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Anthropogenic noise is associated with telomere length and carotenoid-based coloration in free-living nestling songbirds
<p>Growing evidence suggests that anthropogenic noise has deleterious effects on the behavior and physiology of free-living animals. These effects may be particularly pronounced early in life, when developmental trajectories are sensitive to stressors, yet studies investigating developmental effects of noise exposure in free-living populations remain scarce. To elucidate the effects of noise exposure during development, we examined whether noise exposure is associated with shorter telomeres, duller carotenoid-based coloration and reduced body mass in nestlings of a common urban bird, the great tit (Parus major). We also assessed how the noise environment is related to reproductive success. We obtained long-term measurements of the noise environment, over a ~24-h period, and characterized both the amplitude (measured by LAeq, LA90, LA10, LAmax) and variance in noise levels, since more stochastic, as well as louder, noise regimes might be more likely to induce stress. In our urban population, noise levels varied substantially, with louder, but less variable, noise characteristic of areas adjacent to a highway. Noise levels were also highly repeatable, suggesting that individuals experience consistent differences in noise exposure. The amplitude of noise near nest boxes was associated with shorter telomeres among smaller, but not larger, brood members. In addition, carotenoid chroma and hue were positively associated with variance in average and maximum noise levels, and average reflectance was negatively associated with variance in background noise. Independent of noise, hue was positively related to telomere length. Nestling mass and reproductive success were unaffected by noise exposure. Results indicate that multiple dimensions of the noise environment, or factors associated with the noise environment, could affect the phenotype of developing organisms, that noise exposure, or correlated variables, might have the strongest effects on sensitive groups of individuals, and that carotenoid hue could serve as a signal of early-life telomere length.</p>
Data from: Age-related variation in non-breeding foraging behaviour and carry-over effects on fitness in an extremely long-lived bird
1. Senescence has been widely documented in wild vertebrate populations, yet the proximate drivers of age-related declines in breeding success, including allocation trade-offs and links with foraging performance, are poorly understood. For long-lived, migratory species, the non-breeding period represents a critical time for investment in self-maintenance and restoration of body condition, which in many species is linked to fitness. However, the relationships between age, non-breeding foraging behaviour and fitness remain largely unexplored. 2. We performed a cross-sectional study, investigating age-related variation in the foraging activity, distribution and diet of an extremely long-lived seabird, the wandering albatross Diomedea exulans during the non-breeding period, and its links with subsequent reproductive performance. 3. We tracked the distributions of 82 adults aged 8 – 33 years with geolocator-immersion loggers and found an age-related decline in the number of landings (a proxy of foraging effort) during daylight hours. There was a decrease in body feather δ13C values in older males but not females, yet this did not accompany an age-related shift in distributions. Males conducted fewer landings than females, and the sexes were spatially segregated, with males foraging further south, likely due to their differential utilization of winds. 4. While younger (< 20 years) birds had higher foraging activity, all individuals went on to breed successfully the following season. In contrast, among older (20+ years) birds, individuals that landed more often were more likely to defer breeding or fail during incubation, suggesting they have lower foraging success. 5. As far as we are aware, this is the first demonstration of an age-specific carry-over effect of foraging behaviour in the non-breeding period on subsequent reproductive performance. This link between foraging behaviour and fitness in late but not early adulthood indicates that the ability of individuals to forage efficiently outside the breeding period may be an important driver of fitness differences in old age.
Drivers of longitudinal telomere dynamics in the long-lived bat species, Myotis myotis
<p>Age related telomere shortening is considered a hallmark of the ageing process. <a name="_Hlk10395680">However, a recent cross-sectional ageing study of relative telomere length (rTL) in bats failed to detect a relationship between rTL and age in the long-lived genus <i>Myotis</i> (<i>M. myotis</i> and <i>M. bechsteinii</i>), suggesting some other factors are responsible for driving telomere dynamics in these species</a>. Here, we test if longitudinal rTL data show signatures of age-associated telomere attrition in <i>M. myotis</i> and differentiate which intrinsic or extrinsic factors are likely to drive telomere length dynamics.<a name="_Hlk30419416"> </a><a name="_Hlk26682824"></a><a name="_Hlk14445670">Using qPCR, rTL was measured in 504 samples from a marked population, from Brittany, France</a>, captured between 2013 and 2016. These represent 174 individuals with an age range of 0 to 7+ years. We find no significant relationship between rTL and age (<i>p</i> = 0.762), but demonstrate that within-individual rTL is highly variable from year to year. To investigate the heritability of rTL, a population pedigree (n=1744) was constructed from genotype data generated from a 16 microsatellite multiplex, designed from an initial, low coverage, Illumina genome for <i>M. myotis</i>. Heritability was estimated in a Bayesian, mixed model framework, and showed that little of the observed variance in rTL <a name="_Hlk513597000">is heritable (<i>h<sup>2</sup>= </i>0.06 – 0.01)</a>. Rather, correlations of first differences, correlating yearly changes in telomere length and weather variables, demonstrate that, during the spring transition, average temperature, minimum temperature, rainfall and windspeed correlate with changes in longitudinal telomere dynamics. <a name="_Hlk10396857">As such, rTL may represent a useful biomarker to quantify the physiological impact of various environmental stressors in bats.</a></p>
Data from: Parameterizing the robust design in the BUGS language: lifetime carry‐over effects of environmental conditions during growth on a long‐lived bird
1. Since the initial development of the robust design, this capture‐recapture model structure has been modified to estimate temporary emigration, and expanded to include auxiliary information such as band recovery and live resight data using maximum likelihood approaches. These developments have allowed investigators to separately assess individual and group effects on true survival, site fidelity, and temporary emigration. Additionally, recent advances in the BUGS language have allowed researchers to develop increasingly complex, user‐specified models in Bayesian frameworks. 2. The robust design has rarely been implemented in the BUGS language, and previous attempts to parameterize the robust design in BUGS exhibited strong bias in estimates of temporary emigration rates. Given the limitations of current parameterizations of the robust design in Bayesian frameworks, and our research objectives, we have developed a parameterization of the robust design in the BUGS language that produces unbiased estimates of all model parameters. 3. We use this novel model structure to examine lifetime carry‐over effects of environmental conditions during early life on annual breeding probabilities of Pacific black brent (Branta bernicla nigricans) breeding on the Yukon‐Kuskokwim River Delta in western Alaska. We found that individuals that were more structurally developed as goslings bred at increased rates as adults (β = 0.14, f = 0.94), with no effect on adult survival (β = 0.01, f = 0.62). Additionally, we provide evidence for long‐term declines in apparent survival of breeding adult females at the population level (β = ‐0.01, f = 0.90). 4. This novel model structure can be easily expanded (Gibson et al., in review), and has important implications for population modelling at broad scales, where we apply it to a declining population of Pacific black brent. Given long‐term declines in gosling growth on the Yukon‐Kuskokwim Delta, we predict future declines in population trajectories as a result of lifetime carry‐over effects of environmental conditions during growth on adult fecundity, and long‐term declines in adult survival.
Data from: Heritable variation in circulating glucocorticoids and endocrine flexibility in a free-living songbird
Phenotypic flexibility is a central way that organisms cope with challenging and changing environments. As endocrine signals mediate many phenotypic traits, heritable variation in hormone levels, or their context-dependent flexibility, could present an important target for selection. Several studies have estimated the heritability of circulating glucocorticoid levels under acute stress conditions, but little is known about the potential for either baseline hormone levels or rapid endocrine flexibility to evolve. Here we assessed the potential for selection to operate on the elevation (circulating hormone levels) and flexibility of glucocorticoid reaction norms to acute restraint stress. Multivariate animal models revealed low but significant heritability in baseline (h2=0.13-0.14) and stress-induced glucocorticoids (h2=0.18), and moderate heritability in glucocorticoid flexibility in response to acute stress (h2=0.38) in free-living juvenile tree swallows (Tachycineta bicolor; n=408). Baseline glucocorticoids were not genetically correlated with either stress-induced glucocorticoids or glucocorticoid flexibility. These findings indicate that baseline glucocorticoids and the acute stress response are distinct traits that can be independently shaped by selection. Microevolutionary changes that influence the expression or flexibility of these endocrine mediators of phenotype may be an important way that populations adapt to changing environments and novel threats.
Data from: Testing for human impacts in the mismatch of living and dead ostracode assemblages at nested spatial scales in subtropical lakes from the Bahamian archipelago
Naturally time-averaged accumulations of skeletal remains – death assemblages – provide reliable, albeit temporally coarse, information on the species composition and structure of communities in diverse settings, and their mismatch with local living communities usually signals recent human-driven ecological change. Here, we present the first test of live-dead mismatch as an indicator of human stress using ostracodes. On three islands along a gradient of human population density in the Bahamas, we compared the similarity of living and death assemblages in ten lakes with relatively low levels of human stress to live-dead similarity in eleven physically comparable lakes subject to industrial, agricultural, or other human activities currently or in the past. We find that live-dead agreement in pristine lakes is consistently excellent, boding well for using death assemblages in modern-day and paleolimnological biodiversity assessments. In most comparison of physically-similar paired lakes, sample-level live-dead mismatch in both taxonomic composition and species' rank-abundance is on average significantly greater in the stressed lake; live-dead agreement is not lower in all samples from stressed lakes, but is more variable. When samples are pooled for lake-level and island-level comparisons, stressed lakes still yield lower live-dead agreement but the significance of the difference with pristine lakes decreases – species that occur dead-only (or alive-only) in one sample are likely to occur alive (or dead) in other samples. Inter-island differences in live-dead agreement are congruent with, but not significantly correlated with, differences in human population density. This situation arises from heterogeneity in the timing and magnitudes of stresses and in the extent of post-stress recovery. Live-dead mismatch in ostracode assemblages thus may be a reliable indicator of human impact at the sample-level with the potential to be a widely-applicable tool for identifying impacted habitats, and perhaps, monitor the progress of their recovery.
Data from: Long-lived metabolic enzymes in the crystalline lens identified by pulse-labeling of mice and mass spectrometry
<p>The lenticular fiber cells are comprised of extremely long-lived proteins while still maintaining an active biochemical state. Dysregulation of these activities has been implicated in age-related cataracts, and other lens diseases. However, the lenticular protein dynamics underlying health and disease is unclear. We sought to measure the global protein turnover rates in the eye using dietary nitrogen-15 (15N)-labeling of mice between 3 and 15 weeks of age. By performing mass spectrometry we measured the 14N- to 15N-peptide ratios of 248 lens proteins, including Crystallin, Aquaporin, Collagen and Laminin of the lens capsule, and enzymes that catalyze glycolysis as well as oxidation and reduction reactions. Unexpectedly, like the crystallin proteins, many of these enzymes are also exceedingly long-lived. The slow replacement of these enzymes in spite of young age of the mice suggests their potential roles in age-related metabolic changes in the lens.</p>
Data from: Climate change and functional traits affect population dynamics of a long-lived seabird
1. Recent studies unravelled the effect of climate changes on populations through their impact on functional traits and demographic rates in terrestrial and freshwater ecosystems, but such understanding in marine ecosystems remains incomplete. 2. Here, we evaluate the impact of the combined effects of climate and functional traits on population dynamics of a long-lived migratory seabird breeding in the southern ocean: the black-browed albatross (Thalassarche melanophris, BBA). We address the following prospective question: ''Of all the changes in the climate and functional traits, which would produce the biggest impact on the BBA population growth rate?'' 3. We develop a structured matrix population model that includes the effect of climate and functional traits on the complete BBA life cycle. A detailed sensitivity analysis is conducted to understand the main pathway by which climate and functional trait changes affect the population growth rate. 4. The population growth rate of BBA is driven by the combined effects of climate over various seasons and multiple functional traits with carry-over effects across seasons on demographic processes. Changes in Sea Surface Temperature (SST) during late winter cause the biggest changes in the population growth rate, through their effect on juvenile survival. Adults appeared to respond to changes in winter climate conditions by adapting their migratory schedule rather than by modifying their at-sea foraging activity. However, the sensitivity of the population growth rate to SST affecting BBA migratory schedule is small. BBA foraging activity during the pre-breeding period has the biggest impact on population growth rate among functional traits. Finally, changes in SST during the breeding season have little effect on the population growth rate. 5. These results highlight the importance of early life histories and carry-over effects of climate and functional traits on demographic rates across multiple seasons in population response to climate change. Robust conclusions about the roles of various phases of the life cycle and functional traits in population response to climate change rely on an understanding of the relationships of traits to demographic rates across the complete life cycle.
Data from: Select and resequence reveals relative fitness of bacteria in symbiotic and free-living environments
Assays to accurately estimate relative fitness of bacteria growing in multistrain communities can advance our understanding of how selection shapes diversity within a lineage. Here, we present a variant of the "evolve and resequence" approach both to estimate relative fitness and to identify genetic variants responsible for fitness variation of symbiotic bacteria in free-living and host environments. We demonstrate the utility of this approach by characterizing selection by two plant hosts and in two free-living environments (sterilized soil and liquid media) acting on synthetic communities of the facultatively symbiotic bacterium Ensifer meliloti. We find (i) selection that hosts exert on rhizobial communities depends on competition among strains, (ii) selection is stronger inside hosts than in either free-living environment, and (iii) a positive host-dependent relationship between relative strain fitness in multistrain communities and host benefits provided by strains in single-strain experiments. The greatest changes in allele frequencies in response to plant hosts are in genes associated with motility, regulation of nitrogen fixation, and host/rhizobia signaling. The approach we present provides a powerful complement to experimental evolution and forward genetic screens for characterizing selection in bacterial populations, identifying gene function, and surveying the functional importance of naturally occurring genomic variation.
Scan Black Lives Matter mural - Seattle 2020
If you want to get an email each week when we release new photogrammetry models you can subscribe here: https://talekeep.com/newsletter A colorful Black Lives Matters mural on East Pine Street, Seattle, described by one onlooker as a "masterpiece", was completed by anti-racism protesters on June 11, 2020. https://www.youtube.com/watch?v=NTa0hR590PQ The work was carried out by protesters in an area of the city they have occupied and dubbed the Capitol Hill Autonomous Zone (CHAZ). Police have left the area to the protesters, but were still responding to 911 calls there, and seeking to establish dialogue with the protest leaders, the Seattle Times said. Local photographer Kyle Kotajarvi captured the completed mural using a drone before posting the footage on Twitter. In a thread accompanying the footage, he said, "A masterpiece was created in the Capitol Hill Autonomous Zone today." Created in RealityCapture by Capturing Reality from 69 images in 00h:36m:35s. Source: Objaverse 1.0 / Sketchfab
Salvador Dali: The Living Flower
Jewellery by Salvador Dali, currently on exhibition at the Dali Museum in Figueres, Spain. Captured along with its reflection from about 35 photos taken on a Google Pixel 2 XL. VR viewing recommended! Source: Objaverse 1.0 / Sketchfab
ORE 2014 Live Competition Results
<p>The results and logs of the ORE 2014 Live Competition (http://vsl2014.at/meetings/ORE-competition.html). The results can be reproduced with the competition framework, which can be found at GitHub (https://github.com/andreas-steigmiller/ore-2014-competition-framework). Furthermore, the ontologies, the reasoners, and the queries are required, which are all available at Zenodo (https://zenodo.org/record/10791, https://zenodo.org/record/11145, and https://zenodo.org/record/11133, respectively).</p>
ORE 2014 Live Competition Queries
<p>The queries of the ORE 2014 Live Competition (http://vsl2014.at/meetings/ORE-competition.html). The competition framework can be found at GitHub (https://github.com/andreas-steigmiller/ore-2014-competition-framework) and the ontologies and reasoners are also available at Zenodo (https://zenodo.org/record/10791 and https://zenodo.org/record/11145, respectively).</p>
Assembled RADseq Data: "Historical introgression among the American live oaks and the comparative nature of tests for introgression"
<p>Assembled sequence data for Eaton et al. (2015) "Historical introgression among the American live oaks and the comparative nature of tests for introgression". The unassembled sequence data are available on NCBI SRA. </p> <p>Data sets were assembled using pyrad v.2.13 as described in notebook 1 from the study.</p>
Dataset of Axonal Synapses, Acquired using a Two-photon Microscope in the Live Mouse Cortex
<p>This Dataset consists of TIFF 100 images, split in 20 test and 80 training images, of axons with their synapses (boutons) labelled. The labels are in form of ground-truth binary images of the same size, in which the corresponding synapses have been labelled as boxes.</p> <p>This data was collected in the live mouse cortex, using a two-photon microscope, with a 40x objective, at zoom 4, with a resolution of 512 x 512 x 0.147 microns per pixel, and a Point Spread Function characterised by a Full Width at Half Maximum (FWHM) values of 0.45 x 0.45 x 2.5 microns (x, y, z). </p> <p> </p> <p><strong>Please cite the following paper when using this dataset:</strong></p> <p>Bass C, Helkkula P, De Paola V, Clopath C, Bharath AA. Detection of axonal synapses in 3D two-photon images. Giniger E, ed. <em>PLoS ONE</em>. 2017;12(9):e0183309. doi:10.1371/journal.pone.0183309.</p> <p> </p>
Live Coding YouTube - PAT showcase 2017 (Screen Recording)
<p>This is a screen recording of the premiere performance <em>Live Coding YouTube</em>, presented at the Performing Arts and Technology annual showcase, March 2017, McIntosh Theatre, University of Michigan, Ann Arbor. The following is a blurb used for the program note.</p> <p>Music listening has changed greatly with the emergence of music streaming services, such as Spotify or Youtube. However, did it inspire us to make new experimental music? <em>Live Coding YouTube</em> is a response to the anticipation of novel performance practices using streaming media. A live coder uses any available video from YouTube, a video streaming service, as source material to perform an improvised audiovisual piece. The challenge is to manipulate the emerging media that are streamed from a networked service given the limited functionality of the API provided. The piece finds parallels in early experimental music that manipulates magnetic tape and vinyl records. On the contrary, the audiovisual space that a musician can explore on the fly is practically infinite. The performance system is built entirely on a web browser and publicly available in the following address: https://livecodingyoutube.github.io/</p>
Live weight and size measurement of 5 macorinvertebrate species
<p>240 data on 5 macroinvertebrate species :</p> <p>3 species of diplopods : <em>Anadenobolus monilicornis</em> (Von Porat, 1876), <em>Anadenobolus leucostigma</em> (Pocock, 1894) and <em>Trigoniulus coralinus</em> (Gervais, 1847)</p> <p>1 species of earthworm : <em>Pontoscolex corethrurus</em> (Mueller)</p> <p>1 species of earwig : <em>Euborellia caraibea </em>(Hebard, 1921)</p> <p>Body lenght and body width was measured using image analyses software (ImageJ) and body volume was calculated using those measurements.</p> <p>Body live weight wad recorded using a balance up to 0.1mg accuracy.</p>
Cetacean & environmental data collected on Iveragh during LIVE Project (2020-2022)
<p>The data sets consists of cetacean data (sightings and strandings) collected during the LIVE Project, on the Iveragh peninsula, Co. Kerry, Ireland.</p> <p>These include land-based effort watches (October 2021 - September 2022), boat effort surveys (summer 2022), casual sightings reported through LIVE researcher (2020-2022) and data obtained from the Irish Whale and Dolphin Group website (2020-2022).</p> <p>Tidal data from Dingle Harbour and environmental parameters recorded through Buoy M3 are also available here.</p>
LOCKED: A dataset of sociodemographic, economic, living, and health features to measure the impact of the Spanish lockdown during COVID-19 on mental health conditions
<p>A dataset aimed at enhancing the understanding of the mental health effects of the COVID-19 lockdown in Spain. This dataset serves as a valuable resource by integrating psychological assessments, such as the SA-45 pyschological test, with comprehensive socioeconomic, living, and health-related information. By combining these diverse data points, the dataset enables researchers to analyze how various invidual factors influenced nine mental health conditions during the lockdown, providing a robust foundation for further studies on this critical topic.</p>
Primary data of thiotrophic free-living and ectosymbiotic genomes
<p><span>Thiotrophic symbioses between sulfur-oxidizing bacteria and various unicellular and metazoan eukaryotes are widespread in reducing marine environments. The giant colonial ciliate <em>Zoothamnium</em> <em>niveum</em> and its vertically transmitted ectosymbiont <em>Candidatus</em> <em>Thiobius</em> <em>zoothamnicola</em> (short Thiobius), however, is the only thiotrophic mutualism that has been cultivated so far. Because theoretical predictions posit a smaller genome in vertically transmitted endosymbionts compared to free-living relatives, we investigated whether this is true also for an ectosymbiont. We used metagenomics to recover the high-quality draft genome of this bacterial symbiont. For comparison, we have also sequenced a closely related free-living cultured but not formally described strain Milos ODIII6 (short ODIII6). We then performed comparative genomics to assess the functional capabilities at the gene, metabolic pathway, and trait levels. 16S rRNA gene trees and average amino acid identity confirmed the close phylogenetic relationship of both bacteria. Indeed, Thiobius had about a third smaller genome than its free-living relative ODIII6, with reduced metabolic capabilities and fewer functional traits. The functional capabilities of Thiobius were mostly a subset of those of the more versatile ODIII6, which possessed additional genes in the context of oxygen, sulfur, and hydrogen utilization and for the acquisition of phosphorus illustrating the adaptations to instable environmental conditions at hydrothermal vents. In contrast, Thiobius possessed genes for heterotrophy potentially enabling it to utilize lactate and acetate, which may be provided as byproducts by the host. The present study illustrates the effect of strict host-dependence of a bacterial ectosymbiont on genome evolution and host adaptation.</span></p>
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.