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358 results for “fine-scale”
Fine-scale genome-wide signature of Pleistocene glaciation in Thitarodes moths (Lepidoptera: Hepialidae), host of Ophiocordyceps fungus in the Hengduan Mountains
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Data from: Fine-scale genetic structure of small fish populations in islands: The case of brook charr Salvelinus fontinalis (Mitchill, 1814) in Saint-Pierre and Miquelon (France)
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Estimating fine-scale changes in turbulence using the movements of a flapping flier
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Global integration of phylogenomic data and fine-scale partitioning strategies refine the evolutionary tree of Adephaga beetles (Insecta: Coleoptera)
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Data from: Foundation species promote local adaptation and fine-scale distribution of herbaceous plants
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Fine-scale temporal dynamics of flower visitors sheds light on the pollination strategy of a dioecious palm in the Ecuadorian Andes
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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: 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.
Fine-scale genetic structure reflects limited and coordinated dispersal in the colonial monk parakeet, Myiopsitta monachus
<p>The genetic structure of animal populations has considerable behavioural, ecological and evolutionary implications and may arise from various demographic traits. Here, we use observational field data and molecular genetics to determine the genetic structure of an invasive population of monk parakeets, <i><span>Myiopsitta monachus</span></i>, at a range of spatial scales, and investigate the demographic processes that generate the observed structure. Monk parakeets construct large nests that can house several pairs occupying separate chambers; these nests are often aggregated within nesting trees. We determined patterns of relatedness within compound nests, within nesting trees and between trees. Spatial autocorrelation analyses of pairwise genetic relatedness revealed fine-scale genetic structure with relatives of both sexes spatially clustered within, but not beyond, nesting trees. In addition, males were more related to males sharing their compound nests than to other males occupying the same nesting tree. By contrast, males and females within compound nests were not significantly more closely related than elsewhere in the same tree, and we found no evidence for inbreeding. Adults showed high breeding site fidelity between years despite considerable disturbance of nest sites. Natal dispersal was female-biased, but dispersal distances were relatively short with some natal philopatry observed in both sexes. Sibling coalitions, typically of males, were observed amongst both philopatric and dispersing birds. Our results show significant clustering of kin within compound nests and nesting trees resulting from limited and coordinated natal dispersal, with subsequent breeding site fidelity. The resulting genetic structure has implications for social behaviour in this unusual parrot species.</p>
Data from: Fine-scale temperature associated genetic structure between inshore and offshore populations of sea scallop (Placopecten magellanicus)
In the northwest Atlantic Ocean, sea scallop (Placopecten magellanicus) have been characterized by a latitudinal genetic cline with a breakpoint between northern and southern genetic clusters occurring at ~45°N along eastern Nova Scotia, Canada. Using 96 diagnostic single nucleotide polymorphisms (SNPs) capable of discriminating between northern and southern clusters, we examined fine-scale genetic structure of scallops among 27 sample locations, spanning the largest geographic range evaluated in this species to date (~37-51°N). Here, we confirmed previous observations of northern and southern groups, but we show that the boundary between northern and southern clusters is not a discrete latitudinal break. Instead, at latitudes near the previously described boundary, we found unexpected patterns of fine-scale genetic structure occurring between inshore and offshore sites. Scallops from offshore sites, including St. Pierre Bank and the eastern Scotian Shelf, clustered with southern stocks, whereas inshore sites at similar latitudes clustered with northern stocks. Our analyses revealed significant genetic divergence across small spatial scales (i.e., 129 to 221 km distances), and that spatial structure over large and fine scales was strongly associated with temperature during seasonal periods of thermal minima. Clear temperature differences between inshore and offshore locations may explain the fine-scale structuring observed, such as why southern lineages of scallop occur at higher latitudes in deeper, warmer offshore waters. Our study supports growing evidence that fine-scale population structure in marine species is common, often environmentally associated, and that consideration of environmental and genomic data can significantly enhance the identification of marine diversity and management units.
Data from: Fine-scale spatial covariation between infection prevalence and susceptibility in a natural population
The prevalence of infection varies dramatically on a fine spatial scale. Many evolutionary hypotheses are founded on the assumption that this variation is due to host genetics, such that sites with a high frequency of alleles conferring susceptibility are associated with higher infection prevalence. This assumption is largely untested and may be compromised at finer spatial scales where gene flow between sites is high. We put this assumption to the test in a natural snail-trematode interaction in which host susceptibility is known to have a strong genetic basis. A decade of field sampling revealed substantial spatial variation in infection prevalence between 13 sites around a small lake. Laboratory assays replicated over 3 years demonstrate striking variation in host susceptibility among sites in spite of high levels of gene flow between sites. We find that mean susceptibility can explain more than one-third of the observed variation in mean infection prevalence among sites. We estimate that variation in susceptibility and exposure together can explain the majority of variation in prevalence. Overall, our findings in this natural host-parasite system argue that spatial variation in infection prevalence covaries strongly with variation in the distribution of genetically based susceptibility, even at a fine spatial scale.
Data from: Landscape determinants of fine-scale genetic structure of a small rodent in a heterogeneous landscape (Hluhluwe-iMfolozi Park, South Africa)
Small mammals provide ecosystem services, acting, for example, as pollinators and seed dispersers. In addition, they are also disease reservoirs that can be detrimental to human health and they can also act as crop pests. Knowledge of their dispersal preferences is therefore useful for population management and landscape planning. Genetic data were used alongside landscape data to examine the influence of the landscape on the demographic connectedness of the Natal multimammate mouse (Mastomys natalensis) and to identify landscape characteristics that influence the genetic structure of this species across a spatially and temporally varying environment. The most significant landscape features shaping gene flow were aspect, vegetation cover, topographic complexity (TC) and rivers, with western facing slopes, topographic complexity and rivers restricting gene flow. In general, thicket vegetation was correlated with increased gene flow. Identifying features of the landscape that facilitate movement/dispersal in M. natalensis potentially has application for other small mammals in similar ecosystems. As the primary reservoir host of the zoonotic Lassa virus, a landscape genetics approach may have applications in determining areas of high disease risk to humans. Identifying these landscape features may also be important in crop management due to damage by rodent pests.
Data from: Fine-scale kin recognition in the absence of social familiarity in the Siberian jay, a monogamous bird species
Kin recognition is a critical element to kin cooperation, and in vertebrates, it is primarily based on associative learning. Recognition of socially unfamiliar kin occurs rarely, and it is reported only in vertebrate species where promiscuity prevents recognition of first-order relatives. However, it is unknown whether the recognition of socially unfamiliar kin can evolve in monogamous species. Here, we investigate whether genetic relatedness modulates aggression among group members in Siberian jays (Perisoreus infaustus). This bird species is genetically and socially monogamous and lives in groups that are formed through the retention of offspring beyond independence, and the immigration of socially unfamiliar nonbreeders. Observations on feeders showed that genetic relatedness modulated aggression of breeders towards immigrants in a graded manner, in that they chased most intensely the immigrant group members that were genetically the least related. However, cross-fostering experiments showed that breeders were equally tolerant towards their own and cross-fostered young swapped as nestlings. Thus, breeders seem to use different mechanisms to recognize socially unfamiliar individuals and own offspring. As Siberian jays show a high degree of nepotism during foraging and predator encounters, inclusive fitness benefits may play a role for the evolution of fine-scale kin recognition. More generally, our results suggest that fine-graded kin recognition can evolve independently of social familiarity, highlighting the evolutionary importance of kin recognition for social species.
Data from: Nest suitability, fine-scale population structure and male-mediated dispersal of a solitary ground nesting bee in an urban landscape
Bees are the primary pollinators of flowering plants in almost all ecosystems. Worldwide declines in bee populations have raised awareness about the importance of their ecological role in maintaining ecosystem functioning. The naturally strong philopatric behavior that some bee species show can be detrimental to population viability through increased probability of inbreeding. Furthermore, bee populations found in human-altered landscapes, such as urban areas, can experience lower levels of gene flow and effective population sizes, increasing potential for inbreeding depression in wild bee populations. In this study, we investigated the fine-scale population structure of the solitary bee Colletes inaequalis in an urbanized landscape. First, we developed a predictive spatial model to detect suitable nesting habitat for this ground nesting bee and to inform our field search for nests. We genotyped 18 microsatellites in 548 female individuals collected from nest aggregations throughout the study area. Genetic relatedness estimates revealed that genetic similarity among individuals was slightly greater within nest aggregations than among randomly chosen individuals. However, genetic structure among nest aggregations was low (Nei's GST = 0.011). Reconstruction of parental genotypes revealed greater genetic relatedness among females than among males within nest aggregations, suggesting male-mediated dispersal as a potentially important mechanism of population connectivity and inbreeding avoidance. Size of nesting patch was positively correlated with effective population size, but not with other estimators of genetic diversity. We detected a positive trend between geographic distance and genetic differentiation between nest aggregations. Our landscape genetic models suggest that increased urbanization is likely associated with higher levels of inbreeding. Overall, these findings emphasize the importance of density and distribution of suitable nesting patches for enhancing bee population abundance and connectivity in human dominated habitats and highlights the critical contribution of landscape genetic studies for enhanced conservation and management of native pollinators.
Data from: Fine-scale genetic population structure in a mobile marine mammal: inshore bottlenose dolphins in Moreton Bay, Australia
Highly mobile marine species in areas with no obvious geographical barriers are expected to show low levels of genetic differentiation. However, small-scale variation in habitat may lead to resource polymorphisms and drive local differentiation by adaptive divergence. Using nuclear microsatellite genotyping at 20 loci, and mitochondrial control region sequencing, we investigated fine-scale population structuring of inshore bottlenose dolphins (Tursiops aduncus) inhabiting a range of habitats in and around Moreton Bay, Australia. Bayesian structure analysis identified two genetic clusters within Moreton Bay, with evidence of admixture between them (F_ST = 0.05, P = 0.001). There was only weak isolation by distance but one cluster of dolphins was more likely to be found in shallow southern areas and the other in the deeper waters of the central northern bay. In further analysis removing admixed individuals, southern dolphins appeared genetically restricted with lower levels of variation (AR = 3.252, π = 0.003) and high mean relatedness (r = 0.239) between individuals. In contrast, northern dolphins were more diverse (AR = 4.850, π = 0.009) and were mixing with a group of dolphins outside the bay (microsatellite-based STRUCTURE analysis), which appears to have historically been distinct from the bay dolphins (mtDNA Φ_ST = 0.272, P < 0.001). This study demonstrates the ability of genetic techniques to expose fine-scale patterns of population structure and explore their origins and mechanisms. A complex variety of inter-related factors including local habitat variation, differential resource use, social behaviour and learning, and anthropogenic disturbances are likely to have played a role in driving fine-scale population structure amongst bottlenose dolphins in Moreton Bay.
Data from: Male clasping ability, female polymorphism and sexual conflict: fine-scale elytral morphology as a sexually antagonistic adaptation in female diving beetles
During sexual conflict, males and females are expected to evolve traits and behaviours with a sexually antagonistic function. Recently, sexually antagonistic coevolution was proposed to occur between male and female diving beetles (Dytiscidae). Male diving beetles possess numerous suction cups on their forelegs whereas females commonly have rough structures on their elytra. These rough structures have been suggested to obstruct adhesion from male suction cups during mating attempts. However, some diving beetle species are dimorphic, where one female morph has a rough elytra and the other has a smooth elytra. Here, we used biomechanics to study the adhesive performance of male suction cups on the female morphs in two diving beetle species: Dytiscus lapponicus and Graphoderus zonatus. We compared adhesion on the rough and the smooth female morphs to infer the function of the rough elytral modifications. We found that the adhesive force on the rough structures was much lower than on other surfaces. These findings support the suggestion of sexual conflict in diving beetles and a sexually antagonistic function of the rough female structures. In addition, males differed in their adhesive capacity on different female surfaces, indicating a male trade-off between adhering to smooth and rough female morphs.
Data from: Fine-scale belowground species associations in temperate grassland
Evaluating how belowground processes contribute to plant community dynamics is hampered by limited information on the spatial structure of root communities at the scale that plants interact belowground. In this study, roots were mapped to the nearest one mm and molecularly identified by species on vertical (0–15 cm deep) surfaces of soil blocks excavated from dry and mesic grasslands in Yellowstone National Park (YNP) to examine the spatial relationships among species at the scale that roots interact. Our results indicated that average interspecific root – root distances for the majority of species were within a distance (3 mm) that roots have been shown to compete for resources. Most species placed their roots at random, although low root numbers for many species probably led to overestimating the occurrence of random patterns. According to theory, we expected that most of the remaining species would segregate their root systems to avoid competition. Instead we found that more species aggregated than segregated from others. Based on previous investigations, we hypothesize that species aggregate to increase uptake of water, nitrogen and/or phosphorus made available by neighbouring roots, or as a consequence of a reduction in the pathogenicity of soil biota growing in multispecies mixtures. Our results indicate that YNP grassland root communities are organized as closely interdigitating networks of species that potentially can support strong interactions among many species combinations. Future root research should address the prevalence and functional consequences of species aggregation across plant communities.
Data from: Fine-scale genetic structure and helping decisions in a cooperatively breeding bird
In animal societies, characteristic demographic and dispersal patterns may lead to genetic structuring of populations, generating the potential for kin selection to operate. However, even in genetically structured populations, social interactions may still require kin discrimination for cooperative behaviour to be directed towards relatives. Here, we use molecular genetics and long-term field data to investigate genetic structure in an adult population of long-tailed tits Aegithalos caudatus, a cooperative breeder in which helping occurs within extended kin networks, and relate this to patterns of helping with respect to kinship. Spatial autocorrelation analyses reveal fine-scale genetic structure within our population, such that related adults of either sex are spatially clustered following natal dispersal, with relatedness among nearby males higher than that among nearby females, as predicted by observations of male-biased philopatry. This kin structure creates opportunities for failed breeders to gain indirect fitness benefits via redirected helping, but crucially, most close neighbours of failed breeders are unrelated and help is directed towards relatives more often than expected by indiscriminate helping. These findings are consistent with the effective kin discrimination mechanism known to exist in long-tailed tits, and support models identifying kin selection as the driver of cooperation.
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: Polygamy and an absence of fine-scale structure in Dendroctonus ponderosae (Hopk.) (Coleoptera: Curcilionidae) confirmed using molecular markers
An understanding of mating systems and fine-scale spatial genetic structure is required to effectively manage forest pest species such as Dendroctonus ponderosae (mountain pine beetle). Here we used genome-wide single-nucleotide polymorphisms to assess the fine-scale genetic structure and mating system of D. ponderosae collected from a single stand in Alberta, Canada. Fine-scale spatial genetic structure was absent within the stand and the majority of genetic variation was best explained at the individual level. Relatedness estimates support previous reports of pre-emergence mating. Parentage assignment tests indicate that a polygamous mating system better explains the relationships among individuals within a gallery than the previously reported female monogamous/male polygynous system. Furthermore, there is some evidence to suggest that females may exploit the galleries of other females, at least under epidemic conditions. Our results suggest that current management models are likely to be effective across large geographic areas based on the absence of fine-scale genetic structure.
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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.