Find research datasets worth reusing

opencc-by-4.0Jan 2020View details →

Dataset for "Nanopore-led long-read genome assembly of the Australian yabby, Cherax destructor"

Intermediate_Assemblies.tar.gz: Intermediate genome assemblies e.g. raw wtdbg assembly (CD.raw.fa), polished wtdbg assembly (CD.cns.fa), 1st pilon polished assembly (CDF2_pilon1.fasta), 2nd pilon polished assembly (CDF2_pilon2.fasta) and RNA-scaffolded assembly (CDF2_pilon2_prna.fasta). Folders with run_"assembly name" are BUSCO output for each of the assembly. BRAKER2.tar.gz: BRAKER2 genome annotation output containing the initial set of predicted protein-coding genes as well as training intermediate files. BUSCOv3.tar.gz: BUSCO assessment of publicly available Decapod crustacean genome assemblies Cdes.filtered.codingseq: Filtered set of protein-coding sequences Cdes.filtered.faa: Translation of the filtered protein-coding sequences CDF2.NCBI.fasta.masked.gz: Repeat-masked (softmasked) Cherax destructor genome Cqua_transcriptome.tar.gz: rnaSPAdes output (combined fasta) of all Cherax quadricarinatus transcriptomes and its reduced dataset generated by EvidentialGene.  Quast.tar.gz: Quast output of all Decapod crustacean genome assemblies assessed in this study Repeat_Annotation.tar.gz: Repeat annotation (.gff3) based on Cherax destructor-specific de novo repeat library and its summary (.tbl) RepeatLibrary.tar.gz: Cherax destructor-specific de novo repeat library generated by RepeatModeler Wtdbg2_assembly.log: Wtdbg2.5 log file showing exact command used, kmer distribution, memory usage and assembly duration. CAZY_Annotation.tar.gz: dbCAN2 Identification of CAZy in the selected crustacean proteomes as well as list of cellulase-associated GH groups (glycoside hydrolase).  Orthofinder.tar.gz: Orthofinder2 output and proteomes of each crustacean used to infer orthologous clustering. GH9_Analysis.tar.gz: Selected GH9-associated protein sequences, amino acid alignment and IQTree output.  Cdes_mito.gbf: GenBank file of the annotated complete mitogenome Cdes.filtered.codingseq: Cherax destructor protein-coding genes with homology to other crustacean proteomes based on Orthofinder2 orthologous grouping.  Cdes.filtered.faa: Cherax destructor proteins with homology to other crustacean proteomes based on Orthofinder2 orthologous grouping.  Cdes.ortholog.list: List of predicted Cherax destructor proteins with homology to other crustacean proteomes based on Orthofinder2 orthologous grouping.

opencc-by-4.0Jan 2020View details →

Chronicles of Nature Calendar, a Long-term and Large-scale Multitaxon Database on Phenology

We present an extensive, large-scale, long-term and multitaxon database on phenological and climatic variation, involving 506,186 observation dates acquired in 471 localities in Russian Federation, Ukraine, Uzbekistan, Belarus and Kyrgyzstan. The data cover the period 1890-2018, with 96% of the data being from 1960 onwards. The database is rich in plants, birds and climatic events, but also includes insects, amphibians, reptiles and fungi. The database includes multiple events per species, such as the onset days of leaf unfolding and leaf fall for plants, and the days for first spring and last autumn occurrences for birds. The data were acquired using standardized methods by permanent staff of national parks and nature reserves (87% of the data) and members of a phenological observation network (13% of the data). The database is valuable for exploring how species respond in their phenology to climate change. Large-scale analyses of spatial variation in phenological response can help to better predict the consequences of species and community responses to climate change. The recording scheme implemented at nature reserves offers unique opportunities for addressing community-level change across replicate local communities. These data have been systematically collected not as independent monitoring efforts, but using a shared and carefully standardized protocol adapted for each local community. Thus, variability in observation effort is of much less concern than in most other distributed cross-taxon phenological monitoring schemes. To enable analyses of higher-level taxonomical groups, we have included taxonomic classifications for the species in the database. The compilation of the data in a common database was initiated in the context of the project “Linking environmental change to biodiversity change: long-term and large-scale data on European boreal forest biodiversity” (EBFB), funded for 2011-2015 by the Academy of Finland, and continued with the help of other funding to OO since 2016. We organized a series of project meetings that were essential for data acquisition, digitalization and unification. These meetings were organized in Ekaterinburg (Russia) by the Institute of Plant and Animal Ecology, Ural Branch of RAS (Russian Academy of Sciences) in 2011; in Petrozavodsk (Russia) by the Forest Research Institute, at the Karelian Research Center, RAS in 2013; in Miass (Russia) by the Ilmen Nature Reserve in 2014; in Krasnoyarsk (Russia) by the Stolby Nature Reserve in 2014; in Artybash (Russia) by the Altaisky Nature Reserve in 2015; in Listvyanka, Lake Baikal (Russia) by the Zapovednoe Pribajkalje Nature Reserve in 2016; in Roztochja (Ukraine) by the Ministry of Natural Resources of Ukraine in 2016; in Puschino (Russia) by the Prioksko-Terrasnyj Nature Reserve in 2017, in Vyshinino (Russia) by the Kenozero National Park in 2018, and in St Petersburg (Russia) by the Komarov Botanical Institute of the Russian Academy of Sciences in 2019. The compilation of the data in a common database was initiated in the context of the project “Linking environmental change to biodiversity change: long-term and large-scale data on European boreal forest biodiversity” (EBFB), funded for 2011-2015 by the Academy of Finland, and continued with the help of other funding to OO since 2016. We organized a series of project meetings that were essential for data acquisition, digitalization and unification. These meetings were organized in Ekaterinburg (Russia) by the Institute of Plant and Animal Ecology, Ural Branch of RAS (Russian Academy of Sciences) in 2011; in Petrozavodsk (Russia) by the Forest Research Institute, at the Karelian Research Center, RAS in 2013; in Miass (Russia) by the Ilmen Nature Reserve in 2014; in Krasnoyarsk (Russia) by the Stolby Nature Reserve in 2014; in Artybash (Russia) by the Altaisky Nature Reserve in 2015; in Listvyanka, Lake Baikal (Russia) by the Zapovednoe Pribajkalje Nature Reserve in 2016; in Roztochja (Ukraine) by the Ministry of Natural Resources of Ukraine in 2016; in Puschino (Russia) by the Prioksko-Terrasniy Nature Reserve in 2017, in Vyshinino (Russia) by the Kenozero National Park in 2018, and in St Petersburg (Russia) by the Komarov Botanical Institute of the Russian Academy of Sciences in 2019. The compilation of the data into a common database was conducted by the database coordinators (EM and CL) in Helsinki (Finland). Those participants that already held the data in digital format submitted it in the original format, and those that had the data only in paper format digitized it using Excel-based templates developed in the project meetings. Submitted data were processed by the database coordinators according to the following steps:   <ol> <li>The data were formatted so that each observation (the phenological date of a particular event in a particular locality and year) formed one row in the data table (e.g. un-pivoting tables that involved several years as the columns). The phenological event names were split into event type (e.g. “first occurrence“) and species name.</li> <li>The event type names (provided originally typically in Russian) were translated into English and the species names (usually provided in Russian) were identified to scientific names, using dictionaries that were partly developed and verified in the project meetings. All scientific names were periodically verified by mapping them to the Global Biodiversity Information Facility (GBIF) backbone taxonomy.</li> <li>We associated each data record with the following set of information fields: (1) project name, i.e. the source organization, (2) dataset name, (3) locality name, (4) unique taxon identifier, (5) scientific taxon name, and (6) event type.</li> <li>We imported the data records in the main database (maintained as an EarthCape database at <a href="https://ecn.ecdb.io">https://ecn.ecdb.io</a>). During the import, the taxonomic names, locality names, and dataset names were matched against already existing records.</li> </ol> There are at least 200 National Parks and Nature Reserves that collect Chronicles of Nature Book data (in Armenia, Azerbaijan, Belarus, Georgia, Kazakhstan, Kyrgyzstan, Moldova, Russian Federation, Tajikistan, Turkmenistan, Ukraine and Uzbekistan). Out of these, the current database covers data from 62 organizations, with the highest coverage in European Russia. The collection of new data continues in most parks. Thus, the database is not complete, and we aim to support the database with updates, depending on the interest of new partners to join, as well as resources and funding. The technical validation procedures described below will also be applied to any new information included in the database. Data is available as a data package (<a href="http://frictionlessdata.io/docs/data-package/#tabular-data">http://frictionlessdata.io/docs/data-package/#tabular-data</a>) and will be updated with new versions as project goes on.

opencc-by-4.0Feb 2020View details →

Raw Fast5 data for "Microbiota profiling with long amplicons using Nanopore sequencing: full-length 16S rRNA gene and the 16S-ITS-23S of the rrn operon" - PART I

Raw Fast5 data for "Microbiota profiling with long amplicons using Nanopore sequencing: full-length 16S rRNA gene and the 16S-ITS-23S of the rrn operon". See Supplementary Table 2 for associating each sample to its barcode. - FC1_1 includes data for the HM mock community from BEI resources and skin microbiome of the chin in dogs. - FC1_2 includes data for the dorsal skin samples - FC2 includes data for the Zymobiomics mock community and Staphylococcus pseudintermedius isolate

opencc-by-4.0Feb 2020View details →

Rapid and real-time identification of fungi up to the species level with long amplicon Nanopore sequencing from clinical samples

Samples collected from fungal cultures, skin of dogs and ZymoBIOMICSTM mock community (which includes Saccharomyces cerevisiae and Cryptococcus neoformans). The amplicons length of the fungal cultures and ZymoBIOMICSTM mock community is 3,5 Kb and 6 Kb, while the Malassezia spp samples used as control is 3,5 Kb. The amplicons length of the four samples from the skin is 3,5 Kb.

opencc-by-4.0Mar 2020View details →

Long-term effectiveness of sustainable land management practices to control runoff, soil erosion, and nutrient loss and the role of rainfall intensity in Mediterranean rainfed agroecosystems

This data set corresponds to the open-access article "Long-term effectiveness of sustainable land management practices to control runoff, soil erosion, and nutrient loss and the role of rainfall intensity in Mediterranean rainfed agroecosystems" published in CATENA. (<a href="https://doi.org/10.1016/j.catena.2019.104352">https://doi.org/10.1016/j.catena.2019.104352</a>), funded by he European Commission Horizon 2020 project Diverfarming [grant agreement 728003].

opencc-by-4.0Mar 2020View details →

Machine-learning-long-term-wind-power-time-series

In this research work we assess how time-series generated by machine learning models (MLM) compare to Renewables.ninja in terms of their ability to replicate the characteristics of observed nationally aggregated wind power generation for Germany. With this archive, we want to make three machine learning derived time-series available in the Feather format for everyone interested.

opencc-by-4.0May 2020View details →

Dataset S1 of "A long-lived sharp disruption on the lower clouds of Venus"

Simulation with the IPSL Venus GCM. This compressed zip file accompanying the article "A long-lived sharp disruption on the lower clouds of Venus" (DOI: 10.1029/2020GL087221) holds a NetCDF file with a README file describing its structure. The NetCDF file contains the IPSL GCM simulation of the Venus atmosphere for the case of a relaxed zonal wind profile (see subsection 2.4 in main article). Computations were performed on a grid of \(altitude\times latitude\times longitude\) with \(50\times 97\times 96\) elements and along 40 time steps covering 23 Earth days. Calculated physical parameters include: <ol> <li>Atmospheric pressure (Pa).</li> <li>Vertical Wind (m s-1) [positive downward].</li> <li>Air Temperature (K).</li> <li>Zonal Wind (m s-1) [positive westward].</li> <li>Solar radiance at top of the atmosphere (W m-2).</li> </ol>

opencc-by-4.0Jul 2009View details →

copulatory ducts long and s-shaped (9b) in A revision of the African wolf spider genus Amblyothele Simon

copulatory ducts long and s-shaped (9b)

opencc-by-4.0Jul 2009View details →

Palpal tibia long (L/W> 3)(5a) in A revision of the African wolf spider genus Amblyothele Simon

Palpal tibia long (L/W> 3)(5a)

opencc-zeroApr 2020View details →

Data from: Cooperation with closely bonded individuals reduces cortisol levels in long-tailed macaques

Many animal species cooperate with conspecifics in various social contexts. While ultimate causes of cooperation are being studied extensively, its proximate causes, particularly endocrine mechanisms, have received comparatively little attention. Here, we present a study investigating the link between the hormone cortisol, cooperation and social bonds in long-tailed macaques (Macaca fascicularis). We tested 14 macaques in a dyadic cooperation task (loose-string paradigm), each with two partners of different social bond strength and measured their salivary cortisol before and after the task. We found no strong link between the macaques' cortisol level before the task and subsequent cooperative success. In contrast, we did find that the act of cooperating in itself led to a subsequent decrease in cortisol levels, but only when cooperating with closely bonded individuals. Two control conditions showed that this effect was not due to the mere presence of such an individual or the pulling task itself. Consequently, our study shows an intricate way in which the hypothalamic-pituitary-adrenal axis is involved in cooperation. Future studies should reveal whether and how our findings are driven by the anxiolytic effect of oxytocin, which has been associated with social bonding.

opencc-zeroMay 2020View details →

Data from: Single cell RNA-seq analysis reveals that prenatal arsenic exposure results in long-term, adverse effects on immune gene expression in response to Influenza A infection

Arsenic exposure via drinking water is a serious environmental health concern. Epidemiological studies suggest a strong association between prenatal arsenic exposure and subsequent childhood respiratory infections, as well as morbidity from respiratory diseases in adulthood, long after systemic clearance of arsenic. We investigated the impact of exclusive prenatal arsenic exposure on the inflammatory immune response and respiratory health after an adult influenza A (IAV) lung infection. C57BL/6J mice were exposed to 100 ppb sodium arsenite in utero, and subsequently infected with IAV (H1N1) after maturation to adulthood. Assessment of lung tissue and bronchoalveolar lavage fluid (BALF) at various time points post IAV infection reveals greater lung damage and inflammation in arsenic exposed mice versus control mice. Single-cell RNA sequencing analysis of immune cells harvested from IAV infected lungs suggests that the enhanced inflammatory response is mediated by dysregulation of innate immune function of monocyte derived macrophages, neutrophils, NK cells, and alveolar macrophages. Our results suggest that prenatal arsenic exposure results in lasting effects on the adult host innate immune response to IAV infection, long after exposure to arsenic, leading to greater immunopathology. This study provides the first direct evidence that exclusive prenatal exposure to arsenic in drinking water causes predisposition to a hyperinflammatory response to IAV infection in adult mice, which is associated with significant lung damage.

opencc-zeroJun 2020View details →

Data from: Influence of paleolithic range contraction, admixture and long-distance dispersal on genetic gradients of modern humans in Asia

Cavalli-Sforza and coauthors originally explored the genetic variation of modern humans throughout the world and observed an overall east-west genetic gradient in Asia. However, the specific environmental and population genetics processes causing this gradient were not formally investigated and promoted discussion in recent studies. Here we studied the influence of diverse environmental and population genetics processes on Asian genetic gradients and identified which could have produced the observed gradient. To do so, we performed extensive spatially-explicit computer simulations of genetic data under the following scenarios: (i) variable levels of admixture between Paleolithic and Neolithic populations, (ii) migration through long-distance dispersal (LDD), (iii) Paleolithic range contraction induced by the last glacial maximum (LGM) and, (iv) Neolithic range expansions from one or two geographic origins (the Fertile Crescent and the Yangzi and Yellow River Basins). Next, we estimated genetic gradients from the simulated data and we found that they were sensible to the analyzed processes, especially to the range contraction induced by LGM and to the number of Neolithic expansions. Some scenarios were compatible with the observed east-west genetic gradient, such as the Paleolithic expansion with a range contraction induced by the LGM or two Neolithic range expansions from both the east and the west. In general, LDD increased the variance of genetic gradients among simulations. We interpreted the obtained gradients as a consequence of both allele surfing caused by range expansions and isolation by distance along the vast east-west geographic axis of this continent.

opencc-zeroJun 2020View details →

Data from: The ghost of disturbance past: long-term effects of pulse disturbances on community biomass and composition

Current global change is associated with an increase in disturbance frequency and intensity, with the potential to trigger population collapses and to cause permanent transitions to new ecosystem states. However, our understanding of ecosystem responses to disturbances is still incomplete. Specifically, there is a mismatch between the diversity of disturbance regimes experienced by ecosystems and the one-dimensional description of disturbances used in most studies on ecological stability. To fill this gap, we conducted a full factorial experiment on microbial communities, where we varied the frequency and intensity of disturbances affecting species mortality, resulting in twenty different disturbance regimes. We explored the direct and long-term effects of these disturbance regimes on community biomass. While most communities were able to recover biomass and composition states similar to undisturbed controls after a halt of the disturbances, we identified some disturbance thresholds that had long-lasting legacies on communities. Using a model based on logistic growth, we identified qualitatively the sets of disturbance frequency and intensity that had equivalent long-term negative impacts on experimental communities. Our results show that an increase in disturbance intensity is a bigger threat for biodiversity and biomass recovery than the occurrence of more frequent but less intense disturbances.

opencc-zeroJul 2020View details →

Data from: Understanding the social dynamics of breeding phenology: indirect genetic effects and assortative mating in a long distance migrant

Phenological traits, such as the timing of reproduction, are often influenced by social interactions between paired individuals. Such partner effects may occur when pair members affect each other's pre-breeding environment. Partner effects can be environmentally and/or genetically determined, and quantifying direct and indirect genetic effects is important for understanding the evolutionary dynamics of phenological traits. Here, using 26 years of data from a pedigreed population of a migratory seabird, the common tern ( Sterna hirundo ), we investigate male and female effects on female laying date. We find that female laying date harbors both genetic and environmental variation, and is additionally influenced by the environmental, and, to a lower extent, genetic, component of her mate. We demonstrate this partner effect to be largely explained by male arrival date. Interestingly, analyses of mating patterns with respect to arrival date show mating to be strongly assortative and, using simulations, we show that this assortative mating for arrival date leads to overestimation of partner effects. Our study provides evidence for partner effects on breeding phenology in a long distance migrant, while uncovering the potential causal pathways underlying the observed effects and raising awareness for confounding effects due to assortative mating or other common environmental effects.

opencc-zeroJul 2020View details →

No net insect abundance and diversity declines across US Long Term Ecological Research sites

Recent reports of dramatic declines in insect abundance suggest grave consequences for global ecosystems and human society. Most evidence comes from Europe, however, leaving uncertainty about insect population trends worldwide. We used > 5,300 time series for insects and other arthropods, collected over 4-36 years at monitoring sites representing 68 different natural and managed areas, to search for evidence of declines across the United States. Some taxa and sites showed decreases in abundance and diversity while others increased or were unchanged, yielding net abundance and biodiversity trends generally indistinguishable from zero. This lack of overall increase or decline was consistent across arthropod feeding groups, and was similar for heavily disturbed versus relatively natural sites. The apparent robustness of U.S. arthropod populations is reassuring. Yet, this result does not diminish the need for continued monitoring and could mask subtler changes in species composition that nonetheless endanger insect-provided ecosystem services.

Data from: Long-term mechanistic hindcasts predict the structure of experimentally-warmed intertidal communities

Increases in global temperatures are expected to have dramatic effects on the abundance and distribution of species in the coming years. Intertidal organisms, which already experience temperatures at or beyond their thermal limits, provide a model system in which to investigate these effects. We took advantage of a previous study in which experimental plates were deployed in the intertidal zone and passively warmed for 12 years to a daily maximum temperature on average 2.7°C higher than control plots on the adjacent bedrock. We compared the composition of the biological communities on each experimental plate with its neighboring bedrock control. Plate communities showed decreased richness of taxa and percent cover of filamentous algae, mussels and mobile grazers relative to bedrock, and increased percent cover of biofilm. We then used short-term time-series measurements of plate and bedrock temperatures and a mechanistic heat-budget model to hindcast those temperatures back 12 years. Greater differences in long-term average temperature between the experimental plates and bedrock controls were correlated with lower similarity in community composition. Additionally, years with higher average differences between plate and bedrock temperatures were more predictive of current compositional similarity between plate and bedrock communities, even though they occurred farther in the past than did more recent, but cooler, years. We conclude that current intertidal communities reflect their long-term, rather than short-term, thermal histories. Mechanistic heat-budget models based on short-term measurements can provide this valuable, long-term information.

A little damping goes a long way: code and data

It is currently unclear if damping plays a functional role in legged locomotion, and simple models often do not include damping terms. We present a new model with a damping term that is isolated from other parameters: that is, the damping term can be adjusted without retuning other model parameters for nominal motion. We systematically compare how increased damping affects stability in the face of unexpected ground-height perturbations. Unlike most studies, we focus on task-level stability: that is, instead of observing whether trajectories converge back towards a nominal limit-cycle, we quantify the ability to avoid falls using a recently developed mathematical measure. This measure allows trajectories to be compared quantitatively instead of only being separated into a binary classification of "stable" or "unstable". Our simulation study shows that increased damping contributes significantly to task-level stability; however, this benefit quickly plateaus after only a small amount of damping. These results suggest that the low intrinsic damping values observed experimentally may have stability benefits, and are not simply minimized for energetic reasons. All Python code and data needed to generate our results are available open-source.

opencc-by-4.0Aug 2020View details →

Data & R Scripts - Short and long-term effects of low-sulphur fuels on marine zooplankton communities

Data and R scripts associated with "Short and long-term effects of low-sulphur fuels on marine zooplankton communities" https://doi.org/10.1016/j.aquatox.2020.105592

Data from: Ultraconserved yet informative for species delimitation: UCEs resolve long-standing systematic enigma in Central European bees

Accurate and testable species delimitation hypotheses are essential for measuring, surveying and managing biodiversity. Today, taxonomists often rely on mitochondrial DNA barcoding to complement morphological species delimitations. Although COI barcoding has largely proven successful in assisting identifications for most animal taxa, there are nevertheless numerous cases where mitochondrial barcodes do not necessarily reflect the species history. For instance, what is regarded as one single species can be associated with two distinct DNA barcodes, which can point either to cryptic diversity or to deep within-species mitochondrial divergences with no reproductive isolation. In contrast, two or more species can share barcodes, for instance due to mitochondrial introgression. These intrinsic limitations of mitochondrial DNA barcoding can only be addressed with nuclear genomic markers, which are expensive, labour intensive, poorly repeatable, and often require high-quality DNA. To overcome these limitations, we examined the use of ultraconserved nuclear genetic elements (UCEs) as a quick and robust genomic approach to address such problematic cases of species delimitation. This genomic method was assessed using six different bee species complexes suspected to harbour cryptic diversity, mitochondrial introgression, or mitochondrial paraphyly. The sequencing of UCEs recovered between 686 and 1860 homologous nuclear loci and provided explicit species delimitation hypotheses in all investigated species complexes. These results provide strong evidence for the suitability of UCEs as a fast method for species delimitation even in recently diverged lineages. Furthermore, this study provided the first conclusive evidence for both mitochondrial introgression among distinct species, and mitochondrial paraphyly within a single bee species.

Long-term nitrogen addition alters the community and energy channel but not diversity of soil nematodes in a subtropical forest

Summary <ol> <li>Research has indicated that increases in nitrogen (N) deposition can greatly affect ecosystem processes and functions. There is limited information about the effects of long-term N addition on soil nematodes and their functional composition, although nematodes are the most abundant multicellular animals on Earth.</li> <li>We conducted a field experiment in 2004 with four levels of N addition (0, 60, 120, and 240 kg N ha-1 yr-1) in a subtropical Cunninghamia lanceolata forest. Soil samples with three depths (0-20, 20-40 and 40-60 cm) were collected and the community structure, diversity and trophic groups of soil nematodes were determined in 2014.</li> <li>N addition significantly increased the abundance of bacterial- and fungal-feeding nematodes, but decreased the abundance of plant-feeding nematodes at the 0-20 cm soil layer. Accordingly, the plant parasite index and enrichment index decreased but the basal index and channel index increased, which weaken the importance of the plant-based energy channel, but enhance the importance of the fungal-based energy channel. N addition had no effects on the diversity of soil nematodes in three soil depths. Structural equation modeling analysis indicated that N loading directly changed plant-feeding (total r2=0.42) nematodes, or indirectly affected bacterial- (r2=0.43), fungal- (r2=0.31) and plant-feeding nematodes via change soil nutrients, soil water content and pH.</li> <li>These findings suggest that N addition can change the community structure and energy channels soil nematodes, which would affect soil processes and food web functions in forest soils under future environmental change scenarios.</li> </ol>