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opencc-by-4.0May 2020View details →

Geological model of Long Valley Caldera

Borehole lithostratigraphic data (Table S1) and boundary surfaces (surface_01-05) of Long Valley Caldera 3D geological model. This geological model is used in Gola G., Barone A., Castaldo R., Chiodini G., D'Auria L., Garcia-Hernandez R., Pepe S., Solaro G. & Tizzani P. "A novel multidisciplinary approach for the thermo-rheological study of volcanic areas: The case study of Long Valley Caldera", which has been submitted for possible publication in Journal of Geophysical Research - Solid Earth. Coordinates: North America NAD27 UTM Zone 11N Easting: 311000 - 360000 m.; Northing: 4155000 - 4187000 m; XY resolution: 500 m.

opencc-by-4.0May 2020View details →

Thermo-Rheological model of Long Valley Caldera

3D Thermo-Rheological models of Long Valley Caldera presented in Gola G., Barone A., Castaldo R., Chiodini G., D'Auria L., Garcia-Hernandez R., Pepe S., Solaro G. & Tizzani P. "A novel multidisciplinary approach for the thermo-rheological study of volcanic areas: The case study of Long Valley Caldera", which has been submitted for possible publication in Journal of Geophysical Research - Solid Earth. We evaluated the temperature distribution and the brittle-ductile values in a volume of 32×50×30 km3, along East, North and depth directions, respectively. The optimized solution of the conductive-convective model is evaluated with a reservoir permeability of 5.0·10−14 m2, a fault-zone permeability of 5.0·10−14 m2 and a temperature of the magmatic intrusion beneath the caldera of 800°C. The simulated fluid velocity magnitude (mm/year) along x , y and z directions is given positive eastward, northward and upward, respectively. The purely-conductive temperature distribution used as initial condition of the conductive-convective simulation is also given. Finally, we computed the 3D Brittle-Ductile (BD) stratification by considering the optimized conductive-convective thermal model and using a pore fluid factor, a strain rate and a β value equal to 0.36, 1.2, 10–9 s–1, respectively. Further details on the selected petrophysical parameters can be found in the Tables 2 and 3 of the manuscript. The values of the Thermal and Velocity models are gridded with a regular spacing of 0.25 km. The values of the BD model are gridded with a regular spacing of 0.5 km. Coordinates: North America NAD27 UTM Zone 11N Easting: 311000 - 360000 m.; Northing: 4155000 - 4187000 m.

opencc-zeroMay 2020View details →

Data from: Dietary antioxidants attenuate the endocrine stress response during long-duration flight of a migratory bird

Glucocorticoids (GCs) are metabolic hormones that promote catabolic processes, which release stored energy and support high metabolic demands such as during prolonged flights of migrating birds. Dietary antioxidants (e.g., anthocyanins) support metabolism by quenching excess reactive oxygen species produced during aerobic metabolism, and also by activating metabolic pathways that, similar to GCs' function, release stored energy, although the extent of complementarity between GCs and dietary antioxidants is not well known. If anthocyanins complement GCs functions, birds consuming anthocyanin-rich food can be expected to limit the secretion of GCs when coping with a metabolically challenging activity, avoiding the exposure to potential hormonal detrimental effects. We tested this hypothesis in European starlings (Sturnus vulgaris) flying in a windtunnel. We compared levels of corticosterone, the main avian GCs, immediately after a sustained flight and at rest for birds that were fed diets with or without an anthocyanin supplement. As predicted, we found (1) higher corticosterone after flight than at rest in both diet groups, and (2) anthocyanin-supplemented birds had less elevated corticosterone after flight than unsupplemented control birds. This provides novel evidence that dietary antioxidants attenuate the activation of the HPA axis (i.e. increased secretion of corticosterone) during long-duration flight.

opencc-by-4.0Feb 2020View details →

Long-living and highly efficient bio-hybrid light-emitting diodes with zero-thermal-quenching biophosphors

Bio-hybrid light-emitting diodes (Bio-HLEDs) based on color down-converting filters with fluorescent proteins (FPs) have achieved moderate efficiencies (50 lm/W) and stabilities (300 h) due to both thermal- and photo-degradation. Here, we present a significant enhancement in efficiency (~130 lm/W) and stability (>150 days) using a zero-thermalquenching bio-phosphor design. This is achieved shielding the FP surface with a hydrophilic polymer allowing their homogenous integration into the network of a light-guiding and hydrophobic host polymer. We rationalize how the control of the mechanical and optical features of this bio-phosphor is paramount towards highly stable and efficient Bio-HLEDs, regardless of the operation conditions. This is validated by the relationships between the stiffness of the FP-polymer phosphor and the maximum temperature reached under device operation as well as the transmittance of the filters and device efficiency.

opennotspecifiedDec 2002View details →

FIG. 5 in A new species of long·eared bat (Chiroptera, Vespertilionidae) from Sardinia (Italy)

FIG. 5. Cranium (dorsal, ventral, and lateral views) and mandible of the holotype of P. sardus sp. nov.

opennotspecifiedDec 2002View details →

FIG. 1 in A new species of long·eared bat (Chiroptera, Vespertilionidae) from Sardinia (Italy)

FIG. 1. Neighbor-joining tree of European long-eared bats, based on 555 bp of mitochondrial 16S gene fragment (TrN substitution model with I = 0 and γ-shape parameter α = 0.4882); bootstrap support values are indicated for neighbor-joining (left) and maximum parsimony (right) trees; 2,000 replicates were analysed. Abbreviations of haplotypes are the same as in Kiefer et al. (2002) except for the samples from Sardinia Sar1̅Sar22 (see Appendix)

opencc-zeroJun 2020View details →

Data from: Profiling extracellular long RNA transcriptome in human plasma and extracellular vesicles for biomarker discovery

The recent discovery of extracellular RNAs in blood, including RNAs in extracellular vesicles (EVs), combined with low-input RNA-sequencing advances have enabled scientists to investigate their role in human disease. To date, most studies have been focusing on small RNAs, and methodologies to optimize long RNAs measurement are lacking. We used plasma RNA to assess the performance of six long RNA sequencing methods, at two different sites, and we report their differences in reads (%) mapped to the genome/transcriptome, number of genes detected, long RNA transcript diversity, and reproducibility. Using the best performing method, we further compare the profile of long RNAs in the EV- and no-EV-enriched RNA plasma compartments. These results provide insights on the performance and reproducibility of commercially available kits in assessing the landscape of long RNAs in human plasma and different extracellular RNA carriers that may be exploited for biomarker discovery.

opencc-zeroJul 2020View details →

Data from: Mate fidelity improves survival and breeding propensity of a long-lived bird

1. Evolutionary and behavioral ecologists have long been interested in factors shaping the variation in mating behavior observed in nature. Whereas, much of the research on this topic has focused on the consequences of mate choice and mate change on annual reproductive success, studies of a potential positive link between mate fidelity and adult demographic rates have been comparatively rare. This is particularly true for long-lived birds with multi-year, socially monogamous pair bonds. 2. We used a 26-year capture-mark-recapture dataset of 3,330 black brent (Branta bernicla nigricans) to test whether breeding with a familiar mate improved future breeding propensity and survival. We predicted that experienced breeders nesting with a new partner would have rates of survival similar to familiar pairs because long-lived species avoid jeopardizing survival since their lifetime fitness is sensitive to this vital rate. In contrast, we expected that any costs of breeding with a new partner would be paid through skipping the subsequent breeding attempt. 3. We found that unfamiliar pairs had lower subsequent breeding propensity than faithful partners. However, contrary to our expectations, individuals breeding with a new mate also suffered reduced survival. 4. These results add to a small number of studies indicating that a positive relationship between mate retention and adult demographic rates may exist in a diverse array of avian species. Given these results, researchers should consider costs of mate change that extend beyond within-season reproductive success to fully understand the potential adaptive basis for perennial social monogamy. We caution that if mate retention enhances survival prospects, improvements in annual reproductive success with pair-bond length could be a secondary factor favoring perennial social monogamy, particularly in species with slower life history strategies. Further, cases where annual reproductive success does not improve with pair-bond duration, yet multi-year pair bonds are common, could be explained by benefits afforded by mate fidelity to adult vital rates.

opencc-zeroMay 2020View details →

Data from: Fire and grazing controlling a tropical tree line: Effects of long‐term grazing exclusion in Bale Mountains, Ethiopia

Aims: Tropical tree lines are often associated with abrupt shifts in vegetation, soils and disturbance regimes, but the underlying mechanisms are poorly understood. We analysed the role of grazing, fuels and fire in maintaining a sharp tree line with flammable heathland above non-flammable forest. Location: Bale Mountains, Ethiopia. Methods: Grazing exclosures, repeated vegetation sampling, soil analyses and burning and sowing experiments along an altitudinal gradient with Hagenia abyssinica forest, Erica trimera forest and Erica heathland; all heavily grazed, the latter burnt on short rotation. Results: Contrary to expectation, livestock exclusion did not increase forest fuel flammability, but instead resulted in a dense carpet of non-flammable herbs. In the heathland, livestock exclusion led to somewhat faster post-fire fuel recovery, but no major vegetation change. Seeding of tree species resulted in some seedling establishment, but notably Hagenia grew poorly in the heathland, even when protected from livestock. A bioassay, as well as observations of outpost trees on atypical soil above the treeline, suggest that this poor growth is caused by the acidic soils, rather than harsh climate. Despite frequent fires, heathland soils had lower pH and higher organic matter content than forest soils. Below the tree line, tree seedling establishment was successful only in forest gaps, and if livestock was excluded. In both forest and heathland rapid vegetative regeneration in the ground flora after disturbance restricted major species shifts. Conclusions: These results suggest that the contrasting fire potential between heathland and forest, and thus the sharp tree line would be maintained, or possibly even accentuated, in the absence of livestock grazing, and that Hagenia colonisation upwards into the heathland is restricted not only by fire and grazing, but also the acidic soils, a legacy of centuries of Erica dominance.

opencc-zeroJun 2020View details →

Hooded crow genome assembly (PacBio long reads + BioNano optical maps + DoveTail HiC maps)

Structural variation (SV) is an important component of mutations providing the raw material for evolution. Here, we uncover the genome-wide spectrum of intra- and interspecific SV segregating in natural populations of seven songbird species in the genus Corvus. Combining short-read (N = 127) and long-read re-sequencing (N = 31), as well as optical mapping (N = 16), we apply both assembly- and read mapping approaches to detect SV and characterize a total of 220,452 insertions, deletions and inversions. We exploit sampling across wide phylogenetic timescales to validate SV genotypes and assess the contribution of SV to evolutionary processes in an avian model of incipient speciation. We reveal an evolutionary young (~530,000 years) cis-acting 2.25-kb retrotransposon insertion reducing expression of the NDP gene with consequences for premating isolation. Our results attest to the wealth and evolutionary significance of SV segregating in natural populations and highlight the need for reliable SV genotyping.

opencc-zeroJun 2020View details →

Data from: Mating dynamics and multiple paternity in a long-lived vertebrate

Multiple paternity is relatively common across diverse taxa; however, the drivers and implications related to paternal and maternal fitness are not well understood. Several hypotheses have been offered to explain the occurrence and frequency of multiple paternity. One set of hypotheses seeks to explain multiple paternity through direct and indirect benefits including increased genetic diversity or enhanced offspring fitness, whereas another set of hypotheses explains multiple paternity as a byproduct of sexual conflict and population-specific parameters such as density. Here we investigate mating system dynamics in a historically studied population of the American alligator (Alligator mississippiensis) in coastal South Carolina. We examine parentage in 151 nests across 6 years and find that 43% of nests were sired by multiple males and that male reproductive success is strongly influenced by male size. Whereas clutch size and hatchling size did not differ between singly sired and multiple sired nests, fertility rates were observed to be lower in multiply sired clutches. Our findings suggest that multiple paternity may exert cost in regard to female fitness, and raise the possibility that sexual conflict might influence the frequency of multiple paternity in wild alligator populations.

opencc-zeroJul 2020View details →

Data from: Decreased bioefficacy of long-lasting insecticidal nets and the resurgence of malaria in Papua New Guinea

Papua New Guinea (PNG) has the highest malaria transmission outside of Africa. Long-lasting insecticidal nets (LLINs) are believed to have helped to reduce average malaria prevalence in PNG from 15.7% in 2008 to 1% in 2014. Since 2015 malaria indicators in PNG have risen significantly. In the present study, we observed a drastically decreased bioefficacy of unused LLINs with manufacturing dates between 2013 and 2019 collected from villages and LLIN distributors in PNG. Specifically, of the tested n=167 LLINs manufactured between 2013 and 2019 only 16% achieved <a>≥ 80% 24h-mortality or ≥ 95% 60 min-knockdown in cone bioassays </a>conducted with pyrethroid susceptible Anopheles farauti mosquitoes. In contrast, all (100%, n=25) LLINs with manufacturing dates between 2007 and 2012 achieved ≥ 80% 24h-mortality or ≥ 95% 60 min-knockdown. This difference was extremely statistically significant. We hypothesise that decreased bioefficacy of LLINs has contributed to the malaria resurgence in PNG.

Data from: Gene flow at the leading range edge - the long-term consequences of isolation in European Beech (Fagus sylvatica L. Kuhn)

Aim: Isolation is expected to lead to negative impacts on populations due to a reduction in effective population size and gene flow, exacerbating the effects of genetic drift, which might be stronger in peripheral and fragmented populations. Fagus sylvatica (European beech) in southern Sweden presents a gradient of isolation towards the leading range edge of the species. We sought to determine the impact of long-term isolation on genetic diversity and population genetic structure within populations of this species. Location: Samples were obtained from 14 sites towards the northern edge of the native range of beech in Sweden. Taxon: Fagaceae Methods: Using historical sources, we obtained area- and distance-based measures of isolation. We measured genetic diversity and structure by using nuclear microsatellite marker data, and performed parentage analysis to estimate external pollen-mediated gene flow. We implemented a partial least squares regression to determine the effects of isolation on each of the genetic diversity estimators and the measures of external pollen-mediated gene flow. Results: Long-term isolation generally had a negative impact on genetic diversity, which is exacerbated over time, further affecting progeny and suggesting that isolated populations are subject to strong genetic drift, possibly due to the combination of founder events and persistent small population sizes. Bayesian cluster analysis revealed that isolation was also acting as a barrier to gene flow in the north-eastern distribution of beech. Main conclusions: Isolation at the leading range edge of beech in Sweden has created gradients of contemporary gene flow within the species. The long-term cumulative effects of isolation on this wind-pollinated tree species and its negative impacts on genetic diversity and gene flow, could lead to inbreeding depression and higher extinction risk where populations remain small and isolated.

The long-range echo scene of the sperm whale biosonar

Sperm whales use their gigantic nose to produce the most powerful sounds in the animal kingdom, presumably to echolocate deep-sea prey at long ranges and possibly to debilitate prey. To test these hypotheses, we deployed sound recording tags (DTAG-4) on the tip of the nose of three sperm whales. One of these recordings yielded over 6000 echo streams from organisms detected up to 144 m ahead of the whale, supporting a long-range prey detection function of the sperm whale biosonar. The whale navigated this complex acoustic scene by maintaining a stable, long-range acoustic gaze suggesting continual resource evaluation. Less than 10% of the echoic organisms recorded by the tag were targeted for capture and only 18% of the buzzes were emitted within the 50 m depth interval of maximum organism encounter rate, demonstrating echo guided prey selection. Buzzes were initiated >20 m from the prey, showing that sperm whales do not debilitate their prey with sound, but trade echo levels for reduced forward masking and rapid updates on prey location in keeping with the lower manoeuvrability of these large predators. We conclude that the powerful biosonar of sperm whales enables long-range echolocation and selection of prey, but not acoustic debilitation.

opencc-by-4.0Aug 2020View details →

Supporting Information for "How long is too long? Variogram analysis of AERONET data to aid aerosol validation and intercomparison studies"

This contains data sets and their description for the paper "How long is too long? Variogram analysis of AERONET data to aid aerosol validation and intercomparison studies" submitted to the journal Earth and Space Science by this author. This study investigates the uncertainty introduced into comparisons (between e.g. AERONET ground observations, satellite retrievals, or model simulations) of aerosol optical properties due to differences in time of observation between the data sets. This uncertainty source has historically been neglected but is potentially important in some situations.   Journal policies are that Supporting Information data sets can no longer be archived with the paper, but instead should be uploaded to a separate repository. As a result, I have uploaded these data here.   This data set consists of one pdf file describing the data sets, and then two zip archives containing the data (ASCII format). The total size is approximately 10 MB. These data files allow the reproduction of analysis results in this paper, and enable researchers to estimate temporal mismatch uncertainties in their own analyses involving AERONET sites.

Data from: Small tropical forest trees have a greater capacity to adjust carbon metabolism to long‐term drought than large canopy trees

The response of small understory trees to long‐term drought is vital in determining the future composition, carbon stocks and dynamics of tropical forests. Long‐term drought is, however, also likely to expose understory trees to increased light availability driven by drought‐induced mortality. Relatively little is known about the potential for understory trees to adjust their physiology to both decreasing water and increasing light availability. We analysed data on maximum photosynthetic capacity (J max, V cmax), leaf respiration (R leaf), leaf mass per area (LMA), leaf thickness and leaf nitrogen and phosphorus concentrations from 66 small trees across 12 common genera at the world's longest running tropical rainfall exclusion experiment and compared responses to those from 61 surviving canopy trees. Small trees increased J max, V cmax, R leaf and LMA (71%, 29%, 32%, 15% respectively) in response to the drought treatment, but leaf thickness and leaf nutrient concentrations did not change. Small trees were significantly more responsive than large canopy trees to the drought treatment, suggesting greater phenotypic plasticity and resilience to prolonged drought, although differences among taxa were observed. Our results highlight that small tropical trees have greater capacity to respond to ecosystem level changes and have the potential to regenerate resilient forests following future droughts.

Construction of a chromosome-scale long-read reference genome assembly for potato

Background: Worldwide, the cultivated potato, Solanum tuberosum L., is the number one vegetable crop and a critical food security crop. The genome sequence of DM1-3 516 R44, a doubled monoploid clone of S. tuberosum Group Phureja, was published in 2011 using a whole-genome shotgun sequencing approach with short read sequence data. Current advanced sequencing technologies now permit generation of near-complete, high-quality chromosome-scale genome assemblies at a minimal cost. Findings: Here, we present an updated version of the DM1-3 516 R44 genome sequence (v6.1) using Oxford Nanopore Technologies long reads coupled with proximity-by-ligation scaffolding (Hi-C) yielding a chromosome-scale assembly. The new (v6.1) assembly represents 741.6 Mb of sequence (87.8 %) of the estimated 844 Mb genome, of which, 741.5 Mb is non-gapped with 731.2 Mb anchored to the 12 chromosomes. Use of Oxford Nanopore Technologies full-length cDNA sequencing enabled annotation of 32,917 high-confidence protein-coding genes encoding 44,851 gene models that had a significantly improved representation of conserved orthologs compared to the previous annotation. The new assembly has improved contiguity with a 595-fold increase in N50 contig size, 99% reduction in the numbersof contigs, a 44-fold increase in N50 scaffold size, and an LTR Assembly Index score of 13.56, placing it in the category of reference genome quality. The improved assembly also permitted annotation of the centromeres via alignment to sequencing reads derived from CENH3 nucleosomes. Conclusions: Access to advanced sequencing technologies and improved software permitted generation of a high-quality, long-read, chromosome-scale assembly and improved annotation dataset for the reference genotype of potato that will facilitate research aimed at improving agronomic traits and understanding genome evolution.

Shift from short-term competition to facilitation with drought stress is due to a decrease in long-term facilitation

Disentangling short- and long-term neighbour effects, using both removal and observational methods within a single experiment, has strongly improved our understanding of the driving mechanisms of plant-plant interactions. However, there has been no attempt to assess two important underlying processes of their changes along gradients, environmental-severity (changes in target performance without neighbours) and neighbour-traits (changes in performance with neighbours) effects, the former previously shown in alpine communities to be involved in competition and the latter in facilitation. We addressed this goal in an experiment conducted in continental saline depressions (sebkhas) from the Mediterranean arid climate of central Tunisia. We quantified short- and long-term effects of dominant shrubs, transplanting three target grass species in open, nurse and removed-nurse microhabitats of two habitats of different salinity levels in height sebkhas. The design extended geographically from central Tunisia to the Libyan border, 500km southeastward. We used the Relative Interaction Index to calculate short- and long-term effects of neighbours on target species before and after the dry summer seasons and to disentangle environmental-severity from neighbour-trait effects. Short-term effects were slightly negative and long-term effects strongly positive before the dry summer season in the two habitats. Short-term effects switched to positive with increasing drought stress, due to increasing environmental severity (decrease in the response without neighbours), whereas long-term effects decreased due to decreasing environmental mitigation (decrease in the response with neighbours). Soil moisture measurements showed that both changes were due to vanishing shrub soil engineering-effects during the summer drought. We conclude that an increase in short-term facilitation with increasing drought stress through time, apparently supporting the Stress-Gradient-Hypothesis, might be due to a decrease in long-term facilitation. Our study highlights that assessing the effects of neighbours with both the removal and observational methods is crucial for understanding the driving processes of plant-plant interactions in arid systems.

Data from: Long-term ecological legacies in western Amazonia

1. Modifications of Amazonian forests by pre-Columbian peoples are thought to have left ecological legacies that have persisted to the modern day. Most Amazonian palaeoecological records do not, however, provide the required temporal resolution to document the nuanced changes of pre-Columbian disturbance or post-disturbance succession and recovery, making it difficult to detect any direct, or indirect, ecological legacies on tree species. 2. Here, we investigate the fossil pollen, phytolith, and charcoal history of Lake Kumpaka, Ecuador, during the last 2415 years in c. 3-50 year time intervals to assess ecological legacies resulting from pre-Columbian forest modification, disturbance, cultivation, and fire usage. 3. Two cycles of pre-Columbian cultivation (one including slash-and burn cultivation, the other including slash-and-mulch cultivation) were documented in the record around 2150-1430 cal. yr BP and 1250-680 cal. yr BP, with following post-disturbance succession dynamics. Modern disturbance was documented after c. 10 cal. yr BP. The modern disturbance produced a plant composition unlike those of the two past disturbances, as fire frequencies reached their peak in the 2415-year record. The disturbance periods varied in intensity and duration, while the overturn of taxa following a disturbance lasted for hundreds of years. The recovery periods following pre-Columbian disturbance shared some similar patterns of early succession, but the longer-term recovery patterns differed. 4. Synthesis. The trajectories of change after a cessation of cultivation can be anticipated to differ depending on the intensity, scale, duration, and manner of the past disturbance. In the Kumpaka record, no evidence of persistent enrichment or depletion of intentionally altered taxa (i.e. direct legacy effects) was found but indirect legacy effects, however, were documented and have persisted to the modern day. These findings highlight the strengths of using empirical data to reconstruct past change rather than relying solely on modern plant populations to infer past human management and ecological legacies, and challenge some of the current hypotheses involving the persistence of pre-Columbian legacies on modern plant populations.