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Data from: The value of time-series data for conservation planning
<ol> <li>Protected areas (PAs) are increasingly being used worldwide for the conservation and management of wildlife. Systematic conservation planning (SCP) aims at ensuring biodiversity persistence while minimizing the threats faced by the species and/or the economic costs related to protection. To account for spatio-temporal interactions between species and human threats, conservation planning for mobile wildlife requires time-series data derived from monitoring of species and human threats, a process that is costly and technically challenging. Therefore, assessments of the monitoring period needed to ensure sufficient data input in the design of efficient, adequate and representative networks of PAs are crucial.</li> <li>We demonstrated the value of time-series data in conservation planning by implementing SCP and data from different monitoring periods to identify priority conservation areas for highly mobile marine megafauna accounting for their main threat: commercial fishing. Two analyses of ten reserve-design scenarios each, replicated as many times as the data composing each scenario permitted were run in Marxan. The best solutions of the planning scenarios were statistically compared using the Cohen`s Kappa test. We also assessed differences in spatial similarity among and within scenarios using the Wilcoxon non-parametric test and a non-metric multidimensional scaling analysis. Finally, we compared the necessary cost and the area selected for each scenario.</li> <li>Our study highlights the importance of time-series ecological and socioeconomic data for the robust selection of priority conservation areas. The results revealed different thresholds of the minimum temporal data required to design efficient networks of PAs for highly mobile species, demonstrating that the incorporation of data covering longer periods to the scenarios produce a more robust selection of priority conservation areas. Conservation plans using data covering less than three years were missing important priority areas.</li> <li> <i>Synthesis and applications. </i>We provide a method for estimating the minimum number of years of monitoring required to design efficient networks of protected areas that ensure the persistence of highly mobile species such as cetaceans and seabirds. This method can be used within an adaptive management framework to evaluate whether a network of PAs performs as planned, and to test whether management strategies should be altered or adjusted in response to local and global changes.</li> </ol>
Lee and Daunizeau choice data from: Trading mental effort for confidence in the metacognitive control of value-based decision-making
<p>Why do we carefully ponder some decisions, but not others? In this work, we derive a computational model of the metacognitive control of decisions or MCD. In brief, we assume that fast and automatic processes first provide an initial (and largely uncertain) representation of options' values, yielding prior estimates of decision difficulty. This uncertain value representation is then refined by deploying cognitive (e.g., attentional, mnesic) resources, the allocation of which is controlled by an effort-confidence tradeoff. Importantly, the anticipated benefit of allocating resources varies in a decision-by-decision manner according to the prior estimate of decision difficulty. The ensuing MCD model predicts choices, response time, subjective feeling of effort, choice confidence, and choice-induced preference change. We test these predictions in a systematic manner, using a dedicated behavioral paradigm. Our results provide a quantitative link between mental effort, choice confidence, and preference reversals, which could inform interpretations of related neuroimaging findings.</p>
Data from: Mob and rotational grazing influence pasture biomass, nutritive value, and species composition
<p><span> This is digital research data corresponding to a published manuscript, <i>Mob and rotational grazing influence pasture biomass, nutritive value, and species composition</i>, in Agronomy Journal, Vol. 112 p. 2866-2878. </span></p> <p><span> Mob grazing, which uses very high stocking densities for short durations followed by a relatively long rest period, was designed to mimic bison (Bison bison) grazing in western U.S. grassland. This project assessed the suitability of mob grazing for livestock production in the Northeast. Objectives were to compare the effects of mob and rotational grazing on dry matter (DM) mass, nutritive value, and botanical composition across four grazing seasons. Eight, 0.10‐ha paddocks were established in 2014 as a randomized complete block with four replications, and seeded with alfalfa (Medicago sativa L.), white clover (Trifolium repens L.), orchardgrass (Dactylis glomerata L.), narrowleaf plantain (Plantago lanceolata L.), and tall fescue [Schedonorus arundinaceus (Schreb.) Dumort]. Mob‐grazed (MOB) paddocks were grazed by yearling beef cattle twice each year, (70–90–day interval), and rotationally grazed (ROT) paddocks were grazed four to six times each year (when sward height reached 25 cm).</span></p>
Replication files for the Value of Unemployment Insurance
<p>These files enable the replication of all results from The Value of Unemployment Insurance, forthcoming in the Review if Economic Studies</p>
Supplementary material for: Exploring the impact of unstable terminals on branch support values in paleontological data
<p>The dataset consists of a PDF file and two plain-text TNT scripts (*.run files). The PDF includes supporting Figures for the additional analyses conducted by Flores et al. on paleontological datasets. The TNT scripts conduct two complementary sets of analyses: (a) evaluation of taxon instability relative to the incompleteness ("mc.run"), and (b) changes in branch support values after pruning unstable taxa ("avmc.run"). To properly run these files in TNT, the name of the matrix files should be given as arguments (see the TNT documentation webpage for details on the usage of script files). The scripts generate CSV-formatted output for being subsequently read into any other software. Script files are provided as "ready-for-use", and are freely distributable and modifiable. We request that you cite the respective paper and dataset.</p>
Climate influences the value of a plant structural defence against browsing
<ol> <li>The circumstances that select for plant anti-herbivore defences are not well understood. In New Zealand, the "divaricate" cage-like architecture of many woody plants may have arisen as a defence against avian browsing; it also has some ability to deter browsing by introduced deer. Its prominence on alluvial soils in frosty and droughty areas led us to hypothesize that structural defences are of most value where fertile soils coincide with climatic constraints that prevent plants from quickly growing out of the browse zone.</li> <li>We tested this hypothesis by growing seedlings of three divaricate species and their broadleaved congeners on fenced and unfenced plots beneath treefall gaps at three humid frost-free sites in the North Island of New Zealand, and at three colder and drier sites in the South Island. Soil total phosphorus levels were moderate to high at all sites (344 to 961 ppm), and pellet counts indicated similar average deer densities at North and South Island sites, <a name="_Hlk50404021">enabling us to attribute variation in seedling growth and survival primarily to climatic differences between our sites.</a> </li> <li>The circumstances that select for plant anti-herbivore defences are not well understood. In New Zealand, the "divaricate" cage-like architecture of many woody plants may have arisen as a defence against avian browsing; it also has some ability to deter browsing by introduced deer. Its prominence on alluvial soils in frosty and droughty areas led us to hypothesize that structural defences are of most value where fertile soils coincide with climatic constraints that prevent plants from quickly growing out of the browse zone.</li> <li>We tested this hypothesis by growing seedlings of three divaricate species and their broadleaved congeners on fenced and unfenced plots beneath treefall gaps at three humid frost-free sites in the North Island of New Zealand, and at three colder and drier sites in the South Island. Soil total phosphorus levels were moderate to high at all sites (344 to 961 ppm), and pellet counts indicated similar average deer densities at North and South Island sites, <a name="_Hlk50404021">enabling us to attribute variation in seedling growth and survival primarily to climatic differences between our sites.</a> </li> <li>On fenced plots, average relative height growth rates in the North Island exceeded those on the southern sites by 64 %, and growth of broadleaved species averaged 132 % and 99 % greater than that of divaricate congeners at North and South Island sites, respectively. On the northern sites, broadleaved species also held a large (137 %) net height growth advantage over divaricates even on unfenced plots. In contrast, exposure to browsing on the coldest sites resulted in complete loss of the broadleaved net height growth advantage.</li> <li> <a name="_heading=h.30j0zll"></a> <i>Synthesis</i>. Even in the presence of deer, divaricate plants were overgrown on humid frost-free sites, but not on colder and drier sites, where browsing neutralized the superior growth potential of broadleaved species. The cost of structural defences therefore paid off only on sites where climatic adversity reduces the ability of plants lacking such defences to grow quickly out of the browse zone, in agreement with our hypothesis.</li> </ol>
Figure S1. Tear break-up time value in hyaluronic acid (HA) group and non-HA group after excluding the source of publication bias
<p>Figure S1. Tear break-up time value in hyaluronic acid (HA) group and non-HA group after excluding the source of publication bias <br> </p>
MIC values from MBL-producing Enterobacterales collection
<p>Raw minimum inhibitory concentration values (in µg/mL) obtained for the MBL-producing Enterobacterales collection following the agar dilution standard procedure.</p>
TA B L E 2 Estimates of pairwise sequence divergence (cyt-b gene) in pale-bellied Micronycteris, where M. minuta is divided in three clades. Below the diagonal: pairwise distance using the Kimura 2-parameter model (percentage). On the diagonal: within-clade distance using the Kimura 2-parameter model (percentage). Above the diagonal: pairwise p-distance values. Number of specimens sequenced in parenthesis. *Chimeric sequence obtained from two paratypes (Siles et al., 2013). in Revision of the pale-bellied Micronycteris Gray, 1866 (Chiroptera, Phyllostomidae) with descriptions of two new species
TA B L E 2 Estimates of pairwise sequence divergence (cyt-b gene) in pale-bellied Micronycteris, where M. minuta is divided in three clades. Below the diagonal: pairwise distance using the Kimura 2-parameter model (percentage). On the diagonal: within-clade distance using the Kimura 2-parameter model (percentage). Above the diagonal: pairwise p-distance values. Number of specimens sequenced in parenthesis. *Chimeric sequence obtained from two paratypes (Siles et al., 2013).
Supplementary materials for the paper "Benefit of Self-Stabilizing Protocols in Eventually Consistent Key-Value Stores: A Case Study"
<p>Supplementary materials for the paper "Benefit of Self-Stabilizing Protocols in Eventually Consistent Key-Value Stores: A Case Study"</p>
Data from: Comparative spatial genetics and epigenetics of plant populations: heuristic value and a proof of concept
Despite the recent upsurge of interest on natural epigenetic variation of nonmodel organisms, factors conditioning the spatial structure of epigenetic diversity in wild plant populations remain virtually unexplored. We propose that information on processes shaping natural epigenetic variation can be gained using the spatial structure of genetic diversity as null model. Departures of epigenetic isolation-by-distance (IBD) patterns from genetic IBD patterns for the same sample, particularly differences in slope of similarity-distance regressions, will reflect the action of factors that operate specifically on epigenetic variation, including imperfect transgenerational inheritance and responsiveness to environmental factors of epigenetic marks. As a proof of concept, we provide a comparative analysis of spatial genetic and epigenetic structure of 200 mapped individuals of the perennial herb Helleborus foetidus. Plants were fingerprinted using nuclear microsatellites, amplified fragment length polymorphisms (AFLP) and methylation-sensitive AFLP markers. Expectations from individual-level IBD patterns were tested by means of kinship-distance regressions. Both genetic and epigenetic similarity between H. foetidus individuals conformed to theoretical expectations under individual-level IBD models. Irrespective of marker type, there were significant negative linear relationships between the kinship coefficient for plant pairs and their spatial separation. Regression slopes were significantly steeper for epigenetic markers. Epigenetic similarity between individuals was much greater than genetic similarity at shortest distances, such epigenetic 'kinship excess' tending to decrease as plant separation increased. Results suggest that moderate-to-high heritability and responsiveness to local environments are major drivers of epigenetic spatial structure in H. foetidus, and illustrate the heuristic value of comparing genetic and epigenetic spatial structure for formulating and testing hypotheses on forces shaping epigenetic diversity in wild plant populations.
Data from: Parmotrema internexum (Lecanorales: Parmeliaceae): an overlooked macrolichen in southeastern North America highlights the value of basic biodiversity research
Parmotrema internexum is shown to be a morphologically, chemically and phylogenetically distinct species whose occurrence in North America has been previously overlooked and largely based on misidentifications. Prior accounts of the species being similar to P. crinitum but differing in having an adnate thallus, few marginal cilia, and in producing norlobaridone in addition to the stictic acid complex, are confirmed. An extensive review of the taxon, including the use of the name P. internexum in the literature, is provided. Taxonomic treatments of P. crinitum and P. internexum are also provided and both species are illustrated.
Data from: Assessing the conservation value of secondary savanna for large mammals in the Brazilian Cerrado
Debate about the conservation value of secondary habitats has tended to focus on tropical forests, increasingly recognizing the role of secondary forests for biodiversity conservation. However, there remains a lack of information about the conservation value of secondary savannas. Here, we conducted a camera trap survey to assess the effect of secondary vegetation on large mammals in a Brazilian Cerrado protected area, using a single-season occupancy framework to investigate the response of individual species (species-level models) and of all species combined (community-level models). In addition, we investigated the cost effectiveness of different sampling designs to monitor globally threatened species in the study area. At the community level, savanna that regenerated from eucalyptus plantation had similar occupancy estimate as old growth areas. At the species level, none of the ten species individually assessed seemed to respond to succession stage, with greater support for the effect of other covariates on occupancy, such as distance from water and vegetation physiognomy. These results demonstrate that secondary vegetation does not appear to negatively impact large mammals in the study area and suggest that, given a favorable context, Cerrado mammals can recolonize and use secondary savannas that regenerated from clearcut. However, our study area should be considered a best-case scenario, as it retained key ecological attributes of high-value secondary habitats. Our simulations showed that a sampling design with 60 camera trap sites surveyed during nine occasions is appropriate to monitor most globally threatened species in the study area, and could be a useful starting point for new monitoring initiatives in other Cerrado areas.
Data from: High genetic variation and moderate to high values for genetic parameters of Picea abies resistance to Pissodes strobi
Genetic parameters of Picea abies resistance to the white pine weevil (Pissodes strobi Peck) were estimated from 193 full-sib and 166 half-sib families in six 10-year-old progeny trials. The estimated family and individual heritability values for the cumulative weevil attack rate between ages 6 and 10 (CWA6–10) were high and moderate for both full-sib families (0.61 and 0.28, respectively) and half-sib families (0.85 and 0.40, respectively), indicating strong genetic control for this trait in Norway spruce. The fact that specific combining ability (SCA) variance represents 35 % of the general combining ability (GCA) variance suggests that non-additive (dominant) effects are weak. The strong type B correlations found for CWA6–10 (rˆB=0.96 for full-sib families and rˆB=0.81 for half-sib families) indicate that family ranks were stable across sites. For three of the five sites with high attack levels, genetic correlations were not significant between CWA6–10 and tree height at age 5. Moderate positive genetic correlations were detected between CWA6–10 and tree diameter at age 10 (rˆA from 0.29 to 0.60), but specific families showing both high resistance and good diameter growth can be found. These results suggest that the genetic improvement of Norway spruce for resistance to white pine weevil can be achieved successfully without adversely affecting growth.
Data from: Conservation value of low-productive forests measured as the amount and diversity of dead wood and saproxylic beetles
In many managed landscapes, low-productive land comprises most of the remaining relatively untouched areas, and is often over-represented within protected areas. The relationship between the productivity and conservational value of a site is poorly known; however, it has been hypothesized that biodiversity increases with productivity due to higher resource abundance or heterogeneity, and that the species communities of low-productive land are a nested sub-set of communities from more productive land. We tested these hypotheses for dead wood-dependent beetles by comparing their species richness and composition, as well as the amount and diversity of dead wood, between low-productive (potential forest growth < 1 m3 ha-1 year-1) and productive Scots pine-dominated stands in Sweden. We included four stand types: stands situated on (i) thin soils and (ii) mires (both low-productive), (iii) managed stands, and (iv) unmanaged stands set aside for conservation purposes (both productive). Beetle species richness and number of red-listed species were highest in the productive set-asides. Species richness was positively correlated with the volume and diversity of dead wood, but volume appeared to be a better predictor than diversity for the higher species richness in set-asides. Beetle species composition was similar among stand types, and the assemblages in low-productive stands were largely subsets of those in productive set-asides. However, 11% of all species and 40% of red-listed species only occurred in productive stands, while no species were unique to low-productive stands. We conclude that low-productive forests are less valuable for conservation than productive forest land. Given the generally similar species composition among stand types, a comparable conservational effect could be obtained by setting aside a larger area of low-productive forest in comparison to the productive. In terms of dead wood volumes, 1.8–3.6 ha of low-productive forest has the same value as 1 ha of unmanaged productive forest. This figure can be used to estimate the conservation value of low productive forests; however, as productive forests harbored some unique species, they are not completely exchangeable.
Data from: Stimulus discriminability may bias value-based probabilistic learning
Reinforcement learning tasks are often used to assess participants' tendency to learn more from the positive or more from the negative consequences of one's action. However, this assessment often requires comparison in learning performance across different task conditions, which may differ in the relative salience or discriminability of the stimuli associated with more and less rewarding outcomes, respectively. To address this issue, in a first set of studies, participants were subjected to two versions of a common probabilistic learning task. The two versions differed with respect to the stimulus (Hiragana) characters associated with reward probability. The assignment of character to reward probability was fixed within version but reversed between versions. We found that performance was highly influenced by task version, which could be explained by the relative perceptual discriminability of characters assigned to high or low reward probabilities, as assessed by a separate discrimination experiment. Participants were more reliable in selecting rewarding characters that were more discriminable, leading to differences in learning curves and their sensitivity to reward probability. This difference in experienced reinforcement history was accompanied by performance biases in a test phase assessing ability to learn from positive vs. negative outcomes. In a subsequent large-scale web-based experiment, this impact of task version on learning and test measures was replicated and extended. Collectively, these findings imply a key role for perceptual factors in guiding reward learning and underscore the need to control stimulus discriminability when making inferences about individual differences in reinforcement learning.
Data from: Effects of growth rate, size, and light availability on tree survival across life stages: a demographic analysis accounting for missing values and small sample sizes
Background: Plant survival is a key factor in forest dynamics and survival probabilities often vary across life stages. Studies specifically aimed at assessing tree survival are unusual and so data initially designed for other purposes often need to be used; such data are more likely to contain errors than data collected for this specific purpose. Results: We investigate the survival rates of ten tree species in a dataset designed to monitor growth rates. As some individuals were not included in the census at some time points we use capture-mark-recapture methods both to allow us to account for missing individuals, and to estimate relocation probabilities. Growth rates, size, and light availability were included as covariates in the model predicting survival rates. The study demonstrates that tree mortality is best described as constant between years and size-dependent at early life stages and size independent at later life stages for most species of UK hardwood. We have demonstrated that even with a twenty-year dataset it is possible to discern variability both between individuals and between species. Conclusions: Our work illustrates the potential utility of the method applied here for calculating plant population dynamics parameters in time replicated datasets with small sample sizes and missing individuals without any loss of sample size, and including explanatory covariates.
Data from: Value of information in natural resource management: technical developments and application to pink-footed geese
The "value of information" (VOI) is a generic term for the increase in value resulting from better information to guide management, or alternatively, the value foregone under uncertainty about the impacts of management (Yokota and Thompson, Medical Decision Making 2004; 24: 287). The value of information can be characterized in terms of several metrics, including the expected value of perfect information and the expected value of partial information. We extend the technical framework for the value of information by further developing the relationship between value metrics for partial and perfect information and describing patterns of their performance. We use two different expressions for the expected value of partial information to highlight its relationship to the expected value of perfect information. We also develop the expected value of partial information for hierarchical uncertainties. We highlight patterns in the value of information for the Svalbard population of the pink-footed goose (Anser brachyrhynchus), a population that is subject to uncertainty in both reproduction and survival functions. The framework for valuing information is seen as having widespread potential in resource decision making, and serves as a motivation for resource monitoring, assessment, and collaboration.
Data from: A function-valued trait approach to estimating the genetic basis of size at age and its potential role in fisheries induced evolution
Natural selection is inherently a multivariate phenomenon. The selection pressure on size (natural and artificial) and the age at which selection occurs is likely to induce evolutionary changes in growth rates across the entire life history. However, the covariance structure that will determine the path of evolution for size-at-age has been studied in only a few fish species. We therefore estimated the genetic covariance function for size throughout ontogeny using Atlantic silversides (Menidia menidia) as the model system. Over a 3-year period, a total of 542 families were used to estimate the genetic covariance in length at age from hatch through maturity. The function-valued trait approach was employed to estimate the genetic covariance functions. A Bayesian hierarchical model was used to account for the unbalanced design, unequal measurement intervals, unequal sample sizes, and family-aggregated data. To improve mixing, we developed a two-stage sampler using a Gibbs sampler to generate the posterior of a well-mixing approximate model followed by an importance sampler to draw samples from posterior of the completely specified model. We found that heritability of length is age-specific and there are strong genetic correlations in length across ages that last 30d or more. We used these estimates in a hypothetical model predicting the evolutionary response to harvesting following a single generation of selection under both sigmoidal and unimodal patterns of gear selectivity to illustrate the potential outcomes of ignoring the genetic correlations. In these scenarios genetic correlations were found to have a strong effect on both the direction and magnitude of the response to harvest selection.
Data from: Long-term monitoring data provide evidence of declining species richness in a river valued for biodiversity conservation
Free-flowing river segments provide refuges for many imperiled aquatic biota that have been extirpated elsewhere in their native ranges. These biodiversity refuges are also foci of conservation concerns because species persisting within isolated habitat fragments may be particularly vulnerable to local environmental change. We have analyzed long-term (14- and 20-year) survey data to assess evidence of fish species declines in two southeastern U.S. rivers where managers and stakeholders have identified potentially detrimental impacts of current and future land uses. The Conasauga River (Georgia and Tennessee) and the Etowah River (Georgia) form free-flowing headwaters of the extensively dammed Coosa River system. These rivers are valued in part because they harbor multiple species of conservation concern, including three federally endangered and two federally threatened fishes. We have used data sets comprising annual surveys for fish species at multiple, fixed sites located at river shoals to analyze occupancy dynamics and temporal changes in species richness. Our analyses incorporate repeated site-specific surveys in some years to estimate and account for incomplete species detection, and test for species-specific (rarity, mainstem-restriction) and year-specific (elevated frequencies of low- or high-flow days) covariates on occupancy dynamics. In the Conasauga River, analysis of 26 species at 13 sites shows evidence of temporal declines in colonization rates for nearly all taxa, accompanied by declining species richness. Four taxa (including one federally endangered species) have reduced occupancy across the Conasauga study sites, with three of these taxa apparently absent for at least the last 5 years of the study. In contrast, a similar fauna of 28 taxa at 10 sites in the Etowah River shows no trends in species persistence, colonization or occupancy. None of the tested covariates show strong effects on persistence or colonization rates in either river. Previous studies and observations identify contaminants, nutrient loading, or changes in benthic habitat as possible causes for fish species declines in the Conasauga River. Our analysis provides baseline information that could be used to assess effectiveness of future management actions in the Conasauga or Etowah rivers, and illustrates the use of dynamic occupancy models to evaluate evidence of faunal decline from time-series data.
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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.