and relate those changes in diversity to changes in the abiotic environment. Additionally, this study spans a biogeographic transition zone, providing insight into future species assemblages across regions of relatively high species diversity.</span></p> <p><b><span>Location: </span></b><span>Indian River Lagoon, Florida, USA</span></p> <p><b><span>Methods: </span></b><span>Spatial and temporal beta diversity<b> </b>was quantified latitudinally with "best derived breaks" determined by using chronological cluster analyses. Multiple indices of alpha diversity were quantified, including species richness, Shannon diversity, Simpson diversity, and Pielou's evenness. AIC model selection and environmental fit tests were performed to link patterns of diversity and species assemblages with the abiotic environment. </span></p> <p><b><span>Results: </span></b><span>Evidence of a biogeographic transition zone was supported by data spanning the entire study period; the largest break in species assemblage occurred near 28</span><span>°</span><span>N. Fine scale analyses using small and large seine catches were noisier than broad analyses but indicated a northern shift in location of the biogeographic transition zone. Beta-diversity was generally dominated by species turnover/balance versus nestedness/gradient components, implying that changes were driven by species sorting associated with the physical environment. Excluding the summation of all environmental variables, temperature and dissolved oxygen best describe patterns of diversity and species composition. </span></p> <p><b><span>Main Conclusions: </span></b><span>Over years less affected by disturbances, large and small seine catch data suggest the fish community assemblage and location of the biogeographic transition zone has shifted 9 km and 21 km to the north. If the trends observed in these years were to continue from 1999 until the year 2100, a 111 km to 243 km shift in fish communities could be expected. Variation in rates of movement based on gear type suggest novel species assemblages could ensue.</span></p>
Data from: Diversity dynamics of mammals in relation to tectonic and climatic history: comparison of three Neogene records from North America
In modern ecosystems, regions of topographic heterogeneity, when compared with nearby topographically homogeneous regions, support high species densities of mammals and other groups. This biogeographic pattern could be explained by either greater diversification rates or greater accommodation of species in topographically complex regions. In this context, we assess the hypothesis that changes in landscape history have stimulated diversification in mammals. Landscape history includes tectonic and climatic processes that influence topographic complexity at regional scales. We evaluated the influence of changes in topographic complexity and climate on origination and extinction rates of rodents, the most diverse clade of mammals. We compared the Neogene records of rodent diversity for three regions in North America. The Columbia Basin of the Pacific Northwest (Region 1) and the northern Rocky Mountains (Region 2) were tectonically active over much of the Cenozoic and are characterized by high topographic complexity today. The northern Great Plains (Region 3) have been tectonically quiescent, with low relief, throughout the Cenozoic. These three regions have distinctive geologic histories and substantial fossil records. All three regions showed significant changes in diversification and faunal composition over the Neogene. In the montane regions, originations and extinctions peaked at the onset and close, respectively, of the Miocene Climatic Optimum (17–14 Ma), with significant changes in faunal composition accompanying these episodes of diversification. In the Great Plains, rodents showed considerable turnover but infrequent diversification. Peak Neogene diversity in the Great Plains occurred during cooling after the Miocene Climatic Optimum. These histories suggest that climatic changes interacting with increasing topographic complexity intensify macroevolutionary processes. In addition, close tracking of diversity and fossil productivity with the stratigraphic record suggests either large-scale sampling biases or the mutual response of diversity and depositional processes to changes in landscape history.
Data from: Seasonal dynamics of waterbird assembly mechanisms revealed by phylogenetic and functional diversity in a subtropical wetland
Despite growing interest in phylogenetic and functional methods in ecological assembly, less attention has been paid to seasonal variation patterns of migrant species. Migrants can rapidly mediate influences of species interactions and environmental factors through seasonal movement, suggesting dynamical relative importance of different assembly mechanisms among seasons. Here we describe seasonal dynamics in phylogenetic and functional diversity of waterbirds in Mai Po Wetland, in a subtropical region with significant predictable temporal variation. Phylogenetic and functional structure of α diversity varied seasonally. Specifically, phylogenetic structures clustered in summer, while being over-dispersed in winter. However, phylogenetic structure in spring and autumn was intermediate with a transition to random. Functional structure was clustered in spring but showed over-dispersion in the other three seasons. For β diversity, summer and winter assemblages had two distinct groups, while spring and autumn assemblages were mixed. Thus, waterbird assemblages were primarily shaped by interspecific competition in winter. Random processes tended to shape assemblage in spring. Environmental factors played a more important role in summer . In addition, phylogenetic distance of probability of co-occurrence of species pairs was significantly larger in winter than in summer. These results suggest that the relative importance of assemblage mechanisms can vary seasonally in response to changing environmental conditions, suggesting that studies attempting to infer a single dominant assembly mechanism may ignore important assembly processes. Temporal shifts in assembly mechanisms may play an important role in maintaining diversity of subtropical and temperate wetlands and perhaps other dynamic systems.
Data from: Strategies of zooplanktivory shape dynamics and diversity of littoral plankton communities: a mesocosm approach
Planktivorous fish can exert strong top-down control on zooplankton communities. By incorporating different feeding strategies, from selective particulate feeding to cruising filter feeding, fish species target distinct prey. In this study, we investigated the effects of two species with different feeding strategies, the three-spined stickleback (Gasterosteus aculeatus (L.)) and roach (Rutilus rutilus (L.)), on a low-diversity brackish water zooplankton community using a 16-day mesocosm experiment. The experiment was conducted on a small-bodied spring zooplankton community in high-nutrient conditions, as well as a large-bodied summer community in low-nutrient conditions. Effects were highly dependent on the initial zooplankton community structure and hence seasonal variation. In a small-bodied community with high predation pressure and no dispersal or migration, the selective particulate-feeding stickleback depleted the zooplankton community and decreased its diversity more radically than the cruising filter-feeding roach. Cladocerans rather than copepods were efficiently removed by predation, and their removal caused altered patterns in rotifer abundance. In a large-bodied summer community with initial high taxonomic and functional diversity, predation pressure was lower and resource availability was high for omnivorous crustaceans preying on other zooplankton. In this community, predation maintained diversity, regardless of predator species. During both experimental periods, predation influenced the competitive relationship between the dominant calanoid copepods, and altered species composition and size structure of the zooplankton community. Changes also occurred to an extent at the level of nontarget prey, such as microzooplankton and rotifers, emphasizing the importance of subtle predation effects. We discuss our results in the context of the adaptive foraging mechanism and relate them to the natural littoral community.
Data from: An analysis of the impacts of Cretaceous Oceanic Anoxic Events on global molluscan diversity dynamics
Oceanic Anoxic Events (OAEs) are contemporaneous with 11 of the 18 largest Phanerozoic extinction events, but the magnitude and selectivity of their paleoecological impact remains disputed. OAEs are associated with abrupt, rapid warming and increased CO2 flux to the atmosphere, thus insights from this study may clarify the impact of current anthropogenic climate change on the biosphere. We investigated the influence of the Late Cretaceous Bonarelli Event (OAE2; Cenomanian – Turonian stage boundary; ~ 94 Ma) on generic- and species-level molluscan diversity, extinction rates, and ecological turnover. Cenomanian – Turonian results were compared with changes across all Cretaceous stage boundaries, some of which are coincident with less severe OAEs. We found increased generic turnover, but not species-level turnover, associated with several Cretaceous OAEs. The absence of a species-level pattern may reflect species occurrence data that are too temporally coarse to robustly detect patterns. Five hypotheses of ecological selectivity relating anoxia to survivorship were tested across stage boundaries with respect to faunality, mobility and diet using generalized linear models. Increasingly benthic taxa were consistently selected against throughout the Cretaceous regardless of the presence or absence of OAEs. These results suggest that: (1) the Cenomanian – Turonian boundary (OAE2) was associated with a decline in mollusk diversity, and increase in extinction rate, that was significantly more severe than Cretaceous background levels; and (2) no differential ecological selectivity was associated with OAE-related diversity declines among the variables tested here.
Data from: Diversity dynamics of Phanerozoic terrestrial tetrapods at the local-community scale
The fossil record provides one of the strongest tests of the hypothesis that diversity within local communities is constrained over geological timescales. Constraints to diversity are particularly controversial in modern terrestrial ecosystems, yet long-term patterns are poorly understood. Here we document patterns of local richness in Phanerozoic terrestrial tetrapods using a global data set comprising 145,332 taxon occurrences from 27,531 collections. We show that the local richness of non-flying terrestrial tetrapods has risen asymptotically since their initial colonization of land, increasing at most threefold over the last 300 million years. Statistical comparisons support phase-shift models, with most increases in local richness occurring: (1) during the colonization of land by vertebrates, concluding by the late Carboniferous; and (2) across the Cretaceous/Paleogene boundary. Individual groups, such as mammals, lepidosaurs and dinosaurs also experienced early increases followed by periods of stasis often lasting tens of millions of years. Mammal local richness abruptly tripled across the Cretaceous/Paleogene boundary, but did not increase over the next 66 million years. These patterns are consistent with the hypothesis that diversity is constrained at the local-community scale.
Data from: Water level fluctuations and metapopulation dynamics as drivers of genetic diversity in populations of three Tanganyikan cichlid fish species
Understanding how genetic variation is generated and maintained in natural populations, and how this process unfolds in a changing environment, remains a central issue in biological research. In this work, we analyzed patterns of genetic diversity from several populations of three cichlid species from Lake Tanganyika in parallel, using the mitochondrial DNA control region. We sampled populations inhabiting the littoral rocky habitats in both very deep, and very shallow areas of the lake. We hypothesized that the former would constitute relatively older, more stable and genetically more diverse populations, because they should have been less severely affected by the well-documented episodes of dramatic water level fluctuations. In agreement with our predictions, populations of all three species sampled in very shallow shorelines showed traces of stronger population growth than populations of the same species inhabiting deep shorelines. However, contrary to our working hypothesis, we found a significant trend towards increased genetic diversity in the younger, demographically less stable populations inhabiting shallow areas, in comparison to the older and more stable populations inhabiting the deep shorelines. We interpret this finding as the result of the establishment of metapopulation dynamics in the former shorelines, by the frequent perturbation and reshuffling of individuals between populations due to the lake level fluctuations. The repeated succession of periods of allopatric separation and secondary contact is likely to have further increased the rapid pace of speciation in lacustrine cichlids.
Data from: Global gradients in vertebrate diversity predicted by historical area-productivity dynamics and contemporary environment
Broad-scale geographic gradients in species richness have now been extensively documented, but their historical underpinning is still not well understood. While the importance of productivity, temperature, and a scale-dependence of the determinants of diversity is broadly acknowledged, we here argue that limitation to a single analysis scale and data pseudoreplication have impeded an integrated evolutionary and ecological understanding of diversity gradients. We develop and apply a hierarchical analysis framework for global diversity gradients that incorporates an explicit accounting of past environmental variation and provides an appropriate measurement of richness. Due to environmental niche conservatism organisms generally reside in climatically defined bioregions, or "evolutionary arenas", characterized by in situ speciation and extinction. These bioregions differ in age and their total productivity and have varied over time in area and energy available for diversification. We show that, consistently across the four major terrestrial vertebrate groups, current-day species richness of the world's main 32 bioregions is best explained by a model that integrates area and productivity over geological time together with temperature. Adding finer-scale variation in energy availability as an ecological predictor of within-bioregional patterns of richness explains much of the remaining global variation in richness at the 110km grain. These results highlight the separate evolutionary and ecological effects of energy availability and provide a first conceptual and empirical integration of the key drivers of broad-scale richness gradients. Avoiding the pseudo-replication that impedes the evolutionary interpretation of non-hierarchical macroecological analyses, our findings integrate evolutionary and ecological mechanisms at their most relevant scales and offer a new synthesis regarding global diversity gradients.
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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.