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Data from: Genetic diversity, clonality and connectivity in the scleractinian coral Pocillopora damicornis: a multi-scale analysis in an insular, fragmented reef system
Clonality and genetic structure of the coral Pocillopora damicornis sensu lato were assessed using five microsatellites in 12 populations from four islands of the Society Archipelago (French Polynesia) sampled in June 2008. The 427 analysed specimens fell into 132 multilocus genotypes (MLGs), suggesting that asexual reproduction plays an important role in the maintenance of these populations. A haploweb analysis of ITS2 sequences of each MLG was consistent with all of them being conspecific. Genetic differentiation was detected both between and within islands, but when a single sample per MLG was included in the analyses, the populations turned out to be nearly panmictic. These observations provide further evidence of the marked variability in reproductive strategies and genetic structure of P. damicornis throughout its geographic range; comparison with results previously obtained for the congeneric species Pocillopora meandrina underlines the importance of life history traits in shaping the genetic structure of coral populations.
Data from: Scale-dependent strategies for coexistence of mesocarnivores in human-dominated landscapes
Identifying factors influencing the distribution of, and interactions within carnivore communities is important for understanding how they are affected by human activities. Species differ in their ability to adapt to humans depending on their degree of specialization in habitat use and feeding habits. This results in asymmetric changes in the ecology of co-occurring species that can influence their interactions. We investigated whether human infrastructures and free-ranging domestic dogs (a species typically associated with humans) influenced the co-occurrence and habitat use of mesocarnivores in a landscape of high human population density in Maharashtra, India. We used 40 camera trap locations during 233 trapping nights and used Bayesian co-occurrence occupancy models to investigate the habitat use and coexistence of species at different spatial scales. Additionally, we investigated their temporal overlap in space use. Indian foxes altered their habitat use both spatially and temporally in order to avoid free-ranging domestic dogs and other larger competitors. The use of human infrastructure by jackals and jungle cats was limited by the presence of dogs. Our results illustrate how habitat use of smaller carnivore species change both spatially and temporally in order to avoid larger competitors. We also show that the presence of species associated with humans mediates the influence of human infrastructures on the habitat use of mesocarnivores. We highlight the importance of acknowledging the potential impact of urbanization not only on single species, but also on the interactions within the community.
Data from: A degradation debt? large-scale shifts in community composition and loss of biomass in a tropical forest fragment after 40 years of isolation
Habitat loss and fragmentation are among the biggest threats to tropical biodiversity and associated ecosystem services. We examined forest dynamics in a mid-elevation 365-ha fragment in southern Costa Rica. The fragment was isolated in the mid-1970s and belongs to the Las Cruces Biological Station. A 2.25-ha permanent plot was established in the center of the old-growth forest (>400 m to nearest edge boundary) and all plants >5 cm DBH were censused, mapped, and identified to species in two surveys taken ~5–6 years apart (>3,000 stems/survey). Although the reserve maintains high species richness (>200 spp.), with many rare species represented by only one individual, we document a strong shift in composition with a two-fold increase in the number of soft-wooded pioneer individuals. The dominant late-successional understory tree species, Chrysochlamys glauca (Clusiaceae), and most species in the Lauraceae, declined dramatically. Turnover was high: 22.9% of stems in the first survey were lost, and 27.8% of stems in the second survey represented new recruits. Mean tree diameter decreased significantly and there was a 10% decrease in overall biomass. Such alteration has been documented previously but only in smaller fragments or within ~100 m of an edge boundary. Further penetration into this fragment was perhaps driven by a progressive invasion of disturbance-adapted species into the fragment's core over time; the loss of once-dominant late successional species could be a contributing factor. The pattern found is of particular concern given that such fragments represent a substantial portion of today's remaining tropical habitat; further studies in similar-sized fragments that have been isolated for similar prolonged periods are called for.
Data from: Defining conservation units with enhanced molecular tools to reveal fine scale structuring among Mediterranean green turtle rookeries
Understanding the connectivity among populations is a key research priority for species of conservation concern. Genetic tools are widely used for this purpose, but the results can be limited by the resolution of the genetic markers in relation to the species and geographic scale. Here, we investigate natal philopatry in green turtles (Chelonia mydas) from four rookeries within close geographic proximity (~ 200km) on the Mediterranean island of Cyprus. We genotyped hypervariable mtSTRs, a mtDNA control region sequence (CR) and 13 microsatellite loci to genetically characterise 479 green turtles using markers with different modes of inheritance. We demonstrated matrilineal stock structure for the first time among Mediterranean green turtle rookeries. This result contradicts previous regional assessments and supports a growing body of evidence that green turtles exhibit a more precise level of natal site fidelity than has commonly been recognised. The microsatellites detected weak male philopatry with significant stock structure among three of the six pairwise comparisons. The absence of Atlantic CR haplotypes and mtSTRs among these robust sample sizes reaffirm the reproductive isolation of Mediterranean green turtles and supports their status as a subpopulation. A power analysis effectively demonstrated that the mtDNA genetic markers previously employed to evaluate regional stock identity were confounded by an insufficient resolution considering the recent colonisation of this region. These findings improve the regional understanding of stock connectivity and illustrate the importance of using suitable genetic markers to define appropriate units for management and conservation.
Data from: Forest plant community as a driver of soil biodiversity: experimental evidence from collembolan assemblages through large-scale and long-term removal of oak canopy trees Quercus petraea
Plant–soil interactions are increasingly recognized to play a major role in terrestrial ecosystems functioning. However, few studies to date have focused on slow dynamic ecosystems such as forests. As they are vertically stratified by multiple vegetation strata, canopy tree removal by thinning operations could alter forest plant community through tree canopy opening. Very little is known about cascading effects on soil biodiversity. We conducted a large-scale, multi-site assessment of collembolan assemblage response to long-term canopy tree removal in sessile oak Quercus petraea temperate forests. A total of 33 experimental plots were studied covering a large gradient of canopy tree basal area, stand age and local abiotic contexts. Collembolan abundance strongly declined with canopy tree removal in early forest successional stage and this was mediated by negative effect of understory plant community composition changes, i.e. shift from moss and forb to tree seedling, fern, shrub and grass species. Negative effect of this composition shift on collembolan species richness was largely offset by positive effect of the increase in understory plant species richness. This gives support to both the plant mass-ratio and functional diversity hypotheses. Collembolan functional groups had contrasting response patterns, which were mediated by different ecological factors. Epedaphic (r-strategist) abundance and species richness increased with canopy tree removal in relation with the increase in understory plant species richness. In contrast, euedaphic (K-strategist) abundance and species richness declined with canopy tree removal in early forest successional stage in relation with changes in understory plant community composition and species richness, as well as microclimatic conditions. Overall, our study provides experimental evidence that forest plant community can be a strong driver of collembolan assemblages. It also emphasizes the role of trees as foundation species of forest ecosystems that can shape soil biodiversity through their regulation of understory plant community and ecosystem abiotic conditions.
Data from: Fine-scale behavioural adjustments of prey on a continuum of risk
In the wild, prey species often live in the vicinity of predators, rendering the ability to assess risk on a moment-to-moment basis crucial to survival. Visual cues are important as they allow prey to assess predator species, size, proximity and behaviour. However, few studies have explicitly examined prey's ability to assess risk based on predator behaviour and orientation. Using mosquitofish, Gambusia holbrooki, and their predator, jade perch, Scortum barcoo, under controlled conditions, we provide some of the first fine-scale characterisation of how prey adapt their behaviour according to their continuous assessment of risk based on both predator behaviour and angular distance to the predator's mouth. When these predators were inactive and posed less of an immediate threat, prey were often found within the attack cone of the predator showing reductions in speed and acceleration, characteristic of predator-inspection behaviour. However, when predators became active, prey swam faster with greater acceleration and were closer together within the attack cone of predators. Most importantly, this study provides evidence that prey do not adopt a uniform response to the presence of a predator. Instead, we demonstrate that prey are capable of rapidly and dynamically updating their assessment of risk and showing fine-scale adjustments to their behaviour.
Data from: Gynodioecy in structured populations: understanding fine-scale sex ratio variation in Beta vulgaris ssp. maritima
Natural selection, random processes, and gene flow are known to generate sex ratio variations among sexually polymorphic plant populations. In gynodioecious species, in which hermaphrodites and females coexist, the relative effect of these processes on the maintenance of sex polymorphism is still up for debate. The aim of this study was to document sex ratio and cytonuclear genetic variation at a very local scale in wind-pollinated gynodioecious Beta vulgaris ssp. maritima, and attempt to elucidate which processes explained the observed variation. The study sites were characterized by geographically distinct patches of individuals and appeared to be dynamic entities, with recurrent establishment of distinct haplotypes through independent founder events. Along with substantial variation in sex ratio and unexpectedly low gene flow within study sites, our results showed a high genetic differentiation among a mosaic of genetically distinct demes, with isolation by distance or abrupt genetic discontinuities taking place within a few tens of meters. Overall, random founder events with restricted gene flow could be primary determinants of sex structure, by promoting the clumping of sex-determining genes. Such high levels of sex structure provide a landscape for differential selection acting on sex-determining genes, which could modify the conditions of maintenance of gynodioecy in structured populations.
Data from: Identifying fishing grounds from vessel tracks: model-based inference for small scale fisheries
Recent technological developments facilitate the collection of location data from fishing vessels at an increasing rate. The development of low-cost electronic systems allows tracking of small-scale fishing vessels, a sector of fishing fleets typically characterised by many, relatively small vessels. The imminent production of large spatial datasets for this previously data-poor sector, creates a challenge in terms of data analysis. Several methods have been used to infer the spatial distribution of fishing activities from positional data. Here, we compare five approaches using either vessel speed, or speed and turning angle, to infer fishing activity in the Scottish inshore fleet. We assess the performance of each approach using observational records of true vessel activity. Although results are similar across methods, a trip-based Gaussian mixture model provides the best overall performance and highest computational efficiency for our use-case, allowing accurate estimation of the spatial distribution of active fishing (97% of true area captured). When vessel movement data can be validated, we recommend assessing the performance of different methods. These results illustrate the feasibility of designing a monitoring system to efficiently generate information on fishing grounds, fishing intensity, or monitoring of compliance to regulations at a nationwide scale in near-real time.
Data from: Short-term microbial effects of a large-scale mine-tailing storage facility collapse on the local natural environment
We investigated the impacts of the Mount Polley tailings impoundment failure on chemical, physical, and microbial properties of substrates within the affected watershed, comprised of 70 hectares of riparian wetlands and 40 km of stream and lake shore. We established a biomonitoring network in October of 2014, two months following the disturbance, and evaluated riparian and wetland substrates for microbial community composition and function via 16S and full metagenome sequencing. A total of 234 samples were collected from substrates at 3 depths and 1,650,752 sequences were recorded in a geodatabase framework. These data revealed a wealth of information regarding watershed-scale distribution of microbial community members, as well as community composition, structure, and response to disturbance. Substrates associated with the impact zone were distinct chemically as indicated by elevated pH, nitrate, and sulphate. The microbial community exhibited elevated metabolic capacity for selenate and sulfate reduction and an abundance of chemolithoautotrophs in the Thiobacillus thiophilus/T. denitrificans/T. thioparus clade that may contribute to nitrate attenuation within the affected watershed. The most impacted area (a 6km stream connecting two lakes) exhibited 30% lower microbial diversity relative to the remaining sites. The tailings impoundment failure at Mount Polley Mine has provided a unique opportunity to evaluate functional and compositional diversity soon after a major catastrophic disturbance to assess metabolic potential for ecosystem recovery.
Data from: Harnessing stratigraphic bias at the section scale: conodont diversity in the Homerian (Silurian) of the Midland Platform, England
Fossil abundance and diversity in geological successions are subject to bias arising from shifting depositional and diagenetic environments, resulting in variable rates of fossil accumulation and preservation. In simulations, this bias can be constrained based on sequence-stratigraphic architecture. Nonetheless, a practical quantitative method of incorporating the contribution of sequence-stratigraphic architecture in community palaeoecology and diversity analyses derived from individual successions is missing. As a model of faunal turnover affected by the stratigraphic bias, we use the 'Mulde event', a postulated mid-Silurian interval of elevated conodont turnover, which coincides with global eustatic sea-level changes and which has been based on regionally constrained observations. We test whether conodont turnover is highest at the boundary corresponding to the 'event' and post-'event' interval against the alternative that conodont turnover reflects habitat tracking and peaks at facies shifts. Based on the previously documented, parasequence-level stratigraphic framework of sections in the northern and central part of the Midland Platform, the relative controls of sequence-stratigraphic architecture, time and depositional environment over conodont distribution are evaluated using permutational multivariate analysis of variance. The depositional environment controls the largest part of variability in conodont assemblage composition, whereas the postulated 'Mulde event', or genuine temporal change in conodont diversity, cannot be detected. Depending on the binning of the stratigraphic succession, contrasting diversity and turnover patterns can be produced. The simple approach proposed here, emulating partitioning of β diversity into spatial and temporal components, may help to constrain the stratigraphic bias, even at the scale of an individual section.
Data from: Fine-scale genetic structure in a wild bird population: the role of limited dispersal and environmentally-based selection as causal factors
Individuals are typically not randomly distributed in space; consequently ecological and evolutionary theory depends heavily on understanding the spatial structure of populations. The central challenge of landscape genetics is therefore to link spatial heterogeneity of environments to population genetic structure. Here, we employ multivariate spatial analyses to identify environmentally induced genetic structures in a single breeding population of 1174 great tits Parus major genotyped at 4701 single-nucleotide polymorphism (SNP) loci. Despite the small spatial scale of the study relative to natal dispersal we found multiple axes of genetic structure. We built distance-based Moran's eigenvector maps to identify axes of pure spatial variation, which we used for spatial correction of regressions between SNPs and various external traits known to be related to fitness components (avian malaria infection risk, local density of conspecifics, oak tree density and altitude). We found clear evidence of fine-scale genetic structure, with 21, 7 and 9 significant SNPs respectively associated with infection risk by two species of avian malaria (Plasmodium circumflexum and P. relictum) and local conspecific density. Such fine-scale genetic structure relative to dispersal capabilities suggests ecological and evolutionary mechanisms maintain within-population genetic diversity in this population with the potential to drive micro-evolutionary change.
Data from: Studying long-term, large-scale grassland restoration outcomes to improve seeding methods and reveal knowledge gaps
Studies are increasingly investigating effects of large-scale management activities on grassland restoration outcomes. These studies are providing useful comparisons among currently used management strategies, but not the novel strategies needed to rapidly improve restoration efforts. Here we illustrate how managing restoration projects adaptively can allow promising management innovations to be identified and tested. We studied 327 Great Plains fields seeded after coal mining. We modelled plant responses to management strategies to identify the most effective previously used strategies for constraining weeds and establishing desired plants. Then, we used the model to predict responses to new strategies our analysis identified as potentially more effective. Where established, the weed crested wheatgrass (Agropyron cristatum L.) increased through time, indicating a need to manage establishment of this grass. Seeding particular grasses reduced annual weed cover, and because these grasses appeared to become similarly abundant whether sown at low or high rates, low rates could likely be safely used to reduce seeding costs. More importantly, lower than average grass seed rates increased cover of shrubs, the plants most difficult to restore to many grassland ecosystems. After identifying grass seed rates as a driver, we formulated model predictions for rates below the range managers typically use. These predictions require testing but indicated atypically low grass seed rates would further increase shrubs without hindering long-term grass stand development. Synthesis and applications. Designing management around empirically based predictions is a logical next step towards improving ecological restoration efforts. Our predictions are that reducing grass seed rates to atypically low levels will boost shrubs without compromising grasses. Because these predictions derive from the fitted model, they represent quantitative hypotheses based on current understanding of the system. Generating data needed to test and update these hypotheses will require monitoring responses to shifts in management, specifically shifts to lower grass seed rates. A paucity of data for confronting hypotheses has been a major sticking point hindering adaptive management of most natural resources, but this need not be the case with degraded grasslands, because ongoing restoration efforts around the globe are providing continuous opportunities to monitor and manage processes regulating grassland restoration outcomes.
Data from: Population genetic structure of the tree-hole tick Ixodes arboricola (Acari: Ixodidae) at different spatial scales
The endophilic tick Ixodes arboricola infests cavity-nesting birds, and its dispersal strongly depends on the movements of its host. Population genetic structure of I. arboricola was studied with seven polymorphic microsatellite markers. We collected 268 ticks from 76 nest boxes in four woodlots near Antwerp, Belgium. These nest boxes are mainly used by the principal hosts of I. arboricola, the great tit Parus major and the blue tit Cyanistes caeruleus. As these birds typically return to the same cavity for roosting or breeding, ticks within nest boxes were expected to be highly related, and tick populations were expected to be spatially structured among woodlots and among nest boxes within woodlots. In line with the expectations, genetic population structure was found among woodlots and among nest boxes within woodlots. Surprisingly, there was considerable genetic variation among ticks within nest boxes. This could be explained by continuous gene flow from ticks from nearby tree holes, yet this remains to be tested. A pairwise relatedness analysis conducted for all pairs of ticks within nest boxes showed that relatedness among larvae was much higher than among later instars, which suggests that larvae are the most important instar for tick dispersal. Overall, tick populations at the studied spatial scale are not as differentiated as predicted, which may influence the scale at which host–parasite evolution occurs.
FIGURE 27. Paraleptognathia tenuichela ZMH K40632 a. Maxillula, b. Maxilla, c. Mandibles, d. Labrum, e. Labium, f. Maxilliped. Scale bar 0.1 in A revision of the genus Paraleptognathia Kudinova-Pasternak, 1981 (Crustacea: Tanaidacea) and description of four new species
FIGURE 27. Paraleptognathia tenuichela ZMH K40632 a. Maxillula, b. Maxilla, c. Mandibles, d. Labrum, e. Labium, f. Maxilliped. Scale bar 0.1 mm.
FIGURE 25. Paraleptognathia fastuosa ZMH K40629 a. Cheliped. Scale bar 0.25 in A revision of the genus Paraleptognathia Kudinova-Pasternak, 1981 (Crustacea: Tanaidacea) and description of four new species
FIGURE 25. Paraleptognathia fastuosa ZMH K40629 a. Cheliped. Scale bar 0.25 mm. b. Maxillula, c. Epignath, d. Mandibles, e. Labrum, f. Labium, g. Maxilla, h. Maxilliped. Scale bar 0.1 mm.
FIGURE 23. Paraleptognathia benguela ZMH K40619 a. Maxillula, b. Epignath, c. Mandibles, d. Labrum, e. Labium, f. Maxilla, g. Maxilliped. Scale bar 0.1 in A revision of the genus Paraleptognathia Kudinova-Pasternak, 1981 (Crustacea: Tanaidacea) and description of four new species
FIGURE 23. Paraleptognathia benguela ZMH K40619 a. Maxillula, b. Epignath, c. Mandibles, d. Labrum, e. Labium, f. Maxilla, g. Maxilliped. Scale bar 0.1 mm.
FIGURE 19. Paraleptognathia weddellensis ZMH K40603 a. Maxillula, b. Epignath, c. Mandibles, d. Labrum, e. Labium, f. Maxilla, g. Maxilliped. Scale bar 0.1 in A revision of the genus Paraleptognathia Kudinova-Pasternak, 1981 (Crustacea: Tanaidacea) and description of four new species
FIGURE 19. Paraleptognathia weddellensis ZMH K40603 a. Maxillula, b. Epignath, c. Mandibles, d. Labrum, e. Labium, f. Maxilla, g. Maxilliped. Scale bar 0.1 mm.
FIGURE 10. Paraleptognathia gracilis ZMH K40589 a. Maxillula, b. Epignath, c. Mandibles, d. Labrum, e. Labium, f. Maxilla, g. Maxilliped. Scale bar 0.25 in A revision of the genus Paraleptognathia Kudinova-Pasternak, 1981 (Crustacea: Tanaidacea) and description of four new species
FIGURE 10. Paraleptognathia gracilis ZMH K40589 a. Maxillula, b. Epignath, c. Mandibles, d. Labrum, e. Labium, f. Maxilla, g. Maxilliped. Scale bar 0.25 mm for b and e for the rest scale bar 0.1 mm.
FIGURE 16. Paraleptognathia multiserrata ZMUC CRU 7430 a. Body dorsal view, b. Body lateral view. Scale bar 1 in A revision of the genus Paraleptognathia Kudinova-Pasternak, 1981 (Crustacea: Tanaidacea) and description of four new species
FIGURE 16. Paraleptognathia multiserrata ZMUC CRU 7430 a. Body dorsal view, b. Body lateral view. Scale bar 1mm. ZMB 27518 c. Antennule, d. Antenna, e. Pleopod, f. Uropod, g. Cheliped, h. Pereopod 1, i. Pereopod 2, j. Pereopod 3, k. Pereopod 4, l. Pereopod 5, m. Pereopod 6. Scale bar 0.25 mm.
FIGURE 7. Paraleptognathia brachiata ZMUC CRU 3738 a. Body dorsal view b. Body lateral view. Scale bar 1 in A revision of the genus Paraleptognathia Kudinova-Pasternak, 1981 (Crustacea: Tanaidacea) and description of four new species
FIGURE 7. Paraleptognathia brachiata ZMUC CRU 3738 a. Body dorsal view b. Body lateral view. Scale bar 1mm c. Antennule, d. Antennule juvenile male, e. Antenna, f. Pleopod, g. Uropod, h. cheliped, i. Pereopod 1, j. Pereopod 2, k. Pereopod 3, l. Pereopod 4, m. Pereopod 5, n. Pereopod 6. Scale bar 0.25 mm.
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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.