Find research datasets worth reusing

Pace-of-life syndrome: linking personality, metabolism and colour ornamentation in male guppies

Within populations, there commonly exists consistent among-individual differences in behaviour. As a potential mechanism maintaining this variation, the pace-of-life-syndrome (POLS) hypothesis posits that consistent differences in the behaviour of individuals (i.e. 'personality') are intercorrelated and have coevolved with consistent individual differences in metabolism and life-history traits. Here, using adult male guppies, Poecilia reticulata, we tested under laboratory conditions (1) whether behavioural and metabolic traits vary consistently among individuals over time (≤ 7 days) and (2) the POLS prediction that repeatable behavioural traits should be intercorrelated with each other and with repeatable metabolic rate at the among-individual level. Furthermore, based on indicator models of sexual selection, we expected that sexually selected male colour ornamentation would predict individual personality and metabolic rate. We repeatedly assayed three behavioural traits (sociability, boldness, exploration) and three metabolic traits (resting metabolic rate, maximal metabolic rate, aerobic scope) in a set of males that varied in body size and colour ornamentation. All behavioural trait measures were repeatable, consistent with individual personality. Of the three metabolic traits, only resting metabolic rate (RMR) was repeatable. Behavioural trait measures were significantly intercorrelated and thus integrated in a behavioural syndrome. More 'proactive' males were bolder, more exploratory and more sociable than 'reactive' ones. However, contrary to the POLS hypothesis, RMRwas not significantly correlated with any of the behavioural trait measures, suggesting that consistent individual differences in RMR do not drive or support differences in personality, or vice versa. Male colour ornamentation did not covary with behaviour or RMR and thus does not appear to be a reliable predictor of either behavioural or metabolic phenotypes. We therefore did not find any compelling support for the POLS hypothesis, suggesting that individual differences in metabolism do not underlie the evolution and maintenance of among-individual behavioural variation in our study population.

The microbiome of the pelagic tunicate Dolioletta gegenbauri: A potential link between the grazing and microbial food web

Bloom-forming gelatinous zooplankton occur circumglobally and significantly influence the structure of pelagic marine food webs and biogeochemical cycling through interactions with microbial communities. During bloom conditions especially, gelatinous zooplankton are keystone taxa that help determine the fate of primary production, nutrient remineralization, and carbon export. Using the pelagic tunicate Dolioletta gegenbauri as a model system for gelatinous zooplankton, we carried out a laboratory-based feeding experiment to investigate the potential ecosystem impacts of doliolid gut microbiomes and microbial communities associated with doliolid fecal pellets and the surrounding seawater. Targeted metabarcoding (16S rRNA genes recovering Bacteria/Archaea) and qPCR approaches were used to characterize microbiome assemblages. Comparison between sample types revealed distinct patterns in microbial diversity and biomass that were replicable across experiments. These observations support the hypothesis that through their presence and trophic activity, doliolids influence the structure of pelagic food webs and biogeochemical cycling in subtropical continental shelf systems where tunicate blooms are common. Bacteria associated with starved doliolids (representative of the resident gut microbiome) possessed distinct low-biomass and low-diversity microbial assemblages, suggesting that the doliolid microbiome is optimized to support a detrital trophic mode. Bacterial genera Pseudoalteromomas and Shimia were the most abundant potential core microbiome taxa, similar to patterns observed in other marine invertebrates. Exploratory bioinformatic analyses of predicted functional genes suggest that doliolids, via their interactions with bacterial communities, may affect important biogeochemical processes including nitrogen, sulfur, and organic matter cycling.

Linked selection, differential introgression and recombination rate variation promote heterogeneous divergence in a pair of yellow croakers

Understanding the mechanisms underlying heterogeneous genomic divergence is of particular interest in evolutionary biology. Highly differentiated genomic regions, known as genomic islands, often evolve between diverging lineages. These genomic islands may be related to selection promoting adaptation or reproductive isolation. Based on whole genome assembly and genome-wide RAD sequencing in a pair of yellow croakers (genus: Larimichthys), we investigated the evolutionary processes shaping genomic landscapes of divergence. Demographic modelling indicated that the two species diverged following a secondary contact scenario, where differential introgression and linked selection were suggested to be involved in heterogeneous genomic divergence. We identified reduced recombination rate in genomic islands and a relatively good conservation of both genetic diversity and recombination landscapes between species, which highlight the roles of linked selection and recombination rate variation in promoting heterogeneous divergence in the common ancestral lineage of the two species. In addition, we found a positive correlation between differentiation (FST) and absolute sequence divergence (Dxy), and elevated Dxy in genomic islands, which were different from the patterns under linked selection. Restricted gene flow in highly differentiated regions has likely remodeled the landscape of heterogeneous genomic divergence. Moreover, genomic islands showed little evidence of overlapping within and between species, implying that high gene flow and divergent selection when colonizing new habitats have reshaped the patterns of intraspecific divergence. This study highlights that highly differentiated genomic regions can also be from linked selection and variation of recombination rate, and thus are not necessarily related to speciation islands or local adaptation.

opencc-by-4.0Sep 2022View details →

Microbiome network connectivity and composition linked to disease resistance in strawberry plants

The two R data files correspond phyloseq objects used in the study. The file phyloseq_nochim_silva.RData and phyloseq_nochim_unite.RData correspond to bacterial and fungal phyloseq objects, respectively. Both objects include count table, taxonomy table and metadata information.

opencc-by-4.0May 2022View details →

Linked Open Data for the maritime domain

Linked Data in this data set have been compiled from diverse data sources providing information about Trade and Transport locations, protected areas, surveillance data of vessels and vessel characteristics. Data have been transformed into triples according to the vesselAI ontology, using <a href="http://core.ac.uk/download/pdf/212138612.pdf">RDF-Gen</a> . All geometries are provided using <a href="http://www.opengis.net/ont/geosparql">OGC</a> terms. The vesselAI ontology documentation is available<a href="http://83.212.101.70/vesselAI_ontology.html"> here</a> . In a nutshell, this data set comprises data from the following sources: 1. AIS messages of moving objects retrieved from <a href="https://ais-public.kystverket.no/ais-download/">Norwegian Coastal Administration's SafeSeaNet</a> solution, combined with data provided by the <a href="http://web.ais.dk/aisdata/">Danish Maritime Authority</a>. Each record contains the coordinates of the vessel, a timestamp, an identifier for the vessel, its speed and heading. Typically, each vessel reports this information by sending an AIS message every few seconds. Each reported position is also annotated with the corresponding weather conditions according to Copernicus Climate Change Service (C3S) (files: reconstructed_traj.7z, ais202101_part1.7z, ais202101_part2.7z) . The weather variables currently considered as relative to the movement of vessels are: <ul> <li>    '10m_u_component_of_wind',</li> <li>    '10m_v_component_of_wind',</li> <li>    '2m_dewpoint_temperature',</li> <li>    '2m_temperature',</li> <li>    'mean_sea_level_pressure',</li> <li>    'mean_wave_direction',</li> <li>    'mean_wave_period',</li> <li>    'precipitation_type',</li> <li>    'sea_surface_temperature',</li> <li>    'total_precipitation'</li> </ul> 2. Vessel characteristics retrieved from online sources, combined with information about departure and destination seaports. United Nations Code for Trade and Transport Locations (UN/LOCODE), has been also used, to annotate the seaports with their longitude, latitude and Well Known Text (WKT) information, as well as features and facilities available according to online sources (files: vesselsCharacteristics.7z, worldPorts.7z ). 3. Regions of interest in the maritime domain include fishing areas, endangered species habitat areas, exclusive economic zones (EEZ), Natura2000 protected areas. In this snapshot we provide Natura2000 regions (file: natura2000.7z) as well as <a href="https://www.protectedplanet.net/en">World Protected Areas data set</a> (file: wdpa2022.ttl.7z ) Updates and additional data sets can be found <a href="http://83.212.101.70/vesselAI_ontology.html">here</a> . The surveillance and weather data in this data set, are for January 2021 and within the region defined by the degrees: #west: 2.53 #south: 51.50 #north: 60.50 #east: 17.50

Data from: Linking environmental stability with genetic diversity and population structure in two Atlantic Forest palm trees

Spatial patterns of biodiversity in the Atlantic Forest of Brazil are well characterized. However, there is no consensus on the biological processes underlying these patterns, and multiple competing hypotheses have been proposed, several of which center on climatic stability. Here, we ask if Late Quaternary climatic stability predicts contemporary population structure and genomic-level diversity in two palm species: Syagrus botryophora and S. pseudococos (Arecaceae) We first use species occurrence data to model the distribution of suitable environments in 62 time-slice climate projections over the last 120 thousand years, and summarize stability over that period. We then use >25,000 RADseq-generated SNPs to i) describe the spatial patterns of genomic variation in both species, ii) test how well genomic variation is explained by isolation by distance and by the environmental resistance imposed by historical instability (isolation by resistance) and iii) test for a correlation between genetic diversity and historical stability. The contemporary range of S. botryophora has been relatively stable over the last 30 thousand years and there are two isolated regions of high stability for S. pseudococos. The genomic data recovers a clear pattern of isolation by distance in S. botryophora and two structured populations in S. pseudococos. Consequently, the contribution of isolation by resistance to overall genetic structure is much higher in S. pseudococos. Genetic diversity is not significantly correlated with historical stability in either species. Based on the concordance between historical stability and genetic structure, Late Quaternary climate stability may have maintained population connectivity within S. botryophora and promoted intraspecific divergence in S. pseudococos. Conversely, historical stability does not seem to be driving spatial patterns of genetic diversity. This study supports the primary role of climatic stability in determining spatial population structure, but not genetic diversity, in the Atlantic Forest.

opencc-zeroOct 2022View details →

Linking animal behaviour and tree recruitment: Caching decisions by a scatter hoarder corvid determine seed fate in a Mediterranean agroforestry system

1. Seed dispersal by scatter-hoarder corvids is key for the establishment of important tree species from the Holarctic region such as the walnut (Juglans regia). However, the factors that drive animal decisions to cache seeds in specific locations and the consequences of these decisions on seed fate are poorly understood. 2. We experimentally created four distinct, replicated habitat types in a Mediterranean agricultural landscape where the Eurasian magpie (Pica pica) is a common scatter-hoarder: soft bare soil; compacted bare soil; compacted soil with a dense herbaceous cover; and soft linear bare soil made up of the irrigation furrows that separated the rest of the treatments. We also experimentally placed visual landmarks (stones, sticks, and bunches of dry plants) to test if magpies use them to place seed caches. Walnut dispersal from feeders to the habitats was monitored by radio-tracking and camera traps. 3. A sowing experiment simulating natural caches tested the effect of caching type on seed germination and seedling emergence. Seed mass was controlled for the dispersal and sowing experiments. 4. Magpies selected the two habitats with soft soil, and avoided the one with compacted soil, to cache nuts. Seed mass did not affect dispersal distance, germination, or emergence; however, heavier seeds were cached more often under litter and in the habitat with herbaceous cover, whereas lighter seeds were more often buried in the soft bare soil habitat. Seed burial under soil or litter determined seed fate, as there was virtually no emergence from unburied nuts. There was no evidence of any effect of the visual landmarks. 5. Synthesis. The consequences of seed caching for seedling early establishment are driven by a fine decision-making process of the disperser. Magpies seemed to ponder the characteristics of the habitat and the seed itself to determine where and how to cache each nut. By doing so, magpies reinforced the quality of seed dispersal effectiveness, as they cached walnuts in locations that enhanced both seed survival and seedling emergence.

opencc-zeroOct 2022View details →

Data from: Are genetic variation and demographic performance linked?

Quantifying the empirical relationships between genetic variation and population viability is important from both basic biological and applied conservation perspectives, yet few populations have been monitored with both long-term demographic and population genetics approaches. Here, we present eight years of historical demographic data from five populations of Boechera fecunda (Brassicaceae), a rare, self-compatible perennial plant endemic to Montana, USA, and use integral projection models to estimate the stochastic population growth rate (λS) and extinction risk of each population. We combine these demographic estimates with previously published metrics of genetic variation in the same populations to test whether genetic diversity within populations is linked to demographic performance. Our results show that in this predominantly inbred species, genetics and demography are not strongly correlated, suggesting that more inbred populations are not necessarily less viable or at higher extinction risk than more genetically diverse populations. Interestingly, however, a contemporary re-census revealed that, among these populations, genetic rather than demographic parameters were better predictors of current population density, with populations harboring greater genetic diversity maintaining denser populations at present. In the absence of evidence for inbreeding depression decreasing population viability in this species, we recommend conservation of distinct, potentially locally adapted populations of B. fecunda rather than alternatives such as translocations or reintroductions.

opencc-by-4.0Jul 2022View details →

Dataset for "Towards Better Evaluation for Dynamic Link Prediction"

These are the datasets used in Towards Better Evaluation for Dynamic Link Prediction For preparing the datasets, we closely follow the baseline methods' data preparation strategy. The original networks are saved as <network>.csv. The networks are formatted as follows:     * Each edge is denoted in one line.     * Each line has the following format: source_node, destination_node, timestamp, edge_label, comma-separated arrays of edge features.         * Please note that if there is no edge label available, the edge_label column will be filled with 0s only for loading purpose; these labels are not used in the link prediction task.     * The first line denotes the network format.     * Edge features should include at least one feature. If there is no edge feature available, a 0 value is used for all the edges. The network edge-lists are pre-processed for different methods to use them (Specifically, for preprocessing the data, we use the scripts available in "preprocess_data.py" file of the corresponding baseline). Ater preprocessing the network edge-list, there are three files that are used by the models:     * <ml_network>.csv: this file contains the timestamp edge-list.     * <ml_network>.npy: this file contains the edge features in the dense `npy` format that has the features in binary format.     * <ml_network_node>.npy: this file contains the node features in the dense `npy` format that contains the node features in binary format. Please note that when the edge features or node features are absent, we use a vector of zeros is used as the node/edge features in line with the baseline methods.

opencc-zeroOct 2022View details →

Data and codes for: A link model approach to identify congestion hotspots

Congestion emerges when high demand peaks put transportation systems under stress. Understanding the interplay between the spatial organization of demand, the route choices of citizens, and the underlying infrastructures is thus crucial to locate congestion hotspots and mitigate the delay. Here we develop a model where links are responsible for the processing of vehicles, which can be solved analytically before and after the onset of congestion, and provide insights into the global and local congestion. We apply our method to synthetic and real transportation networks, observing a strong agreement between the analytical solutions and the Monte Carlo simulations, and a reasonable agreement with the travel times observed in 12 cities under congested phase. Our framework can incorporate any type of routing extracted from real trajectory data to provide a more detailed description of congestion phenomena and could be used to dynamically adapt the capacity of road segments according to the flow of vehicles, or reduce congestion through hotspot pricing.

opencc-byOct 2017View details →

Early Bronze Age House, Links of Noltland

Early bronze age house discovered during testing at the Links of Noltland. Source: Objaverse 1.0 / Sketchfab

opencc-by-4.0Sep 2015View details →

Linked Open Data at cervantesvirtual.com

The catalogue of the Biblioteca Virtual Miguel de Cervantes contains about 200,000 records which were originally created in compliance with the MARC21 standard. The entries in the catalogue have been recently migrated to a new relational database whose data model adheres to the conceptual models promoted by the International Federation of Library Associations and Institutions (IFLA), in particular, to the FRBR and FRAD specifications. The database content has been later mapped, by means of an automated procedure, to RDF triples which employ mainly the RDA vocabulary (Resource Description and Access) to describe the entities, as well as their properties and relationships. In contrast to a direct transformation, the intermediate relational model provides tighter control over the process for example through referential integrity, and therefore enhanced validation of the output. This RDF-based semantic description of the catalogue is now accessible online.

opencc-zeroMay 2024View details →

Code from: Early survival in Atlantic salmon is associated with parental genotypes at loci linked to timing of maturation

Large effects loci often contain genes with critical developmental functions with potentially broad effects across life-stages. However, the life-stage-specific fitness consequences are rarely explored. In Atlantic salmon, variation in two large-effect loci, six6 and vgll3, is linked to age at maturity, and several physiological and behavioural traits in early life. By genotyping the progeny of wild Atlantic salmon that were planted into natural streams with nutrient manipulations, we tested if genetic variation in these loci is associated with survival in early life. We found that higher early life survival was linked to the genotype associated with late maturation in the vgll3, but with early maturation in the six6 locus. These effects were significant in high-nutrient, but not in in low-nutrient streams. The differences in early survival were not explained by additive genetic effects in the offspring generation, but by maternal genotypes in the six6 locus, and by both parents' genotypes in the vgll3 locus. Our results suggest that indirect genetic effects by large-effect loci can be significant determinants of offspring fitness. This study demonstrates an intriguing case of how large-effect loci can exhibit complex fitness associations across life stages in the wild and indicates that predicting evolutionary dynamics is difficult.

Data associated with manuscript: "Foliar flavonoids across an elevation gradient: plasticity in response to UV, and links with floral pigmentation patterning"

There are two datasets provided in this excel file. The data are flavonoid abundances of Argentina anserina [=Potentilla anserina] exposed to two levels of ultraviolet light in a greenhouse. The "leaf only data" tab has the combined foliar abundances of the major classes of flavonoids detected: chalcone, flavonone, flavone, flavonol, flavon-3-ol, and proanthocyanidin. This dataset was used to analyze the effect of UV treatment and elevation on flavonoid production in leaves. The "leaf and petal matching cmpnds" is the abundance of the major flavonoid classes in leaves and petals for only the compounds that were detected in both tissue types. This dataset was used for all analyses that related leaf flavonoids with petal flavonoids and petal UV pigmentation.

Supplemental Drawings for Cross Linking Workshop/Camp

Supplemental Drawings for Cross Linking Workshop/Camp   Unless specially referenced, all images are available for use/modification by attendees of educational camps

opencc-zeroMay 2024View details →

Data from: Steatotic liver disease induced by TCPOBOP-activated hepatic constitutive androstane receptor: Primary and secondary gene responses with links to disease progression

Constitutive Androstane Receptor (CAR, Nr1i3), a liver nuclear receptor and xenobiotic sensor, induces drug, steroid and lipid metabolizing enzymes, stimulates liver hypertrophy and hyperplasia, and ultimately, hepatocellular carcinogenesis. The mechanisms linking early CAR responses to later disease development are poorly understood. Here we show that exposure of CD-1 mice to TCPOBOP, a halogenated xenochemical and selective CAR agonist ligand, induces pericentral steatosis marked by hepatic accumulation of cholesterol and neutral lipid, and elevated circulating alanine aminotransferase, indicating hepatocyte damage. TCPOBOP-induced steatosis was weaker in the pericentral region but stronger in the periportal region in females compared to males. Early (1-day) TCPOBOP transcriptional responses were enriched for CAR-bound primary response genes, and for lipogenesis and xenobiotic metabolism and oxidative stress protection pathways; late (2-wk) TCPOBOP responses included many CAR binding-independent secondary response genes, with enrichment for macrophage activation, immune response and cytokine and reactive oxygen species production. Late upstream regulators specific to TCPOBOP-exposed male liver were linked to pro-inflammatory responses and hepatocellular carcinoma progression. TCPOBOP administered weekly to male mice using a high corn oil vehicle activated carbohydrate-responsive transcription factor (MLXIPL)-regulated target genes, dysregulated mitochondrial respiratory and translation regulatory pathways, and induced more advanced liver pathology. Overall, TCPOBOP exposure recapitulates histological and gene expression changes characteristic of emerging steatotic liver disease, including secondary gene responses in liver non-parenchymal cells indicative of transition to a more advanced disease state. Upstream regulators of both the early and late TCPOBOP response genes include novel biomarkers for foreign chemical-induced metabolic dysfunction-associated steatotic liver disease.

High temperature properties incuding creep, creep crack growth rate and thermal fatigue linked with chemical composition of alloys derived from 1.4848 refractory stainless steels

The following set of data results from cast alloys modifying chemical composition taking as reference 1.4848 alloy and getting sound samples that have been tested to calculate creep, creep crack growth rate and thermal fatigue data.

Intestinal Blastocystis is linked to healthier diets and more favorable cardiometabolic outcomes in 56,989 individuals from 32 countries

Open the record for dataset details and reuse information.

opencc-zeroMay 2024View details →

Assessing the links between pollinators and the genetic and epigenetic features of plant species with contrasting distribution ranges

In flowering plants, pollinators contribute to gene flow while they also respond to variation in plant traits together determined by genetic, epigenetic and environmental sources of variation. Consequently, a correlation between abundance and diversity of pollinators and the genetic and epigenetic characteristics of plant populations such as diversity or distinctiveness is expected. However, no study has explored these long-term dimensions of plant-pollinator interactions. Mediterranean narrow endemics often exhibit unexpectedly high levels of population genetic and epigenetic diversity. We hypothesize that pollinators may contribute to explain this pattern. Specifically, given the higher sensitivity of small, isolated population to gene flow, we expect a stronger association of pollinators with population genetic and epigenetic variability in narrow endemics than in widely distributed congeners. We studied five pairs of congeneric plant species, consisting of one narrow endemic with a restricted distribution and one widespread congener, found in the Sierra de Cazorla mountains (SE Spain). We characterized the pollinators in up to three populations per species to estimate their diversity and visitation rates. Additionally, we calculated the genetic and epigenetic diversity and distinctiveness of each population using AFLP markers and methylation-sensitive AFLP markers (MSAP), respectively. We assessed the relationship between pollinator diversity and visitation rates. The diversity of pollinators did not vary according to the plant´s distribution range, but visitation rate was higher in widespread species. As predicted, only narrow endemics showed a significant association between pollinators and their population genetic and epigenetic characteristics. Specifically, higher pollinator diversity and visitation rates entailed higher population genetic diversity and lower epigenetic distinctiveness. This work shows the importance of investigating the relationship between pollinator diversity and population genetics and epigenetics to better understand the evolution of plant rarity.