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Data from: Gene expression correlates of facultative predation in the blow fly Chrysomya rufifacies (Diptera: Calliphoridae)
Effects of intraguild predation (IGP) on omnivores and detritivores are relatively understudied when compared to work on predator guilds. Functional genetic work in IGP is even more limited, but its application can help answer a range of questions related to ultimate and proximate causes of this behavior. Here we integrate behavioral assays and transcriptomic analysis of facultative predation in a blow fly (Diptera: Calliphoridae) to evaluate the prevalence, effect, and correlated gene expression of facultative predation by the invasive species Chrysomya rufifacies. Field work observing donated human cadavers indicated facultative predation by C. rufifacies on the native blow fly Cochliomyia macellaria was rare under undisturbed conditions, owing in part to spatial segregation between species. Laboratory assays under conditions of starvation showed predation had a direct fitness benefit (i.e., survival) to the predator. As a genome is not available for C. rufifacies, a de novo transcriptome was developed and annotated using sequence similarity to Drosophila melanogaster. Under a variety of assembly parameters, several genes were identified as being differentially expressed between predators and non-predators of this species, including genes involved in cell-to-cell signaling, osmotic regulation, starvation responses, and dopamine regulation. Results of this work were integrated to develop a model of the processes and genetic regulation controlling facultative predation.
Data from: Correlates of extinction risk in squamate reptiles: the relative importance of biology, geography, threat and range size
Aim Evaluating the relative roles of biological traits and environmental factors that predispose species to an elevated risk of extinction is of fundamental importance to macroecology. Identifying species that possess extinction-promoting traits allows targeted conservation action before precipitous declines occur. Such analyses have been carried out for several vertebrate groups, with the notable exception of reptiles. We identify traits correlating with high extinction risk in squamate reptiles, assess whether these differ with geography, taxonomy and threats, and make recommendations for future Red List assessments. Location Global. Methods We collected data on biological traits and environmental factors for a representative sample of 1139 species of squamate reptiles. We used phylogenetically controlled regression models to identify general correlates of extinction risk, threat-specific correlates of risk and realm-specific correlates of risk. We also assessed the relative importance of range size versus other factors through multiplicative bivariate models, partial regressions and variance partitioning. Results Range size was the most important predictor of extinction risk, reflecting the high frequency of reptiles assessed under range-based IUCN criteria. Habitat specialists occupying accessible ranges were at a greater risk of extinction: although these factors never contributed more than 10% to the variance in extinction risk, they showed significant interactions with range size. The predictive power of our global models ranged from 23% to 29%. The general overall pattern remained the same among geographical, taxonomic and threat-specific data subsets. Main conclusions Proactive conservation requires shortcuts to identify species at high risk of extinction. Regardless of location, squamate reptiles that are range-restricted habitat specialists living in areas highly accessible to humans are likely to become extinct first. Prioritizing species that exhibit such traits could forestall extinction. Integration of data sources on human pressures, such as accessibility of species ranges, may aid robust and time-efficient assessments of species extinction risk.
Data from: Mating status correlates with dorsal brightness in some but not all poison frog populations
Sexual signals are important for intraspecific communication and mate selection, but their evolution may be driven by both natural and sexual selection, and stochastic processes. Strawberry poison frogs (Oophaga pumilio) show strong color divergence among populations, but coloration also varies among individuals of the same population. The importance of coloration for female mate choice has been studied intensely, and sexual selection seems to affect color divergence in strawberry poison frogs. However, the effect of coloration on mating success under field conditions has received very little attention. Furthermore, few studies examined how phenotypic variation among individuals of the same color morph affects mate selection under natural conditions. We measured the spectral reflectance of courting and noncourting individuals and their background substrates in three geographically separated populations. In one population (Sarapiquí, Costa Rica), we found that naturally occurring courting pairs of males and females had significantly brighter dorsal coloration than individual males and females not engaged in courtship interactions. Our field observations suggest that, in the wild, females prefer brighter males while the reason for the higher courtship activity of brighter females remains unclear. Overall our results imply that brightness differences among individuals of the same color morph may actually affect reproductive success in some populations of strawberry poison frogs.
Data from: Convergent and correlated evolution of major life-history traits in the angiosperm genus Leucadendron (Proteaceae)
Natural selection is expected to cause convergence of life histories among taxa as well as correlated evolution of different life-history traits. Here, we quantify the extent of convergence of five key life-history traits (adult fire survival, seed storage, degree of sexual dimorphism, pollination mode, and seed-dispersal mode) and test hypotheses about their correlated evolution in the genus Leucadendron (Proteaceae) from the fire-prone South African fynbos. We reconstructed a new molecular phylogeny of this highly diverse genus that involves more taxa and molecular markers than previously. This reconstruction identifies new clades that were not detected by previous molecular study and morphological classifications. Using this new phylogeny and robust methods that account for phylogenetic uncertainty, we show that the five life-history traits studied were labile during the evolutionary history of the genus. This diversity allowed us to tackle major questions about the correlated evolution of life-history strategies. We found that species with longer seed-dispersal distances tended to evolve lower pollen-dispersal distance, that insect-pollinated species evolved decreased sexual dimorphism, and that species with a persistent soil seed-bank evolved toward reduced fire-survival ability of adults.
Data from: Genetic diversity and differentiation in a wide ranging anadromous fish, American shad (Alosa sapidissima), is correlated with latitude
Studies that span entire species ranges can provide insight into the relative roles of historical contingency and contemporary factors that influence population structure and can reveal patterns of genetic variation that might otherwise go undetected. American shad is a wide ranging anadromous clupeid fish that exhibits variation in demographic histories and reproductive strategies (both semelparity and iteroparity) and provides a unique perspective on the evolutionary processes that govern the genetic architecture of anadromous fishes. Using 13 microsatellite loci, we examined the magnitude and spatial distribution of genetic variation among 33 populations across the species' range to (i) determine whether signals of historical demography persist among contemporary populations and (ii) assess the effect of different reproductive strategies on population structure. Patterns of genetic diversity and differentiation among populations varied widely and reflect the differential influences of historical demography, microevolutionary processes and anthropogenic factors across the species' range. Sequential reductions of diversity with latitude among formerly glaciated rivers are consistent with stepwise postglacial colonization and successive population founder events. Weak differentiation among U.S. iteroparous populations may be a consequence of human-mediated gene flow, while weak differentiation among semelparous populations probably reflects natural gene flow. Evidence for an effect of reproductive strategy on population structure suggests an important role for environmental variation and suggests that the factors that are responsible for shaping American shad life history patterns may also influence population genetic structure.
Data from: Multiple origins of sex chromosome fusions correlated with chiasma localization in Habronattus jumping spiders (Araneae: Salticidae)
Entelegyne spiders rarely show fusions yielding neo-Y chromosomes, which M. J. D. White attributed to a constraint in spiders, namely their proximal chiasma localization acting to upset meiotic segregation in males with fusions. Of the 75 taxa of Habronattus and outgroups studied, 47 have X1X20 sex chromosomes in males, 10 have X1X2Y, 15 have X1X2X3Y, 2 have X0, and one has both X1X20 and X1X2X3Y. Chromosome numbers and behavior suggest neo-Ys formed by an autosome-X fusion to make X1X2Y, with a second fusion to an autosome to make X1X2X3Y. Phylogeny shows at least 8-15 gains (or possibly some losses) of neo-Y (i.e. X-autosome fusions), a remarkable number for such a small clade. In contrast to the many X-autosome fusions, at most one autosome-autosome fusion is indicated. Origins of neo-Y are correlated significantly with distal localization of chiasmata, supporting White's hypothesis that evolution of neo-Y systems is facilitated by looser pairing (distal chiasmata) at meiosis. However, an alternative (or contributing) explanation for the correlation is that X-autosome fusions were selected to permit isolation of male-favored alleles to the neo-Y chromosome, aided by distal chiasmata limiting recombination. This intralocus sexual conflict hypothesis could explain both the many X-autosome fusions, and the stunning complexity of male Habronattus courtship displays.
Data from: Heritability, environmental effects, and genetic and phenotypic correlations of oxidative stress resistance-related enzyme activities during early life stages in Atlantic salmon
Oxidative stress (OS) may pose important physiological constraints on individuals, affecting trade-offs between growth and reproduction or ageing and survival. Despite such evolutionary and ecological importance, the results from studies on the magnitude of individual variation in OS resistance and the underlying causes of this variation such as genetic, environmental, and maternal origins, remain inconclusive. Using a high throughput methodology, we investigated the activity levels in three OS resistance-related enzymes (superoxide dismutase, SOD; glutathione reductase, GR; glutathione S-transferase, GST) during the early life stages of 1000 individuals from 50 paternal half-sib families in two populations of Atlantic salmon. Using animal mixed models, we detected the presence of narrow-sense heritability for SOD and GST; that for GST differed between populations due to differences in environmental variance. We found support for the presence of common environmental variation, including maternal effects, for only GR. Using a bivariate animal model, we detected a positive environmental correlation between activity levels of SOD and GST but were unable to detect an additive genetic correlation. Our results complement previous heritability findings for levels of reactive oxygen species or OS resistance by demonstrating the presence of heritability for OS-related enzyme activities. Our findings provide a foundation for future work, such as investigations on the evolutionary importance of variation in enzyme activities. In addition, our findings emphasise the importance of accounting for developmental stage, environmental variance, and kin relationships when investigating the OS-response at the enzyme activity level.
Data from: Ecological correlates of ghost lineages in ruminants
Integration between phylogenetic systematics and paleontological data has proved to be an effective method for identifying periods that lack fossil evidence in the evolutionary history of clades. In this study we aim to analyze whether there is any correlation between various ecomorphological variables and the duration of these underrepresented portions of lineages, which we call ghost lineages for simplicity, in ruminants. Analyses within phylogenetic (Generalized Estimating Equations) and non-phylogenetic (ANOVAs and Pearson correlations) frameworks were performed on the whole phylogeny of this suborder of Cetartiodactyla (Mammalia). This is the first time ghost lineages are focused in this way. To test the robustness of our data, we compared the magnitude of ghost lineages among different continents and among phylogenies pruned at different ages (4, 8, 12, 16, and 20 Ma). Differences in mean ghost lineage were not significantly related to either geographic or temporal factors. Our results indicate that the proportion of the known fossil record in ruminants appears to be influenced by the preservation potential of the bone remains in different environments. Furthermore, large geographical ranges of species increase the likelihood of preservation.
Supporting information: "Spin-polarization and resonant states in electronic conduction through a correlated magnetic layer"
<p>The supporting information contains the computational details and numerical data for the article. The<br> directory ‘scripts’ of the supplementary material contains the Python code used to create Figures 2–6.<br> The code can be used to exactly reproduce the figures.</p> <p><br> Figures 5 and 6 show interacting data, which requires a computationally involved self-consistent dynamical mean-field theory (DMFT) calculation. The results of this calculation are in the directory ‘DMFT_data’,<br> the subdirectories are named according to the parameters, where ‘tl’ is $t_L$, ‘tc’ is $t_{01}$, and ‘U’ is $U_{0}$.<br> The data is saved as HDF5 files. They can be opened conveniently using Python using the method<br> ‘open_dataset’ given in ‘scripts/dataio.py’.</p> <p> </p>
Data supporting the findings of the study: "Neural correlates of self-other distinction in patients with schizophrenia spectrum disorders: The roles of agency and hand identity"
<p>Data supporting the findings of the study. Details are specified in the readme file.</p>
Data from: Within-group relatedness is correlated with colony-level social structure and reproductive sharing in a social fish.
In group-living species, the degree of relatedness among group members often governs the extent of reproductive sharing, cooperation and conflict within a group. Kinship among group members can be shaped by the presence and location of neighbouring groups, as these provide dispersal or mating opportunities that can dilute kinship among current group members. Here, we assessed how within-group relatedness varies with the density and position of neighbouring social groups in Neolamprologus pulcher, a colonial and group-living cichlid fish. We used restriction site-associated DNA sequencing (RADseq) methods to generate thousands of polymorphic SNPs. Relative to microsatellite data, RADseq data provided much tighter confidence intervals around our relatedness estimates. These data allowed us to document novel patterns of relatedness in relation to colony-level social structure. First, the density of neighbouring groups was negatively correlated with relatedness between subordinates and dominant females within a group, but no such patterns were observed between subordinates and dominant males. Second, subordinates at the colony edge were less related to dominant males in their group than subordinates in the colony centre, suggesting a shorter breeding tenure for dominant males at the colony edge. Finally, subordinates who were closely related to their same-sex dominant were more likely to reproduce, supporting some restraint models of reproductive skew. Collectively, these results demonstrate that within-group relatedness is influenced by the broader social context, and variation between groups in the degree of relatedness between dominants and subordinates can be explained by both patterns of reproductive sharing and the nature of the social landscape.
Data from: Substantia nigra integrity correlates with sequential working memory in Parkinson's disease
<p>Maintaining and manipulating sequential information online is essential for daily activities such as planning. In Parkinson's disease (PD), deficits in sequential working memory have been associated with altered regional activation and functional connectivity within the basal ganglia. This study demonstrated that the substantia nigra (SN) integrity correlates with basal ganglia dysfunction during sequential working memory. We included 29 patients with PD and 29 healthy controls (HC). We assessed the SN integrity using neuromelanin-sensitive MRI and sequential working memory using functional MRI and a digit ordering task. In this task, participants either recalled a sequence of digits in the original order ('pure recall') or rearranged the digits in ascending order and recalled the new sequence ('reorder & recall'). PD showed smaller SN areas than HC, especially on the left side. Compared to HC, PD showed lower task accuracy, hyper-activation of the subthalamic nucleus, hypo-activation of the caudate nucleus and globus pallidus, and weakened functional connectivity between the bilateral SN and all three basal ganglia regions. Moreover, PD showed distinct brain-behavior and structure-function relationships. Ordering-related accuracy cost ('reorder & recall' <i>versus</i> 'pure recall') correlated with the ordering-related subthalamic activation in HC, but with the ordering-related caudate activation in PD. In PD, the caudate activation correlated with the total SN area, whereas the subthalamic activation correlated with daily exposure to D2/3 receptor agonists. In conclusion, damage to the SN may lead to basal ganglia dysfunction sequential working memory deficits even in early PD.</p>
Data from: Evidence of a spatial auto-correlation in the browsing level of four major European tree species
Moran's I of the browsing level of fir, spruce, beech and oak in the Federal State of Baden-Württemberg <p>Data supporting the results publised in "Evidence of a spatial auto-correlation in the browsing level of four major European tree species" by Hagen and Suchant (2020).</p> <p>The contribution of spatial processes to the spatial patterns of ecological systems is widely recognised, but spatial patterns in the ecology of plant-herbivore interactions have rarely been investigated quantitatively owing to limited budget and time associated with ecological research. Studies of the level of browsing on various tree species reported either no spatial auto-correlation or a small effect size. Further, the effects of disturbance events, such as hurricanes, which create large forest openings on spatial patterns of herbivory are not well understood. In this study, we used forest inventory data obtained from the federal state of Baden-Württemberg (Southern Germany) between 2001 and 2009 (grid size: 100×200 m) and thus, after hurricane Lothar struck Southern Germany in 1999. We investigated whether the browsing level of trees (height <= 130 cm) in one location is independent of that of the neighbourhood. Our analyses of 1.758.622 saplings (187.632 sampling units) of oak (Quercus), fir (Abies), spruce (Picea) and beech (Fagus) revealed that the browsing level is characterised by a short distance spatial auto-correlation. The application of indicator variables based on browsed saplings should account for the spatial pattern as the latter may affects the results and therefore also the conclusions of the analysis.</p>
Data from: Electrophysiological correlates of semantic dissimilarity reflect the comprehension of natural, narrative speech
People routinely hear and understand speech at rates of 120–200 words per minute [1, 2]. Thus, speech comprehension must involve rapid, online neural mechanisms that process words' meanings in an approximately time-locked fashion. However, in the context of continuous speech, electrophysiological evidence for such time-locked processing has been lacking. Whilst valuable insights into the semantic processing of speech have been provided by the "N400 component" of the event-related potential [3-6], this literature has been dominated by paradigms using incongruous words within specially constructed sentences, and may not accurately reflect natural, narrative speech comprehension. Building on the discovery that cortical activity "tracks" the dynamics of running speech [7-9], and psycholinguistic work both demonstrating [10-12] and modeling [13-15] how context rapidly impacts on word processing, we describe a new approach for deriving an electrophysiological correlate of natural speech comprehension. We used a computational model [16] to quantify the meaning carried by each word based on how semantically dissimilar it was to its preceding context and then regressed this quantity against electroencephalographic (EEG) data recorded from subjects as they listened to narrative speech. This produced a prominent negativity at a time-lag of 200–600 ms on centro-parietal EEG channels, characteristics common to the N400. Applying this approach to EEG datasets involving time-reversed speech, cocktail party attention and audiovisual speech-in-noise demonstrated that this response was very sensitive to whether or not subjects understood the speech they heard. These findings demonstrate that, when successfully comprehending natural speech, the human brain responds to the contextual semantic content of each word in a relatively time-locked fashion.
Data from - A new tale of lost tails: correlates of tail breakage in the worm lizard Amphisbaena vermicularis
Predator-prey interactions are important evolutionary drivers of defensive behaviours, but they are usually difficult to record. This lack of data on natural history and ecological interactions of species can be overcome through museum specimens, at least for some reptiles. When facing aggressive interactions, reptile species may exhibit the defensive behaviour of autotomy by losing the tail, which is also known as 'urotomy'. The inspection of preserved specimens for scars of tail breakage can reveal possible ecological and biological correlates of urotomy. Herein we investigated how the probability of urotomy in the worm lizard <i>Amphisbaena vermicularis</i> is affected by sex, body size, temperature, and precipitation. We found higher chances of urotomy for specimens with larger body size and from localities with warmer temperatures or lower precipitation. There was no difference in urotomy frequency between sexes. Older specimens likely faced – and survived – more predation attempts through their lifetime than smaller ones. Specimens from warmer regions might be more active both below- and aboveground, increasing the odds to encounter predators, and hence urotomy. Probability of urotomy decreased with increased precipitation. Possibly, in places with heavier rainfall worm lizards come more frequently to the surface when galleries are filled with rainwater, remaining more exposed to efficient predators, which could result in less survival rates and fewer tailless specimens. This interesting defensive behaviour is widespread in squamates, but yet little understood among amphisbaenians. The novel data presented here improve our understanding on the correlates of tail breakage and help us to interpret more tales of lost tails.
Bright correlated twin-beam generation and radiation shaping in high-gain parametric down-conversion with anisotropy
<p>Dataset of the publication “Bright correlated twin-beam generation and radiation shaping in high-gain parametric down-conversion with anisotropy“, M. Riabinin, P. R. Sharapova, and T. Meier, Optics Express 29, 21876 (2021) ( <a href="https://doi.org/10.1364/OE.424977">https://doi.org/10.1364/OE.424977</a> ). The zip file includes the data on which the plots shown in figures 2, 3, 4, 6, 7, and 8 are based.</p>
FIGURE 2 in Phenotypical variation and taxonomic correlates of five closely related Andean species of Poa (Poaceae) along geographic and climatic gradients
FIGURE 2. Plots of PC1 × PC2 and PC1 × PC3 from principal components analysis (PCA) of all specimens in the study. ANFA: P. anfamensis; JUJ: P. jujuyensis; LILL: P. lilloi; PARV: P. parviceps; SCAB: P. scaberula.
FIGURE 1 in Phenotypical variation and taxonomic correlates of five closely related Andean species of Poa (Poaceae) along geographic and climatic gradients
FIGURE 1. DIVA-GIS map of environmental variables and 150 collection sites of Poa specimens from the Andes in South American. A. Elevation. B. Annual mean precipitation. C. Annual mean temperature. D. Annual maximum temperature. E. Annual minimum temperature. Symbols for the Poa species are described in E.
FIGURE 4 in Phenotypical variation and taxonomic correlates of five closely related Andean species of Poa (Poaceae) along geographic and climatic gradients
FIGURE 4. Box plots representing the mean, median, interquartile range, adjacent values (lines), and outliers (dots) of quantitative characters in P. lilloi and P. scaberula.
FIGURE 3 in Phenotypical variation and taxonomic correlates of five closely related Andean species of Poa (Poaceae) along geographic and climatic gradients
FIGURE 3. Plot of discriminant analysis (DA) along the first two discriminant axes obtained from all specimens pertaining to a priori defined species. ANFA: P. anfamensis; JUJ: P. jujuyensis; LILL: P. lilloi; PARV: P. parviceps; SCAB: P. scaberula.
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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.