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358 results for “fine-scale”
Data for "Fine-scale tundra vegetation patterns are strongly related to winter thermal conditions"
<p>This page links to the data and code associated with the publication Niittynen et al. (In Press). "Fine-scale tundra vegetation patterns are strongly related to winter thermal conditions".</p> <p>The dataset contains fine-scale microclimatic, soil and species (vascular plant, bryophyte and lichen) data from three Arctic areas.The environmental data and analyses are describes in the linked publication.</p>
Vegetation growth and landscape genetics of Tillandsia lomas at its dry limits in the Atacama Desert shows fine-scale response to environmental parameters
<p>1. Ecosystems at its dry limits have been studied while focusing on species biology, fitness and interactions of biotic and abiotic parameters; however, the interactive effects of these parameters remain under-explored and, therefore, information is often lacking about the putative effect of global climate change on these ecosystems.</p> <p>2. Here, we conducted an analysis of the interplay of fine-scale landscape genetics and biotic and abiotic factors of terrestrial <i>Tillandsia</i> lomas in the hyperarid Atacama Desert, characterized by a fog-dependent vegetation type consisting of almost one single vascular plant species only.</p> <p>3. We showed that metapopulations of <i>Tillandsia landbeckii</i> are genetically connected over many hundreds of squarekilometres, and despite a large potential to propagate clonally genetic diversity is structured, regionally and locally. On landscape-level genetic diversity correlates well with fitness parameters such as growth, flowering and vegetation density, and we observed also fine-scaled correlation with a 3-D landscape model indicating a positive feedback with saisonal fog occurrence and availability. The various interdependies of biotic and abiotic factors also result in regular linear banding patterns of vegetation arranged orthogonally towards landscape slope. <i>Ex-situ</i> growth experiments indicate that <i>T. landbeckii</i> growths at optimal rates within this extreme, hyperarid environment, and we can extrapolate mean biomass production for this particular ecosystem.</p> <p>4. <i>Synthesis.</i> Our results suggest that the unique ecosystem of terrestrial <i>Tillandsia</i> lomas in the hyperarid Atacama Desert is an evolutionary balanced and fine-scaled system. Vegetation itself is built up by long-lived and persistent modules. We developed a descriptive model of the various interacting factors, thereby highlighting also a severe threat caused by global climate change.</p>
Trait-similarity and trait-hierarchy jointly determine fine-scale spatial associations of resident and invasive ant species
<p>Interspecific competition, a dominant process structuring ecological communities, is influenced by species' phenotypic differences. Limiting similarity theory holds that species with similar traits should compete intensely ("trait-similarity"). In contrast, competing theories including modern coexistence theory emphasize that species with traits conferring competitive advantages should outcompete others ("trait-hierarchy"). Either or both of these mechanisms may drive competitive exclusion, but their relative importance and interacting effects are rarely studied. Here, we explore empirically whether trait-similarity and trait-hierarchy can explain fine-scale spatial associations observed between invasive and native ant species in a tropical assemblage. We find that pairwise co-occurrences between the invasive red imported fire ant Solenopsis invicta and 28 other species across relatively homogenous grasslands can be explained largely by an interaction of trait-similarity and trait-hierarchy in a single morphological trait, relative pronotum width. Specifically, higher trait-hierarchy values are associated with negative co-occurrences; however, these effects are counteracted when species are increasingly dissimilar in their trait ranges. These findings are consistent with the notion that limiting similarity and competitive hierarchies are interactive rather than discrete mechanisms driving competitive exclusion.</p>
Data from: Genetic data reveal fine-scale ecological segregation between larval plethodontid salamanders in replicate contact zones
<p>Contact zones present unique opportunities to investigate ecological divergence, reproductive barriers, and gene flow between species. The two-lined salamander (<em>Eurycea</em> <em>bislineata</em>) species complex is a group of semiaquatic plethodontid salamanders with a reticulate evolutionary history that reflects the reorganization of river drainage basins. Although evidence for widespread, ancient introgression suggests an absence of reproductive isolating mechanisms in the early evolutionary history of the group, modern contact zones reveal a broader diversity of outcomes—with some putative species pairs occurring in sympatry and others exhibiting narrow hybrid zones. Here, we used RADcap data to investigate gene flow and ecological divergence in replicate contact zones between two species in the Appalachian foothills. Our results demonstrate that gene flow between these species is absent or rare, and larvae show strong, fine-scale ecological segregation among riffles, runs, and pools in streams. These results reinforce the more ambiguous conclusions of previous studies that suggested the evolutionary distinctiveness of these two species and underscore the importance of ecological factors in shaping local distributions.</p>
Data from: Outlier SNP markers reveal fine-scale genetic structuring across European hake populations (Merluccius merluccius)
Shallow population structure is generally reported for most marine fish and explained as a consequence of high dispersal, connectivity and large population size. Targeted gene analyses and more recently genome-wide studies have challenged such view, suggesting that adaptive divergence might occur even when neutral markers provide genetic homogeneity across populations. Here, 381 SNPs located in transcribed regions were used to assess large- and fine-scale population structure in the European hake (Merluccius merluccius), a widely distributed demersal species of high priority for the European fishery. Analysis of 850 individuals from 19 locations across the entire distribution range showed evidence for several outlier loci, with significantly higher resolving power. While 299 putatively neutral SNPs confirmed the genetic break between basins (FCT = 0.016) and weak differentiation within basins, outlier loci revealed a dramatic divergence between Atlantic and Mediterranean populations (FCT range 0.275–0.705) and fine-scale significant population structure. Outlier loci separated North Sea and Northern Portugal populations from all other Atlantic samples and revealed a strong differentiation among Western, Central and Eastern Mediterranean geographical samples. Significant correlation of allele frequencies at outlier loci with seawater surface temperature and salinity supported the hypothesis that populations might be adapted to local conditions. Such evidence highlights the importance of integrating information from neutral and adaptive evolutionary patterns towards a better assessment of genetic diversity. Accordingly, the generated outlier SNP data could be used for tackling illegal practices in hake fishing and commercialization as well as to develop explicit spatial models for defining management units and stock boundaries.
Data from: Fine-scale genetic structure and conservation status of American badgers at their northwestern range periphery
Peripheral populations are often characterized by small population size and low genetic diversity, with many at risk of extirpation. These characteristics may be even more pronounced in human-modified landscapes that further reduce the resiliency of populations to environmental change. Situated at the northwestern edge of the species' range, the western American badger (Taxidea taxus jeffersonii) is an endangered mammal in Canada, where it inhabits the interior grassland and open forest ecosystems of British Columbia (BC) and continues to be threatened by severe vehicle-induced mortality rates and other anthropogenic factors. Here, we collected mitochondrial DNA haplotypic and microsatellite genotypic data to investigate the extent and distribution of American badger genetic variation within and among sites in British Columbia, and relative to adjacent populations in the USA, including in Washington state. From these data, we reconstructed population structure and connectivity, and examined current designatable unit status. Patterns of genetic variation for American badgers in British Columbia were as expected for peripheral populations, including reduced genetic diversity, increased population differentiation, and evidence of demographic contraction. Furthermore, we found limited connectivity between regional populations in our study area and identified significant substructure isolating the most northwestern sampling unit (Cariboo), findings that starkly contrast with the high levels of gene flow observed between populations across the species' range core. These results have important implications for current designatable unit status for western American badgers in British Columbia and emphasize the need for further population monitoring and mitigation of potential barriers to gene flow.
Data from: Direct genetic evidence for reproductive philopatry and associated fine-scale migrations in female blacktip reef sharks (Carcharhinus melanopterus) in French Polynesia.
Conservation of top predators has been emphasised as essential in an ecosystem due to their role in trophic chain regulation. Optimization of conservation strategies for these endangered marine top predators requires direct estimates of breeding patterns and connectivity, which are essential to understand their population dynamics. While there have been some attempts to investigate breeding patterns of reef sharks from litter reconstruction using molecular analyses, direct fine-scale migrations of female sharks for parturition as well as connectivity at a medium scale, such as between islands, remain mostly unknown. We used microsatellite DNA markers and a likelihood-based parentage analysis to determine breeding patterns of female blacktip reef sharks in Moorea (Society Islands, French Polynesia). Such an approach demonstrates that while most females gave birth at their home island, some migrated to specific nursery areas outside their home range, sometimes going to another island (up to 50 km across deep ocean). Analysis also revealed that females migrated to the same nursery on every birthing event. Many offspring showed a high level of inbreeding indicating an overall reduced population size, restricted movements and dispersal, or specific mating behaviour. Females represent the vectors that transport the genes at nursery grounds, and their fidelity should thus define reproductive units. As females seem to be philopatric, males could be the ones dispersing genes between metapopulations. These results highlight the need for conservation of coastal zones where female reef sharks seems to exhibit philopatry during the breeding season.
Data from: Fine-scale analysis of an assassin bug's behaviour: predatory strategies to bypass the sensory systems of prey
Some predators sidestep environments that render them conspicuous to the sensory systems of prey. However, these challenging environments are unavoidable for certain predators. Stenolemus giraffa is an assassin bug that feeds on web-building spiders; the web is the environment in which this predator finds its prey, but it also forms part of its preys' sophisticated sensory apparatus, blurring the distinction between environment and sensory systems. Stenolemus giraffa needs to break threads in the web that obstruct its path to the spiders, and such vibrations can alert the spiders. Using laser vibrometry, this study demonstrates how S. giraffa avoids alerting the spiders during its approach. When breaking threads, S. giraffa attenuates the vibrations produced by holding on to the loose ends of the broken thread and causing them to sag prior to release. In addition, S. giraffa releases the loose ends of a broken thread one at a time (after several seconds or minutes) and in this way spaces out the production of vibrations in time. Furthermore, S. giraffa was found to maximally reduce the amplitude of vibrations when breaking threads that are prone to produce louder vibrations. Finally, S. giraffa preferred to break threads in the presence of wind, suggesting that this araneophagic insect exploits environmental noise that temporarily impairs the spiders' ability to detect vibrations. The predatory behaviour of S. giraffa seems to be adaptated in intricate manner for bypassing the sophisticated sensory systems of web-building spiders. These findings illustrate how the physical characteristics of the environment, along with the sensory systems of prey can shape the predatory strategies of animals.
Data from: Fine-scale appendage structure of the Cambrian trilobitomorph Naraoia spinosa and its ontogenetic and ecological implications
<p>Trilobitomorphs are a species-rich Palaeozoic arthropod assemblage that unites trilobites with several other lineages that share similar appendage structure. Post-embryonic development of the exoskeleton is well documented for some trilobitomorphs, especially trilobites, but little is known of the ontogeny of their soft parts, limiting understanding of their autecology. Here we document appendage structure of the Cambrian naraoiid trilobitomorph Naraoia spinosa by computed microtomography, resulting in three-dimensional reconstructions of appendages at both juvenile and adult stages. The adult has dense, strong spines on the protopods of post-antennal appendages, implying a predatory/scavenging behavior. Absence of such gnathobasic structures but instead tiny protopodal bristles and a number of endopodal setae suggests a detritus-feeding strategy for the juvenile. Our data add strong morphological evidence for ecological-niche shifting by Cambrian arthropods during their life cycles. A conserved number of appendages across the sampled developmental stages demonstrates that Naraoia ceased budding off new appendages by the mid-juvenile stage.</p> <p> </p> <p> </p>
Data from: Direct and indirect genetic and fine-scale location effects on breeding date in song sparrows
Quantifying direct and indirect genetic effects of interacting females and males on variation in jointly expressed life-history traits is central to predicting microevolutionary dynamics. However, accurately estimating sex-specific additive genetic variances in such traits remains difficult in wild populations, especially if related individuals inhabit similar fine-scale environments. Breeding date is a key life-history trait that responds to environmental phenology and mediates individual and population responses to environmental change. However, no studies have estimated female (direct) and male (indirect) additive genetic and inbreeding effects on breeding date, and estimated the cross-sex genetic correlation, while simultaneously accounting for fine-scale environmental effects of breeding locations, impeding prediction of microevolutionary dynamics. We fitted animal models to 38 years of song sparrow (Melospiza melodia) phenology and pedigree data to estimate sex-specific additive genetic variances in breeding date, and the cross-sex genetic correlation, thereby estimating the total additive genetic variance while simultaneously estimating sex-specific inbreeding depression. We further fitted three forms of spatial animal model to explicitly estimate variance in breeding date attributable to breeding location, overlap among breeding locations and spatial autocorrelation. We thereby quantified fine-scale location variances in breeding date and quantified the degree to which estimating such variances affected the estimated additive genetic variances. The non-spatial animal model estimated nonzero female and male additive genetic variances in breeding date (sex-specific heritabilities: 0·07 and 0·02, respectively) and a strong, positive cross-sex genetic correlation (0·99), creating substantial total additive genetic variance (0·18). Breeding date varied with female, but not male inbreeding coefficient, revealing direct, but not indirect, inbreeding depression. All three spatial animal models estimated small location variance in breeding date, but because relatedness and breeding location were virtually uncorrelated, modelling location variance did not alter the estimated additive genetic variances. Our results show that sex-specific additive genetic effects on breeding date can be strongly positively correlated, which would affect any predicted rates of microevolutionary change in response to sexually antagonistic or congruent selection. Further, we show that inbreeding effects on breeding date can also be sex specific and that genetic effects can exceed phenotypic variation stemming from fine-scale location-based variation within a wild population.
Data from: Quantifying pursuit-diving seabirds' associations with fine-scale physical features in tidal stream environments
The rapid increase in the number of tidal stream turbine arrays will create novel and unprecedented levels of anthropogenic activity within habitats characterized by horizontal current speeds exceeding 2 ms−1. However, the potential impacts on pursuit-diving seabirds exploiting these tidal stream environments remain largely unknown. Identifying similarities between the fine-scale physical features (100s of metres) suitable for array installations, and those associated with foraging pursuit-diving seabirds, could identify which species are most vulnerable to either collisions with moving components, or displacement from these installations. A combination of vessel-based observational surveys, Finite Volume Community Ocean Model outputs and hydroacoustic seabed surveys provided concurrent measures of foraging distributions and physical characteristics at a fine temporal (15 min) and spatial (500 m) resolution across a tidal stream environment suitable for array installations, during both breeding and non-breeding seasons. These data sets were then used to test for associations between foraging pursuit-diving seabirds (Atlantic puffins Fratercula arctica, black guillemots Cepphus grylle, common guillemots Uria aalge, European shags Phalacrocorax aristotelis) and physical features. These species were associated with areas of fast horizontal currents, slow horizontal currents, high turbulence, downward vertical currents and also hard–rough seabeds. The identity and strength of associations differed among species, and also within species between seasons, indicative of interspecific and intraspecific variations in habitat use. However, Atlantic puffins were associated particularly strongly with areas of fast horizontal currents during breeding seasons, and European shags with areas of rough–hard seabeds and downward vertical currents during non-breeding seasons. Synthesis and applications. Atlantic puffins' strong association with fast horizontal current speeds indicates that they are particularly likely to interact with installations during breeding seasons. Any post-installation monitoring and mitigation measures should therefore focus on this species and season. The multi-species associations with high turbulence and downward vertical currents, which often coincide with fast horizontal current speeds, also highlight useful pre-installation mitigation measures via the omission of devices from these areas, reducing the overall likelihood of interactions. Environmental impact assessments (EIA) generally involve once-a-month surveys across 2-year periods. However, the approaches used in this study show that more focussed surveys can greatly benefit management strategies aiming to reduce the likelihood of negative impacts by facilitating the development of targeted mitigation measures. It is therefore recommended that these approaches contribute towards EIA within development sites.
Data from: Fine-Scale Mapping of Recombination Rate in Drosophila Refines its Correlation to Diversity and Divergence
Regional rates of recombination often correlate with levels of nucleotide diversity, and either selective or neutral hypotheses can explain this relationship. Regional recombination rates also correlate with nucleotide differences between human and chimpanzee, consistent with models where recombination is mutagenic; however, a lack of correlation is observed in the Drosophila melanogaster group, consistent with models invoking natural selection. Here, we revisit the relationship among recombination, diversity, and interspecies difference by generating empirical estimates of these parameters in Drosophila pseudoobscura. To measure recombination rate, we genotyped 1,294 backcross hybrids at 50 markers across the largest assembled linkage group in this species. Genome-wide diversity was estimated by sequencing a second isolate of D. pseudoobscura at shallow coverage. Alignment to the sequenced genome of the closely related species, Drosophila persimilis, provided nucleotide site orthology. Our findings demonstrate that scale is critical in determining correlates to recombination rate: fine-scale cross-over rate estimates are far stronger predictors of both diversity and interspecies difference than broad-scale estimates. The correlation of fine-scale recombination rate to diversity and interspecies difference appears to be genome-wide, evidenced by examination of an X-linked region in greater detail. Because we observe a strong correlation of cross-over rate with interspecies difference, even after correcting for segregating ancestral variation, we suggest that both mutagenic and selective forces generate these correlations, the latter in regions of low crossing over. We propose that it is not cross-overs per se that are mutagenic, but rather repair of DNA double-strand break precursors via crossing over and gene conversion.
Data from: Differential female sociality is linked with the fine-scale structure of sexual interactions in replicate groups of red junglefowl, Gallus gallus
Recent work indicates that social structure has extensive implications for patterns of sexual selection and sexual conflict. However, little is known about the individual variation in social behaviours linking social structure to sexual interactions. Here, we use network analysis of replicate polygynandrous groups of red junglefowl (Gallus gallus) to show that the association between social structure and sexual interactions is underpinned by differential female sociality. Sexual dynamics are largely explained by a core group of highly social, younger females, which are more fecund and more polyandrous, and thus associated with more intense postcopulatory competition for males. In contrast, less fecund females from older cohorts, which tend to be socially dominant, avoid male sexual attention by clustering together and perching on branches, and preferentially reproduce with dominant males by more exclusively associating and mating with them. Collectively, these results indicate that individual females occupy subtly different social niches, and demonstrate that female sociality can be an important factor underpinning the landscape of intra-sexual competition and the emergent structure of animal societies.
Recording fine-scale movement of ground beetles by two methods: Potentials and methodological pitfalls
<p><span><span>Movement trajectories are usually recorded as a sequence of discrete movement events described by two parameters: step length (distance) and turning angle (bearing). One of the most widespread methods to record the geocoordinates of each step is by a GPS device. Such devices have limited suitability for recording fine movements of species with low dispersal ability including flightless carabid beetles at small spatio-temporal scales. As an alternative, the distance-bearing approach can avoid the measurement error of GPS units since it uses directly measured distances and compass azimuths. As no quantification of measurement error between distance-bearing and GPS approaches exists so far, we generated artificial fine-scale trajectories and in addition radio-tracked living carabids in a temperate forest and recorded each movement step by both methods. Trajectories obtained from distance-bearing were compared to those obtained by a GPS device in terms of movement parameters. Consequently, both types of trajectories were segmented by state-switching modeling into two distinct movement stages typical for carabids: random walk and directed movement. We found that the measurement error of GPS compared to distance-bearing was 1.878 m (SEM = 0.181 m) for distances and 31.330° (SEM = 2.066°) for bearings. Moreover, these errors increased under dense forest canopy and rainy weather. Distance error did not change with increasing distance recorded by distance-bearing but bearings were significantly more sensitive to error at short distances. State-switching models showed only slight, not significant, differences in movement states between the two methods in favor of the random walk in the distance-bearing approach. However, the shape of the GPS-measured trajectories considerably differed from those recorded by distance-bearing caused especially by bearing error at short distances. Our study showed that distance-bearing could be more appropriate for recording movement steps not only of ground-dwelling beetles but also other small animals at fine spatio-temporal scales.</span></span></p>
Data from: Cultural transmission of tool use combined with habitat specializations leads to fine-scale genetic structure in bottlenose dolphins
[No abstract entered]
Data from: Causes and consequences of fine-scale population structure in a critically endangered freshwater seal
[No abstract entered]
Supplementary material 2 from: Standovár T, Horváth S, Aszalós R (2017) Temporal changes in vegetation of a virgin beech woodland remnant: stand-scale stability with intensive fine-scale dynamics governed by stand dynamic events. Nature Conservation 17: 35-56. https://doi.org/10.3897/natureconservation.17.12251
Map showing canopy trees in the study area. :
Supplementary material 1 from: Standovár T, Horváth S, Aszalós R (2017) Temporal changes in vegetation of a virgin beech woodland remnant: stand-scale stability with intensive fine-scale dynamics governed by stand dynamic events. Nature Conservation 17: 35-56. https://doi.org/10.3897/natureconservation.17.12251
Map showing the position of sampling plots in 1996 and 2013 :
Figure 7. Fine-scale components RDA 1-3 in Effects of temperature patterns on the spawining phenology and niche overlap of fish assemblages in the water bodies of the Dnipro River basin
Figure 7. Fine-scale components RDA 1-3 of the annual temperature variation. Black line – the original data, colored lines – smoothed data. The abscissa axis – the number of days from 1 July of the previous year to June 31 of the next year.
Supplementary material 1 from: Piry S, Berthier K, Streiff R, Cros-Arteil S, Foucart A, Tatin L, Bröder L, Hochkirch A, Chapuis M-P (2018) Fine-scale interactions between habitat quality and genetic variation suggest an impact of grazing on the critically endangered Crau Plain grasshopper (Pamphagidae: Prionotropis rhodanica). Journal of Orthoptera Research 27(1): 61-73. https://doi.org/10.3897/jor.27.15036
: Explanation note: Supplementary tables and figures.
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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.