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opencc-zeroJun 2022View details →

Deep structure, long-distance migration and admixture in the colour polymorphic land snail Cepaea nemoralis

While snails of the genus Cepaea have historically been important in studying colour polymorphism an ongoing issue is that there is a lack of knowledge of the underlying genetics of the polymorphism, as well as an absence of genomic data to put findings in context. We therefore used phylogenomic methods to begin to investigate the post-glacial history of Cepaea nemoralis, with a long-term aim to understand the roles that selection and drift have in determining both European-wide and local patterns of colour polymorphism. By combining prior and new mitochondrial DNA data from over 1500 individuals with ddRAD genomic data from representative individuals across Europe, we show that patterns of differentiation are primarily due to multiple deeply diverged populations of snails. Minimally, there is a widespread Central European population and additional diverged groups in Northern Spain, the Pyrenees, as well as likely Italy and South Eastern Europe. The genomic analysis showed that the present-day snails in Ireland and possibly some other locations are likely descendants of admixture between snails from the Pyrenees and the Central European group, an observation that is consistent with prior inferences from mtDNA alone. The interpretation is that C. nemoralis may have arrived in Ireland via long-distance migration from the Pyrenean region, subsequently admixing with arrivals from elsewhere. This work therefore provides a baseline expectation for future studies on the genetics of the colour polymorphism, as well as providing a comparator for similar species.

opencc-zeroJun 2022View details →

Landscape conservation as a strategy for recovering biodiversity: lessons from a long-term program of pasture restoration in the southern Atlantic Forest

Although ecological restoration has entered the global agenda to reverse different anthropogenic disturbances, we still know little about how this solution interacts with other conservation strategies, to avoid the progressive loss of species and ecosystem services. Here we evaluate one of the pioneering restoration programs in the southern Brazilian Atlantic Forest, where the combination of conservation and restoration efforts have been carried out for 20 years. Specifically, we tested how landscape characteristics, restoration strategies and environmental characteristics affect the results of the restoration of pastures. We established 65 circular plots (total 4.0 ha) along restoration areas (3-10 years) and sampled trees and shrubs composing the canopy (DBH > 5cm) and understory (DBH< 5cm, height > 1.3m). We analyzed the landscape metrics (proportion of old-growth forests in 200 m, 500m and 1000m buffers around each plot; and area and distance of the nearest-neighboring old-growth forests). We explored the multiple effects of landscape, restoration strategy (reforestation, natural regeneration) and environmental variables (soil, pasture grass types) on the species composition and multiple diversity metrics of restoration areas. The species composition was very similar among restoration ages and restoration strategies. We found positive and strong effects of old-growth forest (200 m buffer) proportion on the species richness and Shannon diversity (canopy and understory), aboveground biomass (canopy) and functional diversity (understory) of restoration areas. The restoration strategies affected forest structure, and, in general, the reforestation strategy increased aboveground biomass, Shannon, functional and phylogenetic diversities (in canopy), and percentage of endemic species and biomass (understory), when compared to natural regeneration. The 20 year-experience in the southern Atlantic Forest showed that programs focused on landscape conservation associated with a mixture of restoration strategies (i.e. natural regeneration in larger areas and active restoration in more disturbed sites) , can be an efficient strategy to ensure biodiversity and ecosystem services in tropical landscapes. Synthesis and applications: To manage degraded tropical lands and achieve global targets for biodiversity and ecosystem services, it is necessary to first ensure the conservation of natural remnants and then use multiple restoration strategies in less resilient areas.

opencc-zeroOct 2022View details →

Data from: Individual heterogeneity in fitness in a long-lived herbivore

Heterogeneity in the intrinsic quality and nutritional condition of individuals affects reproductive success and consequently fitness. Black brant (Branta bernicla nigricans) are long-lived, migratory, specialist herbivores. Long migratory pathways and short summer breeding seasons constrain the time and energy available for reproduction, thus magnifying life-history trade-offs. These constraints, combined with long lifespans and trade-offs between current and future reproductive value, provide a model system to examine the role of individual heterogeneity in driving life-history strategies and individual heterogeneity in fitness. We used hierarchical Bayesian models to examine reproductive trade-offs, modeling the relationships between within-year measures of reproductive energy allocation and among-year demographic rates of individual females breeding on the Yukon-Kuskokwim Delta, Alaska using capture-recapture and reproductive data from 1988 to 2014. We generally found that annual survival tended to be buffered against variation in reproductive investment, while breeding probability varied considerably over the range of clutch size-laying date combinations. We provide evidence for relationships between breeding probability and clutch size, breeding probability and nest initiation date, and an interaction between clutch size and initiation date. Average lifetime clutch size also had a weak positive relationship with apparent survival probability. Our results support the use of demographic buffering strategies for black brant. These results also indirectly suggest associations among environmental conditions during growth, fitness, and energy allocation, highlighting the effects of early growth conditions on individual heterogeneity, and subsequently, lifetime reproductive investment.

opencc-by-4.0May 2022View details →

Latitudinal resource gradient shapes multi-variate defense strategies in a long-lived shrub

Herein lies the data and R code for the analyses for the manuscript titled, "Latitudinal resource gradient shapes multi-variate defense strategies in a long-lived shrub", published in Ecology.

opencc-by-4.0Jun 2022View details →

Bacterial-Type Long-Chain Polyphosphates Bind Human Proteins in the Phosphatidylinositol Signaling Pathway

This dataset consists of 2 tabs. Tab 1: Processed full data This contains the full array data (all proteins), with brightest signals sorted to the top. The data was filtered according to the criteria laid out in the report (see column headers, cells formatted in red if criteria not met). The right side of the table displays the raw data of the duplicate spots on the sample array (incubated with polyP-bio + Strept-532) and the control array (incubated with Strept-532 only).  " Tab 2: Histone Controls This contains the individual fluorescence values for the histone control spots (which are repeated in duplicate on each of the 48 subarrays, i.e. 96 values total), as well as their averages, side by side for sample and control array.

opencc-by-4.0Jun 2022View details →

Long-term observation of the end-of- treatment sludge quality from a Parisian WWTP treating wastewater from 6.5 M inhabitants

Wastewater contains a wide range of biological and chemical markers related to human activity. The collection and analysis of these markers in the effluents (wastewater and sludge) allow to qualify the public health of the population and to evaluate the impact of the chemicals used in daily life on the environment.   In line with these studies, the Innovation Department of SIAAP and its scientific partners (ISA and LEESU) has created an Observatory of the city with the objectives of: • Monitoring the long-term dynamics of known and/or potential pollutants according to French regulations. • Contributing to studies aimed at a better understanding of anthropogenic activities. • Structuring and centralizing data (wastewater and end-of-treatment sludge), ensuring their storage for 10 years. • Providing technical and scientific knowledge by publishing every two years the data generated by the Observatory of the city via the open platform Zenodo. Regarding the end-of-treatment sludge, the Seine Aval (SAV) plant has been chosen as a strategic location, since the catchment area corresponds to the Parisian west catchment (6.5 million inhabitants). Data on the sludge micropollution (in metals, polycyclic aromatic hydrocarbons – PAHs and polychlorinated biphenyls – PCBs) are available since 1980 and are provided in the present datasets.

opencc-zeroJul 2023View details →

Long-read-based draft genome sequence of Indian black gram IPU-94-1 'Uttara': Insights into disease resistance and seed storage protein genes

Black gram [Vigna mungo (L.) Hepper var. mung<a>o</a>] [LAV1] is a warm-season legume highly prized for its protein content along with significant folate and iron proportions. To expedite the genetic enhancement of black gram, a high-quality draft genome from the center of origin of the crop is indispensable. Here, we established a draft genome sequence of an Indian black gram cultivar, 'Uttara' (IPU 94-1), known for its high resistance to mungbean yellow mosaic virus. Pacific Biosciences of California, Inc. (PacBio) single-molecule real-time (SMRT) and Illumina sequencing assembled a draft reference-guided assembly with a cumulative size of ~454.4 Mb, of which, 444.4 Mb was anchored on 11 pseudomolecules corresponding to 11 chromosomes. Uttara assembly denotes features of a high-quality draft genome illustrated through high N50 value (42.88 Mb), gene completeness (benchmarking universal single-copy ortholog [BUSCO] score 94.17%), and low levels of ambiguous nucleotides (N) percent (0.0005%). Gene discovery using transcript evidence predicted 28,881 protein-coding genes, from which, ~95% were functionally annotated. A global survey of genes associated with disease resistance revealed 119 nucleotide binding site–leucine rich repeat (NBS-LRR) proteins, while 23 genes encoding seed storage proteins (SSPs) were discovered in black gram. A large set of microsatellite loci were discovered for marker development in the crop. Our draft genome of an Indian black gram provides the foundational genomic resources for the improvement of important agronomic traits and ultimately will help in accelerating black gram breeding programs.

opencc-zeroJul 2022View details →

Long-term nitrogen fertilization alters arbuscular mycorrhizal fungi community phylogenetic structure in plant roots across fine spatial scales

Purpose: Nitrogen deposition due to human activities is known to have a substantial impact on arbuscular mycorrhizal fungi (AMF) community in plant roots. However, the influence of elevated nitrogen on the phylogenetic structure of AMF across fine spatial scales, as well as the mechanisms behind such alterations, are remained poorly understood. Results: Nitrogen addition significantly increased the phylogenetic alpha diversity (diversity within a plot) and the 'within-treatment' phylogenetic beta diversity (dissimilarity among replicate plots) of AMF communities, which resulted in an increased 'within-treatment' phylogenetic gamma diversity (overall diversity among all the replicate plots within a treatment). These changes were caused by the relative abundance decline of a dominant genus (Glomus) and an increase in non-dominant genera. Mechanically, nitrogen addition affected phylogenetic alpha diversity mainly by influencing soil properties. Likewise, the increased 'within-treatment' dissimilarity of plant community composition and changes in soil properties caused by nitrogen addition and plot distance contributed to an increase in within-treatment phylogenetic beta diversity. Conclusions: We conclude that deterministic environmental filtering (both abiotic and biotic) and dispersal limitation effect played critical roles in AMF community assembly under global change scenarios. Insightfully, this study provides a mechanistic understanding of the response of AMF to nitrogen addition across fine scales.

opencc-by-4.0Mar 2022View details →

Long-term (2003-2020) hourly 0.25° global PM2.5 dataset (DeepCAMS) Part-1: 2003-2011

This is part-I (2003-2011) of our DeepCAMS. Part-II can be found at https://doi.org/10.5281/zenodo.6969598 Usage: The raw data -- (scaling factor: 0.1) --> the true PM2.5 concentration Paper title: Generating a Long-term (2003-2020) hourly 0.25° global PM2.5 dataset via spatiotemporal downscaling of CAMS with deep learning (DeepCAMS) Paper doi: <a href="https://doi.org/10.1016/j.scitotenv.2022.157747">https://doi.org/10.1016/j.scitotenv.2022.157747</a> If you find our work helpful, please cite it, thank you very much!

opencc-zeroAug 2022View details →

Assortative mating by telomere length under different environmental conditions in the brown booby, a long-lived seabird

Life-history strategies covary with a suite of behavioral and physiological responses along a slow-fast continuum, known as pace-of-life-syndrome. Particularly in long-lived species, pace-of-life is expected to influence breeding strategies, making it a potentially important factor in mate choice. It has been proposed that telomere length (TL) may integrate individual physiological components and survival prospects that underlie individual differences in pace-of-life. In the brown booby (Sula leucogaster), a long-lived seabird, we investigated whether TL may indicate individual pace-of-life by examining how it relates to mitochondrial DNA copy number (mtDNAcn), corticosterone (cort) levels, and skin coloration—a condition-dependent sexual trait. Then, we tested whether there is assortative mating by TL, and whether the degree of TL similarity between partners influences an individual's likelihood of changing mates and physiological state (mtDNAcn and cort levels). Because environmental conditions may have important effects on the individual pace-of-life, the study was performed in two colonies with contrasting breeding conditions. We found that TL was positively related to mtDNAcn (but not cort levels), suggesting that individuals with shorter telomeres have reduced mitochondrial activity and aerobic capacity. TL was reflected in sexual coloration, but only in the colony with good breeding conditions. There was positive assortative mating by TL, however the degree of assortative mating was unrelated to mtDNAcn, cort levels and the probability of mate change, which greatly varied between the two colonies. Our results suggest that TL might be an indicator of the individual pace-of-life and may influence mating patterns. Importantly, contrasting environmental conditions influenced the link between TL and sexual coloration and the propensity of individuals to change mate, highlighting the importance of environmental variation on breeding strategies.

opencc-zeroAug 2022View details →

Improving citizen science data for long-term monitoring of plant species

In 2012, a new volunteer-based recording scheme for vascular plants was launched in the Netherlands. Its purpose is to track the changes in the number of occupied 1-km grid cells for as many native plant species as possible between survey rounds of 8 years. We did not prescribe a strict field protocol to minimize variation in observer effort, but instead chose to statistically correct for this variation with occupancy models. These models require replicated visits to a grid cell per season, which was implemented by having two independent observers survey grid cells and record all plant species observed. Now that a first survey round has ended (2012–2019), we evaluate our approach, i.e. we tested whether the scheme has the potential to produce proper trend estimates. The number of occupied grid cells in the first round was estimated per species, using an occupancy model with day of year, visit duration and observer experience as covariates for detection. The detection probability, which was 0.43 on average, strongly depended on visit duration and day of year. It was possible to estimate the number of occupied grid cells quite precisely for several hundreds of species, such that the statistical power is expected to be high enough to detect changes of 10% between survey rounds. For rare species, however, the power to detect changes is expected to be quite low. We conclude that the approach works well, but further improvements are suggested.

opencc-by-4.0Aug 2022View details →

Archive data supporting the results in the paper: Increase in carbon input by enhanced fine root turnover in a long-term warmed forest soil

This is the archive data supporting the results in the paper: Increase in carbon input by enhanced fine root turnover in a long-term warmed forest soil; submitted to the Journal Science of the Total Environment.

opencc-by-4.0Aug 2022View details →

Combined U-series and in situ U-Pb dating of fault-related carbonates for reconstructing a long-term history of fault activity in response to SE Tibetan Plateau brittle deformation

Table S1. Analytical conditions for LA-ICP-MS U-Pb dating Table S2. Analytical conditions for LA-ICP-MS elemental mapping Table S3. In situ calcite LA-ICAPMS U-Pb dating data

Long-term proliferation of large annual thistles in dry Mediterranean rangelands

Data set 1: 2005-2018, climate, treatments, total plot biomass, Carthamus glaucus cover & biomas, Scolymus maculatus cover & biomass Data set 2: 2019, treatments, Carthamus glaucus biomas, Scolymus maculatus biomass

Genome-resolved metagenomics using short-, long-read and metaHiC sequencing

Reference-quality metagenome-assembled genomes (MAGs) are the key to exploring microbial compositions and microbe-phenotype associations. They can be recovered by different sequencing technologies and computational tools, which need an unbiased and comprehensive assessment to identify best practices. This work systematically evaluates 40 distinct strategies to recover high-quality MAGs generated by eight assemblers, eight metagenomics binners, and four sequencing technologies, including short-, long-read and metaHiC sequencing. We notice that the hybrid assemblies of short- and long-reads outperform either short- or long-read assemblies and generate more contigs with high contiguity. When the hybrid assemblies are combined with metaHiC-based binning (Hybrid-HiC), more high-quality MAGs with higher taxonomic diversity are recovered, and more tRNA and rRNA genes, phages, plasmids and antibiotic resistance genes are identified in the mock, simulated and real datasets.

opencc-zeroAug 2022View details →

Supplementary materials: Return of the pika: American pikas re-occupy long-extirpated, warm locations

To accompany: Return of the pika: American pikas re-occupy long-extirpated, warm locations by Constance I. Millar and Andrew T. Smith, Nature Notes. American pika re-colonization sites identified in this study Bodie State Historic Park – Noonday Mine 38.004 N; -119.1005 W; 2,615 m Site also clearly identified in maps in Smith (1974a), Smith & Gilpin (1997), Smith & Nagy (2015). North Mono Craters Site 37.9116 N; -118.9985 W; 2,145-2,250 m

Zircon dates long-lived plume dynamics in oceanic islands

Here we present a new data set from ten islands of the hot-spot related Galapagos Archipelago. That includes zircon U-Pb geochronology and δ18O - εHf(t) isotope geochemistry and whole rock geochemistry. The methodology includes different analytical technics like SHRIMP II, LA-MC-ICPMS, ICP, and XRD. This repository contains the following files: Table S1. LA-MC-ICPMS Lu-Hf isotope data of Galápagos zircons measured at Hong Kong University. Table S2. LA-MC-ICPMS Lu-Hf isotope data of Galápagos zircons measured at Frankfurt University. Table S3. Major and trace element concentrations for Galápagos samples. Table S4. Oxygen isotope ratios for Galápagos zircons. Table S5. Thermo-mechanical properties of the rock phase. Table S6. List of the numerical experiments. Table S7: List of the experiments used to calibrate the permeable boundary condition. Table S8.  (A) Hf Isotope Ratios in Galapagos Lavas (After (Blichert-Toft & White, 2001). (B) Oxygen isotopic ratios of plagioclase separates from Galapagos lavas and xenoliths (Geist et al., 1998). (C) Oxygen isotope compositions of olivine grains from subaerial lavas (Peterson et al., 2019). (D) Hf Isotope Compositions (±2s) of Submarine Ridges in the Panama Basin and of CLIP (Caribbean Large Igneous Province) rocks (Geldmacher et al., 2003). Movie S1

opencc-zeroSep 2022View details →

Simulated data from: Reference-free assembly of long-read transcriptome sequencing data with RNA-Bloom2

Long-read sequencing technologies have improved significantly since their emergence. Their read lengths, potentially spanning entire transcripts, is advantageous for reconstructing transcriptomes. Existing long-read transcriptome assembly methods are primarily reference-based and to date, there is little focus on reference-free transcriptome assembly. We introduce RNA-Bloom2, a reference-free assembly method for long-read transcriptome sequencing data. RNA-Bloom2 is available on GitHub at: <a href="https://github.com/bcgsc/RNA-Bloom">https://github.com/bcgsc/RNA-Bloom</a>. We benchmarked the assembly quality and the computational performance of RNA-Bloom2 on simulated data. We prepared two mouse simulated datasets with Trans-NanoSim for the cDNA and dRNA sequencing protocols model on experimental ONT data. The datasets were simulated based on the mouse ENSEMBL annotation for GRCm39. To investigate the effect of sequencing depth, we subsampled each dataset to 2, 10, and 18 million reads, resulting in a total of six sets of reads for our benchmarking experiments. Using the simulated data, we showed that the transcriptome assembly quality of RNA-Bloom2 is competitive to those of reference-based methods.

Taxonomic classification of seabird long bones using 3D shape: A method with wider potential in zooarchaeology

Dataset of manually-placed landmark (.pts) files.  Fixed landmarks and semilandmarks were placed on 3D digitised (.ply) models and exported in .pts file format from Landmark Editor 3.0 (Institute of Data Analysis and Visualization IDAV, University California Davis, USA) (Wiley et al., 2005). The .pts files can be read into R (R Core Team., 2021) using the Morpho::read.pts function (Schlager, 2017).     R Core Team. (2021). R: A language and environment for statistical computing. (Version 4.0.2). R Foundation for Statistical Computing, Vienna, Austria. <a href="https://www.r-project.org/">https://www.r-project.org/.</a> Schlager, S. (2017). Morpho and Rvcg–Shape Analysis in R: R-Packages for geometric morphometrics, shape analysis and surface manipulations. In Statistical shape and deformation analysis (pp. 217-256). Elsevier. Wiley, D. F., Amenta, N., Alcantara, D. A., Ghosh, D., Kil, Y. J., Delson, E., Harcourt-Smith, W., Rohlf, F. J., St. John, K., & Hamann, B. (2005). Evolutionary morphing. IEEE Visualization 2005 - (VIS'05), pp.55.

Long-term testing of alkaline electrolyser single cell using Raney Ni electrodes

Chronopotentiometry and polarization curves of alkaline electrolyser single cell using Raney Ni electrodes.