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Figure 2 in Potential seed dispersal of cumbaru (Dipteryx alata) by fruit-eating bats (Artibeus sp.) in a Brazilian urban context
Figure 2: Potential seed dispersal of Dipteryx alata by Artibeus sp. (A) Cerrado riparian forest located in an urban area of the municipality of Cáceres,Mato Grosso (Brazil) where potentially cumbaru tree (D. alata) is present, (B) roosting site used by two individuals of Artibeus sp. monitored for 21 consecutive days to quantify cumbaru frugivory and seed dispersal (C and D).
Identifying in vitro toxicity testing approaches for (novel) proteins in the context of food and feed risk assessment
<p>Annexes to EFSA external scientific report Identifying <em>in vitro</em> toxicity testing approaches for (novel) proteins in the context of food and feed risk assessment</p>
Data from: Epidemiological interactions between urogenital and intestinal human schistosomiasis in the context of praziquantel treatment across three West African countries
Background: In many parts of sub-Saharan Africa, urogenital and intestinal schistosomiasis co-occur, and mixed species infections containing both Schistosoma haematobium and S. mansoni can be common. During co-infection, interactions between these two species are possible, yet the extent to which such interactions influence disease dynamics or the outcome of control efforts remains poorly understood. Methodology/Principal Findings: Here we analyse epidemiological data from three West African countries co-endemic for urogenital and intestinal schistosomiasis (Senegal, Niger and Mali) to test whether the impact of praziquantel (PZQ) treatment, subsequent levels of re-infection or long-term infection dynamics are altered by co-infection. In all countries, positive associations between the two species prevailed at baseline: infection by one species tended to predict infection intensity for the other, with the strength of association varying across sites. Encouragingly, we found little evidence that co-infection influenced PZQ efficacy: species-specific egg reduction rates (ERR) and cure rates (CR) did not differ significantly with co-infection, and variation in treatment success was largely geographical. In Senegal, despite positive associations at baseline, children with S. mansoni co-infection at the time of treatment were less intensely re-infected by S. haematobium than those with single infections, suggesting competition between the species may occur post-treatment. Furthermore, the proportion of schistosome infections attributable to S. mansoni increased over time in all three countries examined. Conclusions/Significance: These findings suggest that while co-infection between urinary and intestinal schistosomes may not directly affect PZQ treatment efficacy, competitive interspecific interactions may influence epidemiological patterns of re-infection post-treatment. While re-infection patterns differed most strongly according to geographic location, interspecific interactions also seem to play a role, and could cause the community composition in mixed species settings to shift as disease control efforts intensify, a situation with implications for future disease management in this multi-species system.
Data from: A phylogenetic and morphologic context for the radiation of an endemic fauna in a long-lived lake: Corbulidae (Bivalvia; Myoida) in the Miocene Pebas Formation of western Amazonia
The Corbulidae are one of a handful of a primarily marine bivalve clades that exhibit a remarkable radiation, marked by increased species richness and divergent morphologies, within a long-lived lake. For corbulids, this diversification occurred within the lower to middle Miocene Pebas Formation of western Amazonia. Only one taxon associated with this radiation (Anticorbula) remains extant. We conducted a series of phylogenetic analyses to characterize diversification of Corbulidae within the Pebas Formation and relate that diversification to geologically older freshwater corbulids from the Paleocene Fort Union Formation of the northern Great Plains (United States). We used these results, as well as a quantitative examination of morphospace occupation, to infer whether Pebasian corbulids represent a true species flock, and whether the lacustrine system represented by the Pebas Formation represents a cradle of, or reservoir for, freshwater corbulid diversity. We conducted two sets of phylogenetic analyses using shell morphology characters. A genus-level data set incorporated type species of freshwater corbulid genera, any Paleocene representatives of these genera, and selected brackish and marine corbulid genera. A species-level analysis added all described freshwater corbulid taxa to the genus-level matrix. Our results were highly resolved (few most-parsimonious trees), but not particularly robust (low branch support). For the genus-level matrix, we used a taxon jackknife procedure to explore the effects of taxon sampling on tree stability and topology. Jackknife results recover a subclade of freshwater taxa (including both Anticorbula and Pachydon species and the Paleocene Ostomya sp.) in 92.4% of trees, although placement of this subclade across the ingroup varies, as do the topologic positions of other freshwater species. Freshwater and marine corbulids also are morphologically distinct from each other, a factor that likely reduced the robustness of our phylogenetic results. By combining these results with paleoecologic, stratigraphic, and morphologic data, we infer that freshwater corbulids arose once within the family, prior to the Cenozoic, with three distinct freshwater lineages present at their first appearance in the late Paleocene of North America. Within the Miocene Pebas system of South America, we reconstruct supralimital morphologic evolution within three lineages as freshwater taxa became variously adapted to the fluid, dysoxic muds characterizing lake-bottom facies representative of the Pebas lacustrine system. In addition, corbulids apparently successfully coped with high predation pressures from co-occurring shellcrushing predators. Finally, we consider that freshwater Corbulidae were primarily fluvial taxa throughout their geologic history, with a relatively ephemeral radiation within the Pebasian lake system, thus making the Pebasian system a cradle of diversity for several corbulid lineages.
Data from: Microenvironment and functional-trait context dependence predict alpine plant community dynamics
Predicting the structure and dynamics of communities is difficult. Approaches linking functional traits to niche boundaries, species co‐occurrence and demography are promising, but have so far had limited success. We hypothesized that predictability in community ecology could be improved by incorporating more accurate measures of fine‐scale environmental heterogeneity and the context‐dependent function of traits. We tested these hypotheses using long term whole‐community demography data from an alpine plant community in Colorado. Species distributions along microenvironmental gradients covaried with traits important for below‐ground processes. Positive associations between species distributions across life stages could not be explained by abiotic microenvironment alone, consistent with facilitative processes. Rates of growth, survival, fecundity and recruitment were predicted by the direct and interactive effects of trait, microenvironment, macroenvironment and neighbourhood axes. Synthesis. Context‐dependent interactions between multiple traits and microenvironmental axes are needed to predict fine‐scale community structure and dynamics.
Data from: History matters more when explaining genetic diversity within the context of the core-periphery hypothesis
The core–periphery hypothesis (CPH) predicts that populations located at the periphery of a species' range should have lower levels of genetic variation than those at the centre of the range. However, most of the research on the CPH focuses on geographic distance and not on ecological distance, or uses categorical definitions of core and periphery to explain the distribution of genetic diversity. We use current climate data and historical climate data from the last glacial maxima to develop quantitative estimates of contemporary and historical ecological suitability using ecological niche models. We analysed genetic diversity using 12 polymorphic microsatellites to estimate changes in heterozygosity, allelic richness and population differentiation in 31 populations of the wood frog (Lithobates sylvaticus) spanning the species' entire eastern clade (33o to 45o latitude) from Alabama, USA, to Nova Scotia, Canada. Our data support predictions based on the CPH. Populations showed significant differences in genetic diversity across the range, with lower levels of genetic variation at the geographic range edge and in areas with lower levels of historical and contemporary ecological suitability. However, history and geography (not current ecological suitability) best explain the patterns. This study highlights the importance of examining more than just geography when assessing the CPH, and the importance of historical ecological suitability in the maintenance of genetic diversity and population differentiation.
Data from: How symbiosis and ecological context influence the variable expression of transgenerational wing induction upon fungal infection of aphids
Aphids, like most animals, mount a diverse set of defenses against pathogens. For aphids, two of the best studied defenses are symbiont-conferred protection and transgenerational wing induction. Aphids can harbor bacterial symbionts that provide protection against pathogens, parasitoids and predators, as well as against other environmental stressors. In response to signals of danger, aphids also protect not themselves but their offspring by producing more winged than unwinged offspring as a way to ensure that their progeny may be able to escape deteriorating conditions. Such transgenerational wing induction has been studied most commonly as a response to overcrowding of host plants and presence of predators, but recent evidence suggests that pea aphids (Acyrthosiphon pisum) may also begin to produce a greater proportion of winged offspring when infected with fungal pathogens. Here, we explore this phenomenon further by asking how protective symbionts, pathogen dosage and environmental conditions influence this response. Overall, while we find some evidence that protective symbionts can modulate transgenerational wing induction in response to fungal pathogens, we observe that transgenerational wing induction in response to fungal infection is highly variable. That variability cannot be explained entirely by symbiont association, by pathogen load or by environmental stress, leaving the possibility that a complex interplay of genotypic and environmental factors may together influence this trait.
Data from: Microhabitat partitioning in seagrass mesograzers is driven by consistent species choices across multiple predator and competitor contexts
Explanations for the coexistence of multiple species from the same functional group or taxonomic clade frequently include fine-scale resource partitioning. However, despite the hypothesized importance of niche partitioning, we know relatively little about the underlying mechanisms. For example, differences in resource use may be fixed consequences of organism traits, or they may be achieved via context-dependent behaviors. In this study we investigated mechanisms of microhabitat partitioning using eight species of marine mesograzers inhabiting seagrass and algae habitats, using laboratory trials to measure microhabitat use in the presence and absence of both predators and competitors. We found clear evidence for microhabitat partitioning between the species, which account for over 60% of the mesograzers commonly found in this system and vary in both body size and the ability to build tubes on habitat substrates. Species-specific microhabitat use was poorly predicted by these two traits, but remained remarkably consistent across contexts. Habitat use was not affected by the presence of fish predators common in this system, even though predation pressure is thought to place strong constraints on microhabitat in communities of plant-associated arthropods. The presence of competing species also did not affect the relative separation of microhabitat use. Behavioral responses to potential competitors did cause significant changes in microhabitat use in all of the smallest species, but these changes did not depend on competitor identity and were relatively small compared to among-species patterns of microhabitat partitioning. The consistency of species-specific microhabitat use, regardless of the presence of predators or competitors, should make coexistence most likely among species that differ in these choices. For these species, it appears that the benefits accrued from their selected microhabitats are not affected by species interactions, or that any benefits of alternative microhabitat use are outweighed by risks associated with movement.
Data from: Context-dependent colonisation of terrestrial habitat 'islands' by a long-distance migrant bird
Landscape context can affect how individuals perceive patch quality during colonisation. However, although context-dependent colonisation has been observed in aquatic environments it has rarely been studied in terrestrial environments or at large spatial scales. Here, we assessed how landscape context influenced colonisation rates in a large-scale (c.7000 km2) terrestrial system where colonisers (Willow Warbler Phylloscopus trochilus) are capable of rapid, long-distance movements. Bioacoustic recorders were used to detect first song dates (an indicator of colonisation or re-colonisation) and settlement in 23 naturally replicated habitat patches. We compared support for three competing hypotheses describing colonisation patterns that depend on landscape context ('redirection', 'landscape-selection' and 'relative patch size') with two patch-level hypotheses (patch 'quality' and 'heterospecific attraction'). First song was earlier when habitat availability in the landscape was low, supporting the 'redirection' hypothesis. Settlement probability was best predicted by patch 'quality' and was lower in woodlands with a dense understorey. Results suggest that colonisation of habitat patches by male P. trochilus after spring migration is spatially hierarchical. First, initial colonisation depends on landscape context, and settlement is then determined by fine-scale vegetation characteristics. More broadly, we suggest that patterns observed in fragmented aquatic environments (e.g. 'redirection') can, in some circumstances, be extended to large-scale terrestrial environments.
Data from: Statistical context dictates the relationship between feedback-related EEG signals and learning
Learning should be adjusted according to the surprise associated with observed outcomes but calibrated according to statistical context. For example, when occasional changepoints are expected, surprising outcomes should be weighted heavily to speed learning. In contrast, when uninformative outliers are expected to occur occasionally, surprising outcomes should be less influential. Here we dissociate surprising outcomes from the degree to which they demand learning using a predictive inference task and computational modeling. We show that the P300, a stimulus-locked electrophysiological response previously associated with adjustments in learning behavior, does so conditionally on the source of surprise. Larger P300 signals predicted greater learning in a changing context, but less learning in a context where surprise indicated a one-off outlier (oddball). Our results suggest that the P300 provides a surprise signal that is interpreted by downstream learning processes differentially according to statistical context in order to appropriately calibrate learning across complex environments.
Context-dependent dispersal determines relatedness and genetic structure in a patchy amphibian population
<p>Dispersal is a central process in ecology and evolution with far reaching consequences for the dynamics and genetics of spatially structured populations (SSPs). Individuals can adjust their decisions to disperse according to local fitness prospects, resulting in context-dependent dispersal. By determining dispersal rate, distance, and direction, these individual-level decisions further modulate the demography, relatedness, and genetic structure of SSPs. Here, we examined how context-dependent dispersal influences the dynamics and genetics of a Great Crested Newt (<i>Triturus cristatus</i>) SSP. We collected capture-recapture data of 5564 individuals and genetic data of 950 individuals across a SSP in northern Germany. We added genetic data from six sites outside this SSP to assess genetic structure and gene flow at a regional level. Dispersal rates within the SSP were high but dispersal distances were short. Dispersal was context-dependent: individuals preferentially immigrated into high-quality ponds where breeding probabilities were higher. The studied SSP behaved like a patchy population, where subpopulations at each pond were demographically interdependent. High context-dependent dispersal led to weak but significant spatial genetic structure and relatedness within the SSP. At the regional level, a strong hierarchical genetic structure with very few first-generation migrants as well as low effective dispersal rates suggest the presence of independent demographic units. Overall, our study highlights the importance of habitat quality for driving context-dependent dispersal and therefore demography and genetic structure in SSPs. Limited capacity for long-distance dispersal seems to increase genetic structure within a population and leads to demographic isolation in anthropogenic landscapes.</p>
Data and statistical code from: Population differences in the effect of context on personality in an invasive lizard
<p>Within populations, individuals often differ consistently in their average level of behavior (i.e. animal personality), as well as their response to environmental change (i.e. behavioral plasticity). Thus, changes in environmental conditions might be expected to mediate the structure of animal personality traits. However, it is currently not well understood how personality traits change in response to environmental conditions, and whether this effect is consistent across multiple populations within the same species. Accordingly, we investigated variation in personality traits across two ecological contexts in the invasive delicate skink (<i>Lampropholis delicata</i>). Specifically, lizards from three different populations were repeatedly measured for individual activity in group behavioral assays under differing levels of food availability. We found that environmental context had a clear effect on the structure of lizard personality, where activity rates were not repeatable in the absence of food, but were repeatable in the presence of food resources. The difference in repeatability of activity rates across contexts appeared to be largely driven by an increase in among-individual variance when tested in the presence of food resources. However, this was only true for one of the populations tested, with food context having no effect on the expression of personality traits in the other two populations. Our results highlight the important role of environmental context in mediating the structure of animal personality traits and suggest that this effect may vary among populations.</p>
FIGURE 5 in Nucleus patterns of zoea I larvae (Crustacea: Decapoda) in the context of taxonomy
FIGURE 5. Telson of Xantho hydrophilus viewed from dorsally (a., c., e.) and Xantho pilipes viewed from ventrally (b., d., f.), corresponding views made with different techniques. a., b. DAPI stained, c., d. conventional light microscopy, e., f. Scanning EM. An, anus; B, bristles; F, furca branch; PLP, posteriolateral process; Ps3-5, pleon segments 3-5; Se, setae; arrowheads, small lateral processes on setae.
FIGURE 4 in Nucleus patterns of zoea I larvae (Crustacea: Decapoda) in the context of taxonomy
FIGURE 4. Telson of Pisidia longicornis viewed from dorsally (a., c., e.) and Porcellana platycheles viewed from ventrally (b., d., f.), corresponding views made with different techniques. (a.,b.) DAPI stained, (c., d.) conventional light microscopy, (e.,f.) Scanning EM. An, anus, PLP, posteriolateral process; Ps4 and Ps5, pleon segments 4 and 5; Se, setae; T, telson.
FIGURE 1 in Nucleus patterns of zoea I larvae (Crustacea: Decapoda) in the context of taxonomy
FIGURE 1. Survey of DAPI stained zoeas. a. Palaemon elegans, viewed from dorsally. b. Porcellana platycheles, viewed from laterally. c. Xantho incisus, viewed from laterally. Arrowheads regions with intensely stained nuclei.
FIGURE 2 in Nucleus patterns of zoea I larvae (Crustacea: Decapoda) in the context of taxonomy
FIGURE 2. Confocal microscopy of telson of Palaemon elegans viewed from dorsally. a., survey of telson, b., detail. Arrowehads, dense arrangement of nuclei at the telson edge (a.) and nucleus clusters at the base of setae (b.); B, bristles; Se, setae.
FIGURE 3 in Nucleus patterns of zoea I larvae (Crustacea: Decapoda) in the context of taxonomy
FIGURE 3. Telson of Palaemon elegans viewed from dorsally (a., c., e.) and Palaemon adspersus viewed from ventrally (b., d., f.), corresponding views made with different techniques. a., b. DAPI stained, c., d. conventional light microscopy, e., f. Scanning EM. An, anus; B, bristles; PLP, posteriolateral process; Ps5 and Ps6, pleon segments 5 and 6; Se, setae; arrowheads, nuclei in setae (b.) and feather-like lateral branches on setae (e.), arrows, dense arrangement of nuclei at the telson edge.
Context dependent fitness costs of reproduction despite stable body mass costs in an Arctic herbivore
<p class="western">1. The cost of reproduction on demographic rates is often assumed to operate through changing body condition. Several studies have found that reproduction depresses body mass more if the current conditions are severe, such as high population densities or adverse weather, than under benign environmental conditions. However, few studies have investigated the association between the fitness and body mass costs of reproduction.</p> <p class="western">2. Using 25 years of individual-based capture-recapture data from Svalbard reindeer (<i>Rangifer tarandus platyrhynchus</i>), we built a novel Bayesian state-space model that jointly estimated inter-annual change in mass, annual reproductive success, and survival, while accounting for incomplete observations. The model allowed us to partition the differential effects of intrinsic and extrinsic factors on both non-reproductive mass change and the body mass cost of reproduction and to quantify their consequences on demographic rates.</p> <p class="western">3. Contrary to our expectation, the body mass cost of reproduction (mean = 5.8 kg) varied little between years (CV = 0.08) whereas the between-year variation in body mass changes, that were independent of the previous year's reproductive state, varied substantially (CV = 0.4) in relation to autumn temperature and the amount of rain-on-snow in winter. This mass loss led to a cost of reproduction on the next reproduction, which was amplified by the same environmental covariates, from a 10% reduction in reproductive success in benign years, to a 50% reduction in harsh years. The reproductive mass loss also resulted in a small reduction in survival.</p> <p class="western">4. Our results show how demographic costs of reproduction, driven by inter-annual fluctuations in individual body condition, result from the balance between body mass costs of reproduction and body mass changes that are independent of previous reproductive state. We illustrate how a strong context dependent fitness cost of reproduction can occur, despite a relatively fixed body mass cost of reproduction. This suggests that female reindeer display a very conservative energy allocation strategy, either aborting their reproductive attempt at an early stage or weaning at a relatively constant cost. Such a strategy might be common in species living in a highly stochastic food limited environment.</p>
Effect of Light Wavelength on Soybean Growth and Development in a Context of Speed Breeding
<p>Soybean breeding involves crossing and inbreeding for multiple generations to develop genetically-stable lines. The long generation times and the absence of easily-scalable double-haploid technologies cause early generations to be the major bottleneck in soybean breeding. Here we tested the effect of red and blue lights (RB) and full spectrum white lights (FS) generated by light emitting diode (LED) panels, coupled with 12 h light (29 °C) / 12 h darkness (27 °C) photothermal conditions, on the growth and development of soybean lines and breeding materials of diverse maturity groups in a context of speed breeding. We observed that RB light, when compared to FS light, reduced plant height by an average of 17.3 cm but did not affect vegetative biomass, pods and seeds per plants, nor the ability to meet a minimum of one seed per plant. Overall, the RB light treatment reduced days after planting (DAP) to physiological maturity (R7) by 1.5 d as compared to FS. The period between planting and the harvest of seeds (cycle time) of mid- and late-maturity soybean ranged from 63 to 81 d in the greenhouse, as compared to approximately 120 d typically observed in field conditions. Also, DAP to R7 was dependent on soybean maturity group. The use of RB lights, coupled with photothermal conditions herein reported, would allow to advance up to 5 generations of US-adapted soybean under a controlled environment, instead of the 1-3 generations currently possible. This methodology is simple and easily scalable for it maintains stable growing conditions throughout the crop cycle and it allows for simultaneous planting and harvesting within the same growth room. This could have a significant impact in genetic gain of U.S. soybean breeding programs.</p>
Data for: Testing the match-mismatch hypothesis in bighorn sheep in the context of climate change
<p><span><span><span><span><span><span><span><span><span><span><span>In species with long gestation, females commit to reproduction several months before parturition. If cues driving conception date are uncoupled from spring conditions, parturition could be mistimed. Mismatch may increase with global change if the rate of temporal changes in autumn cues differs from the rate of change in spring conditions. Using 17 years of data on climate and vegetation phenology, we show that autumn temperature and precipitation, but not vegetation phenology, explain parturition date in bighorn sheep. Although autumn cues drive the timing of conception, they do not predict conditions at parturition in spring. We calculated the mismatch between individual parturition date and spring green-up, assessed whether mismatch increased over time and investigated the consequences of mismatch on lamb neonatal survival, weaning mass and overwinter survival. Mismatch fluctuated over time but showed no temporal trend. Temporal changes in green-up date did not lead to major fitness consequence of mismatch. Detailed data on individually marked animals revealed no effect of mismatch on neonatal or overwinter survival, but lamb weaning mass was negatively affected by mismatch. Capital breeders might be less sensitive to mismatch than income breeders because they are less dependent on daily food acquisition. Herbivores in seasonal environments may access sufficient forage to sustain lactation before or after the spring 'peak' green-up, and partly mitigate the consequences of a mismatch. Thus, the effect of phenological mismatch on fitness may be affected by species life-history, highlighting the complexity in quantifying trophic mismatches in the context of climate change. </span></span></span></span></span></span></span></span></span></span></span></p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.