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opencc-zeroMar 2023View details →

Genetic diversity and population structure from a Peruvian nucleus cattle herd using SNP data

New-generation sequencing technologies, among them SNP chips for massive genotyping, have proven to be useful for the effective management of genetic resources. Also, developing nucleus herds is an effective method for genetic improvement work. To date, molecular studies in Peruvian cattle are still in their infancy. To close this gap, we here employed two SNP panels (BovineHD and Bovine100K) to determine for the first time the Peruvian nucleus herd's genetic diversity and population structure that belong to INIA. This nucleus comprises Brahman (N=16), Braunvieh (N=14), Gyr (N=11), and Fleckvieh (N=22) breeds. Additionally, samples from a locally adapted creole cattle, the Arequipa Fighting Bull (AFB, N=12), were incorporated into the study. The genetic diversity indices in all breeds showed a high proportion of polymorphic SNPs, varying from 69.37% in Gyr to 80.81% in Braunvieh. Also, Braunvieh possessed the highest observed heterozygosity (0.53±0.17), while Brahman possessed the lowest (0.44±0.10), indicating that the former is more diverse compared to the other cattle breed groups. According to the molecular variance analysis, 83.92% of the variance occurs within individuals, whereas 16.0% occurs between populations. The pairwise FST estimates between breeds showed values that ranged from 0.054 (Braunvieh vs AFB) to 0.266 (Brahman vs AFB). Pairwise Reynold's distance showed a pattern similar to the one obtained with the FST statistics, with values ranging from 0.058 to 0.309. A dendrogram was constructed using the Neighbor-Joining clustering algorithm, and similar to the principal coordinate analysis, three groups were identified. Results showed a clear separation between Bos indicus (Brahman and Gyr) and B. taurus breeds (Braunvieh and Fleckvieh). For Fleckvieh and Braunvieh, there were two subgroups each one of them grouping with the AFB group. Similar results were obtained with ADMIXTURE analysis with K= 3 as the most optimal number for the inferred genetic structure of the populations. The results from the current study would contribute to the appropriate management avoiding loss of genetic variability in these breeds and to future improvements for this nucleus. Additional work is needed to speed up the breeding process in the Peruvian cattle system.

opencc-by-4.0Mar 2023View details →

Original Data for Publication: Exceptionally Stable Dimers and Trimers of Au25 Clusters Linked with a Bidentate Dithiol: Synthesis, Structure and Chirality Study.

Original Data for Publication: Exceptionally Stable Dimers and Trimers of Au25 Clusters Linked with a Bidentate Dithiol: Synthesis, Structure and Chirality Study. Angewandte Chemie, 2023

opencc-by-4.0Mar 2023View details →

Fits Data of "Multiple Rings and Asymmetric Structures in the Disk of SR 21"

This is the fits data of the paper "Multiple Rings and Asymmetric Structures in the Disk of SR 21".

opencc-by-4.0Mar 2023View details →

Data for "Structure and drivers of social networks and their links with health in older adults"

Data, supplementary material and scripts for the paper "Structure and drivers of social networks and their links with health in older adults" Social network is an important factor in promoting healthy aging. However, the mechanisms linking social capital to health are complex. Moreover, most of the social network analysis studies on older adults consider only participants’ relationships and not how these relationships are themselves connected. In this study, we went further than current ego-centered network studies by determining global social network metrics and the structure of relationships among older adult participants of the RECORD Cohort using the Veritas-Social questionnaire. The aim of this study is to identify key dimensions of social networks of older adults, and to evaluate how these dimensions relate to depressive symptoms, life satisfaction, and well-being. Using Principal Component Analyses (PCA), we identified four social network dimensions with psychological meanings. Dimension 1 (homophily) was positively linked with perceived accessibility to services in one’s residential neighborhood but negatively linked with the level of study. Dimension 2 (social integration) as Dimension 3 (social support) was only linked to the number of people living with ego. Dimension 4 was linked with perceived accessibility to local services. Finally, and rather surprisingly, we found that none of the four network dimensions, even the degree, was linked to the three health status metrics.

Data from: Bat activity is related to habitat type and structure in managed pine barrens in New England

Background. Several insectivorous bat species are found in New England, yet research on them is still scarce. Current research shows the ecological importance of bats due to their control of insect populations, but they are endangered by habitat loss and White Nose Syndrome, among other threats. Pine barrens are an uncommon ecosystem found in New England that supports other rare taxa and could be important for these bat species. Methods. With hand-held audio recorders, we surveyed for bats in Montague Plains Wildlife Management Area in Massachusetts and Concord Pine Barrens in New Hampshire in June 2022. Our study objectives were to 1) describe the most common bat species and 2) compare bat activity across different habitat types at two managed pine barrens in New England. In particular, we examined bat activity related to habitat type (scrub oak, mature pitch pine, treated pitch pine, hardwood forest), habitat structure (i.e., canopy closure), and time since prescribed fire. We analyzed our data through linear mixed effects modeling and Fisher’s exact tests. Results. Overall, we were able to measure the presence of five out of the nine total species found in the area, including the endangered Myotis lucifugus (little brown bat). We recorded 293 bat calls, with the majority of calls from big brown bats (71%). We found significant differences (P < 0.05) in bat activity in relation to habitat types and structure. The index of bat activity was greatest in pitch pine and hardwood forests and lowest in scrub oak and treated pitch pine habitats. With preliminary data, we also found that there was more bat activity in areas that had not been burned recently. Discussion. These findings demonstrate the importance of pine barrens as an ecosystem that supports bats in New England. According to the activity of bats in our study, closed canopy and mature pitch pine habitats may be prioritized in conservation efforts at managed barrens for bat species. Further research is recommended to better understand the relationship between prescribed fires, which are common in managed barrens, and bat activity.

Sn velocity model and original catalogue data for essay "Uppermost mantle structure of the Japan subduction zone from Sn tomography"

Sn velocity model and original catalogue data for essay “Uppermost mantle structure of the Japan subduction zone from Sn tomography”

Computational Data for "Synthesis, Structures and Photophysical Properties of Tetra- and Hexanuclear Zinc Complexes Supported by Tridentate Schiff Base Ligands"

Computational data used for the article "Synthesis, Structures and Photophysical Properties of Tetra- and Hexanuclear Zinc Complexes Supported by Tridentate Schiff Base Ligands". This Includes the geometries, optimizations, and the TD-DFT calculations of all mentioned structures and simulated UV-Vis spectra.

opencc-zeroDec 2022View details →

Data from: Network structure of avian mixed-species flocks decays with elevation and latitude across the Andes

Birds in mixed-species flocks benefit from greater foraging efficiency and reduced predation but also face costs related to competition and activity matching. Because this cost-benefit trade-off is context-dependent (e.g., abiotic conditions, habitat quality), the structure of flocks is expected to vary along elevational, latitudinal, and disturbance gradients. Specifically, we predicted that the connectivity and cohesion of flocking networks would (1) decline towards tropical latitudes and lower elevations, where competition and activity matching costs are higher, and (2) increase with lower forest cover and greater human disturbance. We analysed the structure of 84 flock networks across the Andes and assessed the effect of elevation, latitude, forest cover and human disturbance on network characteristics. We found that Andean flocks are overall open-membership systems (unstructured), though the extent of network structure varied across gradients. Elevation was the main predictor of structure, with more connected and less modular flocks upslope. As expected, flocks in areas with higher forest cover were less cohesive, with better-defined flock subtypes. Flocks also varied across latitude and disturbance gradients as predicted, but effect sizes were small. Our findings indicate that the unstructured nature of Andean flocks might arise as a strategy to cope with harsh environmental conditions.

Structuring the End of the Data Life Cycle - Datasets

Additional data for paper "Structuring the End of the Data Life Cycle".

Figure data for "Layered structures in the upper several hundred meters of the Moon along the Chang'E-4 rover's first 1000-m traverse"

These are the raw data and derived data used to generate figures in the paper "Layered structures in the upper several hundred meters of the Moon along the Chang'E-4 rover's first 1000-m traverse." The data files are in the .mat format, and each column in the channel 1 files represents one trace, which contains 8192 rows (samples). Channel 1 has a time window of 20480 ns, with a sampling interval of 2.5 ns. The CE4-channel-2-imaging-result file refers to the subsurface profile of the regolith along the traverse, with a distance resolution of 3.74 cm and a depth resolution of 2.54 cm.

opencc-by-4.0May 2023View details →

Ground Gamma-ray Spectrometry Data of the Cerro do Jarau Impact Structure

This is gamma-ray dataset that was collected during two field campaings in the Cerro do Jarau impact structure in Brazil. The Cerro do Jarau structure is a ~13.5 km diameter impact structure located in southern Brazil and formed on Cretaceous continental flood basalts of the Serra Geral Formation and underlying sedimentary strata. The available file provides the raw dataset in counts per unit of time; concentration values of K, U along with their respective histograms; and calibration crossplots for each channel.

Obuasi case study data: Performance of neutral SNP barcodes to determine genetic diversity and structure of Plasmodium falciparum in Africa

A small number of informative biallelic single nucleotide polymorphisms (SNPs) have been proposed to be an economical method to fast-track the genotyping and relatedness analysis of Plasmodium falciparum in malaria-endemic areas. Whilst used successfully in low-transmission areas where infections are monoclonal and highly related, we present the first study to evaluate the performance of these 24- and 96-SNP molecular barcodes in African countries characterised by moderate-to-high transmission. Using haplotypes generated from the MalariaGEN P. falciparum Community Project version 6 database, 52.3% of infections were multiclonal, generating high frequencies of mixed-allele calls (MACs) per isolate. Both multiclonality and low heterozygosity of SNPs impeded haplotype construction for analyses of relatedness. Although fewer SNPs provided usable data, these SNP barcodes weakly identified genetic differentiation across large geographic distances. However, both minor and major alleles' frequencies were temporally unstable. We conclude that these standardised SNP barcodes are vulnerable to ascertainment bias. While large numbers of SNPs acquired by whole-genome sequencing and computational methods to construct haplotypes present a way forward, these approaches may not be practical or cost-effective for surveillance on large scales in malaria-endemic areas.

Social network and fitness data from age-structured populations of forked fungus beetles

We investigated the relationships between age, social behavior, and fitness at three levels of organization: the individual, the local social environment, and the population. Replicate groups of forked fungus beetles (Bolitotherus cornutus) were engineered to have either young- or old- biased age structures, and both social and reproductive behaviors were recorded.

Raw data from: Environmental variation structures reproduction and recruitment in long-lived mega-herbivores: Galapagos Giant Tortoises

Understanding drivers of vital rates is important for testing life history theory, predicting population dynamics, and guiding conservation. Migratory, long-lived animals are important to life history theory because they present an extreme among trade-offs in vital rates: delayed maturity, low fecundity, variable recruitment rates, and long generation times. Understanding how vital rates respond to environmental variation has been elusive for such species because of difficulties in studying wide-ranging animals over extended periods. Populations that live on elevation gradients can provide tractable study systems because considerable environmental change occurs over small geographic distances. Galapagos tortoises are an iconic example; they are long-lived, migrate seasonally, face multiple anthropogenic threats, and have cryptic early life history stages for which vital rates are unknown. From 2012–2021, we studied the reproductive ecology of two species of Galapagos tortoises along elevation gradients that coincided with substantial change in climate and vegetation productivity. Specifically, we 1) measured physical and reproductive condition of adult females, 2) tracked the movements of 33 adult females using GPS telemetry, and re-located them seasonally to measure condition, 3) recorded nest temperatures, clutch characteristics, and egg survival from 107 nests, and 4) used radio telemetry to re-locate 104 hatchlings to monitor growth, survival, and movements. We also monitored temperature, rainfall, and primary productivity from field and remotely sensed data along the elevation gradient. Adult females were either elevational migrants or year-round lowland residents. Migrants had higher body condition than residents, and body condition was positively correlated with fecundity. Nests occurred in the hottest, driest part of the tortoise's range, between 6–165m elevation. Clutch size increased with elevation, egg survival declined, and hatchling survival and growth were highest at intermediate elevations. Hatchlings dispersed rapidly between 100–750 m from their nests before becoming sedentary in ranges <0.05 ha. Environmental variability mediated by elevation influenced adult fecundity and juvenile recruitment. Predicted future climates will profoundly impact the relationships between elevation and vital rates of Galapagos tortoises and other species living on elevation gradients. Resilience will be maximized by ensuring connectivity of foraging and reproductive areas within current and possible future elevational ranges of these species.

opencc-by-4.0May 2023View details →

Simulation Data for "GPR161 structure uncovers the redundant role of sterol-regulated ciliary cAMP signaling in the Hedgehog pathway"

Molecular dynamics simulation data for "GPR161 structure uncovers the redundant role of sterol-regulated ciliary cAMP signaling in the Hedgehog pathway"

Axiom canine microarray data from Australian dingoes and domestic dogs for admixture and population structure analysis

Admixture between species is a cause for concern in wildlife management. Canids are particularly vulnerable to inter-specific hybridisation, and genetic admixture has shaped their evolutionary history. Microsatellite DNA testing, relying on a small number of genetic markers and geographically restricted reference populations, has identified extensive domestic dog admixture in Australian dingoes and driven conservation management policy. There has been concern that geographic variation in dingo genotypes could confound ancestry analyses that use a small number of genetic markers. Here we apply genome-wide single nucleotide polymorphism (SNP) genotyping to a set of 385 wild and captive dingoes from across Australia and then carry out comparisons to domestic dogs, and perform ancestry modelling and biogeographic analyses to characterize population structure in dingoes and investigate the extent of admixture between dingoes and dogs in different regions of the continent. We show that there are at least five distinct dingo populations across Australia. We observed limited evidence of dog admixture in wild dingoes, challenging previous reports regarding the occurrence and extent of dog admixture in dingoes, as our ancestry analyses show that previous assessments severely overestimate the degree of domestic dog admixture in dingo populations, particularly in southeastern Australia. These findings strongly support the use of genome-wide SNP genotyping as a refined method for wildlife managers and policy makers to assess and inform dingo management policy and legislation moving forwards.

Data for: Environments and hosts structure the bacterial microbiomes of fungus-gardening ants and their symbiotic fungus gardens

The fungus gardening-ant system is considered a complex, multi-tiered symbiosis between the ants, their fungus, and microorganisms associated with either ants or fungus. We examine the bacterial microbiome of Trachymyrmex septentrionalis and Mycetomoellerius turrifex ants and their symbiotic fungus garden, using 16S rRNA Illumina sequencing, over a large geographical region. Typically microorganisms can be acquired from a parent colony (vertical transmission) or from the environment (horizontal transmission). Because the symbiosis is characterized by co-dispersal of the ants and fungus, elements of both ant and fungus garden microbiome could be characterized by vertical transmission, for example. The goals of this study were to explore how both the ant and fungus garden bacterial microbiome were acquired. The main findings were that different mechanisms appear to explain the structure the microbiomes of ants and their symbiotic fungus gardens. Ant associated microbiomes had a strong host ant signature, which suggests vertical inheritance of the ant associated bacterial microbiome. On the other hand, the bacterial microbiome of the fungus garden was more complex in that some components appear to be structured by the ant host species whereas other by fungal lineage or region. Thus bacteria in fungus gardens appear to be acquired both horizontally and vertically.

Data for: Honey bees (Apis mellifera) modify plant-pollinator network structure, but do not alter wild species' interactions

Honey bees (Apis mellifera) are widely used for honey production and crop pollination, raising concern for wild pollinators, as honey bees may compete with wild pollinators for floral resources. The first sign of competition, before changes appear in wild pollinator abundance or diversity, may be changes to wild pollinator interactions with plants. Such changes for a community can be measured by looking at changes to metrics of resource use overlap in plant-pollinator interaction networks. Studies of honey bee effects on plant-pollinator networks have usually not distinguished whether honey bees alter wild pollinator interactions, or if they merely alter total network structure by adding their own interactions. To test this question, we experimentally introduced honey bees to a Canadian grassland and measured plant-pollinator interactions at varying distances from the introduced hives. We found that honey bees increased the network metrics of pollinator and plant functional complementarity and decreased interaction evenness. However, in networks constructed from just wild pollinator interactions, honey bee abundance did not affect any of the metrics calculated. Thus, all network structural changes to the full network (including honey bee interactions) were due only to honey bee-plant interactions, and not to honey bees causing changes in wild pollinator-plant interactions. Given widespread and increasing use of honey bees, it is important to establish whether they affect wild pollinator communities. Our results suggest that honey bees did not alter wild pollinator foraging patterns in this system, even in a year that was drier than the 20-year average.

Data from: Positive plant diversity effects on soil microbial drought resistance are linked to variation in labile carbon and microbial community structure

Biodiversity loss and drought are substantially altering both above-and belowground terrestrial ecosystem functioning, but mechanistic understanding of plant diversity effects on the drought resistance of soil microbial biomass remains limited. We designed a mesocosm experiment to examine drought resistance of soil microbial biomass along a plant species richness gradient (five plant species richness levels based on old-field communities). We calculated resistance of microbial biomass to drought and recorded key belowground properties which may influence microbial resistance to drought (i.e., microbial diversity, microbial community structure, soil carbon stocks and root biomass). Plant species richness had a positive effect on microbial resistance to drought. Variation in microbial resistance to drought was linked to properties of the fungal community in ambient soil (Shannon diversity, arbuscular mycorrhizal fungal richness and abundance) but not soil bacterial diversity. Moreover, microbial resistance to drought increased with increasing root biomass and dissolved organic carbon recorded under ambient conditions. These results highlight the importance of plant diversity for microbial biomass stability in our old-field study system with implications for biogeochemical cycling, and suggest that indirect effects of plant species richness on labile soil carbon and soil fungi may drive resistance of soil microbial biomass to drought.

Data for: Antibiotic-degrading resistance changes bacterial community structure via species-specific responses

Some bacterial resistance mechanisms degrade antibiotics, potentially protecting neighbouring susceptible cells from antibiotic exposure. We do not yet understand how such effects influence bacterial communities of more than two species, which are typical in nature. Here, we used experimental multispecies communities to test the effects of clinically important pOXA-48-plasmid-encoded resistance on community-level responses to antibiotics. We found that resistance in one community member reduced antibiotic inhibition of other species, but some benefitted more than others. Further experiments with supernatants and pure-culture growth assays showed the susceptible species profiting most from detoxification were those that grew best at degraded antibiotic concentrations (greater than zero, but lower than the starting concentration). This pattern was also observed on agar surfaces, and the same species also showed relatively high survival compared to most other species during the initial high-antibiotic phase. By contrast, we found no evidence of a role for higher-order interactions or horizontal plasmid transfer in community-level responses to detoxification in our experimental communities. Our findings suggest carriage of an antibiotic-degrading resistance mechanism by one species can drastically alter community-level responses to antibiotics, and the identities of the species that profit most from antibiotic detoxification are predicted by their intrinsic ability to survive and grow at changing antibiotic concentrations.