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739 results for “data loss”
Data from: Replicated evolutionary divergence in the cuticular hydrocarbon profile of male crickets associated with the loss of song in the Hawaiian archipelago
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Data from: Short-term genetic consequences of habitat loss and fragmentation for the neotropical palm Oenocarpus bataua
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Data from: Automated integration of trees and traits: a case study using paired fin loss across teleost fishes
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Spatio-temporal analysis of remotely sensed forest loss data in the Cordillera Administrative Region, Philippines
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Data from: Convergent regulatory evolution and loss of flight in palaeognathous birds
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Data from: Direct and indirect effects of sexual signal loss on female reproduction in the Pacific field cricket (Teleogryllus oceanicus)
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Data from: Loss of animal seed dispersal increases extinction risk in a tropical tree species due to pervasive negative density dependence across life stages
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Data from: Cannibalism and intraguild predation community dynamics: coexistence, competitive exclusion and the loss of alternative stable states
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Data from: Repeated alpine flight loss within the widespread New Zealand stonefly Nesoperla fulvescens
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Raw data for: "Abrupt declines marine phytoplankton production driven by warming and biodiversity loss in a microcosm experiment"
<p><strong>Raw data for the article:</strong> Bestion, E, Barton, S, García, FC, Warfield, R, Yvon-Durocher, G (2020). Abrupt declines in marine phytoplankton production driven by warming and biodiversity loss in a microcosm experiment. Ecology Letters. 2020.</p> <p><br> <strong>This data should be cited as:</strong> Bestion, E, Barton, S, García, FC, Warfield, R, Yvon-Durocher, G (2020). Raw data for: "Abrupt declines marine phytoplankton production driven by warming and biodiversity loss in a microcosm experiment" [Data set]. Bestion et al 2020 Ecology Letters. Zenodo. http://doi.org/10.5281/zenodo.3555223<br> -----------------------------</p> <p><strong>The data is composed of two datasets:</strong><br> -----------------------------------------<br> - Biodiversity_ecosystem_function_data.csv<br> - Cell_traits_data.csv</p> <p> </p> <p><strong>Composition of the Biodiversity ecosystem function dataset</strong><br> ------------------------------------------------------------<br> The dataset contains 27 columns<br> - Temperature: the temperature treatment, either 15, 25or 30°C<br> - R: the community richness (1, 2, 4, 8 or 16 species)<br> - log2_R: the log2-scaled richness<br> - M: the community identity (e.g. ABCD is a community composed of 4 species, species A, B, C and D)<br> - P: the partition id (5 independent partitions of the species pool were drawn, following Bell et al 2009)<br> - Q: the partitioned species pool id (following Bell et al 2009)<br> - R: the replicate id (3 replicates per community within a partition, named 1 to 3)<br> - SA to SP: the species presence-absence status for each of the 16 species (species A to species P), with 1: species present within the community, 0: species absent<br> - Abundance: number of cells per ml at the end of the experiment<br> - ln_Abundance: log-transformed Abundance<br> - Chl_a : chlorophyll a content at the end of the experiment in pg ml-1<br> - ln_Chl_a : log-transformed chlorophyll a</p> <p><br> <strong>Composition of the Cell traits dataset</strong><br> -----------------------------------------<br> The dataset contains 9 columns<br> - Species_alpha: the alphanumeric id of the species used in the Biodiversity ecosystem function dataset<br> - Species_name: species identity<br> - Phylum: the phylum<br> - ln.c: the ln transformed metabolic rate b(Tc) at the reference temperature Tc = 293.15°K from the Sharpe-Schoolfield equation (eq. 4 in the article) in µgO2 cell-1 hour-1<br> - Ea: the activation energy (eV) from the Sharpe-Schoolfield equation<br> - Eh: the deactivation energy (eV) from the Sharpe-Schoolfield equation<br> - Th: the temperature at which half of the enzyme have become non functional (°K) from the Scharpe-Schoolfield equation<br> - Topt: the optimum temperature from differentiating the Sharpe-Schoolfield equation. It is presented in °C to be easier to link to the temperature treatments in the experiment<br> - cell_volume: the cell volume, in µm3</p>
Data from: Rapid loss of self-incompatibility in experimental populations of the perennial outcrossing plant Linaria cavanillesii
Transitions from self-incompatibility (SI) to self-compatibility (SC) in angiosperms may be frequently driven by selection for reproductive assurance when mates or pollinators are rare, and are often succeeded by loss of inbreeding depression by purging. Here we use experimental evolution to investigate the spread of SC from one such population of the perennial plant Linaria cavanillesii into SI populations that still have high inbreeding depression. We introduced SC individuals at different frequencies into replicate experimental populations of L. cavanillesii that varied in access to pollinators. Our experiment revealed a rapid shift to SC in all replicates, driven by both greater seed set and greater outcross siring success of SC individuals. We discuss our results in the light of computer simulations that confirm the tendency of SC to spread into SI populations under the observed conditions. Our study illustrates the ease with which SC can spread among populations, a requisite for species-wide transitions from SI to SC.
Data from: Habitat loss and thermal tolerances influence the sensitivity of resident bird populations to winter weather at regional scales
<p>1. Climate change and habitat loss pose the greatest contemporary threats to biodiversity, but their impacts on populations largely vary across species. These differential responses could be caused by complex interactions between landscape and climate change and species-specific sensitivities.</p> <p>2. Understanding the factors that determine which species are most vulnerable to the synergistic effects of climate change and habitat loss is a high conservation priority. Here, we ask (a) whether and to what extent land cover moderates the impacts of winter weather on population dynamics of wintering birds, and (b) what role species' physiology might play in modifying their responses to changing weather conditions.</p> <p>3. To address these questions, we used thousands of observations collected by citizen scientists participating in Project FeederWatch to build dynamic occupancy models for 14 species of wintering birds.</p> <p>4. Populations of wintering birds were more dynamic, having higher rates of local extinction and colonization, in more forested landscapes during extreme cold – presumably enabling them to better track resources. However, urban areas appeared to provide refuge for some species, as demonstrated by increased local colonization during the harshest winter weather. Lastly, we found that species-specific differences in thermal tolerances strongly influenced occupancy dynamics such that species that are less cold-tolerant were more likely to go locally extinct at colder sites and during colder periods throughout winter.</p> <p>5. Together, our results suggest species that are less cold-tolerant and populations occupying less forested landscapes are most vulnerable to extreme winter weather. 11-Jun-2020</p>
Data from: The environmental determinants of total evaporative water loss in birds at multiple temperatures
<p>Endotherms dissipate heat to the environment to maintain a stable body temperature at high ambient temperatures, which requires them to maintain a balance between heat dissipation and water conservation. Birds are relatively small, contain a large amount of metabolically expensive tissue, and are mostly diurnal, making them susceptible to physiological challenges related to water balance and heat dissipation. We compiled total evaporative water loss (TEWL) measurements for 172 species of birds exposed to different temperatures and used comparative methods to examine their relationships with body size, ambient temperature, precipitation, diet, and diel activity cycle. TEWL in the thermoneutral zone (TNZ) was associated primarily with body mass and activity phase. Larger and more active-phase birds, with their higher metabolic rates, lost more water through evaporation than smaller, resting-phase birds, particularly at higher thermal exposures. However, maximum temperature of the natural habitat became an important determinant of TEWL when birds were exposed to temperatures exceeding the TNZ. Species from hotter climates exhibited higher TEWL. Adaptation to arid climates did not restrict evaporative water loss at thermal conditions within the TNZ, but promoted evaporative water loss at exposures above the TNZ. The TEWL of granivores, which ingest food with low water content, differed little from species with other food habitats under all thermal conditions. The effects of environmental covariates of TEWL was dissimilar across thermal exposures, suggesting no evidence for a trade-off between water conservation in the TNZ and heat dissipation at exposure to higher temperatures. Thus, birds may be able to acclimate when climate change results in the need to increase heat dissipation due to warming, except perhaps in hot, arid environments where species will need to depend heavily upon evaporative cooling to maintain homeothermy.</p>
Data from: Early maternal loss affects diurnal cortisol slopes in immature but not mature wild chimpanzees
<p>Biological embedding of stress experienced early in life is a mechanism proposed to explain the fitness costs of maternal loss in mammals. This embedding is expected to lead to long-term alterations of the hypothalamic pituitary adrenal (HPA) axis activity. This idea has, however, rarely been tested in wild long-lived animals. We assessed whether, as in humans, maternal loss had short and long-term impacts on orphan wild chimpanzee urinary cortisol levels and diurnal urinary cortisol slopes, both indicative of the HPA axis functioning. Immature orphan chimpanzees who experienced early maternal loss had diurnal cortisol slopes indicative of high activation of the HPA axis and recently orphaned immatures had elevated cortisol levels. However, unlike in humans, the cortisol profiles did not differ between orphan and non-orphan adult male chimpanzees. Our study highlights that long-term alteration of stress physiology related to early life adversity may not be viable in some wild animal populations. </p>
Data from: Loss of sweet taste despite the conservation of sweet receptor genes in insectivorous bats
<p>The evolution of taste perception is usually associated with the ecology and dietary changes of organisms. However, mismatches between feeding ecology and taste receptor evolution have been identified in some vertebrate animals. One example is the sweet taste receptor gene <em>Tas1r2</em>. Previous analysis of partial sequences has revealed that <em>Tas1r2</em> has undergone equally strong purifying selection between insectivorous and frugivorous bats. To test whether the sweet taste function is also important in bats with contrasting diets, we examined the complete coding sequences of both sweet taste receptor genes (<em>Tas1r2</em> and <em>Tas1r3</em>) in 34 representative bat species. Although these two genes are highly conserved between frugivorous and insectivorous bats at the sequence level, our behavioral experiments revealed that an insectivorous bat (<em>Myotis ricketti</em>) showed no preference for natural sugars, whereas the frugivorous species (<em>Rousettus leschenaultii</em>) showed strong preferences for sucrose and fructose. Furthermore, while both sweet taste receptor genes are expressed in the taste tissue of insectivorous and frugivorous bats, our cell-based assays revealed striking functional divergence: the sweet taste receptors of frugivorous bats are able to respond to natural sugars whereas those of insectivorous bats are not, which is consistent with the behavioral preference tests, suggesting that functional evolution of sweet taste receptors is closely related to diet. This comprehensive study suggests that using sequence conservation alone could be misleading in inferring protein and physiological function, and highlights the power of combining behavioral experiments, expression analysis, and functional assays in molecular evolutionary studies. </p>
Data from: Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists
To elucidate the genetic bases of mycorrhizal lifestyle evolution, we sequenced new fungal genomes, including 13 ectomycorrhizal (ECM), orchid (ORM) and ericoid (ERM) species, and five saprotrophs, which we analyzed along with other fungal genomes. Ectomycorrhizal fungi have a reduced complement of genes encoding plant cell wall–degrading enzymes (PCWDEs), as compared to their ancestral wood decayers. Nevertheless, they have retained a unique array of PCWDEs, thus suggesting that they possess diverse abilities to decompose lignocellulose. Similar functional categories of nonorthologous genes are induced in symbiosis. Of induced genes, 7–38% are orphan genes, including genes that encode secreted effector-like proteins. Convergent evolution of the mycorrhizal habit in fungi occurred via the repeated evolution of a 'symbiosis toolkit', with reduced numbers of PCWDEs and lineage-specific suites of mycorrhiza-induced genes.
Data from: Plastid genome sequences of legumes reveal parallel inversions and multiple losses of rps16 in papilionoids
To date, publicly available plastid genomes of legumes have for the most part been limited to the subfamily Papilionoideae. Here we report 13 new plastid genomes of legumes spanning all three subfamilies. The genomes representing Caesalpinioideae and Mimosoideae are highly conserved in gene content and gene order, similar to the ancestral angiosperm genome organization. Genomes within the Papilionoideae, however, have reduced sizes due to deletions in nine intergenic spacers primarily in the large single copy region. Our study also indicates that rps16 has been independently lost at least five times in legumes, with additional gene and intron losses scattered among the papilionoids. Additionally, genera from two distinct lineages within the papilionoids, Lupinus and Robinia, have a parallel inversion of 36 kb and 39 kb, respectively. This parallel inversion is novel as it appears to be caused by a 29 bp repeat within two trnS genes. This repeat is present in all available legume plastid genomes indicating that there is the potential for this inversion to be present in more species. This case of a homoplasious inversion is also evidence that some inversion events may not be reliable phylogenetic markers.
Data from: Normal vision can compensate for the loss of the circadian clock.
Circadian clocks are thought to be essential for timing the daily activity of animals, and consequently increase fitness. This view was recently challenged for clock-less fruit flies and mice that exhibited astonishingly normal activity rhythms under outdoor conditions. Compensatory mechanisms appear to enable even clock mutants to live a normal life in nature. Here, we show that gradual daily increases/decreases of light in the laboratory suffice to provoke normally timed sharp morning (M) and evening (E) activity peaks in clock-less flies. We also show that the compound eyes, but not Cryptochrome (CRY), mediate the precise timing of M and E peaks under natural-like conditions, as CRY-less flies do and eyeless flies do not show these sharp peaks independently of a functional clock. Nevertheless, the circadian clock appears critical for anticipating dusk, as well as for inhibiting sharp activity peaks during midnight. Clock-less flies only increase E activity after dusk and not before the beginning of dusk, and respond strongly to twilight exposure in the middle of the night. Furthermore, the circadian clock responds to natural-like light cycles, by slightly broadening Timeless (TIM) abundance in the clock neurons, and this effect is mediated by CRY.
Data from: Importance of mixotrophic bacterivory can be predicted by light and loss rates
Recent observational studies form oligotrophic waters provide ample evidence that mixotrophic flagellates often account for the bulk of bacterivory. However, we lack a general framework that allows a mechanistic understanding of success of mixotrophs in the competition with heterotrophic bacterivores. This is especially needed for integrating mixotrophy in models of the microbial loop. Based on general tradeoffs linked to the combined resource use in mixotrophs (generalist versus specialist), we propose a concept where mixotrophs are favored by conditions of high light – low losses, corresponding to the situation found in the surface waters of oligotrophic oceans. Under such conditions, they can achieve positive net growth at very low resource levels, allowing simultaneous competition with specialized protists. Conversely, heterotrophic bacterivores and photoautotrophs should be especially favored in more productive and low-light conditions. We show experimentally that the combined effect of light and loss rates (dilution) predicts the success of mixotrophic bacterivorous flagellates. Moreover, our results suggest that total bacterivory, contrary as seen in the traditional microbial loop concept, has a more intricate coupling to light.
Data from: NDH expression marks major transitions in plant evolution and reveals coordinate intracellular gene loss
Background: Key innovations have facilitated novel niche utilization, such as the movement of the algal predecessors of land plants into terrestrial habitats where drastic fluctuations in light intensity, ultraviolet radiation and water limitation required a number of adaptations. The NDH (NADH dehydrogenase-like) complex of Viridiplantae plastids participates in adapting the photosynthetic response to environmental stress, suggesting its involvement in the transition to terrestrial habitats. Although relatively rare, the loss or pseudogenization of plastid NDH genes is widely distributed across diverse lineages of photoautotrophic seed plants and mutants/transgenics lacking NDH function demonstrate little difference from wild type under non-stressed conditions. This study analyzes large transcriptomic and genomic datasets to evaluate the persistence and loss of NDH expression across plants. Results: Nuclear expression profiles showed accretion of the NDH gene complement at key transitions in land plant evolution, such as the transition to land and at the base of the angiosperm lineage. While detection of transcripts for a selection of non-NDH, photosynthesis related proteins was independent of the state of NDH, coordinate, lineage-specific loss of plastid NDH genes and expression of nuclear-encoded NDH subunits was documented in Pinaceae, gnetophytes, Orchidaceae and Geraniales confirming the independent and complete loss of NDH in these diverse seed plant taxa. Conclusion: The broad phylogenetic distribution of NDH loss and the subtle phenotypes of mutants suggest that the NDH complex is of limited biological significance in contemporary plants. While NDH activity appears dispensable under favorable conditions, there were likely sufficiently frequent episodes of abiotic stress affecting terrestrial habitats to allow the retention of NDH activity. These findings reveal genetic factors influencing plant/environment interactions in a changing climate through 450 million years of land plant evolution.
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.