Find research datasets worth reusing

Data from: Parameterizing the robust design in the BUGS language: lifetime carry‐over effects of environmental conditions during growth on a long‐lived bird

1. Since the initial development of the robust design, this capture‐recapture model structure has been modified to estimate temporary emigration, and expanded to include auxiliary information such as band recovery and live resight data using maximum likelihood approaches. These developments have allowed investigators to separately assess individual and group effects on true survival, site fidelity, and temporary emigration. Additionally, recent advances in the BUGS language have allowed researchers to develop increasingly complex, user‐specified models in Bayesian frameworks. 2. The robust design has rarely been implemented in the BUGS language, and previous attempts to parameterize the robust design in BUGS exhibited strong bias in estimates of temporary emigration rates. Given the limitations of current parameterizations of the robust design in Bayesian frameworks, and our research objectives, we have developed a parameterization of the robust design in the BUGS language that produces unbiased estimates of all model parameters. 3. We use this novel model structure to examine lifetime carry‐over effects of environmental conditions during early life on annual breeding probabilities of Pacific black brent (Branta bernicla nigricans) breeding on the Yukon‐Kuskokwim River Delta in western Alaska. We found that individuals that were more structurally developed as goslings bred at increased rates as adults (β = 0.14, f = 0.94), with no effect on adult survival (β = 0.01, f = 0.62). Additionally, we provide evidence for long‐term declines in apparent survival of breeding adult females at the population level (β = ‐0.01, f = 0.90). 4. This novel model structure can be easily expanded (Gibson et al., in review), and has important implications for population modelling at broad scales, where we apply it to a declining population of Pacific black brent. Given long‐term declines in gosling growth on the Yukon‐Kuskokwim Delta, we predict future declines in population trajectories as a result of lifetime carry‐over effects of environmental conditions during growth on adult fecundity, and long‐term declines in adult survival.

opencc-zeroApr 2020View details →

Data from: Insect pollinators show constancy for different flower traits between the most‐ and less‐preferred plants: a case study of the long‐proboscid tangle‐veined fly

1. The coevolution of insect pollinators and their host plants is a typical example of natural selection; however, it remains unclear as to how insect pollinators avoid overdependence on one peculiar plant. As most insect pollinators exhibit a diet breadth when showing flower constancy, to determine the difference and similarity of most and less-preferred flowers by insect pollinators may be helpful to understand their trade-off between flower constancy and overdependence. 2. We addressed this question in the long-proboscid tangle-veined fly (Nemetrinus spp.). Dietary investigation indicates that the flies show constancy for the morphological characteristic of the Delphinium caeruleum, which is the most preferred plant for this Nemestrinidae fly that has blue, long-tubed flowers. 3. In a colour selection experiment, focal individuals showed obvious preference for white, which is the colour of less-preferred flowers by the fly in the natural environment. In a scent selection experiment, focal individuals showed obvious preference for D. caeruleum and Dracocephalum heterophyllum, but avoidance to Dasiphora fruticosa and Dasiphora davurica. This indicates that long-proboscid tangle-veined flies can forage on other flowers, even the existing of constancy for D. caeruleum, as long as they do not hate the scent. It seems that long-proboscid tangle-veined flies can maximize foraging efficiency by showing constancy for the morphological characteristic of the most preferred plant and for the scent and colour of less-preferred plants. 4. The tradeoff of long-proboscid tangle-veined fly in selection of nectar sources may be an adaptation to the risk of overdependence on one plant in evolution.

Data from: Plant demographic and functional responses to management intensification: a long-term study in a Mediterranean rangeland

1. Understanding how functional traits, which are key for plant functioning, relate to demographic parameters of populations is central to tackle pending issues in plant ecology such as the forecast of the fate of populations and communities in a changing world, the quantification of community assembly processes or the improvement of species distribution models. We addressed this question in the case of species from a Mediterranean rangeland of southern France. 2. Changes in species abundance in response to management intensification (fertilization and increased grazing pressure) were followed over a 28-year period. Probabilities of presence, and elasticities of the changes in the probability of space occupancy to colonization and survival, which are analogues of demographic parameters, were calculated for 53 species from the time series of abundance data using a space occupancy model. Nine quantitative traits pertaining to resource use, plant morphology, regeneration and phenology were measured on these species and related to demographic parameters. 3. The long-term dynamics of species in response to management intensification was associated with major changes in functional traits and strategies. Changes in the probability of occurrence – analogous to population growth rate - were correlated with traits describing the fast-slow continuum of leaf functioning. The elasticity of population growth rate to colonization was significantly related to reproductive plant height and seed mass, and to a lower extent, to leaf carbon isotopic ratio. 4. Synthesis. The functional response of species to management intensification corresponds to a shift along the second axis of a recently identified global spectrum of plant form and function, which maps, to some extent, onto the fast-slow continuum of life-history strategies. By contrast, the elasticity of colonization relates to the global spectrum axis capturing the size of organs. Seed mass contributes to this axis and is assumed to relate to one of the important traits structuring the reproductive strategy axis of life histories as well, namely net reproductive rate. While this mapping between functional and life-history traits is appealing, further tests in contrasting types of communities are required to assess its degree of generality.

opencc-zeroDec 2019View details →

A Test of the Repeatability of Measurements of Relative Fitness in the Long-Term Evolution Experiment with Escherichia coli

Experimental studies of evolution using microbes have a long tradition, and these studies have increased greatly in number and scope in recent decades. Most such experiments have been short in duration, typically running for weeks or months. A venerable exception, the long-term evolution experiment (LTEE) with Escherichia coli has continued for 30 years and 70,000 bacterial generations. The LTEE has become one of the cornerstones of the field of experimental evolution, in general, and the BEACON Center for the Study of Evolution in Action, in particular. Science laboratories and experiments usually have finite lifespans, but we hope that the LTEE can continue far into the future. There are practical issues associated with maintaining such a long-term experiment. One issue, which we address here, is whether key measurements made at one time and place are reproducible, within reasonable limits, at other times and places. This issue comes to the forefront when one considers moving an experiment like the LTEE from one lab to another. To that end, the Barrick lab at the University of Texas at Austin, measured the fitness values of samples from the 12 LTEE populations at 2,000, 10,000, and 50,000 generations and compared the new data to data previously obtained at Michigan State University. On balance, the datasets agree very well. More generally, this finding shows the value of simplicity in experimental design, such as using a chemically defined growth medium and appropriately storing samples from microbiological experiments. Even so, one must be vigilant in checking assumptions and procedures given the potential for uncontrolled factors (e.g., water quality) to affect outcomes. This vigilance is perhaps especially important for a trait like fitness, which integrates all aspects of organismal performance and may therefore be sensitive to any number of subtle environmental influences.

opencc-zeroDec 2015View details →

Data from: Long-term climate and competition explain forest mortality patterns under extreme drought

Rising temperatures are amplifying drought-induced stress and mortality in forests globally. It remains uncertain, however, whether tree mortality across drought-stricken landscapes will be concentrated in particular climatic and competitive environments. We investigated the effects of long-term average climate [i.e. 35-year mean annual climatic water deficit (CWD)] and competition (i.e. tree basal area) on tree mortality patterns, using extensive aerial mortality surveys conducted throughout the forests of California during a 4-year statewide extreme drought lasting from 2012 to 2015. During this period, tree mortality increased by an order of magnitude, typically from tens to hundreds of dead trees per km2, rising dramatically during the fourth year of drought. Mortality rates increased independently with average CWD and with basal area, and they increased disproportionately in areas that were both dry and dense. These results can assist forest managers and policy-makers in identifying the most drought-vulnerable forests across broad geographic areas.

opencc-zeroMar 2020View details →

Roadside diversity in relation to age and surrounding source habitat: evidence for long time lags in valuable green infrastructure

1. The severe and ongoing decline in semi-natural grassland habitat during the past two centuries means that it is important to consider how other, marginal grassland habitat elements can contribute to landscape-level biodiversity, and under what circumstances. 2. To examine how habitat age and the amount of core grassland habitat in the surrounding landscape affect diversity in green infrastructure, we carried out inventories of 36 rural road verges that were either historical (pre-1901) or modern (established post-1901 and before 1975), and were surrounded by relatively high (>15%) or low (<5%) levels of grassland habitat. We recorded the number of plant species, grassland specialists, grassland conservation species and the fraction of the landscape's species and specialists found in the road verge. 3. Road verge communities were characterised by high levels of grassland specialist species (35% of the 161 species recorded), with road verge sites supporting 15-20% of the specialist species found in the surrounding 25 km2 landscape. 4. Richness of species and specialists were more closely related to road age than to the amount of surrounding habitat. Higher diversity in historical roads, despite the majority of modern roads being at least 60 years old, suggests a long time lag in the establishment of grassland communities in marginal grassland habitats. We identified no effect of historical surrounding land use on present day diversity in road verges. 5. Road verge richness was not affected by the amount of surrounding grassland. This could be due to the relatively low amounts of grassland remaining in all landscapes, together with dispersal limitation commonly found in grassland plant communities contributing to a potential time lag. 6. We identified road verges as potentially very important habitats for grassland communities. Because of the high levels of grassland specialists present, these and other marginal grasslands and grassland green infrastructure should be explicitly considered in landscape-scale conservation management. Practitioners looking to identify the most species-rich road verges should aim to find the oldest possible, while long time lags in community assembly suggests that seed sowing may be appropriate to enhance roadside diversity, even in decades-old road verges.

opencc-by-4.0Jun 2021View details →

Impact of increased resolution on long-standing biases in HighResMIP-PRIMAVERA climate models

This contains the data and plot scripts to reproduce the figures of the manuscript: Impact of increased resolution on long-standing biases in HighResMIP-PRIMAVERA climate models. Authors: Eduardo Moreno-Chamarro1*, Louis-Philippe Caron1,2, Saskia Loosveldt Tomas1, Oliver Gutjahr3,4 , Marie-Pierre Moine5, Dian Putrasahan3 , Christopher D. Roberts6, Malcolm J. Roberts7, Retish Senan6, Laurent Terray5, Etienne Tourigny1, Pier Luigi Vidale8 1 Barcelona Supercomputing Center (BSC), Barcelona, Spain. 2 Ouranos, Montreal, H3A 1B9, Canada. 3 Max Planck Institute for Meteorology. Hamburg, Germany. 4 Now at Institut für Meereskunde, Universität Hamburg, Hamburg, Germany. 5 CECI, Université de Toulouse, CERFACS/CNRS, Toulouse, France. 6 ECMWF European Centre for Medium-Range Weather Forecasts, Reading, United Kingdom. 7 Met Office, Exeter EX1 3PB, United Kingdom. 8 NCAS-Climate, Department of Meteorology, University of Reading, Reading, United Kingdom. Correspondence to: Eduardo Moreno-Chamarro (eduardo.moreno@bsc.es) Abstract. We examine the impacts of increased resolution on four long-standing biases using five different climate models developed within the PRIMAVERA project. Atmospheric resolution is increased from ~100–200 km to ~25–50 km, and ocean resolution is increased from ~1° (i.e., eddy-parametrized) to ~0.25° (i.e., eddy-present). For one model, ocean resolution is also increased to 1/12° (i.e., eddy-rich). Fully-coupled general circulation models and their atmosphere-only versions are compared with observations and reanalysis of near-surface temperature, precipitation, cloud cover, net cloud radiative effect, and zonal wind over the period 1980–2014. Both the ensemble mean and the individual models are analyzed. Increased resolution especially in the atmosphere helps reduce the surface warm bias over the tropical upwelling regions in the coupled models, with further improvements in the cloud cover and precipitation biases over the tropical Atlantic particularly. Related to this and to the improvement in the precipitation distribution over the western tropical Pacific, the double ITCZ bias also weakens with resolution. Overall, increased ocean resolution from 1° to 0.25° offers limited improvements or even bias degradation in some models, although an eddy-rich ocean resolution seems beneficial to reduce the North Atlantic cold bias and the Gulf Stream path. Despite the improvements, however, large biases in precipitation and cloud cover persist over the whole tropics as well as in the upper-troposphere zonal winds at mid-latitudes in both coupled and atmosphere-only models at higher resolutions. The SO warm bias also worsens or persists in some coupled models. And a new warm bias emerges in the Labrador Sea in all the high-resolution coupled models. The analysis of the PRIMAVERA models therefore suggests that, to reduce biases, i) increased atmosphere resolution up to ~25–50 km alone might not be sufficient and ii) an eddy-rich ocean resolution might be needed. The study thus adds to evidence that further improved model physics and tuning might be necessary in addition to increased resolution to mitigate biases.

opencc-zeroMay 2019View details →

Data from: Ancient polymorphisms contribute to genome-wide variation by long-term balancing selection and divergent sorting in Boechera stricta

Background: Genomic variation is widespread, and both neutral and selective processes can generate similar patterns in the genome. These processes are not mutually exclusive, so it is difficult to infer the evolutionary mechanisms that govern population and species divergence. Boechera stricta,is a perennial relative of Arabidopsis thaliana native to largely undisturbed habitats with two geographic and ecologically divergence subspecies. Here we delineate the evolutionary processes driving genetic diversity and population differentiation in this species. Results: Using whole genome re-sequencing data from 517 Boechera stricta accessions, we identify four genetic groups that diverged around 30 - 180 thousand years ago, with long-term small effective population sizes and recent population expansion after the Last Glacial Maximum. We find three genomic regions with elevated nucleotide diversity, totaling about 10% of the genome. These three regions of elevated nucleotide diversity show excess of intermediate-frequency alleles, higher absolute divergence (dXY) and lower relative divergence (FST) than genomic background, and significant enrichment in immune-related genes, reflecting long-term balancing selection. Scattered across the genome we also find regions with both high FST and DXY among groups, termed FST-islands. Population genetic signatures indicate that FST-islands with elevated divergence, which have experienced directional selection, are derived from divergent sorting of ancient polymorphisms. Conclusions: Our results suggest that long-term balancing selection on disease resistance genes may have maintained ancestral haplotypes across different geographical lineages, and unequal sorting of balanced polymorphisms may have generated genomic regions with elevated divergence. This study highlights the importance of ancestral balanced polymorphisms as crucial components of genome-wide variation.

Data from: Rare long-distance dispersal of a marine angiosperm across the Pacific Ocean

Aim: Long-distance dispersal (LDD) events occur rarely but play a fundamental role in shaping species biogeography. Lying at the heart of island biogeography theory, LDD relies on unusual events to facilitate colonisation of new habitats and range expansion. Despite the importance of LDD, it is inherently difficult to quantify due to the rarity of such events. We estimate the probability of LDD of the seagrass Heterozostera nigricaulis, a common Australian species, across the Pacific Ocean to colonise South America.Location: Coastal Chile, Australia and the Pacific Ocean. Methods: Genetic analysis of H. nigricaulis collected from Chile and Australia were used to assess the relationship between the populations and levels of clonality. Ocean surface current models were used to predict the probability of propagules dispersing from South East Australia to Central Chile and shipping data used to determine the likelihood of anthropogenic dispersal. Results: Our study infers that the seagrass H. nigricaulis dispersed from Australia across the entire width of the Pacific (~14,000 km) to colonise South America on two occasions. Genetic analyses reveal that these events led to two large isolated clones, one of which covers a combined area of 3.47 km2. Oceanographic models estimate the arrival probability of a dispersal propagule within 3 years to be at most 0.00264%. Early shipping provides a potential alternative dispersal vector, yet few ships sailed from SE Australia to Chile prior to the first recording of H. nigricaulis and the lack of more recent and ongoing introductions demonstrate the rarity of such dispersal. Main Conclusion: These findings demonstrate LDD does occur over extreme distance despite very low probabilities. The large number of propagules (100s of millions) produced over 100s of years suggests that the arrival of propagules in Chile was inevitable and confirms the importance of LDD for species distributions and community ecology.

opencc-zeroDec 2016View details →

Data from: Long-term in situ persistence of biodiversity in tropical sky-islands revealed by landscape genomics

Tropical mountains are areas of high species richness and endemism. Two historical phenomena may have contributed to this: (1) fragmentation and isolation of habitats may have promoted the genetic differentiation of populations and increased the possibility of allopatric divergence and speciation, and; (2) the mountain areas may have allowed long-term population persistence during global climate fluctuations. These two phenomena have been studied using either species occurrence data or estimating species divergence times. However, only few studies have used intraspecific genetic data to analyse the mechanisms by which endemism may emerge at the microevolutionary scale. Here, we use landscape analysis of genomic SNP data sampled from two high-elevation plant species from an archipelago of tropical sky-islands (the Transmexican Volcanic Belt) to test for population genetic differentiation, synchronous demographic changes and habitat persistence. We show that genetic differentiation can be explained by the degree of glacial habitat connectivity among mountains, and that mountains have facilitated the persistence of populations throughout glacial/interglacial cycles. Our results support the ongoing role of tropical mountains as cradles for biodiversity by uncovering cryptic differentiation and limits to gene flow.

opencc-by-nc-4.0Feb 2021View details →

Figure 3 in Ilha Grande, one of the locations with the most records of bat species (Mammalia, Chiroptera) in Rio de Janeiro state: results of a long-term ecological study

Figure 3. Relationship between number of species in the Phyllostomidae family (A) and number of captures in the Phyllostomidae family, (B) and capture effort (h.m²) in bat inventories in Rio de Janeiro state. Numbers correspond to locations listed in Table IV. Dots: cross = study 1 on Ilha Grande; square = study 2 on Ilha Grande; star = study 3 on Ilha Grande; triangle = study 4 on Ilha Grande; black circle = study 5 on Ilha Grande; grey circle = other studies in Rio de Janeiro state.

opencc-by-nc-4.0Feb 2021View details →

Figure 1 in Ilha Grande, one of the locations with the most records of bat species (Mammalia, Chiroptera) in Rio de Janeiro state: results of a long-term ecological study

Figure 1. Map of Ilha Grande with sampling points of the five studies described in this paper, conducted between 1998 and 2018 on Ilha Grande, Angra dos Reis, Rio de Janeiro state, Brazil. A map of South America is shown, detailing the location of the state of Rio de Janeiro, in southeastern Brazil, while in the enlargement is shown the state of Rio de Janeiro detailing the location of Ilha Grande.

opencc-by-nc-4.0Feb 2021View details →

Figure 2 in Ilha Grande, one of the locations with the most records of bat species (Mammalia, Chiroptera) in Rio de Janeiro state: results of a long-term ecological study

Figure 2. Locations in Rio de Janeiro state where bat inventories have been conducted. Numbers correspond to locations in Table 4. A map of South America is shown, detailing the location of the state of Rio de Janeiro in southeastern Brazil.

opencc-zeroMar 2020View details →

Multiple abiotic and biotic drivers of long-term wood decomposition within and among species in semiarid inland dunes: a dual role for stem diameter

This is wood decomposition data conducted in an semiarid inland dune including mass loss, initial wood traits and k values of combinations between five diameter classes and four shrub species under different treatments including UV and litter position. We found that after 34 months of in situ incubation, the mass loss of buried woody litters was three times faster than those of suspended and surface woody litters (53.5 ± 2.7 %, 17.0 ± 1.0 % and 14.4± 1.2 %, respectively). In surface and suspended positions, litter decomposition rates were almost equally low and most mass loss was during the first two years, when bark was still attached and UV radiation had no significant effect on woody litter mass loss.

opencc-zeroJun 2021View details →

Plant dispersal syndromes are unreliable as predictors of zoochory and long-distance dispersal by ungulates and waterbirds

Plant dispersal syndromes are allocated based on diaspore morphology and used to predict mechanisms of dispersal. Many authors assume that only angiosperms with endozoochory, epizoochory or anemochory syndromes have a long-distance dispersal (LDD) mechanism. Too much faith is often placed in classical syndromes to explain historical dispersal events and to predict future ones. The "endozoochory syndrome" is actually a "frugivory syndrome" and has often diverted attention from endozoochory by non-frugivores (e.g. waterbirds and large herbivores) that disperse a broad range of angiosperms, for which they likely provide the maximum dispersal distances. Neither the endozoochory nor the epizoochory syndromes provide helpful predictions of which plants non-frugivores disperse, or by which mechanism. We combined data from Albert et al. (2015a), Soons et al. (2016) and Julve (1998) to show that only 4% of European plant species dispersed by ungulate endozoochory belong to the corresponding syndrome, compared to 36% for ungulate epizoochory and 8% for endozoochory by migratory ducks. In contrast, the proportions of these species that are assigned to an "unassisted syndrome" are 37%, 31% and 28%, respectively. Since allocated syndromes do not adequately account for zoochory, empirical studies often fail to find the expected relationship between syndromes and LDD events such as those underlying the colonization of islands or latitudinal migration. We need full incorporation of existing zoochory data into dispersal databases, and more empirical research into the relationship between plant traits and the frequency and effectiveness of different dispersal mechanisms (paying attention to unexpected vectors). Acknowledging the broad role of non-frugivores in facilitating LDD is crucial to improve predictions of the consequences of global change, such as how plant distributions respond to climate change, and how alien plants spread. Networks of dispersal interactions between these vertebrates and plants are a vital but understudied part of the Web of Life. The datasets we present here illustrate these limitations of syndromes, and include data from Brochet et al. (2010) regarding the syndromes of plants dispersed by Eurasian Teal via epizoochory or endozoochory.

opencc-zeroDec 2019View details →

Data from: Long-lived metabolic enzymes in the crystalline lens identified by pulse-labeling of mice and mass spectrometry

The lenticular fiber cells are comprised of extremely long-lived proteins while still maintaining an active biochemical state. Dysregulation of these activities has been implicated in age-related cataracts, and other lens diseases. However, the lenticular protein dynamics underlying health and disease is unclear. We sought to measure the global protein turnover rates in the eye using dietary nitrogen-15 (15N)-labeling of mice between 3 and 15 weeks of age. By performing mass spectrometry we measured the 14N- to 15N-peptide ratios of 248 lens proteins, including Crystallin, Aquaporin, Collagen and Laminin of the lens capsule, and enzymes that catalyze glycolysis as well as oxidation and reduction reactions. Unexpectedly, like the crystallin proteins, many of these enzymes are also exceedingly long-lived. The slow replacement of these enzymes in spite of young age of the mice suggests their potential roles in age-related metabolic changes in the lens.

Data from: Climate change and functional traits affect population dynamics of a long-lived seabird

1. Recent studies unravelled the effect of climate changes on populations through their impact on functional traits and demographic rates in terrestrial and freshwater ecosystems, but such understanding in marine ecosystems remains incomplete. 2. Here, we evaluate the impact of the combined effects of climate and functional traits on population dynamics of a long-lived migratory seabird breeding in the southern ocean: the black-browed albatross (Thalassarche melanophris, BBA). We address the following prospective question: ''Of all the changes in the climate and functional traits, which would produce the biggest impact on the BBA population growth rate?'' 3. We develop a structured matrix population model that includes the effect of climate and functional traits on the complete BBA life cycle. A detailed sensitivity analysis is conducted to understand the main pathway by which climate and functional trait changes affect the population growth rate. 4. The population growth rate of BBA is driven by the combined effects of climate over various seasons and multiple functional traits with carry-over effects across seasons on demographic processes. Changes in Sea Surface Temperature (SST) during late winter cause the biggest changes in the population growth rate, through their effect on juvenile survival. Adults appeared to respond to changes in winter climate conditions by adapting their migratory schedule rather than by modifying their at-sea foraging activity. However, the sensitivity of the population growth rate to SST affecting BBA migratory schedule is small. BBA foraging activity during the pre-breeding period has the biggest impact on population growth rate among functional traits. Finally, changes in SST during the breeding season have little effect on the population growth rate. 5. These results highlight the importance of early life histories and carry-over effects of climate and functional traits on demographic rates across multiple seasons in population response to climate change. Robust conclusions about the roles of various phases of the life cycle and functional traits in population response to climate change rely on an understanding of the relationships of traits to demographic rates across the complete life cycle.

opencc-by-4.0May 2020View details →

Intaglio. Long oval intaglio in cornelian engraved with a brāhmī inscription in three characters and a trident.

Intaglio. Long oval intaglio in cornelian engraved with a brāhmī inscription in three characters and a trident. British Museum 1892,1103.125.

opencc-byJan 2021View details →

Alibates Petroglyph - Long Foot - Enhanced

An enhanced view of a boulder with a foot petroglyph and a number of cupules. [The unenhanced version is here.](https://skfb.ly/6XSON) Source: Objaverse 1.0 / Sketchfab