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304 results for “scale pattern”
Data from: Unravelling large-scale patterns and drivers of biodiversity in dry rivers
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Data from: Mast seeding patterns are asynchronous at a continental scale
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Large-scale exploration of nitrogen utilization efficiency in Asia region for rice crop: variation patterns and determinants
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FIGURE 6. Scale-shaped sclerites under polarized light showing concentric extinction patterns. A in A review of the genus Trichogorgia (Cnidaria, Octocorallia), including descriptions of new species
FIGURE 6. Scale-shaped sclerites under polarized light showing concentric extinction patterns. A: Stephanogorgia diomedea (USNM 75108); B: Trichogorgia lyra (USNM 52875); C: S. wainwrighti (USNM 1112682); D: T. muzikae sp. nov. (USNM 77155, holotype).
Data from: Endemism patterns are scale dependent
<p>Areas of endemism are important in biogeography because they capture facets of biodiversity not represented elsewhere. However, the scales at which they are relevant to research and conservation are poorly analysed. Here, we calculate weighted endemism (WE) and phylogenetic endemism (PE) separately for all birds and amphibians across the globe. We show that scale dependence is widespread for both indices and manifests across grain sizes, spatial extents and taxonomic treatments. Variations in taxonomic opinions – whether species are treated by systematic 'lumping' or 'splitting' – can profoundly affect the allocation of WE hotspots. Global patterns of PE can provide insights into complex evolutionary processes but this congruence is lost at the continental to country extents. These findings are explained by environmental heterogeneity at coarser grains, and to a far lesser extent at finer resolutions. Regardless of scale, we find widespread deficits of protection for endemism hotspots. Our study presents a framework for assessing areas for conservation that are robust to assumptions on taxonomy, spatial grain and extent.</p>
Broad-scale patterns of the Afro-Palearctic landbird migration
Aim: Animal migration strategies balance trade-offs between mortality and reproduction in seasonal environments. Knowledge of broad-scale biogeographical patterns of animal migration is important for understanding ecological drivers of migratory behaviours. Here we present a flyway-scale assessment of the spatial structure and seasonal dynamics of the Afro-Palearctic bird migration system and explore how phenology of the environment guides long-distance migration. Location: Europe and Africa. Time period: 2009–2017. Major taxa studied: Birds. Methods: We compiled an individual-based dataset comprising 23 passerine and near-passerine species of 55 European breeding populations where a total of 564 individuals were tracked migrating between Europe and sub-Saharan Africa. In addition, we used remote sensed observations on primary productivity (NDVI) to estimate the timing of vegetation green-up in spring and senescence in autumn across Europe. First, we described how individual breeding and non-breeding sites and the migratory flyways link geographically. Second, we examined how migration timing along the two major Afro-Palearctic flyways is tuned with vegetation phenology en route and at the breeding sites. Results: While we found the longitudes of individual breeding and non-breeding sites to be strongly positively related, the latitudes of breeding and non-breeding sites were negatively related. In autumn, timing of migration was similar along the Western and the Eastern flyways and happened ahead of the autumnal senescence of vegetation. In spring, migration timing was approximately two weeks later along the Eastern flyway than on the Western flyway which coincided with the later spring green-up in Eastern Europe. Main Conclusions: Migration of the Afro-Palearctic landbirds follows a longitudinally parallel leap-frog migration pattern where migrants track vegetation green-up in spring and depart before vegetation senescence in autumn. However, the ongoing global change have the potential to disrupt this spatiotemporal synchronization between migration timing and spring green-up with variable effects on different migrant populations.
Effect of ecological factors on fine-scale patterns of social structure in African lions
1. Environmental variations can influence the extent to which individuals interact with other individuals by changing the value of grouping. It is well known that many species can form and disband groups, often in response to the distribution and abundance of resources. 2. While previous studies showed that resources influence the broad-scale structure of animal groups, knowledge gaps remain on whether they affect fine-scale patterns of association among individuals within groups. 3. We quantify association patterns in African lions while simultaneously monitoring the abundance and distribution of prey. We test how social and ecological factors, including individual trait (age, sex, reproductive state) similarity and prey availability (prey abundance, dispersion, herd size and body size) affect within-pride social structure in African lions. 4. We found that individual decisions about associates depended on resource availability with individuals associating equally across all members of the pride when prey herds were scarce, aggregated or large bodied, and associating more exclusively (in subgroups of preferred associates) when prey herds were abundant, dispersed or small bodied. Individuals within lion prides seemed to be buffering against changes in prey availability by modulating their strength and density of connections with conspecifics when prides split into subgroups. The strength and density of connections among individuals within subgroups was greater when prey herds were large and lower when prey herds were dispersed or large bodied. 5. Our findings suggest that individual lions are making social decisions at both the subgroup level and the pride level, with decisions representing putatively fitness-enhancing strategies. Individuals were typically shifting between having few strong connections and having many weaker connections depending on prevailing ecological conditions, with prey abundance, dispersion and body size having the greatest impact on decisions about splitting into subgroups. The maintenance of connections within prides and subgroups in the face of ecological change suggests that the fission-fusion nature of lion prides might be essential for the long-term maintenance of social connections even when short-term conditions do not allow them. More broadly, our study reveals how fission-fusion dynamics and ecological factors can simultaneously have an effect on animals across multiple levels of sociality. 29-Jul-2020
Data from: Contrasting patterns of population structure at large and fine scales in an avian disturbance specialist of braided river ecosystems
Aim: To understand the population structure and its potential drivers at different spatial scales in a migratory bird, the black-fronted tern (Chlidonias albostriatus); a specialist of the spatially and temporally dynamic environments of braided rivers. Location: New Zealand Methods: We used a three-pronged approach based on 17 microsatellites, two mitochondrial loci (cytochrome b / control region), and phenotypic data (head-bill length, bill depth, wing length, weight). We determined large-scale genetic structure throughout the whole breeding range (approx. 150,000 km2), calculated genetic divergence of breeding populations, and tested for isolation-by-distance between populations. We investigated the level of fine-scale genetic structure based on spatial autocorrelation analyses and assessed the presence of a body size cline based on phenotypic data. Lastly, we compared phenotypic divergence (PST) and the level of divergence by genetic drift (FST) among breeding populations to test for underlying mechanisms of population differentiation. Results: Nuclear and mitochondrial DNA showed that across their range black-fronted terns were effectively panmictic, with low genetic divergence between breeding colonies overall and no isolation-by-distance. However, at fine geographical scales black-fronted terns accrued significant genetic structure for distances up to 75 km, primarily driven by males, indicating more frequent female dispersal. Furthermore, a phenotypic cline in accordance with Bergmann's rule was evident. PST exceeded FST in three traits, suggestive of local adaptation. Main conclusions: Significant fine-scale structure can be present in highly mobile, specialist species while not affecting spatial structures at larger scales. Hence, methodologies applied to both whole landscapes and local scales are important to appropriately estimate connectivity in dynamic metapopulations and investigate the processes behind connectivity. Conservation management will need to include protecting currently uninhabited patches to facilitate natural colonisation of suitable habitat. For black-fronted terns, managing whole catchments throughout the entire breeding range would be preferable to managing single patches.
Data from: Helianthus maximiliani and species fine-scale spatial pattern affect diversity interactions in reconstructed tallgrass prairies
1. Biodiversity and Ecosystem Function analyses aim to explain how individual species and their interactions affect ecosystem function. With this study we asked in what ways do species interact, are these interactions affected by species planting pattern, and are initial (planted) proportions or previous year (realized) proportions a better reference point for characterizing grassland diversity effects? 2. We addressed these questions with experimental communities compiled from a pool of 16 tallgrass prairie species. We planted all species in monocultures and mixtures that varied in their species richness, evenness, and spatial pattern. We recorded species-specific biomass production over three growing seasons and fitted Diversity-Interactions (DI) models to annual plot biomass yields. 3. In the establishment season, all species interacted equally to form the diversity effect. In years 2 and 3, each species contributed a unique additive coefficient to its interaction with every other species to form the diversity effect. These interactions were affected by H. maximiliani and the species planting pattern. Models based on species planted proportions better-fit annual plot yields than models based on species previous contributions to plot biomass. 4. Outcomes suggest that efforts to plant tallgrass prairies to maximize diversity effects should focus on the specific species present and in what arrangement they are planted. Furthermore, for particularly diverse grasslands, the effort of collecting annual species biomass data may not be necessary when quantifying diversity effects with Diversity-Interactions models.
Data from: Geographic isolation and larval dispersal shape seascape genetic patterns differently according to spatial scale
Genetic variation, as a basis of evolutionary change, allows species to adapt and persist in different climates and environments. Yet, a comprehensive assessment of the drivers of genetic variation at different spatial scales is still missing in marine ecosystems. Here, we investigated the influence of environment, geographic isolation, and larval dispersal on the variation in allele frequencies, using an extensive spatial sampling (47 locations) of the striped red mullet (Mullus surmuletus) in the Mediterranean Sea. Univariate multiple regressions were used to test the influence of environment (salinity and temperature), geographic isolation, and larval dispersal on Single Nucleotide Polymorphisms (SNPs) allele frequencies. We used Moran's Eigenvector Maps (db-MEMs) and Asymmetric Eigenvector Maps (AEMs) to decompose geographic and dispersal distances in predictors representing different spatial scales. We found that salinity and temperature had only a weak effect on the variation in allele frequencies. Our results revealed the predominance of geographic isolation to explain variation in allele frequencies at large spatial scale (> 1,000km) while larval dispersal was the major predictor at smaller spatial scale (< 1,000km). Our findings stress the importance of including spatial scales to understand the drivers of spatial genetic variation. We suggest that larval dispersal allows to maintain gene flows at small to intermediate scale, while at broad scale, genetic variation may be mostly shaped by adult mobility, demographic history or multi-generational stepping stone dispersal. These findings bring out important spatial scale considerations to account for in the design of a protected areas network that would efficiently enhance protection and persistence capacity of marine species.
Data from: Small- to large-scale patterns of ground-dwelling spider (Araneae) diversity across northern Canada
We examined how Arctic spider (Araneae) biodiversity is distributed at multiple spatial scales in Northern Canada using a standardized hierarchical sampling design. We investigated which drivers, environmental or spatial, influence the patterns observed. Spatial patterns of species richness and composition of Arctic spiders were assessed in 12 sites located in Arctic, Subarctic, and North-Boreal regions, across 30 degrees of latitude and 80 degrees of longitude. Variation of diversity was partitioned in relation to multiple environmental and spatial drivers of diversity patterns. Over 23, 000 adult spiders, representing 306 species in 14 families, were collected in Northern Canada, with 107 species (35% of the total species collected) representing new Territorial or Provincial records. Spider diversity was structured at the regional scale across ecoclimatic regions but not with latitude. Longitudinal patterns of spider diversity across Canada may be explained by post-glacial dispersal. At local scales, diversity was non-randomly distributed, and possibly limited by biotic interactions. We recommend the use of ecoclimatic regions as a framework for conservation of biodiversity in Northern Canada and spiders as useful bioindicators which can help us understand the effects of climate change across ecoclimatic regions of northern Canada.
Data from: Continental-scale patterns reveal potential for warming-induced shifts in cattle diet
In North America, it has been shown that cattle in warmer, drier grasslands have lower quality diets than those cattle grazing cooler, wetter grasslands, which suggests warming will increase nutritional stress and reduce weight gain. Yet, little is known about how the plant species that comprise cattle diets change across these gradients and whether these shifts in dietary quality coincide with shifts in dietary composition, i.e. the relative abundance of different plant species consumed by cattle. To quantify geographic patterns in dietary composition, we analyzed the dietary composition and dietary quality of unsupplemented cattle from 289 sites across the central US by sequence-based analyses of plant DNA isolated from cattle fecal samples. Overall, assuming that the percentage of reads for a species in a sample corresponds to the percentage of protein derived from the species, only 45% of the protein intake for cattle was derived from grasses. Within the Great Plains, northern cattle relied more on grasses than southern cattle, which derived a greater proportion of their protein from herbaceous and woody eudicots. Eastern cattle were also more likely to consume a unique assemblage of plant species than western cattle. High dietary protein was not strongly tied to consumption of any specific plant species, which suggests that efforts to promote individual plant species may not easily remedy protein deficiencies. A few plant species were consistently associated with lower quality diets. For example, the diets of cattle with high amounts of Elymus or Hesperostipa were more likely to have lower crude protein concentrations than diets with less of these grasses. Overall, our analyses suggest that climatic warming will increase the reliance of cattle on eudicots as protein concentrations of grasses decline. Monitoring cattle diet with this DNA-based sequencing approach can be an effective tool for quantifying cattle diet to better increase animal performance and guide mitigation strategies to changing climates.
Data from: A porous convection model for small-scale grass patterns
Spatial ecological patterns are usually ascribed to Turing‐type reaction‐diffusion or scale‐dependent feedback processes, but morphologically indistinguishable patterns can be produced by instabilities in fluid flow. We present a new hypothesis that suggests that fluid convection and chill damage to plants could form vegetation patterns with wavelengths ≈1–2 times the plant height. Previous hypotheses for small‐scale vegetation pattern formation relied on a Turing process driven by competition for water, which is thought to occur in large vegetation patterns. Predictions of the new hypothesis were consistent with properties of natural grass patterns in North Carolina, contradicting the Turing hypothesis. These results indicate that similarities in pattern morphology should not be interpreted as implying similarities in the pattern‐forming processes, that small‐wavelength vegetation patterns may arise from mechanisms that are distinct from those generating long‐wavelength vegetation patterns, and that fluid instabilities should be recognized as a cause of ecological patterns.
Data from: Nonlinear thermal gradients shape broad-scale patterns in geographic range size and can reverse Rapoport's rule
Aim: Species living at latitudes that have greater annual temperature variations are expected to achieve broader geographic ranges than species living at latitudes that have smaller annual temperature variations, generating a positive relationship between range size and latitude (Rapoport's rule). However, this prediction fails to take into account the greater latitudinal extent of tropical temperatures relative to those at higher latitudes. Here we model the contributions of the broader latitudinal extent of equal-temperature habitats at low latitudes and the greater annual temperature variation at high latitudes to the range size–latitude relationship, and test whether the latitudinal variation in geographic range size in marine bivalves can be explained by models that account for both annual temperature variation and the steepness of latitudinal thermal gradients. Location: Western Pacific, eastern Pacific and western Atlantic. Methods: We use a null model where geographic ranges are placed on the ocean surface independently of thermal gradients, and a range-expansion model where the minimum and maximum temperatures encompassed by the geographic range of a species (macroecological thermal ranges) are positively related to annual temperature minima and maxima at the location where the species originated. We compare results with a database containing 40,820 occurrences of 4760 marine bivalve species. Result: Models incorporating temperature-limited range expansion along realistic thermal gradients predict an inverse relationship between range size and latitude, in opposition to Rapoport's rule. The distribution patterns of marine bivalves match this prediction. Main conclusions: The poleward trend in latitudinal range size is determined by the nonlinearity of the latitudinal gradient of temperature minima and maxima and less by the latitudinal gradient of the local seasonal range in temperatures. Although tropical species do have narrower macroecological thermal ranges than high-latitude species, the nearly constant temperatures over wide areas of the tropics allow tropical species to achieve broad latitudinal ranges.
Data from: Atoll-scale patterns in coral reef community structure: Human signatures on Ulithi Atoll, Micronesia
The dynamic relationship between reefs and the people who utilize them at a subsistence level is poorly understood. This paper characterizes atoll-scale patterns in shallow coral reef habitat and fish community structure, and correlates these with environmental characteristics and anthropogenic factors, critical to conservation efforts for the reefs and the people who depend on them. Hierarchical clustering analyses by site for benthic composition and fish community resulted in the same 3 major clusters: cluster 1–oceanic (close proximity to deep water) and uninhabited (low human impact); cluster 2–oceanic and inhabited (high human impact); and cluster 3–lagoonal (facing the inside of the lagoon) and inhabited (highest human impact). Distance from village, reef exposure to deep water and human population size had the greatest effect in predicting the fish and benthic community structure. Our study demonstrates a strong association between benthic and fish community structure and human use across the Ulithi Atoll (Yap State, Federated States of Micronesia) and confirms a pattern observed by local people that an 'opportunistic' scleractinian coral (Montipora sp.) is associated with more highly impacted reefs. Our findings suggest that small human populations (subsistence fishing) can nevertheless have considerable ecological impacts on reefs due, in part, to changes in fishing practices rather than overfishing per se, as well as larger global trends. Findings from this work can assist in building local capacity to manage reef resources across an atoll-wide scale, and illustrates the importance of anthropogenic impact even in small communities.
Data from: Morphology and genetics reveal an intriguing pattern of differentiation at a very small geographic scale in a bird species, the forest thrush Turdus lherminieri
Mobile organisms are expected to show population differentiation only over fairly large geographical distances. However, there is growing evidence of discrepancy between dispersal potential and realized gene flow. Here we report an intriguing pattern of differentiation at a very small spatial scale in the forest thrush (Turdus lherminieri), a bird species endemic to the Lesser Antilles. Analysis of 331 individuals from 17 sampling sites distributed over three islands revealed a clear morphological and genetic differentiation between these islands isolated by 40–50 km. More surprisingly, we found that the phenotypic divergence between the two geographic zones of the island of Guadeloupe was associated with a very strong genetic differentiation (Fst from 0.073–0.153), making this pattern a remarkable case in birds given the very small spatial scale considered. Molecular data (mitochondrial control region sequences and microsatellite genotypes) suggest that this strong differentiation could have occurred in situ, although alternative hypotheses cannot be fully discarded. This study suggests that the ongoing habitat fragmentation, especially in tropical forests, may have a deeper impact than previously thought on avian populations.
Data from: Variation in fine-scale genetic structure and local dispersal patterns between peripheral populations of a South American passerine bird
The distribution of suitable habitat influences natal and breeding dispersal at small spatial scales, resulting in strong micro-geographic genetic structure. Although environmental variation can promote inter-population differences in dispersal behavior and local spatial patterns, the effects of distinct ecological conditions on within-species variation in dispersal strategies and in fine-scale genetic structure remain poorly understood. We studied local dispersal and fine-scale genetic structure in the thorn-tailed rayadito (Aphrastura spinicauda), a South American bird that breeds along a wide latitudinal gradient. We combine capture-mark-recapture data from eight breeding seasons and molecular genetics to compare two peripheral populations with contrasting environments in Chile: Navarino Island, a continuous and low density habitat, and Fray Jorge National Park, a fragmented, densely populated and more stressful environment. Natal dispersal showed no sex bias in Navarino, but was female-biased in the more dense population in Fray Jorge. In the latter, male movements were restricted and some birds seemed to skip breeding in their first year, suggesting habitat saturation. Breeding dispersal was limited in both populations, with males being more philopatric than females. Spatial genetic autocorrelation analyses using 13 polymorphic microsatellite loci confirmed the observed dispersal patterns: a fine-scale genetic structure was only detectable for males in Fray Jorge for distances up to 450 m. Furthermore, two-dimensional autocorrelation analyses and estimates of genetic relatedness indicated that related males tended to be spatially clustered in this population. Our study shows evidence for context-dependent variation in natal dispersal and corresponding local genetic structure in peripheral populations of this bird. It seems likely that the costs of dispersal are higher in the fragmented and higher density environment in Fray Jorge, particularly for males. The observed differences in micro-geographic genetic structure for rayaditos might reflect the genetic consequences of population-specific responses to contrasting environmental pressures near the range limits of its distribution.
Data from: Patterns of local community composition are linked to large-scale diversification and dispersal of clades
At any location, a group of organisms may be represented by several clades. What determines which clades will dominate local communities in terms of their species richness? Here, this relatively neglected question is addressed by analyzing 166 local assemblages of snakes distributed globally. For most regions, local assemblages are dominated by clades with higher global-scale diversification rates and more frequent dispersal into each region, and not by clades that have been present in that region longer. This result contrasts with many other studies of local richness (in other organisms), which show strong impacts of regional colonization time on overall local species richness of clades. Furthermore, even though local assemblages are assembled independently on different continents, most regions have converged on similar patterns of proportional richness. Specifically, a few rapidly diversifying clades dominate most communities around the world. The high diversification rates of these clades are then linked to their high dispersal rates. Similar patterns may occur in many groups, such as plants, frogs, salamanders, birds, and mammals.
Data from: From animal tracks to fine-scale movement modes: a straightforward approach for identifying multiple, spatial movement patterns
1. Thanks to developments in animal tracking technology, detailed data on the movement tracks of individual animals are now attainable for many species. However, straightforward methods to decompose individual tracks into high-resolution, spatial modes are lacking but are essential to understand what an animal is doing. 2. We developed an analytical approach that combines separately-validated methods into a straightforward tool for converting animal GPS tracks to short-range movement modes. Our three-step analytical process comprises: (1) decomposing data into separate movement segments using behavioural change point analysis; (2) defining candidate movement modes and translating them into non-linear or linear equations between net squared displacement (NSD) and time; and (3) fitting each candidate equation to NSD segments and determining the best-fitting modes using Concordance Criteria, Akaike's Information Criteria and other fine-scale segment characteristics. We illustrate our approach for three sub-adults, male wild boar Sus scrofa tracked at 15 min intervals over 4 months using GPS collars. We defined five candidate movement modes based on previously published studies of short-term movements: encamped, ranging, round trips (complete and partial), and wandering. 3. Our approach successfully classified over 80% of the tracks into these movement modes lasting between 5 and 54 hours and covering between 300 m to 20 km. Repeated analyses of GPS data resampled at different rates indicated that one positional fix every 3-4 h was sufficient for >70% classification success. Classified modes were consistent with published observations of wild boar movement, further validating our method. 4. The proposed approach advances the status quo by permitting classification into multiple movement modes (where these are adequately discernable from spatial fixes) facilitating analyses at high temporal and spatial resolutions, and is straightforward, largely objective, and without restrictive assumptions, necessary parameterizations or visual interpretation. Thus, it should capture the complexity and variability of tracked animal movement mode for a variety of taxa across a wide range of spatial and temporal scales.
Data from: Spatial patterns of self-recruitment of a coral reef fish in relation to island-scale retention mechanisms
Oceanographic features influence the transport and delivery of marine larvae, and physical retention mechanisms, such as eddies, can enhance self-recruitment (i.e. the return of larvae to their natal population). Knowledge of exact locations of hatching (origin) and settlement (arrival) of larvae of reef animals provides a means to compare observed patterns of self-recruitment 'connectivity' with those expected from water circulation patterns. Using parentage inference based on multiple sampling years in Moorea, French Polynesia, we describe spatial and temporal variation in self-recruitment of the anemonefish Amphiprion chrysopterus, evaluate the consistency of net dispersal distances of self-recruits against the null expectation of passive particle dispersal and test the hypothesis that larvae originating in certain reef habitats (lagoons and passes) would be retained and thus more likely to self-recruit than those originating on the outer (fore) reef. Estimates of known self-recruitment were consistent across the sampling years (~25–27% of sampled recruits). For most (88%) of these self-recruits, the net distance between hatching and settlement locations was within the maximum dispersal distance expected for a neutrally buoyant passive particle based on the longest duration of the larval dispersive phase and the average direction and speed of current flow around Moorea. Furthermore, a parent of a given body size on the outer (fore) reef of Moorea was less likely to produce self-recruits than those in passes. Our findings show that even a simple dispersal model based on net average flow and direction of alongshore currents can provide insight into landscape-scale retention patterns of reef fishes.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.