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6,569 results for “Long-term”
Data from: A shift in the long-term mode of foraminiferan size evolution caused by the end-Permian mass extinction
Size is among the most important traits of any organism, yet the factors that control its evolution remain poorly understood. In this study, we investigate controls on the evolution of organismal size using a newly compiled database of nearly 25,000 foraminiferan species and subspecies spanning the past 400 million years. We find a transition in the pattern of foraminiferan size evolution from correlation with atmospheric pO2 during the Paleozoic (400-250 Mya) to long-term stasis during the post-Paleozoic (250 Mya to present). Thus, a dramatic shift in the evolutionary mode coincides with the most severe biotic catastrophe of the Phanerozoic (543 Mya to present). Paleozoic tracking of pO2 was confined to Order Fusulinida, whereas Paleozoic lagenides, miliolids, and textulariids were best described by the stasis model. Stasis continued to best describe miliolids and textulariids during post-Paleozoic time, while random walk was the best supported mode for the other diverse orders. The shift in evolutionary dynamics thus appears to have resulted primarily from the selective elimination of fusulinids at the end of the Permian Period. These findings illustrate the potential for mass extinction to alter macroevolutionary dynamics for hundreds of millions of years.
Data from: Pattern of polyphenol intake and the long-term risk of dementia in older persons
Objective: To investigate the optimal combination of dietary polyphenols associated with the long-term risk of dementia in a large prospective French cohort of older persons, the Three-City (3C) Study. Methods: We included 1,329 non-demented older adults from the 3C Study with assessment of intake of 26 polyphenol subclasses and followed for 12 years for dementia. Using Partial Least Square for Cox models, we identified a pattern of polyphenol intake associated with dementia risk. Results: The pattern combined several flavonoids (dihydroflavonols, anthocyanins, isoflavonoids, flavanones), stilbenes (including resveratrol), lignans and other subclasses (hydroxybenzaldehydes, naphtoquinones, furanocoumarins). Compared with participants in the lower quintile of pattern score, those in the higher quintile had a 50% lower risk of dementia (95% CI 20%; 68%, p-trend <0.01) in multivariate models. Conclusions: In this French cohort, a polyphenol pattern provided by a diet containing specific plant products (nuts, citrus, berries, leafy vegetables, soy, cereals, olive oil) accompanied with red wine and tea was associated with lower dementia risk.
Data from: Forest plant community as a driver of soil biodiversity: experimental evidence from collembolan assemblages through large-scale and long-term removal of oak canopy trees Quercus petraea
Plant–soil interactions are increasingly recognized to play a major role in terrestrial ecosystems functioning. However, few studies to date have focused on slow dynamic ecosystems such as forests. As they are vertically stratified by multiple vegetation strata, canopy tree removal by thinning operations could alter forest plant community through tree canopy opening. Very little is known about cascading effects on soil biodiversity. We conducted a large-scale, multi-site assessment of collembolan assemblage response to long-term canopy tree removal in sessile oak Quercus petraea temperate forests. A total of 33 experimental plots were studied covering a large gradient of canopy tree basal area, stand age and local abiotic contexts. Collembolan abundance strongly declined with canopy tree removal in early forest successional stage and this was mediated by negative effect of understory plant community composition changes, i.e. shift from moss and forb to tree seedling, fern, shrub and grass species. Negative effect of this composition shift on collembolan species richness was largely offset by positive effect of the increase in understory plant species richness. This gives support to both the plant mass-ratio and functional diversity hypotheses. Collembolan functional groups had contrasting response patterns, which were mediated by different ecological factors. Epedaphic (r-strategist) abundance and species richness increased with canopy tree removal in relation with the increase in understory plant species richness. In contrast, euedaphic (K-strategist) abundance and species richness declined with canopy tree removal in early forest successional stage in relation with changes in understory plant community composition and species richness, as well as microclimatic conditions. Overall, our study provides experimental evidence that forest plant community can be a strong driver of collembolan assemblages. It also emphasizes the role of trees as foundation species of forest ecosystems that can shape soil biodiversity through their regulation of understory plant community and ecosystem abiotic conditions.
Data from: A framework for the identification of long-term social avoidance in longitudinal datasets
Animal sociality is of significant interest to evolutionary and behavioural ecologists, with efforts focused on the patterns, causes and fitness outcomes of social preference. However, individual social patterns are the consequence of both attraction to (preference for) and avoidance of conspecifics. Despite this, social avoidance has received far less attention than social preference. Here, we detail the necessary steps to generate a spatially explicit, iterative null model which can be used to identify non-random social avoidance in longitudinal studies of social animals. We specifically identify and detail parameters which will influence the validity of the model. To test the usability of this model, we applied it to two longitudinal studies of social animals (Eastern water dragons (Intellegama leseurii) and bottlenose dolphins (Tursiops aduncus) to identify the presence of social avoidances. Using this model allowed us to identify the presence of social avoidances in both species. We hope that the framework presented here inspires interest in addressing this critical gap in our understanding of animal sociality, in turn allowing for a more holistic understanding of social interactions, relationships and structure.
Data from: Studying long-term, large-scale grassland restoration outcomes to improve seeding methods and reveal knowledge gaps
Studies are increasingly investigating effects of large-scale management activities on grassland restoration outcomes. These studies are providing useful comparisons among currently used management strategies, but not the novel strategies needed to rapidly improve restoration efforts. Here we illustrate how managing restoration projects adaptively can allow promising management innovations to be identified and tested. We studied 327 Great Plains fields seeded after coal mining. We modelled plant responses to management strategies to identify the most effective previously used strategies for constraining weeds and establishing desired plants. Then, we used the model to predict responses to new strategies our analysis identified as potentially more effective. Where established, the weed crested wheatgrass (Agropyron cristatum L.) increased through time, indicating a need to manage establishment of this grass. Seeding particular grasses reduced annual weed cover, and because these grasses appeared to become similarly abundant whether sown at low or high rates, low rates could likely be safely used to reduce seeding costs. More importantly, lower than average grass seed rates increased cover of shrubs, the plants most difficult to restore to many grassland ecosystems. After identifying grass seed rates as a driver, we formulated model predictions for rates below the range managers typically use. These predictions require testing but indicated atypically low grass seed rates would further increase shrubs without hindering long-term grass stand development. Synthesis and applications. Designing management around empirically based predictions is a logical next step towards improving ecological restoration efforts. Our predictions are that reducing grass seed rates to atypically low levels will boost shrubs without compromising grasses. Because these predictions derive from the fitted model, they represent quantitative hypotheses based on current understanding of the system. Generating data needed to test and update these hypotheses will require monitoring responses to shifts in management, specifically shifts to lower grass seed rates. A paucity of data for confronting hypotheses has been a major sticking point hindering adaptive management of most natural resources, but this need not be the case with degraded grasslands, because ongoing restoration efforts around the globe are providing continuous opportunities to monitor and manage processes regulating grassland restoration outcomes.
Data from: Temperature effects on long-term population dynamics in a parasitoid-host system
Long-term environmental changes will likely alter the strengths of interactions between species and consequently their population dynamics, leading to changes in the stability of ecological systems. While an increasing number of empirical studies have shown that environmental changes can alter the strengths of species interactions, these studies are typically short (<1–2 generations) and therefore give only partial information about longer term population dynamics. To focus on longer term dynamics, we investigated population cycles of pea aphids and their most common parasitoid, Aphidius ervi, in Wisconsin, USA. Data collected over three years in alfalfa fields showed an apparent host–parasitoid population cycle. Furthermore, higher pea aphid population growth rates and increased parasitism were correlated with higher naturally occurring temperatures. While these effects were observed with seasonal fluctuations in temperature, they beg the question of how long-term changes in mean annual temperature might change aphid–parasitoid population cycles, a question which we further pursued with laboratory experiments. To quantify temperature-dependent demographic parameters, we used short-term (<1 generation) experiments conducted at 20°C and 27°C. The higher temperature increased aphid and parasitoid development rates, adult aphid life span and fecundity, and parasitoid attack rates. We then conducted multi-generation population-level laboratory experiments to reveal the effects of temperature (20°C vs. 27°C) on population dynamics. We fit the resulting time series data using a nonlinear age-structured state-space model to estimate population-level processes that could not be estimated in short-term laboratory experiments. Using the model, we parsed out the demographic rates that had the largest impacts on aphid–parasitoid population cycles. This analysis showed that there were frequent contrasts in the effects of temperature operating through different demographic rates. For example, the temperature-dependent increase in aphid development rate decreased cycle amplitude, while the increase in parasitoid attack rate increased cycle amplitude. There were also striking interactions among demographic rates. For example, the temperature-dependent increase in aphid development rate could either increase or decrease the cycle period depending on the values of other demographic rates. Although these complexities make predictions difficult, overall they suggest that increasing long-term mean temperature will decrease the period, increase the amplitude, and tend to destabilize pea aphid–A. ervi dynamics.
Data from: Using a full annual cycle model to evaluate long-term population viability of the conservation-reliant Kirtland's warbler after successful recovery
Long-term management planning for conservation-reliant migratory songbirds is particularly challenging because habitat quality in different stages and geographic locations of the annual cycle can have direct and carry-over effects that influence the population dynamics. The Neotropical migratory songbird Kirtland's warbler Setophaga kirtlandii (Baird 1852) is listed as endangered under the U.S. Endangered Species Act and Near Threatened under the IUCN Red List. This conservation-reliant species is being considered for U.S. federal delisting because the species has surpassed the designated 1000 breeding pairs recovery threshold since 2001. To help inform the delisting decision and long-term management efforts, we developed a population simulation model for the Kirtland's warbler that incorporated both breeding and wintering grounds habitat dynamics, and projected population viability based on current environmental conditions and potential future management scenarios. Future management scenarios included the continuation of current management conditions, reduced productivity and carrying capacity due to the changes in habitat suitability from the creation of experimental jack pine Pinus banksiana (Lamb.) plantations, and reduced productivity from alteration of the brown-headed cowbird Molothrus ater (Boddaert 1783) removal programme. Linking wintering grounds precipitation to productivity improved the accuracy of the model for replicating past observed population dynamics. Our future simulations indicate that the Kirtland's warbler population is stable under two potential future management scenarios: (i) continuation of current management practices and (ii) spatially restricting cowbird removal to the core breeding area, assuming that cowbirds reduce productivity in the remaining patches by ≤41%. The additional future management scenarios we assessed resulted in population declines. Synthesis and applications. Our study indicates that the Kirtland's warbler population is stable under current management conditions and that the jack pine plantation and cowbird removal programmes continue to be necessary for the long-term persistence of the species. This study represents one of the first attempts to incorporate full annual cycle dynamics into a population viability analysis for a migratory bird, and our results indicate that incorporating wintering grounds dynamics improved the model performance.
Data from: Long-term evolution of the natural isolate of Escherichia coli 536 in the mouse gut colonized after maternal transmission reveals convergence in the constitutive expression of the lactose operon.
In vitro experimental evolution has taught us many lessons on the molecular bases of adaptation. To move towards more natural settings, evolution in the mice gut has been successfully performed. Yet, these experiments suffered from the use of laboratory strains as well as the use of axenic or streptomycin treated mice to maintain the inoculated strains. To circumvent these limitations, we conducted a one-year experimental evolution in vivo using a natural isolate of E. coli, strain 536, in conditions mimicking as much as possible natural environment with mother to offspring microbiota transmission. Mice were then distributed in 24 independent cages and separated in two different diets: a regular one (Chow diet, CD) and high-fat high-sugar one (Western diet, WD). Genome sequences revealed an early and rapid selection during the breast-feeding period that selected the constitutive expression of the well-characterized lactose operon. E. coli was lost significantly more in CD than WD, however, we could not detect any genomic signature of selection, nor any diet specificities during the later part of the experiments. The apparently neutral evolution presumably due to low population size maintained nevertheless at high frequency the early selected mutations affecting lactose regulation. The rapid loss of lactose operon regulation challenges the idea that plastic gene expression is both optimal and stable in the wild.
Estimating the long-term repeatability of food-hoarding behaviours in an avian predator
Food-hoarding behaviour is widespread in the animal kingdom and enables predictable access to food resources in unpredictable environments. Within-species, consistent variation among individuals in food-hoarding behaviours may indicate the existence of individual strategies, as it likely captures intrinsic differences in how individuals cope with risks (e.g. starvation, pilferage). Using 17 years of data, we estimated the long-term repeatability of 10 food-hoarding behaviours in a population of Eurasian pygmy owls (Glaucidium passerinum), a small avian predator subject to high temporal fluctuations in its main prey abundance. We found low repeatability in the proportion of shrews and the average prey mass stored for both sexes while females were moderately repeatable in the mass and the number of preys stored. These two pairs of behaviours were tightly correlated among-individuals and might represent two different sets of individual strategies to buffer against starvation risks. Whether the existence of such strategies can facilitate populations' persistence and adaptation to climate change remains to be investigated.
Data from: Long-term and interactive effects of different mammalian consumers on growth, survival and recruitment of dominant tree species
<p>Throughout the world, numerous tree species are reported to be in decline, either due to increased mortality of established trees or reduced recruitment. The situation appears especially acute for oaks, which are dominant features of many landscapes in the northern hemisphere. Although numerous factors have been hypothesized to explain reductions in tree performance, vertebrate herbivores and granivores may serve as important drivers of these changes. Here, using data from 8- and 14-year-old exclosure experiments, we evaluated the individual and interactive effects of large and small mammalian herbivores on the performance of three widespread oak species in California – coast live oak (<i>Quercus agrifolia</i>), California black oak (<i>Q. kelloggii</i>) and Oregon white oak (<i>Q. garryana</i>). Although impacts varied somewhat by species and experiment, herbivory by black-tailed deer (<i>Odocoileus hemionus columbianus</i>) reduced the height and survival of juvenile coast live oaks and altered their architecture, as well as reduced the abundance of black oak seedlings, the richness of woody species and the cover of non-oak woody species. Small mammals (<i>Microtus californicus</i> and <i>Peromyscus maniculatus</i>) had even more widespread effects, reducing the abundance of black oak seedlings and the height and cover of all three oak species. We also detected numerous interactions between small mammals and deer, with one herbivore having positive or negative effects on oak abundance and cover when the other herbivore was either present or absent. For example, deer often had negative effects on seedling abundance only when, or even more so when, small mammals were present. In summary, mammalian consumers play crucial roles in limiting oak recruitment by reducing seedling abundance, maintaining trees in stunted states and preventing them from reaching sapling stages and becoming reproductive. Interactions between large and small mammals can also alter the intensity and direction of their effects on trees.</p>
Liquidity Risk and Long-Term Finance: Evidence from a Natural Experiment
<p>This package contains all the code necessary to reproduce figures and tables in Choudhary and Limodio (forthcoming). "Liquidity Risk and Long-Term Finance: Evidence from a Natural Experiment" in the Review of Economic Studies. Instructions are also given about accessing the data.</p>
Data from: Long-term persistence of wildlife populations in a pastoral area
<p>Facilitating coexistence between people and wildlife is a major conservation challenge in East Africa. Some conservation models aim to balance the needs of people and wildlife, but the effectiveness of these models is rarely assessed. Using a case-study approach, we assessed the ecological performance of a pastoral area in northern Tanzania (Manyara Ranch) and established a long-term wildlife population monitoring programme (carried out intermittently from 2003-2008 and regularly from 2011-2019) embedded in a distance sampling framework. By comparing density estimates of the road-transect based long-term monitoring to estimates derived from systematically distributed transects, we found that the bias associated with non-random placement of transects was non-significant. Overall, cattle, and sheep and goat reached the greatest densities and several wildlife species occurred at densities similar (zebra, wildebeest, waterbuck, Kirk's dik-dik) or possibly even greater (giraffe, eland, lesser kudu, Grant's gazelle, Thomson's gazelle) than in adjacent national parks in the same ecosystem. Generalized linear mixed models suggested that most wildlife species (8 out of 14) reached greatest densities during the dry season, that wildlife population densities either remained constant or increased over the 17-year period, that herbivorous livestock species remained constant, while domestic dog population decreased over time. Cross-species correlations did not provide evidence for interference competition between grazing or mixed livestock species and wildlife species but indicate possible negative relationships between domestic dog and warthog populations. Overall, wildlife and livestock populations in Manyara Ranch appear to coexist over the 17-year span. Most likely, this is facilitated by existing connectivity to adjacent protected areas, effective anti-poaching efforts, spatio-temporal grazing restrictions, favourable environmental conditions of the ranch and spatial heterogeneity of surface water and habitats. This long-term case study illustrates the potential of rangelands to simultaneously support wildlife conservation and human livelihood goals if livestock grazing is restricted in space, time and numbers.</p>
Figure 10 in A long-term survey of spring monarch butterflies in north-central Florida
Figure 10. The yearly decline in oviposition rate at Cross Creek from 1994 to 2017, recorded as average eggs/stem (500 plant minimum each year) for the four weeks from 22 March to 18 April. (F = 11.501, p = 0.003, R2 = 0.390). Excluding the extraordinary high value in 1995, the decline by 1,18 linear regression is about 78%. Based on a total of 3545 eggs.
Figure 2 in A long-term survey of spring monarch butterflies in north-central Florida
Figure 2. View across Hogan's pasture showing numerous flowering Asclepias humistrata plants. 28 April 2010. Photo by K. Sims Dunford.
Figure 6 in A long-term survey of spring monarch butterflies in north-central Florida
Figure 6. Appearance of adults at Cross Creek calculated as the number captured per hour, averaged for each week from 1994 through 2017 (excluding 1997, 2000–2001, 2003). The earliest arrival was 14 March (week of 8–14 March). Not all weeks were surveyed in each year. Means are shown with 95% CI. Based on observations of a total of 865 adults.
Figure 9 in A long-term survey of spring monarch butterflies in north-central Florida
Figure 9. Egg abundance through the spring, recorded as mean eggs/stem for each week from 1994 through 2017 (50 plants per sample, minimum of 500 plants examined each year; excludes 1997, 2001, and 2004). Means are shown with 95% CI calculated from 3545 eggs found during 44,753 surveys of stems.
Figure 5 in A long-term survey of spring monarch butterflies in north-central Florida
Figure 5. Variation in flowering phenology of Asclepias humistrata at Cross Creek across three years; 2002 was a typical year, 2008 was an early year, and 2010 was a late year.
Figure 11 in A long-term survey of spring monarch butterflies in north-central Florida
Figure 11. Phenology of immatures at Cross Creek, totalled for 1994–2017. Larvae are divided into 1st through 3rd and 4th and 5th instar. Based on totals of 3444 eggs and 1295 larvae.
Figure 1 in A long-term survey of spring monarch butterflies in north-central Florida
Figure 1. Satellite view of Hogan's pasture (X) and the roadsides in Cross Ck, Alachua Co., FL, where the density, health, stage and number of Asclepias humistrata plants and stems and the spring breeding populations of monarch butterflies were assessed.
Figure 7 in A long-term survey of spring monarch butterflies in north-central Florida
Figure 7. Wing wear of monarchs for each week through the spring flight period, from a total of 302 adults combined for 2005–2017 using a scale from 1 (very fresh with no scale loss) to 5 (worn, many scales missing). Two measures are shown for each week: the median determined from all butterflies and the proportion of adults with wing wear 1s and 2s. Individuals in early April were mostly fresh.
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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.