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208 results for “spatial association”
Spatial-numerical associations in humans
<p>Number sense requires an ability to estimate values and respective differences - although how brains most efficiently processes information remains unknown. We tested if participants demonstrate processing preferences for horizontal or vertical representations during paired number comparisons. For numbers above the subitizing range of 1-4 with the largest number positioned upwards, participants demonstrated significantly faster and more accurate responses. </p>
The Pacific lamprey genomic divergence, association mapping, temporal Willamette Falls, spatial rangewide datasets
<p>High rates of dispersal can breakdown coadapted gene complexes. However, concentrated genomic architecture (i.e., genomic islands of divergence) can suppress recombination to allow evolution of local adaptations despite high gene flow. Pacific lamprey (<em>Entosphenus tridentatus</em>) is a highly dispersive anadromous fish. Observed trait diversity and evidence for genetic basis of traits suggests it may be locally adapted. We addressed whether concentrated genomic architecture could influence local adaptation for Pacific lamprey. Using two new whole genome assemblies and genotypes from 7,716 single nucleotide polymorphism (SNP) loci in 518 individuals from across the species range, we identified four genomic islands of divergence (on chromosomes 01, 02, 04, and 22). We determined robust phenotype-by-genotype relationships by testing multiple traits across geographic sites. These trait associations likely explain genomic divergence across the species' range. We genotyped a subset of 302 broadly distributed SNPs in 2,145 individuals for association testing for adult body size, sexual maturity, migration distance and timing, adult swimming ability, and larval growth. Body size traits were strongly associated with SNPs on chromosomes 02 and 04. Moderate associations also implicated SNPs on chromosome 01 as being associated with variation in female maturity. Finally, we used candidate SNPs to extrapolate a heterogeneous spatiotemporal distribution of these predicted phenotypes based on independent datasets of larval and adult collections. These maturity and body size results guide future elucidation of factors driving regional optimization of these traits for fitness. Pacific lamprey is culturally important and imperiled. This research addresses biological uncertainties that challenge restoration efforts.</p>
Plasmodium falciparum genomic surveillance reveals spatial and temporal trends, association of genetic and physical distance, and household clustering
<p>Molecular epidemiology using genomic data can help identify relationships between malaria parasite population structure, malaria transmission intensity, and ultimately help generate actionable data to assess the effectiveness of malaria control strategies. Genomic data, coupled with geographic information systems data, can further identify clusters or hotspots of malaria transmission, parasite genetic and spatial connectivity, and parasite movement by human or mosquito mobility over time and space. In this study, we performed longitudinal genomic surveillance in a cohort of 70 participants over four years from different neighborhoods and households in Thiès, Senegal—a region of exceptionally low malaria transmission (entomological inoculation rate (EIR) less than 1). Genetic identity (identity by state) was established using a 24 single nucleotide polymorphism molecular barcode and a multivariable linear regression model was used to establish genetic and spatial relationships. Our results show clustering of genetically similar parasites within households and a decline in genetic similarity of parasites with increasing distance. One household showed extremely high diversity and warrants further investigation as to the source of these diverse genetic types. This study illustrates the utility of genomic data with traditional epidemiological approaches for surveillance and detection of trends and patterns in malaria transmission not only by neighborhood but also by household. This approach can be implemented regionally and countrywide to strengthen and support malaria control and elimination efforts. </p>
Spatial plant-plant associations from a Mediterranean grassland and associated analyses
<p>This dataset contains data documenting plant spatial patterns in a Mediterranean grassland (la Crau, France) along a grazing and nutrient enrichment gradient, along with accessory data documenting soil characteristics. It has been used to compute spatial association networks for plant communties to investigate changes in plant-plant interactions with grazing. Results show that association networks become closer to random expectations as grazing pressure increases.</p>
Data from: Ecological and spatial patterns associated with diversification of the shrub genus Tetraglochin along Southern-Central Andes (Rosaceae)
In addition to the degree of geographical isolation (sympatry, parapatry, allopatry and peripatry), ecology can be an important factor promoting diversification of lineages, both by niche divergence as well as niche conservatism. Tetraglochin is a genus of shrubs with six species distributed along the Southern and Central Andes, from Peru to southern Argentina and central Chile. Although monophyly of the genus as the identity of its species are well established, spatiotemporal framework for its diversification and the potential role of the ecology and geography in the speciation process remain unknown. In the present study we analyzed diversification times and historical biogeography of the genus, and conducted different climatic niche and geographical range comparisons among its species to determine possible patterns associated with speciation. Results support the Pleistocene diversification, early along the Southern Andes and the Patagonian Steppe and subsequently in the Central Andes. Climatic niche divergence did not prove to be a major factor promoting speciation, but rather the phylogenetic niche conservatism. Our analyses also favored the sympatric model of speciation, although patterns from geographical range evolution are difficult to interpret due to the lability on the ancestral distributions, and therefore micro-allopatric or parapatric divergence associated with the glacial-interglacial cycles and climatic oscillations throughout the Quaternary should not be discarded. Other potential factors associated with diversification of Tetraglochin are also discussed.
Spatial variation in diet-microbe associations across populations of a generalist North American carnivore
1. Generalist species, by definition, exhibit variation in niche attributes that promote survival in changing environments. Increasingly, phenotypes previously associated with a species, particularly those with wide or expanding ranges, are dissolving and compelling greater emphasis on population-level characteristics. 2. In the present study, we assessed spatial variation in diet characteristics, gut microbiome, and the association between these two ecological traits across populations of coyotes (Canis latrans). We highlight the influence of the carnivore community in shaping these relationships, as the coyote varied from being an apex predator to a subordinate, mesopredator across sampled populations. 3. We implemented a scat survey across three distinct coyote populations in Michigan, USA. We used carbon (δ13C) and nitrogen (δ15N) isotopic values to reflect consumption patterns and trophic level, respectively. Corresponding samples were also paired with 16S rRNA sequencing to describe the microbial community and correlate with isotopic values. 4. Though consumption patterns were comparable, we found spatial variation in trophic level among coyote populations. Specifically, δ15N was highest where coyotes were the apex predator and lowest where coyotes co-occurred with gray wolves (Canis lupus). 5. The gut microbial community exhibited marked spatial variation across populations with the lowest OTU diversity found where coyotes occurred at their lowest trophic level. Bacteriodes and Fusobacterium dominated the microbiome and were positively correlated across all populations. We found no correlation between δ13C and microbial community attributes. However, positive associations between δ15N and specific microbial genera increased as coyotes ascended trophic levels. 6. Coyotes provide a model for exploring implications of niche plasticity because they are a highly adaptable, wide-ranging omnivore. As coyotes continue to vary in trophic position and expand their geographic range, we might expect increased divergence within their microbial community, changes in physiology, and alterations in behavior. 05-May-2020
Data from: Transatlantic secondary contact in Atlantic salmon, comparing microsatellites, a SNP array, and Restriction Associated DNA sequencing for the resolution of complex spatial structure
Identification of discrete and unique assemblages of individuals or populations is central to the management of exploited species. Advances in population genomics provide new opportunities for re-evaluating existing conservation units but comparisons among approaches remain rare. We compare the utility of RAD-seq, a single nucleotide polymorphism (SNP) array and a microsatellite panel to resolve spatial structuring under a scenario of possible trans-Atlantic secondary contact in a threatened Atlantic Salmon, Salmo salar, population in southern Newfoundland. Bayesian clustering indentified two large groups subdividing the existing conservation unit and multivariate analyses indicated significant similarity in spatial structuring among the three data sets. mtDNA alleles diagnostic for European ancestry displayed increased frequency in southeastern Newfoundland and were correlated with spatial structure in all marker types. Evidence consistent with introgression among these two groups was present in both SNP data sets but not the microsatellite data. Asymmetry in the degree of introgression was also apparent in SNP data sets with evidence of gene flow towards the east or European type. This work highlights the utility of RAD-seq based approaches for the resolution of complex spatial patterns, resolves a region of trans-Atlantic secondary contact in Atlantic Salmon in Newfoundland and demonstrates the utility of multiple marker comparisons in identifying dynamics of introgression.
Data from: Spatial and seasonal influences on culturable endophytic mycobiota associated with different tissues of Eugenia jambolana Lam. and their antibacterial activity against MDR strains
Background: Present study focuses on diversity and distribution analysis of endophytic fungi associated with different tissues of Eugenia jambolana. The influence of season and geographical location on diversity and distribution of endophytic fungi has been analyzed. Antibacterial activity of isolated fungal species has also been investigated against MDR bacterial strains. Result: A total of 1896 endophytic fungal isolates were obtained from healthy, surface sterilized tissues of leaf, stem and petiole tissues during summer, monsoon and winter season. Out of 24 fungal species isolated, 20 species belong to class Ascomycetes, 2 to Basidiomycetes and 2 to Zygomycetes. Maximum species diversity was in rainy season whereas colonization frequency was in winter. All the diversity indices showed maximum species diversity at site 5 (Yamunanager), rainy among the seasons and leaf among the tissues studied. Aspergillus genus was most frequently isolated. Aspergillus niger and Alternaria alternata were most dominant species. Three way ANOVA results showed that effect of season was highly significant on species diversity in relation to sites and tissues. 60% endophytic fungal extracts showed significant antibacterial activity against one or more than one MDR bacterial strain. Conclusion: Different fungal species were recovered from different sites but the inter-site comparisons were not significant according to Jaccard similarity coefficient. Diversity of such fungal endophytes indicates that Eugenia jambolana plant acts as an ecosystem facilitating survival of many microbes with impressive antibacterial potential.
Data from: Ecological divergence among colour morphs mediated by changes in spatial network structure associated with disturbance
1. Differences in individual behaviour affect social interactions and contribute to the spatial structuring of animal populations. However, disturbance should also affect spatial networks by altering habitat heterogeneity and resource availability. Variation in resource availability should perturb the frequency and nature of social and ecological interactions within a population by affecting the spatial distribution of individuals. 2. In disturbed habitats where resources are limiting, spatial relationships should reflect behavioural differences among individuals, with higher-quality resources controlled by dominant individuals. In contrast, all individuals may exploit preferred resources in resource-rich habitats. Environmental variation and population reorganisation may also result in variation in morphological, behavioural, and ecological traits, which ultimately affect fitness. 3. We addressed these considerations for male tree lizards (Urosaurus ornatus) at three sites that differ in levels of disturbance. The habitats at these localities differed in the availability of live trees, the preferred microhabitat of U. ornatus. In addition, male U. ornatus exhibit a polymorphism in dewlap colour linked with differences in aggression, which should influence their position in a network and access to resources. We applied a network framework to characterise the spatial organisation of male morphs at each site and quantified male aggressive behaviour in the laboratory. We also compared body size, body condition, number of bite marks, parasite load, and the microhabitat use and diet, of males among the sites. 4. We detected no significant differences in spatial network structure between unburned and infrequently burned sites. However, at a frequently-burned site, the network shifted towards geographically closer, heteromorphic male neighbour associations. Males at this site were also larger, more aggressive, and had more bite marks but fewer parasites than males at the other sites. Moreover, we detected divergence in microhabitat use and diet among the morphs at the frequently-burned site that reflected the shift in spatial network structure and differences in morph behaviour. That is, only more-aggressive morphs usurped trees and consumed prey from higher trophic levels. 5. We conclude that environmental variation may influence animal spatial network structure. Jointly, behavioural and environmental variation may promote despotic social dynamics and ecological divergence in resource-limited habitats.
Data from: Temporal and spatial activity-associated energy partitioning in free-swimming sea snakes
1. Partitioning energy between critical basal functions and activity-associated behaviours is a primary determinant of animal survival. Consequently, habitat selection is likely to be driven by the efficiency with which resources can be acquired from a heterogeneous energy landscape. 2. Determining how energy partitioning is achieved across temporal and spatial scales is particularly challenging in aquatic animals due to the logistical limitations in estimating field metabolic rates (FMR) while simultaneously examining habitat choice. 3. Here, accelerometry telemetry and bimodal respirometry were used to correlate vectorial dynamic body acceleration (<i>VeDBA</i>) with oxygen consumption rates (<i>V̇o<sub>2</sub></i>) of sea snakes (<i>Hydrophis curtus</i> and <i>H. elegans</i>) across an ecologically-relevant temperature range. Subsequently, <i>VeDBA</i> of free-roaming snakes was used to estimate activity-associated FMR within a near-shore environment over diel, seasonal and spatial scales. 4. Diel changes in activity explained short-term patterns in FMR, whereas seasonal changes in water temperature drove long-term patterns. Spatial analyses demonstrated that activity-associated FMR was elevated in productive seagrass and mudflat habitats, indicative of a concentration of foraging efforts. 5. Our findings illustrate for the first time how sea snakes partition activity-associated FMR across time and space, providing an approach by which we can monitor the impacts of, and vulnerabilities to, natural and anthropogenic disturbances like warming and trawl fisheries.
Data from: Low spatial genetic differentiation associated with rapid recolonization in the New Zealand fur seal Arctocephalus forsteri
Population declines resulting from anthropogenic activities are of major consequence for the long-term survival of species because the resulting loss of genetic diversity can lead to extinction via the effects of inbreeding depression, fixation of deleterious mutations, and loss of adaptive potential. Otariid pinnipeds have been exploited commercially to near extinction with some species showing higher demographic resilience and recolonization potential than others. The New Zealand fur seal (NZFS) was heavily impacted by commercial sealing between the late 18th and early 19th centuries, but has recolonized its former range in southern Australia. The species has also recolonized its former range in New Zealand, yet little is known about the pattern of recolonization. Here, we first used 11 microsatellite markers (n = 383) to investigate the contemporary population structure and dispersal patterns in the NZFS (Arctocephalus forsteri). Secondly, we model postsealing recolonization with 1 additional mtDNA cytochrome b (n = 261) marker. Our data identified 3 genetic clusters: an Australian, a subantarctic, and a New Zealand one, with a weak and probably transient subdivision within the latter cluster. Demographic history scenarios supported a recolonization of the New Zealand coastline from remote west coast colonies, which is consistent with contemporary gene flow and with the species' high resilience. The present data suggest the management of distinct genetic units in the North and South of New Zealand along a genetic gradient. Assignment of individuals to their colony of origin was limited (32%) with the present data indicating the current microsatellite markers are unlikely sufficient to assign fisheries bycatch of NZFSs to colonies.
Data from: Differential divergence in autosomes and sex chromosomes is associated with intra-island diversification at a very small spatial scale in a songbird lineage
<p>Recently diverged taxa showing marked phenotypic and ecological diversity are optimal systems to understand the genetic processes underlying speciation. We used genome-wide markers to investigate the diversification of the Reunion grey white eye (<i>Zosterops borbonicus</i>) on the small volcanic island of Reunion (Mascarene archipelago), where this species complex exhibits four geographic forms that are parapatrically distributed across the island and differ strikingly in plumage colour. One form restricted to the highlands is separated by a steep ecological gradient from three distinct lowland forms which meet at narrow hybrid zones that are not associated with environmental variables. Analyses of genomic variation based on SNP data from genotyping-by-sequencing and pooled RADseq approaches, reveal that signatures of selection associated with elevation can be found at multiple regions across the genome, whereas most loci associated with the lowland forms are located on the Z sex chromosome. We identified <i>TYRP1</i>, a Z-linked colour gene, as a likely candidate locus underlying colour variation among lowland forms. Tests of demographic models revealed that highland and lowland forms diverged in the presence of gene flow, and divergence has progressed as gene flow was restricted by selection at loci across the genome. This system is promising to investigate how natural selection and reproductive isolation shape the genomic landscape of divergence at multiple stages of the speciation process.</p>
How manual object exploration is associated with 7- to 8-month-old infants' visual prediction abilities in spatial object processing.
<p>Data set of Kubicek, C., Jovanovic, B., & Schwarzer, G. (in press). How manual object exploration is associated with 7- to 8-month-old infants’ visual prediction abilities in spatial object processing. <em>Infancy.</em></p>
Population divergence associated with spatial asynchrony in precipitation in neotropical frogs
<p><span>Aim</span><span>: To test the role of asynchrony in precipitation patterns among populations –a proxy for asynchronous breeding– as a driver of intraspecific genetic divergence across 38 species of Neotropical frogs. In addition, to examine whether regions with more asynchronous precipitation regimes across space have higher frog species richness and have experienced greater speciation rates than regions with more spatially synchronous precipitation regimes.</span></p> <p><strong><span>Location</span></strong><span><strong>: </strong>Central and South America</span></p> <p><strong><span>Taxon</span></strong><span><strong>:</strong> Anurans</span></p> <p><strong><span>Methods</span></strong><span><strong>: </strong>For microevolutionary analyses, we assessed the relationship between spatial asynchrony in precipitation and mtDNA genetic divergence accounting for ecological connectivity using multiple regression and phylogenetic meta-analyses. For macroevolutionary analyses, we assessed the relationship between species richness, speciation rates estimated from a comprehensive molecular phylogeny, and the degree of spatial asynchrony in precipitation using generalized linear models.</span></p> <p><strong><span>Results and Main conclusions:</span></strong><span><strong> </strong>Beyond a generalized effect of ecological connectivity on intraspecific genetic divergence, we found that spatial asynchrony in precipitation is positively associated with genetic differentiation in 39% of the species tested, resulting in a weak cross-species effect. However, the effect of asynchrony in precipitation on population divergence seems not to scale to macroevolutionary patterns because spatial asynchrony in precipitation was not associated with geographical patterns of species richness nor present-day speciation rates. Our results indicate that asynchronous breeding may promote genetic divergence even in the absence of geographic barriers in species where breeding is associated with water availability, but such effects may not be stable enough through time to influence macroevolutionary patterns.</span></p>
FIGURE 16 in First records of Leucania rawlinsi Adams and L. senescens M̂schler (Lepidoptera: Noctuidae) in Brazil: redescription, potential association with Bt maize, larval parasitoids, and spatial and temporal distribution
FIGURE 16. Distribution of the abundance of Leucania rawlinsi and L. senescens in different Brazilian biomes based on standardized collections.
FIGURE 14 in First records of Leucania rawlinsi Adams and L. senescens M̂schler (Lepidoptera: Noctuidae) in Brazil: redescription, potential association with Bt maize, larval parasitoids, and spatial and temporal distribution
FIGURE 14. Abundance of Leucania rawlinsi and L. senescens in Brazil based on standardized collections and data from entomological collections.
FIGURE 15 in First records of Leucania rawlinsi Adams and L. senescens M̂schler (Lepidoptera: Noctuidae) in Brazil: redescription, potential association with Bt maize, larval parasitoids, and spatial and temporal distribution
FIGURE 15. Relative abundance of Leucania rawlinsi and L. senescens based on standardized collections in Brazil. Abbreviations of states are in the Material and Methods section. MS–C: Chapadṳo do Sul, Mato Grosso do Sul; MS–M: Miranda, Mato Grosso do Sul; ES–A: Alegre; ES–D: Domingos Martins.
FIGURES 11–12 in First records of Leucania rawlinsi Adams and L. senescens M̂schler (Lepidoptera: Noctuidae) in Brazil: redescription, potential association with Bt maize, larval parasitoids, and spatial and temporal distribution
FIGURES 11–12. Female genitalia in ventral (left) and lateral view (right) of species of Leucania. 11, L. rawlinsi from Petrópolis, Rio de Janeiro, Brazil (DZ 31.118). 12, L. senescens from Chapadṳo do Sul, Mato Grosso do Sul, Brazil (EMBRAPA 4372). Scale bar: 1mm.
FIGURES 9–10 in First records of Leucania rawlinsi Adams and L. senescens M̂schler (Lepidoptera: Noctuidae) in Brazil: redescription, potential association with Bt maize, larval parasitoids, and spatial and temporal distribution
FIGURES 9–10. Male genitalia in posterior (left) and lateral view (right) and aedeagus of species of Leucania. 9, L. rawlinsi from Conquista d'Oeste, Mato Grosso, Brazil (DZ 40.187). 10, L. senescens from Parque Estadual de Campos do Jordṳo, Campos do Jordṳo, Sṳo Paulo, Brazil (MZUSP). The vesica is about 70% smaller than remaining genitalia. Scale bar: 1mm.
FIGURES 5–8 in First records of Leucania rawlinsi Adams and L. senescens M̂schler (Lepidoptera: Noctuidae) in Brazil: redescription, potential association with Bt maize, larval parasitoids, and spatial and temporal distribution
FIGURES 5–8. Anterior view of the head (upper) and dorsal view of the thorax (bottom) of species of Leucania. 5–6, L. rawlinsi, male from Estrada da Graciosa, Morretes, Paraná, Brazil (DD 357). 7–8, L. senescens, male from Parque Estadual de Campos do Jordṳo, Campos do Jordṳo, Sṳo Paulo, Brazil (MZUSP). Scale bar: 2mm.
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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.