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739 results for “data loss”
Data from: Tail loss and telomeres: consequences of large-scale tissue regeneration in a terrestrial ectotherm.
Large-scale tissue regeneration has potential consequences for telomere length through increases in cell division and changes in metabolism which increase the potential for oxidative stress damage to telomeres. The effects of regeneration on telomere dynamics have been studied in fish and marine invertebrates, but the literature is scarce for terrestrial species. We experimentally induced tail autotomy in a lizard (Niveoscincus ocellatus) and assessed relative telomere length (RTL) in blood samples before and after partial tail regeneration while concurrently measuring reactive oxygen species (ROS) levels. The change in ROS levels was a significant explanatory variable for the change in RTL over the sixty-day experiment. At the average value of ROS change, the mean RTL increased significantly in the control group (intact tails), but there was no such evidence in the regenerating group. In contrast, ROS levels decreased significantly in the regenerating group, but there was no such evidence in the control group. Combined, these results suggest that tail regeneration following autotomy involves a response to oxidative stress and this potentially comes at a cost to telomere repair. This change in telomere maintenance demonstrates a potential long-term cost of tail regeneration beyond the re-growth of tissue itself.
Data from: Interacting effects of wildlife loss and climate on ticks and tick-borne disease
Both large-wildlife loss and climatic changes can independently influence the prevalence and distribution of zoonotic disease. Given growing evidence that wildlife loss often has stronger community-level effects in low-productivity areas, we hypothesized that these perturbations would have interactive effects on disease risk. We experimentally tested this hypothesis by measuring tick abundance and the prevalence of tick-borne pathogens (Coxiella burnetii and Rickettsia spp.) within long-term, size-selective, large-herbivore exclosures replicated across a precipitation gradient in East Africa. Total wildlife exclusion increased total tick abundance by 130% (mesic sites) to 225% (dry, low-productivity sites), demonstrating a significant interaction of defaunation and aridity on tick abundance. When differing degrees of exclusion were tested for a subset of months, total tick abundance increased from 170% (only mega-herbivores excluded) to 360% (all large wildlife excluded). Wildlife exclusion differentially affected the abundance of the three dominant tick species, and this effect varied strongly over time, likely due to differences among species in their host associations, seasonality, and other ecological characteristics. Pathogen prevalence did not differ across wildlife exclusion treatments, rainfall levels, or tick species, suggesting that exposure risk will respond to defaunation and climate change in proportion to total tick abundance. These findings demonstrate interacting effects of defaunation and aridity that increase disease risk, and they highlight the need to incorporate ecological context when predicting effects of wildlife loss on zoonotic disease dynamics.
Data from: Trait independence primes convergent trait loss
The repeated, independent evolution of traits (convergent evolution) is often attributed to shared environmental selection pressures. However, developmental dependencies among traits can limit the phenotypic variation available to selection and bias evolutionary outcomes. Here we determine how changes in developmentally correlated traits may impact convergent loss of the tympanic middle ear, a highly labile trait within toads that currently lack adaptive explanation. The middle ear's lability could reflect evolutionary trade-offs with other skull features under selection, or the middle ear may evolve independently of the rest of the skull, allowing it to be modified by active or passive processes without pleiotropic trade-offs with other skull features. We compare the skulls of 55 species (39 eared, 16 earless) within the family Bufonidae, spanning six hypothesized independent middle ear transitions. We test whether shared or lineage-specific changes in skull shape distinguish earless species from eared species and whether earless skulls lack other late-forming skull bones. We find no evidence for pleiotropic trade-offs between the middle ear and other skull structures. Instead, middle ear loss in anurans may provide a rare example of developmental independence contributing to evolutionary lability of a sensory system.
Data from: Ultrafast evolution and loss of CRISPRs following a host shift in a novel wildlife pathogen, Mycoplasma gallisepticum
Measureable rates of genome evolution are well documented in human pathogens but are less well understood in bacterial pathogens in the wild, particularly during and after host switches. Mycoplasma gallisepticum (MG) is a pathogenic bacterium that has evolved predominantly in poultry and recently jumped to wild house finches (Carpodacus mexicanus), a common North American songbird. For the first time we characterize the genome and measure rates of genome evolution in House Finch isolates of MG, as well as in poultry outgroups. Using whole genome sequences of 12 House Finch isolates across a 13-year serial sample and an additional four newly sequenced poultry strains, we estimate a nucleotide diversity in House Finch isolates of only ~2% of ancestral poultry strains and a nucleotide substitution rate of 0.8 – 1.2 X 10-5 per site per year both in poultry and in House Finches, an exceptionally fast rate rivaling some of the highest estimates reported thus far for bacteria. We also found high diversity and complete turnover of CRISPR arrays in poultry MG strains prior to the switch to the House Finch host, but after the invasion of House Finches, there is progressive loss of CRISPR repeat diversity, and recruitment of novel CRISPR repeats ceases. Recent (2007) House Finch MG strains retain only ~50% of the CRISPR repertoire founding (1994-95) strains and have lost the CRISPR-associated genes required for CRISPR function. Our results suggest that genome evolution in bacterial pathogens of wild birds can be extremely rapid and in this case is accompanied by apparent functional loss of CRISPRs.
Data from: A degradation debt? large-scale shifts in community composition and loss of biomass in a tropical forest fragment after 40 years of isolation
Habitat loss and fragmentation are among the biggest threats to tropical biodiversity and associated ecosystem services. We examined forest dynamics in a mid-elevation 365-ha fragment in southern Costa Rica. The fragment was isolated in the mid-1970s and belongs to the Las Cruces Biological Station. A 2.25-ha permanent plot was established in the center of the old-growth forest (>400 m to nearest edge boundary) and all plants >5 cm DBH were censused, mapped, and identified to species in two surveys taken ~5–6 years apart (>3,000 stems/survey). Although the reserve maintains high species richness (>200 spp.), with many rare species represented by only one individual, we document a strong shift in composition with a two-fold increase in the number of soft-wooded pioneer individuals. The dominant late-successional understory tree species, Chrysochlamys glauca (Clusiaceae), and most species in the Lauraceae, declined dramatically. Turnover was high: 22.9% of stems in the first survey were lost, and 27.8% of stems in the second survey represented new recruits. Mean tree diameter decreased significantly and there was a 10% decrease in overall biomass. Such alteration has been documented previously but only in smaller fragments or within ~100 m of an edge boundary. Further penetration into this fragment was perhaps driven by a progressive invasion of disturbance-adapted species into the fragment's core over time; the loss of once-dominant late successional species could be a contributing factor. The pattern found is of particular concern given that such fragments represent a substantial portion of today's remaining tropical habitat; further studies in similar-sized fragments that have been isolated for similar prolonged periods are called for.
Data from: Functional diversity is a passenger but not driver of drought-related plant diversity losses in annual grasslands
1. Effects of climate change on plant community functional diversity are of interest since experiments have found functional diversity to predict ecosystem function. Functional diversity has been hypothesized to confer resilience to plant communities (as a "driver" of community change), but in unmanipulated natural communities, it might alternatively (or additionally) act as a "passenger" by responding to changes in plant diversity caused by extrinsic factors such as climate. 2. We examined trends in plant functional diversity in annual grasslands in Northern California over a 19-year period, during which a trend toward drier winters had previously been associated with the losses of drought-intolerant species. We tested whether functional diversity decreased over the period of the study (acting as a passenger), and also whether initial site functional diversity influenced the degree of community change over the study period (acting as a driver). 3. Initial community functional diversity was not related to species richness loss or community variability. We found that functional diversity declined as plant species richness and community mean specific leaf area declined over the course of the study, and all of these trends were associated with declining precipitation, indicating that functional diversity acted as a passenger of community change. 4. Synthesis. This study is among the first to demonstrate that recent climatic trends may drive loss of functional diversity. Our findings highlight that functional diversity does not necessarily confer community resilience when its variation is shaped by the environment rather than by experimental treatments.
Data from: The microbially-mediated soil organic carbon loss under degenerative succession in an alpine meadow
Land-cover change has long been recognized as having marked effect on the amount of soil organic carbon (SOC). However, the microbially-mediated processes and mechanisms on SOC are still unclear. In this study, the soil samples in a degenerative succession from alpine meadow to alpine steppe meadow in the Qinghai-Tibetan Plateau were analyzed using high-throughput technologies, including Illumina sequencing and GeoChip functional gene arrays. The soil microbial community structure and diversity were significantly (P < 0.05) different between alpine meadow and alpine steppe meadow, the microbial ɑ-diversity in alpine steppe meadow was significantly (P < 0.01) higher than in alpine meadow. Molecular ecological network analysis indicated that the microbial community structure in alpine steppe meadow was more complex and tighter than in the alpine meadow. The relative abundance of soil microbial labile carbon degradation genes (e.g., pectin and hemicellulose) was significantly higher in alpine steppe meadow than in alpine meadow, but the relative abundance of soil recalcitrant carbon degradation genes (e.g. chitin and lignin) showed the opposite tendency. The Biolog Ecoplate experiment showed that microbially-mediated soil carbon utilization was more active in alpine steppe meadow than in alpine meadow. Consequently, more soil labile carbon might be decomposed in alpine steppe meadow than in alpine meadow. Therefore, the degenerative succession of alpine meadow because of climate change or anthropogenic activities would most likely decreased SOC and nutrients medicated by changing soil microbial community structure and their functional potentials for carbon decomposition.
Data from: Ageing and reproduction: antioxidant supplementation alleviates telomere loss in wild birds
Reproduction is inherently costly. Environmental stressors, such as infection and limited food resources, can compromise investment at each breeding attempt. For example, recent data on captive birds showed that increased reproductive effort accelerates ageing. However, the effects of nutritional status and infection on ageing remain unknown. Telomeres function as protective caps at the ends of eukaryotic chromosomes, and changes in telomere length is a commonly used proxy for ageing. To partially address the mechanisms of ageing following reproduction, we supplemented, medicated or administered a combined treatment to wild blue tits (Cyanistes caeruleus) breeding in central Spain during 2012. The nutritional supplement consisted of two different antioxidants, while the medication was an antimalarial treatment against blood parasites. We evaluated the effect of these manipulations on reproductive success and parasite loads in the first breeding season, and on changes in telomere length between two consecutive breeding seasons. Supplemented birds showed no reduction in blood parasite infections in 2012, although they exhibited higher body mass and fledging success. The antimalarial drugs reduced infections by several parasite species, but this had no effect on fitness parameters. In the following season, telomeres from supplemented birds had shortened less. Altogether, we found that supplementation with antioxidants provided fitness benefits in the short term and reduced telomere loss a year following treatment. Our results provide indirect empirical support for accelerated telomere loss as a cost of reproduction.
Data from: Grafting or pruning in the animal tree: lateral gene transfer and gene loss?
Background: Lateral gene transfer (LGT), also known as horizontal gene transfer, into multicellular eukaryotes with differentiated tissues, particularly gonads, continues to be met with skepticism by many prominent evolutionary and genomic biologists. A detailed examination of 26 animal genomes identified putative LGTs in invertebrate and vertebrate genomes, concluding that there are fewer predicted LGTs in vertebrates/chordates than invertebrates, but there is still evidence of LGT into chordates, including humans. More recently, a reanalysis of a subset of these putative LGTs into vertebrates concluded that there is not horizontal gene transfer in the human genome. One of the genes in dispute is an N-acyl-aromatic-L-amino acid amidohydrolase (ENSG00000132744), which encodes ACY3. This gene was initially identified as a putative bacteria-chordate LGT but was later debunked as it has a significant BLAST match to a more recently deposited genome of Saccoglossus kowalevskii, a flatworm, Metazoan, and hemichordate. Results: Using BLAST searches, HMM searches, and phylogenetics to assess the evidence for LGT, gene loss, and rate variation in ACY3/ASPA homologues, the most parsimonious explanation for the distribution of ACY3/ASPA genes in eukaryotes involves both gene loss and bacteria-animal LGT, albeit LGT that occurred hundreds of millions of years ago prior to the divergence of gnathostomes. Conclusions: ACY3/ASPA is most likely a bacteria-animal LGT. LGTs at these time scales in the ancestors of humans are not unexpected given the many known, well-characterized, and adaptive LGTs from bacteria to insects and nematodes.
Data and R code from: Fire-induced loss of the world's most biodiverse forests in Latin America
<p>Fire plays a dominant role in deforestation, particularly in the tropics, but the relative extent of transformations and influence of fire frequency on eventual forest loss remain unclear. Here we analyze the frequency of fire and its influence on post-fire forest trajectories between 2001-2018. We account for ~1.1% of Latin American forests burnt in 2002-2003 (8,465,850 ha). Although 40.1% of forests (3,393,250 ha) burned only once, by 2018~48% of the evergreen forests converted to other, primarily grass-dominated uses. While greater fire frequency yielded more transformation, our results reveal the staggering impact of even a single fire. Increasing fire frequency imposes greater risks of irreversible forest loss, transforming forests into ecosystems increasingly vulnerable to disturbance and degradation. Reversing this trend is indispensable to both mitigate and adapt to climate change globally. As climate change transforms fire regimes across the region, key actions are needed to conserve Latin American forests.</p>
Data from: Convergent regulatory evolution and loss of flight in palaeognathous birds
A core question in evolutionary biology is whether convergent phenotypic evolution is driven by convergent molecular changes in proteins or regulatory regions. We combined phylogenomic, developmental, and epigenomic analysis of 11 new genomes of paleognathous birds, including an extinct moa, to show that convergent evolution of regulatory regions, more so than protein-coding genes, is prevalent among developmental pathways associated with independent losses of flight. A Bayesian analysis of 284,001 conserved noncoding elements, 60,665 of which are corroborated as enhancers by open chromatin states during development, identified 2355 independent accelerations along lineages of flightless paleognaths, with functional consequences for driving gene expression in the developing forelimb. Our results suggest that the genomic landscape associated with morphological convergence in ratites has a substantial shared regulatory component.
Data from: Species loss drives ecosystem function in experiments, but in nature the importance of species loss depends on dominance
<p>Aim: Decades of experimental research have conclusively shown a positive relationship between species richness and ecosystem function. However, authoritative reviews find no consensus on how species loss affects function in natural communities. We analyse experimental and observational data in an identical way and test whether they produce similar results.</p> <p>Location: North America and Europe (experimental communities); global (natural communities).</p> <p>Time period: Experimental communities: 1998–2013; natural communities: 1982–2018.</p> <p>Major taxa studied: </p> <p>Experimental communities: temperate grassland plants; natural communities: temperate grassland plants, tropical forest trees, kelp forest producers<br> and native bees.</p> <p>Methods: We used an approach inspired by the Price equation to analyse 129 datasets from experimental and natural communities worldwide. We tested how the<br> effects of species loss on ecosystem function varied with dominance and the nonrandomness<br> of species loss and, in turn, how these two factors differed between<br> experiments and observations.</p> <p>Results: Studies carried out in experimental and natural communities reached different conclusions regarding the effects of species loss. First, species loss had greater effects on ecosystem function in experiments than in nature. Second, the importance of species loss was negatively correlated with dominance in nature because as dominance increased, lost species were increasingly those contributing little to ecosystem function. Although experimental and natural communities exhibited similar levels of dominance, an analogous relationship was not possible in experiments because the order of species loss was randomized by design. Main conclusions: Species loss was sometimes, but not always, the major driver of loss of function in nature. Variation in the importance of species loss was not messy and context dependent; instead, it was predicted by functional dominance. Although results from experimental and natural communities were similar in several key ways, they differed in that species loss was a consistent predictor of ecosystem function in experiments and not in nature.</p>
Data for manuscript "Influence of Photochemical Loss of VOCs on Understanding Ozone Formation Mechanism"
<p>Data for manuscript "Influence of Photochemical Loss of VOCs on Understanding Ozone Formation Mechanism"</p>
Data from: The sensitivity of Neotoma to climate change and biodiversity loss over the late Quaternary
<p>The late Quaternary was a time of considerable environmental change in North America. Not only was climate highly variable, but a megafaunal extinction at the terminal Pleistocene led to considerable loss of biodiversity. These combined perturbations likely had cascading effects across communities and ecosystems. Here, we focus on a detailed fossil record on the Edwards Plateau in Texas and the response of <em>Neotoma</em>, a genus of herbivorous rodents, to these environmental and ecological perturbations. We characterized changes in <em>Neotoma</em> body mass and diet across the past 20,000 years; body mass was estimated using measurements of fossil teeth and diet quantified using stable isotope analysis of carbon and nitrogen isotope from fossil bone collagen. We found that prior to ~7,000 cal yr BP, maximum mass was positively and significantly correlated to precipitation and negatively correlated to temperature. Independently, body mass was significantly and negatively correlated to communtiy composition becoming more similar to modern over time. Moreover, while <em>Neotoma</em> diet in the Pleistocene was primarily sourced from C<sub>3</sub> resources, it became progressively more reliant on C<sub>4</sub> (and potentially CAM) plants through the Holocene. The combination of decreasing population body mass and higher C<sub>4</sub>/CAM consumption was associated with a regional transition from a mesic forest to a xeric savanna grassland. Our results suggest that <em>Neotoma</em> during the terminal Pleistocene were responding to climatic factors through changes in body size, while changes in local resource availability during the Holocene likely led to changes in the relative abundance of different <em>Neotoma</em> species in the community. </p>
Codes and data regarding "Temporal dissipative structures in optical Kerr resonators with transient loss fluctuation"
<p>Here we upload codes and figure data relate to the article "Temporal dissipative structures in optical Kerr resonators with transient loss fluctuation" that was published on Optics Express (<a href="https://doi.org/10.1364/OE.439212">https://doi.org/10.1364/OE.439212</a>)</p> <p>Please note that the codes have been tested using Matlab in the version of 2019a.</p> <p>The ".opj" and ".opju" files in the folder "Figure_data" can be opened via <a href="https://www.originlab.com/viewer/">the Origin viewer</a> (a free app published by Originlab)</p>
Data from: Repeated alpine flight loss within the widespread New Zealand stonefly Nesoperla fulvescens
<p><span>Flight loss is a common feature of upland insect assemblages, with recent studies detecting parallel wing reduction events across independent alpine lineages. However, the geographic scale over which such repeated evolution can operate remains unclear. In this study, we use genotyping-by-sequencing</span> to assess the genomic relationships among vestigial-winged and full-winged populations of the widespread New Zealand stonefly <em>Nesoperla</em> <em>fulvescens</em>, to test for repeated wing loss events over small spatial scales. Biogeographic analyses indicate that alpine wing loss in this widespread species is restricted to a single, narrow mountain range. Intriguingly, our coalescent analyses indicate that upland vestigial-winged <em>N</em>. <em>fulvescens</em> populations are not sister to one another, suggesting wings have been lost independently in disjunct populations of this species, over a <30 km scale. Our results suggest that selection against flight above the alpine treeline can drive rapid and repeated adaptation even across narrow spatial scales. We propose that such repetitive processes may represent a far more pervasive feature of alpine insect adaptation than is currently recognised.</p>
Data from: Density-dependent dispersal strategy of pollinator moderates the adverse effect of habitat loss on plant reproduction
<p><span>1. </span><span>Major challenges for plant conservation are predicting the effect of habitat loss on pollination success and plant reproduction </span><span>potential</span><span>. Most studies report that pollinator movement is affected by quantitative and spatial characteristics of landscapes. However, little is known about the role of pollinator movement, impacted by floral volatiles and intraspecies interaction, on plant reproduction in fragmented landscapes.</span></p> <p><span>2. </span><span>To clarify the effect of pollinator movement on plant reproduction </span><span>relative to </span><span>habitat loss, we developed an integrated model incorporating pollinator's foraging response with its </span><span>dispersal</span> <span>process mediated by a density-dependent dispersal (DDD) strategy</span><span>.</span> <span>This model</span> <span>performed better in capturing behaviorals response of pollinators than do current methods. The integrated model was verified with field results of pollinator visitation and plant reproduction of saltcedar (<em>Tamarix</em> <em>chinensis</em>) inhabiting the Yellow River Delta, and then was compared against a dispersal strategy called density-independent dispersal (DID). The model was applied to landscapes with various non-habitat percentage (<em>NHP</em>) to explore the effect of habitat loss on plant reproduction.</span></p> <p><span>3. </span><span>Results suggested that saltcedar populations differ in their responses to habitat loss, which depended on the spatial scales considered. At landscape scale, increasing <em>NHP</em> significantly inhibited the dispersion extent of floral volatiles and therefore reduced pollinator visitation and subsequent seed production, especially when <em>NHP</em> exceeded the critical threshold of 0.6.</span> <span>However, at patch scale, comparing with DID strategy, the DDD strategy enabled pollinators to increase their utilization of flowers by 43.42% and 6.79% in low-density and distant plant patches, whereas their utilization was reduced by 7.75% and 2.24% in high-density and central patches, respectively. </span><span>Plant reproduction was improved correspondingly</span> <span>in low-density and distant patches under different <em>NHP</em>s.</span></p> <p><span>4. </span><span>Consequently, habitat loss inhibits the volatiles dispersion and interferes with the foraging success of pollinators, a major factor influencing plant reproduction at landscape scale. At patch scale, adaptive utilization of pollinators exhibiting DDD strategy alleviates the negative effect of habitat loss on plant production and maintains plant population persistence. Since pollinator behavioral response is critical to plant reproduction, we recommend the use of the here-presented integrated model to assess the impact of habitat loss on plant reproduction.</span></p>
Data and Code for "Comparing the Impacts of Ozone-Depleting Substances and Carbon Dioxide on Arctic Sea Ice Loss"
<p>This upload contains data and code related to the submitted manuscript "Comparing the Impacts of Ozone-Depleting Substances and Carbon Dioxide on Arctic Sea Ice Loss" by Bushuk, Polvani, and England. See README.txt for a description of the datasets and code.</p>
Data and code for: "Sea level rise from West Antarctic mass loss significantly modified by large snowfall anomalies"
<p>Data and code required to reproduce results in paper: "Sea level rise from West Antarctic mass loss significantly modified by large snowfall anomalies"</p>
Hydrological Response of Andean Catchments to Recent Glacier Mass Loss (data)
<p>Data related to the article in review (The Cryosphere journal)</p>
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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.
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DANDI Archive for NWB datasets
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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.