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7,742 results for “individuals”
Data from: An integrated assessment model of seabird population dynamics: can individual heterogeneity in susceptibility to fishing explain abundance trends in Crozet wandering albatross?
1. Seabirds have been incidentally caught in distant-water longline fleets operating in the Southern Ocean since at least the 1970s, and breeding numbers for some populations have shown marked trends of decline and recovery concomitant with longline fishing effort within their distributions. However, lacking is an understanding of how forms of among-individual heterogeneity may interact with fisheries bycatch and influence population dynamics. 2. We develop a model that uses comprehensive data on the spatial and temporal distributions of fishing effort and seabird foraging to estimate temporal overlaps, fishery catchability and consequent bycatch. We apply a population model that is structured by age, sex, life stage and spatially to Crozet Island wandering albatross and explore how heterogeneity in susceptibility to capture may have influenced the population's demography over time. 3. A model where some birds were assumed to be more susceptible to fisheries bycatch was able to successfully replicate the observed trend in breeding pairs. Considerably poorer fits were found without this assumption. Results suggested that the more susceptible birds may have been removed from the population by the 1990s. 4. The model was also able to highlight areas, times and fleets prone to increased bycatch. Knowledge of these factors should assist fisheries and conservation management bodies to quantify and reduce seabird bycatch through spatial management and fleet-specific mitigation efforts. 5. Synthesis and application. Many seabirds show complex life histories that make them highly susceptible to additional incidental mortality from fishing vessels. By applying a population model that integrates key aspects of seabird and fishery dynamics, we were able to explain the observed trends in the breeding population of Crozet wandering albatross and identify key areas and fleets where further mitigation may be required. In addition, the potential removal of a category of birds that shows increased susceptibility to capture has important implications for the conservation management of this population and other iconic species incidentally caught by large-scale commercial fisheries.
Data from: Encountering a bait is necessary but insufficient to explain individual variability in vulnerability to angling in two freshwater benthivorous fish in the wild
Fish personality traits, such as swimming activity, or personality related emergent behavioural properties, such as space use, should affect encounter rates between fish and fishing gear. Increased encounters should in turn drive vulnerability to capture by passively operated fishing gears. However, empirical evidence documenting a relationship between activity-based behaviours and vulnerability to capture in the wild is limited. Using whole-lake acoustic telemetry, we first documented significant repeatabilities over several months of a suite of encounter rate-associated behaviours (swimming distance, activity space size, time on baited feeding sites, switching frequency among baited feeding sites, distance to the lake bottom) in two recreationally important benthivorous cyprinid species, the common carp (Cyprinus carpio) and tench (Tinca tinca). We then experimentally targeted both species using standard angling gear on baited feeding sites. Individual fish regularly visited the angling sites, documenting that the fishes encountered the angling baits. Carp were readily hooked within the first few days, after which catchability dropped to low levels characteristic of tench from the onset of the angling experiment. When attempting to explain individual variation in vulnerability, we failed to document significant relationships among a suite of repeatable encounter-based behaviours and vulnerability to angling for both species. There was also no evidence for size selection or for energetically less conditioned carp to be more vulnerable than their counterparts. The data cumulatively suggest that fine-scale behaviours after encountering a bait (e.g., frequency of bait intake, or degree of spitting baited hooks following ingestion) are ultimately decisive for determining vulnerability to angling in both species. We therefore conclude that encountering a stationary bait in angling for benthivorous cyprinids is a necessary, but insufficient condition for determining the likelihood of capture of an individual fish. Hence, fishing-induced selection on encounter-based behaviours in recreational angling for benthivorous fish in the wild appears unlikely.
Data from: Practical low-coverage genomewide sequencing of hundreds of individually barcoded samples for population and evolutionary genomics in nonmodel species
Today most population genomic studies of nonmodel organisms either sequence a subset of the genome deeply in each individual or sequence pools of unlabelled individuals. With a step-by-step workflow, we illustrate how low-coverage whole-genome sequencing of hundreds of individually barcoded samples is now a practical alternative strategy for obtaining genomewide data on a population scale. We used a highly efficient protocol to generate high-quality libraries for ~6.5 USD from each of 876 Atlantic silversides (a teleost fish with a genome size ~730 Mb) that we sequenced to 1–4× genome coverage. In the absence of a reference genome, we developed a bioinformatic pipeline for mapping the genomic reads to a de novo assembled reference transcriptome. This provides an 'in silico' method for exome capture that avoids the complexities and expenses of using wet chemistry for target isolation. Using novel tools for analysis of low-coverage data, we extracted population allele frequencies, individual genotype likelihoods and polymorphism data for 2 504 335 SNPs across the exome for the 876 fish. To illustrate the use of the resulting data, we present a preliminary analysis of geographical patterns in the exome data and a comparison of complete mitochondrial genome sequences for each individual (constructed from the low-coverage data) that show population colonization patterns along the US east coast. With a total cost per sample of less than 50 USD (including sequencing) and ability to prepare 96 libraries in only 5 h, our approach adds a viable new option to the population genomics toolbox.
Data from: Individual diet differences in a molluscivore shorebird are associated with the size of body instruments for internal processing rather than for feeding
Especially in birds, it is widely found that the size of individual prey items follows the size of the instruments of prey capture, handling and processing, i.e. bill size. In fact, this is the natural history basis of major discoveries on adaptative evolution in the face of changing food resources. In some birds, e.g. the molluscivore shorebirds ingesting hard-shelled prey, most of the prey processing process takes place within the digestive tract. This study of a salvaged sample of actively feeding great knots Calidris tenuirostris accidentally drowned in fishing nets in northern China, is the first documentation of diet selection at the level of the individual in previously well-studied molluscivore shorebirds. Diet composition was not associated with the length of the bill, but with the mass of the muscular gizzard. Gizzard mass, which unlike bill length is a phenotypically flexible trait, enables great knots to adjust to changing food resources as an individual, i.e. instantly responding to the food on offer. For migratory species like great knots which rely on seasonal sequences of inter distant feeding areas offering prey with a variety of characteristics, the capacity to individually adjust appears a key adaptation.
Data from: Becoming pure: identifying generational classes of admixed individuals within lesser and greater scaup populations
Estimating the frequency of hybridization is important to understand its evolutionary consequences and its effects on conservation efforts. In this study, we examined the extent of hybridization in two sister species of ducks that hybridize. We used mitochondrial control region sequences and 3,589 double-digest restriction-associated DNA sequences (ddRADseq) to identify admixture between wild lesser scaup (Aythya affinis) and greater scaup (A. marila). Among 111 individuals, we found one introgressed mitochondrial DNA haplotype in lesser scaup and four in greater scaup. Likewise, based on the site-frequency spectrum from autosomal DNA, gene flow was asymmetrical, with higher rates from lesser into greater scaup. However, using ddRADseq nuclear DNA all individuals were assigned to their respective species with > 0.95 posterior assignment probability. To examine the power for detecting admixture, we simulated a breeding experiment in which empirical data were used to create F1 hybrids and nine generations (F2-F10) of backcrossing. F1 hybrids and F2, F3, and most F4 backcrosses were clearly distinguishable from pure individuals, but evidence of admixed histories was effectively lost after the fourth generation. Thus, we conclude that low interspecific assignment probabilities (0.011 – 0.043) for two lesser and nineteen greater scaup were consistent with admixed histories beyond the F3 generation. These results indicate that the propensity of these species to hybridize in the wild is low and largely asymmetric. When applied to species-specific cases, our approach offers powerful utility for examining concerns of hybridization in conservation efforts, especially for determining the generational time until admixed histories are effectively lost through backcrossing.
Data from: A comparison of individual-based genetic distance metrics for landscape genetics
A major aim of landscape genetics is to understand how landscapes resist gene flow and thereby influence population genetic structure. An empirical understanding of this process provides a wealth of information that can be used to guide conservation and management of species in fragmented landscapes, and also to predict how landscape change may affect population viability. Statistical approaches to infer the true model among competing alternatives are based on the strength of the relationship between pairwise genetic distances and landscape distances among sampled individuals in a population. A variety of methods have been devised to quantify individual genetic distances, but no study has yet compared their relative performance when used for model selection in landscape genetics. In this study, we used population genetic simulations to assess the accuracy of 16 individual-based genetic distance metrics under varying sample sizes and degree of population genetic structure. We found most metrics performed well when sample size and genetic structure was high. However, it was much more challenging to infer the true model when sample size and genetic structure was low. Under these conditions, we found genetic distance metrics based on principal components analysis were the most accurate (though several other metrics performed similarly), but only when they were derived from multiple principal component axes (the optimal number varied depending on the degree of population genetic structure). Our results provide guidance for which genetic distance metrics maximize model selection accuracy and thereby better inform conservation and management decisions based upon landscape genetic analysis.
Improving intra- and inter-annual GPP predictions by using individual-tree inventories and leaf growth dynamics
<p>Carbon sequestration is a key ecosystem service provided by forests. Inventory data based on individual trees are considered to be the most accurate method for estimating forest productivity. However, estimations of forest photosynthesis itself from inventory data remains understudied, particularly when considering the growth and development of individual trees under the background of global change. Here, we used the leaf growth process with phenology and non-structural carbohydrates (NSC) storage to revise an individual-tree based carbon model, FORCCHN. This model couples leaf development and biomass to quantify gross primary productivity (GPP) in the forests, where growth is decoupled from photosynthesis in daily step. The model was initialized with inventory-based forest data rather than the more widely used satellite-based data. We tested the model against measured aboveground woody biomass, growth of leaf biomass, daily gross ecosystem exchange (GEE), and yearly GEE at five representative forest sites in the Northern Hemisphere. We also compared the results from the original model and the revised model at five forest sites. Including leaf growth dynamics and inventory-based initialization improved the predicted performance (r2) of GPP by an average of 33%. Synthesis and applications. Our results suggest that the appropriate vegetation data sources (i.e. inventory or satellite selection) and the effective predictions of the growth process should be considered when developing future carbon cycle models and forest carbon estimation options. Applying and improving such carbon models to evaluate carbon sequestration is an important part of forest carbon sink management.</p>
Data from: Use of a microfluidic platform to uncover basic features of energy and environmental stress responses in individual cells of Bacillus subtilis
Bacteria use a variety of stress-sensing systems to sense and respond to diverse stressors and to ensure their survival under adverse conditions. The gram-positive bacterium Bacillus subtilis responds to energy stress (ATP depletion) and to environmental stressors using two distinct stress-sensing pathways that converge on the alternative sigma factor σB to provoke a general stress response. Past efforts to study the σB stress response in bulk culture and on agarose pads were unable to visualize the responses of individual cells under tightly controlled conditions for extended periods of time. Here we use a microfluidics-based strategy to discern the basic features of σB activation in single cells in response to energy and environmental stress, both immediately upon stressor exposure and for tens of generations thereafter. Upon energy stress at various levels of stressor, cells exhibited fast, transient, and amplitude-modulated responses but not frequency modulation as previously reported. Upon environmental stress, which is mediated by the stressosome complex, wild-type cells primarily exhibited a transient and amplitude-modulated response. However, mutant cells producing only one of the four paralogous RsbR stressosome proteins showed striking and previously unseen differences. Whereas RsbRA-only cells mimicked the wild type, RsbRC-only cells displayed a slower but sustained overall response composed of repeated activation events in single cells.
FIGURES 97–100 in Facial affect recognition in individuals at clinical high risk for psychosis
FIGURES 97–100. Geographical distributions of Parasthetops species.
FIGURES 115–116 in Facial affect recognition in individuals at clinical high risk for psychosis
FIGURES 115–116. Geographical distributions of Mesoceration species.
FIGURE 77 in Facial affect recognition in individuals at clinical high risk for psychosis
FIGURE 77. Mesoceration littlekarroo, dorsal and lateral habitus of holotype.
FIGURE 62 in Facial affect recognition in individuals at clinical high risk for psychosis
FIGURE 62. Mesoceration bicurvum, dorsal and lateral habitus of holotype.
FIGURE 59 in Facial affect recognition in individuals at clinical high risk for psychosis
FIGURE 59. Mesoceration integer, dorsal and lateral habitus of holotype.
FIGURE 53 in Facial affect recognition in individuals at clinical high risk for psychosis
FIGURE 53. Mesoceration semicarinulum, dorsal and lateral habitus of holotype.
FIGURE 52 in Facial affect recognition in individuals at clinical high risk for psychosis
FIGURE 52. Mesoceration incarinum, dorsal and lateral habitus of holotype.
FIGURE 45 in Facial affect recognition in individuals at clinical high risk for psychosis
FIGURE 45. Mesoceration periscopum, dorsal and lateral habitus of holotype.
FIGURE 44 in Facial affect recognition in individuals at clinical high risk for psychosis
FIGURE 44. Mesoceration rapidensis, dorsal and lateral habitus of holotype.
FIGURE 76 in Facial affect recognition in individuals at clinical high risk for psychosis
FIGURE 76. Mesoceration tabulare, dorsal and lateral habitus of holotype.
FIGURE 67 in Facial affect recognition in individuals at clinical high risk for psychosis
FIGURE 67. Mesoceration bispinum, dorsal and lateral habitus of holotype.
FIGURE 38 in Facial affect recognition in individuals at clinical high risk for psychosis
FIGURE 38. Mesoceration durabilis, dorsal and lateral habitus of holotype.
ScienceDex guides
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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.