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9,882 results for “Scale”
Data from: A model of urban scaling laws based on distance dependent interactions
Socio-economic related properties of a city grow faster than a linear relationship with the population, in a log–log plot, the so-called superlinear scaling. Conversely, the larger a city, the more efficient it is in the use of its infrastructure, leading to a sublinear scaling on these variables. In this work, we addressed a simple explanation for those scaling laws in cities based on the interaction range between the citizens and on the fractal properties of the cities. To this purpose, we introduced a measure of social potential which captured the influence of social interaction on the economic performance and the benefits of amenities in the case of infrastructure offered by the city. We assumed that the population density depends on the fractal dimension and on the distance-dependent interactions between individuals. The model suggests that when the city interacts as a whole, and not just as a set of isolated parts, there is improvement of the socio-economic indicators. Moreover, the bigger the interaction range between citizens and amenities, the bigger the improvement of the socio-economic indicators and the lower the infrastructure costs of the city. We addressed how public policies could take advantage of these properties to improve cities development, minimizing negative effects. Furthermore, the model predicts that the sum of the scaling exponents of social-economic and infrastructure variables are 2, as observed in the literature. Simulations with an agent-based model are confronted with the theoretical approach and they are compatible with the empirical evidences.
Data from: Fine scale genetic correlates to condition and migration in a wild Cervid
The relationship between genetic variation and phenotypic traits is fundamental to the study and management of natural populations. Such relationships often are investigated by assessing correlations between phenotypic traits and heterozygosity or genetic differentiation. Using an extensive data set compiled from free-ranging mule deer (Odocoileus hemionus), we combined genetic and ecological data to (i) examine correlations between genetic differentiation and migration timing, (ii) screen for mitochondrial haplotypes associated with migration timing, and (iii) test whether nuclear heterozygosity was associated with condition. Migration was related to genetic differentiation (more closely related individuals migrated closer in time) and mitochondrial haplogroup. Body fat was related to heterozygosity at two nuclear loci (with antagonistic patterns), one of which is situated near a known fat metabolism gene in mammals. Despite being focused on a widespread panmictic species, these findings revealed a link between genetic variation and important phenotypes at a fine scale. We hypothesize that these correlations are either the result of mixing refugial lineages or differential mitochondrial haplotypes influencing energetics. The maintenance of phenotypic diversity will be critical to enable the potential tracking of changing climatic conditions, and these correlates highlight the need to consider evolutionary mechanisms in management, even in widely distributed panmictic species.
Data from: Large-scale proteomics of the cassava storage root and identification of a target gene to reduce post-harvest deterioration
Cassava (Manihot esculenta) is the most important root crop in the tropics, but rapid postharvest physiological deterioration (PPD) of the root is a major constraint to commercial cassava production. We established a reliable method for image-based PPD symptom quantification and used label-free quantitative proteomics to generate an extensive cassava root and PPD proteome. Over 2600 unique proteins were identified in the cassava root, and nearly 300 proteins showed significant abundance regulation during PPD. We identified protein abundance modulation in pathways associated with oxidative stress, phenylpropanoid biosynthesis (including scopoletin), the glutathione cycle, fatty acid α-oxidation, folate transformation, and the sulfate reduction II pathway. Increasing protein abundances and enzymatic activities of glutathione-associated enzymes, including glutathione reductases, glutaredoxins, and glutathione S-transferases, indicated a key role for ascorbate/glutathione cycles. Based on combined proteomics data, enzymatic activities, and lipid peroxidation assays, we identified glutathione peroxidase as a candidate for reducing PPD. Transgenic cassava overexpressing a cytosolic glutathione peroxidase in storage roots showed delayed PPD and reduced lipid peroxidation as well as decreased H2O2 accumulation. Quantitative proteomics data from ethene and phenylpropanoid pathways indicate additional gene candidates to further delay PPD. Cassava root proteomics data are available at www.pep2pro.ethz.ch for easy access and comparison with other proteomics data.
Data from: A theoretical foundation for multi-scale regular vegetation patterns
Self-organized regular vegetation patterns are widespread1 and thought to mediate ecosystem functions such as productivity and robustness, but the mechanisms underlying their origin and maintenance remain disputed. Particularly controversial are landscapes of overdispersed (evenly spaced) elements, such as North American Mima mounds, Brazilian murundus, South African heuweltjies, and, famously, Namibian fairy circles. Two competing hypotheses are currently debated. On the one hand, models of scale-dependent feedbacks, whereby plants facilitate neighbours while competing with distant individuals, can reproduce various regular patterns identified in satellite imagery. Owing to deep theoretical roots and apparent generality, scale-dependent feedbacks are widely viewed as a unifying and near-universal principle of regular-pattern formation, despite scant empirical evidence. On the other hand, many overdispersed vegetation patterns worldwide have been attributed to subterranean ecosystem engineers such as termites, ants, and rodents. Although potentially consistent with territorial competition, this interpretation has been challenged theoretically and empirically and (unlike scale-dependent feedbacks) lacks a unifying dynamical theory, fuelling scepticism about its plausibility and generality. Here we provide a general theoretical foundation for self-organization of social-insect colonies, validated using data from four continents, which demonstrates that intraspecific competition between territorial animals can generate the large-scale hexagonal regularity of these patterns. However, this mechanism is not mutually exclusive with scale-dependent feedbacks. Using Namib Desert fairy circles as a case study, we present field data showing that these landscapes exhibit multi-scale patterning—previously undocumented in this system—that cannot be explained by either mechanism in isolation. These multi-scale patterns and other emergent properties, such as enhanced resistance to and recovery from drought, instead arise from dynamic interactions in our theoretical framework, which couples both mechanisms. The potentially global extent of animal-induced regularity in vegetation—which can modulate other patterning processes in functionally important ways—emphasizes the need to integrate multiple mechanisms of ecological self-organization.
Data from: Outcomes of stroke patients treated with thrombolysis according to prestroke Rankin Scale scores
Background: It is common practice to withhold intravenous thrombolysis (IVT) for acute ischemic stroke in patients with preexisting disabilities. To test the hypothesis of an association of IVT and good clinical outcome also in patients with preexisting disabilities without an increase in mortality we analyzed data of 52,741 patients (15,317 treated with IVT) depending on prestroke Rankin Scale (pRS) score. Methods: We performed an observational study based on a consecutive stroke registry covering 10.8 million inhabitants. The outcome at discharge of stroke patients admitted in the time window of potential eligibility for IVT (<4.5h after stroke onset) was compared between patients treated and not treated with thrombolysis, stratified by pRS. Logistic regression analysis was used to estimate adjusted odds ratios (OR) along with 95% confidence intervals (CI) for favorable clinical outcome, defined as returning to the baseline pRS score or a score of 0 or 1 and mortality. Sensitivity analyses for subgroups of mildly and severely affected stroke patients were performed and influence of treatment duration was assessed. Results: Among included patients IVT rates were 32% for patients with pRS 0-1 and 20% for patients with pRS 2-5. IVT in patients with pRS of 0-4 was associated with a higher chance of returning to the baseline pRS (or a modified RS of 0/1), with ORs ranging between 1.42 (pRS 2; CI 1.16-1.73) and 1.73 (pRS 0; CI 1.61-1). The OR observed in patients with a pRS of 5 was 0.65 (CI 0.25-1.70). Observed associations remained consistent in sensitivity analyses. Subgroup analyses revealed no evidence of bias due to potential floor and ceiling effects. No evidence of elevated in-hospital mortality of patients treated with thrombolysis was observed. Conclusions: Our study suggests that IVT can be effective even in patients with severe preexisting disabilities, provided that they were not bedridden before stroke onset. Withholding IVT on the sole ground of prestroke disabilities may not be justified.
Data from: Resolving basal lamiid phylogeny and the circumscription of Icacinaceae with a plastome-scale data set
PREMISE OF THE STUDY: Major relationships within Lamiidae, an asterid clade with ∼40000 species, have largely eluded resolution despite two decades of intensive study. The phylogenetic positions of Icacinaceae and other early-diverging lamiid clades (Garryales, Metteniusaceae, and Oncothecaceae) have been particularly problematic, hindering classification and impeding our understanding of early lamiid (and euasterid) character evolution. METHODS: To resolve basal lamiid phylogeny, we sequenced 50 plastid genomes using the Illumina sequencing platform and combined these with available asterid plastome sequence data for more comprehensive phylogenetic analyses. KEY RESULTS: Our analyses resolved basal lamiid relationships with strong support, including the circumscription and phylogenetic position of the enigmatic Icacinaceae. This greatly improved basal lamiid phylogeny offers insight into character evolution and facilitates an updated classification for this clade, which we present here, including phylogenetic definitions for 10 new or converted clade names. We also offer recommendations for applying this classification to the Angiosperm Phylogeny Group (APG) system, including the recognition of a reduced Icacinaceae, an expanded Metteniusaceae, and two orders new to APG: Icacinales (Icacinaceae + Oncothecaceae) and Metteniusales (Metteniusaceae). CONCLUSIONS: The lamiids possibly radiated from an ancestry of tropical trees with inconspicuous flowers and large, drupaceous fruits, given that these morphological characters are distributed across a grade of lineages (Icacinaceae, Oncothecaceae, Metteniusaceae) subtending the core lamiid clade (Boraginales, Gentianales, Lamiales, Solanales, Vahlia). Furthermore, the presence of similar morphological features among members of Aquifoliales suggests these characters might be ancestral for the Gentianidae (euasterids) as a whole.
Data from: Patterns of size variation in bees at a continental scale: does Bergmann's rule apply?
Body size latitudinal clines have been widley explained by the Bergmann's rule in homeothermic vertebrates. However, there is no general consensus in poikilotherms organisms in particular in insects that represent the large majority of wildlife. Among them, bees are a highly diverse pollinators group with high economic and ecological value. Nevertheless, no comprehensive studies of species assemblages at a phylogenetically larger scale have been carried out even if they could identify the traits and the ecological conditions that generate different patterns of latitudinal size variation. We aimed to test Bergmann's rule for wild bees by assessing relationships between body size and latitude at continental and community levels. We tested our hypotheses for bees showing different life history traits (i.e. sociality and nesting behaviour). We used 142,008 distribution records of 615 bee species at 50 km x 50 km (CGRS) grids across the West Palearctic. We then applied Generalized Least Squares fitted linear model (GLS) to assess the relationship between latitude and mean body size of bees, taking into account spatial autocorrelation. For all bee species grouped, mean body size increased with higher latitudes, and so followed Bergmann's rule. However, considering bee genera separately, four genera were consistent with Bergmann's rule, while three showed a converse trend, and three showed no significant cline. All life history traits used here (i.e. solitary, social and parasitic behaviour; ground and stem nesting behaviour) displayed a Bergmann's cline. In general there is a main trend for larger bees in colder habitats, which is likely to be related to their thermoregulatory abilities and partial endothermy, even if a "season length effect" (i.e. shorter foraging season) is a potential driver of the converse Bergmann's cline particularly in bumblebees.
Data from: Scientific output scales with resources. A comparison of US and European Universities
By using a comprehensive dataset of US and European universities, we demonstrate super-linear scaling between university revenues and their volume of publications and (field-normalized) citations. We show that this relationship holds both in the US and in Europe. In terms of resources, our data show that three characteristics differentiate the US system: (1) a significantly higher level of resources for the entire system, (2) a clearer distinction between education-oriented institutions and doctoral universities and (3) a higher concentration of resources among doctoral universities. Accordingly, a group of US universities receive a much larger amount of resources and have a far higher number of publications and citations when compared to their European counterparts. These results demonstrate empirically that international rankings are by and large richness measures and, therefore, can be interpreted only by introducing a measure of resources. Implications for public policies and institutional evaluation are finally discussed.
Data from: Allometric convergence in savanna trees and implications for plant scaling models in variable ecosystems
Theoretical models of allometric scaling provide frameworks for understanding and predicting how and why the morphology and function of organisms vary with scale. It remains unclear, however, if the predictions of 'universal' scaling models for vascular plants hold across diverse species in variable environments. Phenomena such as competition and disturbance may drive allometric scaling relationships away from theoretical predictions based on an optimized tree. Here, we use a hierarchical Bayesian approach to calculate tree-specific, species-specific, and 'global' (i.e. interspecific) scaling exponents for several allometric relationships using tree- and branch-level data harvested from three savanna sites across a rainfall gradient in Mali, West Africa. We use these exponents to provide a rigorous test of three plant scaling models (Metabolic Scaling Theory (MST), Geometric Similarity, and Stress Similarity) in savanna systems. For the allometric relationships we evaluated (diameter vs. length, aboveground mass, stem mass, and leaf mass) the empirically calculated exponents broadly overlapped among species from diverse environments, except for the scaling exponents for length, which increased with tree cover and density. When we compare empirical scaling exponents to the theoretical predictions from the three models we find MST predictions are most consistent with our observed allometries. In those situations where observations are inconsistent with MST we find that departure from theory corresponds with expected tradeoffs related to disturbance and competitive interactions. We hypothesize savanna trees have greater length-scaling exponents than predicted by MST due to an evolutionary tradeoff between fire escape and optimization of mechanical stability and internal resource transport. Future research on the drivers of systematic allometric variation could reconcile the differences between observed scaling relationships in variable ecosystems and those predicted by ideal models such as MST.
Data from: Colony-level differences in the scaling rules governing wood ant compound eye structure
Differential organ growth during development is essential for adults to maintain the correct proportions and achieve their characteristic shape. Organs scale with body size, a process known as allometry that has been studied extensively in a range of organisms. Such scaling rules, typically studied from a limited sample, are assumed to apply to all members of a population and/or species. Here we study scaling in the compound eyes of workers of the wood ant, Formica rufa, from different colonies within a single population. Workers' eye area increased with body size in all the colonies showing a negative allometry. However, both the slope and intercept of some allometric scaling relationships differed significantly among colonies. Moreover, though mean facet diameter and facet number increased with body size, some colonies primarily increased facet number whereas others increased facet diameter, showing that the cellular level processes underlying organ scaling differed among colonies. Thus, the rules that govern scaling at the organ and cellular levels can differ even within a single population.
Data from: Improving short-term information spreading efficiency in scale-free networks by specifying top large-degree vertices as the initial spreaders.
The positive function of initially influential vertices could be exploited to improve spreading efficiency for short-term spreading in scale-free networks. However, the selection of initial spreaders depends on the specific scenes. The selection of initial spreaders needs to offer low complexity and low power consumption for short-term spreading. In this paper, we propose a selection strategy for efficiently spreading information by specifying a set of top large-degree vertices as the initially informed vertices. The essential idea behind the proposed selection strategy is to exploit the significant diffusion of the top large-degree vertices at the beginning of spreading. To evaluate the positive impact of initially influential vertices, we first build an information spreading model in the Barabási-Albert (BA) scale-free network; next, we design 54 comparative Monte Carlo experiments based on a benchmark strategy and the proposed selection strategy in different BA scale-free network structures. Experimental results indicate that (1) the proposed selection strategy significantly can improve spreading efficiency in the short-term spreading and (2) both network size and number of hubs have a strong impact on spreading efficiency, while the number of initially informed vertices has a weak impact. The proposed selection strategy can be employed in short-term spreading, such as sending warnings or crisis information spreading or information spreading in emergency training or realistic emergency scenes.
Data from: Species-specific responses to habitat conversion across scales synergistically restructure Neotropical bird communities
Ecologists are increasingly exploring methods for preserving biodiversity in agricultural landscapes. Yet because species vary in how they respond to habitat conversion, ecological communities in agriculture and more natural habitats are often distinct. Unpacking the heterogeneity in species responses to habitat conversion will be essential for predicting and mitigating community shifts. Here, we analyze two years of bird censuses at 150 sites across gradients of local land cover, landscape forest amount and configuration, and regional precipitation in Costa Rica to holistically characterize species responses to habitat conversion. Specifically, we used Poisson-binomial mixture models to (1) delineate groups of species that respond similarly to environmental gradients, (2) explore the relative importance of local versus landscape-level habitat conversion, and (3) determine how landscape context influences species' local habitat preferences. We found that species fell into six groups: habitat generalists, abundant and rare forest specialists, and three groups of agricultural specialists that differed in their responses to landscape forest cover, fragmentation, and regional precipitation. Birds were most sensitive to local forest cover, but responses were contingent on landscape context. Specifically, forest specialists benefitted most when local forest cover increased in forested landscapes, while habitat generalists exhibited compensatory dynamics, peaking at sites with either local or landscape-level forest, but not both. Our study demonstrates that species responses to habitat conversion are complex but predictable. Characterizing species-level responses to environmental gradients represents a viable approach for forecasting the winners and losers of global change and designing interventions to minimize the ongoing restructuring of Earth's biota.
Data from: A newly recognised species that has been confused with the global polyphagous pest scale insect, Coccus hesperidum Linnaeus (Hemiptera: Coccomorpha: Coccidae)
Coccus hesperidum L. (Hemiptera: Coccomorpha: Coccidae), the type species of the soft scale genus Coccus L., the family Coccidae and the whole of the scale insects (Coccoidea), is a cosmopolitan plant pest. Using DNA sequence data and morphological comparisons, we determine that there is a distinct species that is morphologically very similar to C. hesperidum. Here, we describe the species as Coccus praetermissus Lin & Tanaka sp. n., based on adult female specimens from Australia, Malaysia and Thailand. The adult female of C. praetermissus sp. n. differs from C. hesperidum in having dorsal setae with bluntly rounded tips, whereas they are sharply pointed in C. hesperidum. A detailed description of the newly recognised species is provided, incorporating adult female morphology and DNA sequences from mitochondrial and nuclear loci. Our examination of slides from The Natural History Museum, London, and several Australian institutions indicates that C. praetermissus sp. n. has been confused sometimes with C. hesperidum s. s. These findings have potential relevance to plant biosecurity and quarantine because C. hesperidum is cosmopolitan whereas C. praetermissus sp. n., which is also polyphagous and the two species can share many host plants, currently appears to be more geographically restricted. Additionally, there is deep genetic divergence within C. praetermissus sp. n. that might indicate that it is a cryptic species complex, but wider geographic sampling is required to test this possibility.
Data from: Hiding behavior in Christmas tree worms on different time scales
Many animals escape predators by hiding. Hiding decisions are economic in that individuals trade off the physiological costs of hiding with the benefits of increased security. The number of conspecifics may increase competition, security, or attract predators, influencing predation risk. We studied hiding time in Christmas tree worms (Spirobranchus giganteus), sessile marine invertebrates, which lived with 0–17 other worms within 20cm. Competition and predation risk reduction both predict a shorter latency to re-emerge given the necessity to feed and potential for safety in numbers, respectively. In contrast, if grouped worms attract more predators, individuals should hide longer. We experimentally induced hiding in 174 worms and found a significant, positive relationship between hiding time and number of conspecifics. We repeated the test 4 consecutive times in 1 day on a subset of 30 worms that were either solitary or lived with one other untested worm. We found that worms with longer hiding times habituated more quickly than worms with shorter hiding times, and that the individual worm explained 55.8% of the variation in hiding time. When we conducted the trials for 4 days, we found that the individual worm explained 41.75% of the variation, but no evidence of behavioral plasticity. Worm antipredator responses were consistently individualistic, but behavioral plasticity was only evident over short time scales. For sessile marine invertebrates, higher densities may attract predators, enhancing rather than diluting predation risk. Worms that cannot move away from their neighbors, thus seemingly modify antipredator behavior in consistent ways.
Data from: Research on the mechanical behavior of shale based on multi-scale analysis
In view of the difficulty in obtaining the mechanical properties of shale, the multi-scale analysis of shale was performed on a shale outcrop from the Silurian Longmaxi Formation in the Changning area, Sichuan Basin, China. The nano/micro indentation test is an effective method for multi-scale mechanical analysis. In this paper, effective criteria for the shale indentation test were evaluated. The elastic modulus was evaluated at a multi-scale and the engineering validation of drilling cuttings was performed. The porosity tests showed that the pore distribution of shale from the nano-scale to macro-pore could be better displayed by the nuclear magnetic resonance test. The micro-scale elastic modulus and hardness increased nonlinearly with the increase in the clay packing density. It was observed that the size effect of the micro-hardness was based on porosity and composition. The partial spalling of shale at the micro-scale could lead to irregular bulges or steps in a load–displacement curve. The elastic modulus of pure clay minerals was 24.2 GPa on the parallel bedding plane, and 15.8 GPa on the vertical bedding plane. The contact hardness (pure clay minerals) was 0.51 GPa. The indentation results showed that the micro elastic modulus of shale obeyed the normal distribution, and the statistical average could predict the macro mechanical properties effectively. The present work provides a novel idea regarding the cognitive mechanics state of shale in the formation.
Data from: Genomic-scale capture and sequencing of endogenous DNA from feces
Genomic-level analyses of DNA from non-invasive sources would facilitate powerful conservation and evolutionary studies in natural populations of endangered and otherwise elusive species. However, the typical low quantity and poor quality of DNA that is extracted from non-invasive samples have generally precluded such work. Here we apply a modified DNA capture protocol that, when used in combination with massively-parallel sequencing technology, facilitates efficient and highly-accurate resequencing of megabases of specified nuclear genomic regions from fecal DNA samples. We validated our approach by comparing genetic variants identified from corresponding fecal and blood DNA samples of six western chimpanzees (Pan troglodytes verus) across more than 1.5 megabases of chromosome 21, chromosome X, and the complete mitochondrial genome. Our results suggest that it is now feasible to conduct genomic studies in natural populations for which constraints on invasive sampling have otherwise long been a barrier. The data we collected also provided an opportunity to examine western chimpanzee genetic diversity at unprecedented scale. Despite high mitochondrial genome diversity (pi = 0.585%), western chimpanzees have a low ratio (0.42) of X chromosomal (pi = 0.034%) to autosomal (chromosome 21 pi = 0.081%) sequence diversity, a pattern that may reflect an unusual demographic history of this subspecies.
Data from: Testing the scaling effects and mechanisms of N-induced biodiversity loss: evidence from a decade-long grassland experiment
Although extensive studies demonstrate that nitrogen (N) enrichment frequently reduces plant diversity within small quadrats (0.5 –4 m2), only a few studies have evaluated N effects on biodiversity across different spatial scales. We conducted the first experimental test of the scale dependence of N effects on species richness from a 10-year N treatment (1.75- 28 g N m−2 yr−1) in a typical steppe. We used species area relationship (SAR) to analyze the scale dependence of species loss with power model S = cAz (S is species number, A is area, c is intercept, and z is slope). Absolute species loss decreased at sampling area > 8 m2. Proportional species loss (compared to control) decreased and critical threshold (Ncrit) for biodiversity losses increased with sampling areas. These scale dependences were quantified as increasing slope (z-value) of SAR with N addition. Through SAR decomposition, we found that this overall positive effect was in response to positive effects of changes to the species abundance distribution over negative effects of overall species richness losses. Synthesis. As nitrogen (N) enrichment typically occurs at scales much larger than individual plots, understanding how N enrichment affects the scaling patterns of biodiversity is necessary for biodiversity conservation and ecosystem management in response to anthropogenic N deposition.
Data from: The Urban Heat Island and its spatial scale dependent impact on survival and development in butterflies of different thermal sensitivity
Climate alteration is one of the most cited ecological consequences of urbanization. However, the magnitude of this impact is likely to vary with spatial scale. We investigated how this alteration affects the biological fitness of insects, which are especially sensitive to ambient conditions and well-suited organisms to study urbanization-related changes in phenotypic traits. We monitored temperature and relative air humidity in wooded sites characterized by different levels of urbanization in the surroundings. Using a split-brood design experiment, we investigated the effect of urbanization at the local (i.e., 200 × 200 m) and landscape (i.e., 3 × 3 km) scale on two key traits of biological fitness in two closely related butterfly species that differ in thermal sensitivity. In line with the Urban Heat Island concept, urbanization led to a 1°C increase in daytime temperature and an 8% decrease in daytime relative humidity at the local scale. The thermophilous species Lasiommata megera responded at the local scale: larval survival increased twofold in urban compared to rural sites. Urbanized sites tended to produce bigger adults, although this was the case for males only. In the woodland species Pararge aegeria, which has recently expanded its ecological niche, we did not observe such a response, neither at the local, nor at the landscape scale. These results demonstrate interspecific differences in urbanization-related phenotypic plasticity and larval survival. We discuss larval pre-adaptations in species of different ecological profiles to urban conditions. Our results also highlight the significance of considering fine-grained spatial scales in urban ecology.
Data from: Scale and direction of adaptive introgression between black cottonwood (Populus trichocarpa) and balsam poplar (P. balsamifera)
Introgression can introduce novel genetic variation at a faster rate than mutation alone, and result in adaptive introgression when adaptive alleles are maintained in the recipient genome over time by natural selection. A previous study from our group demonstrated adaptive introgression from Populus balsamifera into P. trichocarpa in a target genomic region. Here we expanded our local ancestry analysis to the whole genome of both parents to provide a comprehensive, unbiased view of introgression patterns and to identify additional candidate regions for adaptive introgression genome-wide. Populus trichocarpa is a large, fast-growing tree of mild coastal regions of the Pacific northwest, whereas P. balsamifera is a smaller stature tree of continental and boreal regions with intense winter-cold. The species are parapatric with extensive hybridization. Here, using local ancestry analysis, we detected asymmetric patterns of introgression across the whole genome of these two species of poplar trees adapted to contrasting environments, with stronger introgression from P. balsamifera to P. trichocarpa than vice versa. Admixed P. trichocarpa individuals showed more genomic regions with unusually high levels of introgression (19 regions) compared with admixed P. balsamifera (9 regions) but also the largest introgressed peak (1.02 Mb). Our analysis also revealed numerous candidate regions for adaptive introgression with strong signals of selection, notably related to disease resistance, and enriched for genes that may play crucial roles for survival and adaptation. Furthermore, we revealed overrepresentation of subtelomeric regions in P. balsamifera introgression into P. trichocarpa and possible protection of the sex-determining regions from interspecific gene flow.
Data from: Comparative analysis of encephalization in mammals reveals relaxed constraints on anthropoid primate and cetacean brain scaling
There is a well-established allometric relationship between brain and body mass in mammals. Deviation of relatively increased brain size from this pattern appears to coincide with enhanced cognitive abilities. To examine whether there is a phylogenetic structure to such episodes of changes in encephalization across mammals, we used phylogenetic techniques to analyse brain mass, body mass and encephalization quotient (EQ) among 630 extant mammalian species. Among all mammals, anthropoid primates and odontocete cetaceans have significantly greater variance in EQ, suggesting that evolutionary constraints that result in a strict correlation between brain and body mass have independently become relaxed. Moreover, ancestral state reconstructions of absolute brain mass, body mass and EQ revealed patterns of increase and decrease in EQ within anthropoid primates and cetaceans. We propose both neutral drift and selective factors may have played a role in the evolution of brain–body allometry.
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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.