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Data from: Butterfly abundance declines over 20 years of systematic monitoring in Ohio, USA
Severe insect declines make headlines, but they are rarely based on systematic monitoring outside of Europe. We estimate the rate of change in total butterfly abundance and the population trends for 81 species using 21 years of systematic monitoring in Ohio, USA. Total abundance is declining at 2% per year, resulting in a cumulative 33% reduction in butterfly abundance. Three times as many species have negative population trends compared to positive trends. The rate of total decline and the proportion of species in decline mirror those documented in three comparable long-term European monitoring programs. Multiple environmental changes such as climate change, habitat degradation, and agricultural practices may contribute to these declines in Ohio and shift the makeup of the butterfly community by benefiting some species over others. Our analysis of life-history traits associated with population trends shows an impact of climate change, as species with northern distributions and fewer annual generations declined more rapidly. However, even common and invasive species associated with human-dominated landscapes are declining, suggesting widespread environmental causes for these trends. Declines in common species, although they may not be close to extinction, will have an outsized impact on the ecosystem services provided by insects. These results from the most extensive, systematic insect monitoring programs in North America demonstrate an ongoing defaunation in butterflies that on an annual scale might be imperceptible, but cumulatively has reduced butterfly numbers by a third over 20 years.
Data from: Persistent near real-time passive acoustic monitoring for baleen whales from a moored buoy: system description and evaluation
1. Managing interactions between human activities and marine mammals often relies on an understanding of the real-time distribution or occurrence of animals. Visual surveys typically cannot provide persistent monitoring because of expense and weather limitations, and while passive acoustic recorders can monitor continuously, the data they collect are often not accessible until the recorder is recovered. 2. We have developed a moored passive acoustic monitoring system that provides near real-time occurrence estimates for humpback, sei, fin, and North Atlantic right whales from a single site for a year, and makes those occurrence estimates available via a publicly accessible website, email and text messages, a smartphone/tablet app, and the U.S. Coast Guard's maritime domain awareness software. We evaluated this system using a buoy deployed off the coast of Massachusetts during 2015-2016 and redeployed again during 2016-2017. Near real-time estimates of whale occurrence were compared to simultaneously collected archived audio as well as whale sightings collected near the buoy by aerial surveys. 3. False detection rates for right, humpback, and sei whales were 0% and nearly 0% for fin whales, while missed detection rates at daily time scales were modest (12-42%). Missed detections were significantly associated with low calling rates for all species. We observed strong associations between right whale visual sightings and near real-time acoustic detections over a monitoring range of 30-40 km and temporal scales of 24-48 hours, suggesting that silent animals were not especially problematic for estimating occurrence of right whales in the study area. There was no association between acoustic detections and visual sightings of humpback whales. 4. The moored buoy has been used to reduce the risk of ship strikes for right whales in a U.S. Coast Guard gunnery range, and can be applied to other mitigation applications.
Data from: Challenges of NGS in conservation management: insights from long-term monitoring of corridor effects on the genetic diversity of mouse lemurs in a fragmented landscape
Long-term genetic monitoring of populations is essential for efforts aimed at preserving genetic diversity of endangered species. Here, we employ a framework of long-term genetic monitoring to evaluate the effects of fragmentation and the effectiveness of the establishment of corridors in restoring population connectivity and genetic diversity of mouse lemurs Micocebus ganzhorni. To this end, we supplement estimates of neutral genetic diversity with the assessment of adaptive genetic variability of the MHC. In addition, we address the challenges of long-term genetic monitoring of functional diversity by comparing the genotyping performance and estimates of MHC variability generated by SSCP/Sanger-sequencing with those obtained by high throughput sequencing (NGS, Illumina), an issue that is particularly relevant when previous work serves as a baseline for planning management strategies that aim to ensure the viability of a population. We report that SSCP greatly underestimates individual diversity and that discrepancies in estimates of MHC diversity attributable to the comparisons of traditional and NGS genotyping techniques can influence the conclusions drawn from conservation management scenarios. Evidence of migration among fragments in Mandena suggests that mouse lemurs are robust to the process of fragmentation and that the effect of corridors is masked by ongoing gene flow. Nonetheless, results based on a larger number of shared private alleles at neutral loci between fragment pairs found after the establishment of corridors in Mandena suggest that gene flow is augmented as a result of enhanced connectivity. Our data points out that despite low effective population size, M. ganzhorni maintains high individual heterozygosity at neutral loci and at MHC II DRB gene and that selection plays a predominant role in maintaining MHC diversity. These findings highlight the importance of long-term genetic monitoring in order to disentangle between the processes of drift and selection maintaining adaptive genetic diversity in small populations.
Data from: AudioMoth: evaluation of a smart open acoustic device for monitoring biodiversity and the environment
1. The cost, usability and power efficiency of available wildlife monitoring equipment currently inhibits full ground-level coverage of many natural systems. Developments over the last decade in technology, open science, and the sharing economy promise to bring global access to more versatile and more affordable monitoring tools, to improve coverage for conservation researchers and managers. 2. Here we describe the development and proof-of-concept of a low-cost, small-sized and low-energy acoustic detector: 'AudioMoth'. The device is open-source and programmable, with diverse applications for recording animal calls or human activity at sample rates of up to 384kHz. We briefly outline two ongoing real-world case studies of large-scale, long-term monitoring for biodiversity and exploitation of natural resources. These studies demonstrate the potential for AudioMoth to enable a substantial shift away from passive continuous recording by individual devices, towards smart detection by networks of devices flooding large and inaccessible ecosystems. 3. The case studies demonstrate one of the smart capabilities of AudioMoth, to trigger event logging on the basis of classification algorithms that identify specific acoustic events. An algorithm to trigger recordings of the New Forest cicada (Cicadetta montana) demonstrates the potential for AudioMoth to vastly improve the spatial and temporal coverage of surveys for the presence of cryptic animals. An algorithm for logging gunshot events has potential to identify a shotgun blast in tropical rainforest at distances of up to 500 m, extending to 1km with continuous recording. 4. AudioMoth is more energy efficient than currently available passive acoustic monitoring (PAM) devices, giving it considerably greater portability and longevity in the field with smaller batteries. At a build cost of ~US$43 per unit, AudioMoth has potential for varied applications in large-scale, long-term acoustic surveys. With continuing developments in smart, energy-efficient algorithms and diminishing component costs, we are approaching the milestone of local communities being able to afford to remotely monitor their own natural resources.
Data from: Monitoring the effective population size of a brown bear (Ursus arctos) population using new single-sample approaches
The effective population size (Ne) could be the ideal parameter for monitoring populations of conservation concern as it conveniently summarizes both the evolutionary potential of the population and its sensitivity to genetic stochasticity. However, tracing its change through time is difficult in natural populations. We applied four new methods for estimating Ne from a single sample of genotypes to trace temporal change in Ne for bears in the Northern Dinaric Mountains. We genotyped 510 bears using 20 microsatellite loci, and determined their age. The samples were organized into cohorts with regard to the year when the animals were born and yearly samples with age categories for every year when they were alive. We used the Estimator by Parentage Assignment (EPA) to directly estimate both Ne and generation interval for each yearly sample. For cohorts, we estimated the effective number of breeders (Nb) using Linkage Disequilibrium, Sibship Assignment and Approximate Bayesian Computation methods, and extrapolated these estimates to Ne using the generation interval. The Ne estimate by EPA is 276 (183-350 95% CI), meeting the inbreeding-avoidance criterion of Ne > 50 but short of the long-term minimum viable population goal of Ne > 500. The results obtained by the other methods are highly consistent with this result, and all indicate a rapid increase in Ne probably in the late 1990s and early 2000s. The new single-sample approaches to estimation of Ne provide efficient means for including Ne in monitoring frameworks, and will be of great importance for future management and conservation.
Data from: Genetic monitoring and complex population dynamics: insights from a 12-year study of the Rio Grande silvery minnow
The endangered Rio Grande silvery minnow persists as a remnant population in a highly fragmented and regulated arid-land river system. The species is subject to dramatic fluctuations in density. Since 2003, the wild population has been supplemented by hatchery-reared fish. We report on a 12-year (1999 – 2010) monitoring study of genetic diversity and effective population size (Ne) of wild and hatchery stocks. Our goals were to evaluate how genetic metrics responded to changes in wild fish density and whether they corresponded to the number and levels of diversity of hatchery-reared repatriates. Genetic diversity and all measures of Ne in the wild population did not correlate with wild fish density until hatchery supplementation began in earnest. Estimates of variance and inbreeding effective size were not correlated. Our results suggest source-sink dynamics where captive stocks form a genetically diverse source and the wild population behaves as a sink. Nevertheless, overall genetic diversity of silvery minnow has been maintained over the last decade and we attribute this to a well designed and executed propagation management plan. When multiple factors like environmental fluctuation and hatchery supplementation act simultaneously on a population, interpretation of genetic monitoring data may be equally complex and require considerable ecological data.
Data from: The roles of joint tissues and jaw muscles in palatal biomechanics of the Savannah monitor (Varanus exanthematicus) and their significance for cranial kinesis
Many vertebrates exhibit cranial kinesis, or movement between bones of the skull other than at the jaw joint. Many kinetic species possess a particular suite of features to accomplish this movement, including flexible cranial joints and protractor musculature. Whereas the skeletal anatomy of these kinetic systems is well understood, how these joints are biomechanically loaded, how different soft tissues affect joint loading and kinetic capacity, and how the protractor musculature loads the skull remain poorly understood. Here we developed a Finite Element Model of the savannah monitor, Varanus exanthematicus, a modestly kinetic lizard, to better elucidate the roles of soft tissue in mobile joints and protractor musculature on cranial loading. We described the 3D resultants of jaw muscles and histology of palatobasal, otic and jaw joints. We tested the effects of joint tissue types, bite point, and muscle loads to evaluate the biomechanical role of muscles have on the palate and braincase. We found the jaw muscles have significant mediolateral components and resultants that can impart stability across palatocranial joints. We found articular tissues affect the magnitude of strains experienced across the palatobasal and otic joints. We found that without protractor muscle loading, the palate, quadrate and braincase experience higher strains suggesting this muscle helps insulate the braincase and palatoquadrate from high loads. Finally, we found the cross-sectional properties of the bones of Varanus exanthematicus is well suited for performing under torsional loads. These findings suggest that torsion may be a significant driver in the evolution of cranial kinesis in lepidosaurs.
Data from: Systematic site selection for multispecies monitoring networks
The importance of monitoring biodiversity to detect and understand changes throughout time and to inform management is increasingly recognized. Monitoring schemes should be globally unified, spatially integrated across scales, long term, and cost-efficient. We propose a framework to design optimized multispecies-targeted monitoring networks over large areas. The method builds upon previous developments on systematic conservation planning in terms of optimizing resource allocation in space, and comprises seven steps: (a) determine which questions will be addressed, (b) define species to be monitored, (c) compile occurrence data for all defined species, (d) predict the overall distribution of each species, (e) collect relevant environmental data and identify homogeneous strata, (f) set targets for the minimum number of monitoring sites per species and/or stratum and (g) identify optimal monitoring sites. We tested whether the monitoring networks designed with our framework have increased performance when compared to networks obtained with simple-random or stratified-random sampling by using a set of different indicators. To that end, we designed monitoring networks using optimized and non-optimized sampling schemes, applied to a case study in Portugal, where the goal was to design a monitoring network for amphibians and reptiles, to complement the one currently established in Spain. Results allowed us to conclude that monitoring networks designed with our method tend to outperform the non-optimized ones, in terms of higher species diversity (i.e. higher number of species and equity across monitoring sites), higher representation of environmental strata, and particularly higher coverage of rare species, with less survey effort. Synthesis and applications. We developed a framework to allocate monitoring sites for multiple species at broad scales using predictive models and optimization algorithms currently applied in systematic conservation planning. This framework presents field survey cost-efficiency advantages when compared to other standard sampling designs and can significantly contribute to improving the design of monitoring schemes. Thus, we recommend its application to design new multispecies monitoring networks or to extend existing ones.
Data from: Environmental monitoring through protist NGS metabarcoding: assessing the impact of fish farming on benthic foraminifera communities
The measurement of species diversity represents a powerful tool for assessing the impacts of human activities on marine ecosystems. Traditionally, the impact of fish farming on the coastal environment is evaluated by monitoring the dynamics of macrobenthic infaunal populations. However, taxonomic sorting and morphology-based identification of the macrobenthos demands highly trained specialists and is extremely time-consuming and costly, what makes it unsuitable for large-scale biomonitoring efforts involving numerous samples. Here, we propose to alleviate this laborious task by developing protist metabarcoding tools based on next-generation sequencing (NGS) of environmental DNA and RNA extracted from sediment samples. In this study, we analysed the response of benthic foraminiferal communities to the variation of environmental gradients associated with salmon farms in Scotland. We investigated the foraminiferal diversity based on ribosomal minibarcode sequences generated by the Illumina NGS technology. We compared the molecular data with morphospecies counts and with environmental gradients, including distance to cages and Redox used as a proxy for sediment oxygenation. Our study revealed high variations between foraminiferal communities collected in the vicinity of fish farms and at distant locations. We found evidence for alpha diversity loss in strongly impacted sites, especially visible in the RNA data. We also detected some candidate bioindicator foraminiferal species. Based on this proof-of-concept study, we conclude that NGS metabarcoding using foraminifera and other protists has considerable potential to become a new tool for surveying the impact of aquaculture and other industrial activities in the marine environment.
Data from: DIY meteorology: use of citizen science to monitor snow dynamics in a data-sparse city
Cities are under pressure to operate their services effectively and project costs of operations across various timeframes. In high-latitude and high-altitude urban centers, snow management is one of the larger unknowns and has both operational and budgetary limitations. Snowfall and snow depth observations within urban environments are important to plan snow clearing and prepare for the effects of spring runoff on cities' drainage systems. In-house research functions are expensive, but one way to overcome that expense and still produce effective data is through citizen science. In this paper, we examine the potential to use citizen science for snowfall data collection in urban environments. A group of volunteers measured daily snowfall and snow depth at an urban site in Saskatoon (Canada) during two winters. Reliability was assessed with a statistical consistency analysis and a comparison with other data sets collected around Saskatoon. We found that citizen-science-derived data were more reliable and relevant for many urban management stakeholders. Feedback from the participants demonstrated reflexivity about social learning and a renewed sense of community built around generating reliable and useful data. We conclude that citizen science holds great potential to improve data provision for effective and sustainable city planning and greater social learning benefits overall.
Data from: Pollination on the dark side: acoustic monitoring reveals impacts of a total solar eclipse on flight behavior and activity schedule of foraging bees
The total solar eclipse of 21 August 2017 traversed ~5000 km from coast to coast of North America. In its 90-min span, sunlight dropped by three orders of magnitude and temperature by 10–15°C. To investigate impacts of these changes on bee (Hymenoptera: Apoidea) pollinators, we monitored their flights acoustically in natural habitats of Pacific Coast, Rocky Mountain, and Midwest regions. Temperature changes during the eclipse had little impact on bee activity. Most of the explained variation (R2) in buzzing rate was attributable to changes in light intensity. Bees ceased flying during complete darkness at totality, but flight activity was unaffected by dim light in partial phases before and after totality. Flights of bees during partial phases of the eclipse lasted longer than flights made under full sun, showing that behavioral plasticity matched bee flight properties to changes in light intensity during the eclipse. Efforts of citizen scientists, including hundreds of school children, contributed to the scope and educational impact of this study.
Data from: Discovery of 20,000 RAD–SNPs and development of a 52-SNP array for monitoring river otters
Many North American river otter (Lontra canadensis) populations are threatened or recovering but are difficult to study because they occur at low densities, it is difficult to visually identify individuals, and they inhabit aquatic environments that accelerate degradation of biological samples. Single nucleotide polymorphisms (SNPs) can improve our ability to monitor demographic and genetic parameters of difficult to study species. We used restriction site associated DNA (RAD) sequencing to discover 20,772 SNPs present in Montana, USA, river otter populations, including 14,512 loci that were also variable in at least one other population range-wide. After applying careful filtering criteria meant to minimize ascertainment bias and identify high quality, highly heterozygous (H o = 0.2–0.50) SNPs, we developed and tested 52 independent SNP qPCR genotyping assays, including 41 that performed well with diluted DNA. The 41 loci provided high power for population assignment tests with only 1 misassignment (1.6 %) between closely neighboring populations. Our SNPs showed high power to differentiate individuals and assign them to population of origin, as well as strong concordance of genotypes from high and diluted concentrations of DNA, and between original RAD and the SNP qPCR array.
Data from: Long-term genetic monitoring reveals contrasting changes in the genetic composition of newly established populations of the intertidal snail Bembicium vittatum
Newly established populations are susceptible to founder events that reduce genetic variation. This may be counterbalanced by gene flow after populations become established or founders coming from genetically different populations. However, initial gains in genetic diversity may be short-lived if there is limited mixing between lineages and subsequent inbreeding or if one lineage sweeps to fixation through selection or genetic drift. Here, we report on the genetic changes taking place within two newly established populations of intertidal snail over a 15-year period (~ 10 generations). Each translocation was set up using multiple, genetically distinct source populations. Our data show that higher levels of variation in the translocated populations compared to the source populations were maintained over time for both nuclear (microsatellite) and mitochondrial genes. Small changes in allele and haplotype frequencies were observed in the source populations and in one of the translocated populations, but marked changes were evident in the other, where there was a dramatic shift towards the genetic make-up of one of the source populations. These genetic changes occurred despite relatively large numbers of founders (200- 374 adults) and no evidence of the population experiencing a severe reduction in effective population size. Our study shows that the genetic composition of newly established populations can vary greatly over time and that genetic outcomes can be highly variable, and significantly different to expectations, even when they are established using high numbers of individuals and involve source populations from the same geographic regions.
Data from: Random versus game trail-based camera trap placement strategy for monitoring terrestrial mammal communities
Camera trap surveys exclusively targeting features of the landscape that increase the probability of photographing one or several focal species are commonly used to draw inferences on the richness, composition and structure of entire mammal communities. However, these studies ignore expected biases in species detection arising from sampling only a limited set of potential habitat features. In this study, we test the influence of camera trap placement strategy on community-level inferences by carrying out two spatially and temporally concurrent surveys of medium to large terrestrial mammal species within Tanzania's Ruaha National Park, employing either strictly game trail-based or strictly random camera placements. We compared the richness, composition and structure of the two observed communities, and evaluated what makes a species significantly more likely to be caught at trail placements. Observed communities differed marginally in their richness and composition, although differences were more noticeable during the wet season and for low levels of sampling effort. Lognormal models provided the best fit to rank abundance distributions describing the structure of all observed communities, regardless of survey type or season. Despite this, carnivore species were more likely to be detected at trail placements relative to random ones during the dry season, as were larger bodied species during the wet season. Our findings suggest that, given adequate sampling effort (> 1400 camera trap nights), placement strategy is unlikely to affect inferences made at the community level. However, surveys should consider more carefully their choice of placement strategy when targeting specific taxonomic or trophic groups.
Data from: Repertoire-based individual acoustic monitoring of a migratory passerine bird with complex song as an efficient tool for tracking territorial dynamics and annual return rates
In field ecological and behavioural studies, it is often necessary to identify specific individuals. In birds, colour rings are frequently used to mark individuals; however, rings are often difficult to observe, especially in small species and dense habitats. Acoustic-based monitoring detecting individuals by their characteristic vocalization is a potentially suitable alternative, but this approach is challenging in species with complex songs. On the example of the Tree Pipit (Anthus trivialis), a small migratory passerine often singing in flight or from perches obscured by foliage, we demonstrate that acoustic monitoring based on the syllable repertoire can be very efficient tool for individual recognition. During a 3-year study, we obtained over 500 recordings from males from one study population (a number of them returning after winter). Males banded with colour rings were repeatedly recorded throughout the seasons, and syllable repertoires were determined from spectrograms for each recording. The repertoire of each unambiguously identified male was distinct and stable within as well as between seasons; and males with similar syllable repertoires differed in syntax. Based on the congruence between identification based solely on spectrogram assessment, and that based on observation of colour rings, we inferred that reliable identification of singing males (including non-ringed ones) was possible in the studied population from assessing a repertoire and song syntax of <5-min recording (containing 20–30 songs). The acoustic-based data: (i) increased the overall estimated number of territorial males at the study locality (from 49 ringed to 61), and improved the estimates of the period of their presence; (ii) revealed dynamic within-season changes in territory occupancy that would otherwise be missed; and (iii) allowed identification of returning birds (including non-ringed ones and those actively avoiding approaching humans). Our results suggest that some commonly used methods may substantially underestimate return rates of migratory bird species. Individual acoustic monitoring should be applicable on various bird species with complex song and stable repertoires, and may be particularly useful for those living in dense habitat or sensitive to handling.
Data from: Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding
To manage and conserve biodiversity, one must know what is being lost, where, and why, as well as which remedies are likely to be most effective. Metabarcoding technology can characterise the species compositions of mass samples of eukaryotes or of environmental DNA. Here, we validate metabarcoding by testing it against three high-quality standard data sets that were collected in Malaysia (tropical), China (subtropical) and the United Kingdom (temperate) and that comprised 55,813 arthropod and bird specimens identified to species level with the expenditure of 2,505 person-hours of taxonomic expertise. The metabarcode and standard data sets exhibit statistically correlated alpha- and beta-diversities, and the two data sets produce similar policy conclusions for two conservation applications: restoration ecology and systematic conservation planning. Compared with standard biodiversity data sets, metabarcoded samples are taxonomically more comprehensive, many times quicker to produce, less reliant on taxonomic expertise and auditable by third parties, which is essential for dispute resolution.
Data from: A high-resolution panorama camera system for monitoring colony-wide seabird nesting behaviour
1. Obtaining accurate and representative demographic metrics for animal populations is critical to many aspects of wildlife monitoring and management. However, at remote animal colonies, metrics derived from sequential counts or other continuous monitoring are often subject to logistical, weather and disturbance challenges.The development of remote camera technologies has assisted monitoring, but limitations in spatial and temporal resolution and sample sizes remain. 2. Here we describe the application of a robotic camera system (Gigapan) which takes a tiled sequence of photographs that are automatically stitched together to form high-resolution panoramas. We demonstrate the application of the Gigapan using data collected during field-testing at a shy albatross colony on Albatross Island in northwest Tasmania. 3. We took daily panoramas over five days to estimate mean incubation shift-duration, an indirect measure for foraging trip duration, in an existing study area. Similar numbers of occupied nests could be observed at a distance of ~100m in the Gigapan panoramas compared to ground-based counts (115 and 117 respectively). Of these, birds on 90% of nests visible in the panoramas could be unambiguously identified as marked or unmarked with a small daub of paint throughout the study period and thus a shift change reliably recorded. Gigapan-based shift duration was estimated using a novel instantaneous statistical method and were longer than estimates earlier in the egg brooding period, potentially revealing a new pattern in shift duration. 4. This example field application provides proof-of-concept and demonstration that the relatively low cost Gigapan system provides the spatial advantages of satellite or aerial photos with the detail and temporal replication of land-based camera systems. The Gigapan system can extend or enhance traditional data collection methods, particularly for simultaneous observations, at distance, of the behaviour of many surface nesting colonial seabirds..
Data from: Scaling of processes shaping the clonal dynamics and genetic mosaic of seagrasses through temporal genetic monitoring
Theoretically, the dynamics of clonal and genetic diversities of clonal plant populations are strongly influenced by the competition among clones and rate of seedling recruitment, but little empirical assessment has been made of such dynamics through temporal genetic surveys. We aimed to quantify 3 years of evolution in the clonal and genetic composition of Zostera marina meadows, comparing parameters describing clonal architecture and genetic diversity at nine microsatellite markers. Variations in clonal structure revealed a decrease in the evenness of ramet distribution among genets. This illustrates the increasing dominance of some clonal lineages (multilocus lineages, MLLs) in populations. Despite the persistence of these MLLs over time, genetic differentiation was much stronger in time than in space, at the local scale. Contrastingly with the short-term evolution of clonal architecture, the patterns of genetic structure and genetic diversity sensu stricto (that is, heterozygosity and allelic richness) were stable in time. These results suggest the coexistence of (i) a fine grained (at the scale of a 20 × 30 m quadrat) stable core of persistent genets originating from an initial seedling recruitment and developing spatial dominance through clonal elongation; and (ii) a local (at the scale of the meadow) pool of transient genets subjected to annual turnover. This simultaneous occurrence of initial and repeated recruitment strategies highlights the different spatial scales at which distinct evolutionary drivers and mating systems (clonal competition, clonal growth, propagule dispersal and so on) operate to shape the dynamics of populations and the evolution of polymorphism in space and time.
Data from: Genetic and population monitoring of two small black bear (Ursus americanus) populations in Alabama, within a regional context.
One of the major concerns in conservation today is the loss of genetic diversity which is a frequent consequence of population isolation and small population sizes. Fragmentation of populations and persecution of carnivores has posed a substantial threat to the persistence of free ranging carnivores in North America since the arrival of European settlers. Black bears have seen significant reductions in range size from their historic extent, which is most pronounced in the southeastern United States and even more starkly in Alabama where until recently bears were reduced to a single geographically isolated population in the Mobile River Basin. Recently a second population has naturally re-established itself in northeastern Alabama. We sought to determine size, genetic diversity and genetic connectivity for these two populations in relation to other regional populations. Both populations of black bears in Alabama had small population sizes and had moderate to low genetic diversity, but showed different levels of connectivity to surrounding populations of bears. The Mobile River Basin population had a small population size at only 86 individuals (76-124, 95% C.I.), the lowest genetic diversity of compared populations (richness =2.33, Ho and He =0.33), and showed near complete genetic isolation from surrounding populations across multiple tests. The newly recolonizing population in northeastern Alabama had a small but growing population doubling in 3 years (34 individuals 26-43, 95% C.I.), relatively moderate genetic diversity compared to surrounding populations (richness = 3.32, Ho =0.53, He =0.65), and showed a high level of genetic connectivity with surrounding populations.
Data from: Smart nest box: a tool and methodology for monitoring of cavity-dwelling animals
1.Camera recording and video analysis have emerged as a successful non-invasive method for collecting a wide range of biological data on many different taxa of animals. However, camera monitoring has rarely been applied to long term surveillance of cavity or box-nesting species and ordinary off-the-shelf cameras are employed. 2.We present methodology and data on the effectiveness of nest box monitoring using a camera system embedded in four "smart nest boxes" (SNBoxes). We applied the SNBoxes to eight Tengmalm's owl (Aegolius funereus) nests in the Czech Republic during a five-month period in 2014. Each SNBox consisted of a pair of cameras with infrared lighting, an event detector, a radio-frequency identification reader, auxiliary sensors, and a 60 Ah 12 V battery to power the whole system. All devices used were centrally managed by an embedded computer with specifically developed software. 3.Using four SNBoxes, we observed owl nesting continually during the incubation, nestling, and fledgling phases, in total 309 days, resulting in 3382 owl video events. Batteries were changed every 6.5 days. A memory of 4 GB was found sufficient to store monthly data. We identified 12 types of male and female parental activities and their timing, the diet composition and frequency of prey delivery, the manner of prey storage, the light intensity at the time of each parental activity, the temperature inside the clutch and outside the box, and the duration of nestling period of each young. We also produced a video on owl nesting for the general public. 4.The SNBox and related methodology show enormous potential as a non-invasive tool for monitoring animals using boxes or natural cavities. The main advantage of the SNBox is the possibility to study both nocturnal and diurnal animal species and great flexibility in use of the software and hardware for different tasks. As a result, the SNBox provides an opportunity for novel insights into the breeding, roosting, hibernating, and food storage activities of a wide range of cavity-living birds, mammals, and reptiles.
ScienceDex guides
Understand access before you commit
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.