Find research datasets worth reusing

Data for: Population structure of a grassland songbird (Dolichonyx oryzivorus) to inform conservation units

Understanding the patterns and processes driving population structure is crucial for conservation planning. Spatial conservation units (CUs) for one or more species have been defined using similarities in communities, habitats, and resource management concerns. Additionally, CU boundaries can be informed by population genetic structure. Here, we determined the population structure of the Bobolink (Dolichonyx oryzivorus), a migratory grassland bird. Its breeding range spans longitudinally across most of North America in the northern U.S. and southern Canada, and its population has declined by 59% from 1971 to 2014. We sampled blood from Bobolinks at seven breeding sites and used a ddRAD sequencing approach to identify 3236 SNPs for population genetic analyses. Using the Bayesian clustering approach, STRUCTURE, we found low levels of genetic differentiation across the breeding range. F st values ranged from 0.002 to 0.036 among all population pairs, and genetic structure followed an isolation-by-distance model. Despite low levels of genetic differentiation, we found evidence for four genetic groupings— breeding populations in Oregon and British Columbia were distinct from each other as well as from Central and eastern North American breeding populations. Investigating the demographic history of the populations using approximate Bayesian computation, we found evidence that western Bobolink populations are not relict populations but instead were founded during a recent westward range expansion, possibly enabled by agricultural expansion. We identify four genetics-based CUs that may serve as a complementary spatial framework, broader in scale compared to the commonly-used Bird Conservation Regions, for defining and achieving population objectives.

Data for: Surrounding landscape, habitat and hybridization dynamics drive population structure and genetic diversity in the Saltmarsh Sparrow (Ammospiza caudacuta)

Determining factors that shape a species' population genetic structure is beneficial for identifying effective conservation practices. We assessed population structure and genetic diversity for Saltmarsh Sparrow (Ammospiza caudacuta), an imperiled tidal marsh specialist, using 13 microsatellite markers and 964 individuals sampled from 24 marshes across the breeding range. We show that Saltmarsh Sparrow populations are structured regionally by isolation-by-distance, with gene flow occurring among marshes within ~110-135 km of one another. Isolation-by-resistance and isolation-by-environment also shape genetic variation; several habitat and landscape features are associated with genetic diversity and genetic divergence among populations. Human development in the surrounding landscape isolates breeding marshes, reducing genetic diversity and increasing population genetic divergence, while surrounding marshland and patch habitat quality (proportion high marsh and sea-level-rise trend) have the opposite effect. The distance of the breeding marsh to the Atlantic Ocean also influences genetic variation, with marshes farther inland being more divergent than coastal marshes. In northern marshes, hybridization with Nelson's Sparrow (A. nelsoni) strongly influences Saltmarsh Sparrow genetic variation, by increasing genetic diversity in the population; this has a concomitant effect of increasing genetic differentiation of marshes with high levels of introgression. From a conservation perspective, we found that the majority of population clusters have low effective population sizes, suggesting a lack of resiliency. To conserve the representative breadth of genetic and ecological diversity and to ensure redundancy of populations, it will be important to protect a diversity of marsh types across the latitudinal gradient of the species range, including multiple inland, coastal and urban populations, which we have shown to exhibit signals of genetic differentiation. It will also require maintaining connectivity at a regional level, by promoting high marsh habitat at the scale of gene flow (~130 km), while also ensuring "stepping stone" populations across the range.

Data from: Insight into the structural and magnetotransport properties of epitaxial alpha-Fe2O3/Pt(111) heterostructures: The role of the reversed layer sequence

We report on the chemical structure and spin Hall magnetoresistance (SMR) in epitaxial α-Fe2O3(hematite)(0001)/Pt(111) bilayers with hematite thicknesses of 6 nm and 15 nm grown by molecular beam epitaxy on a MgO(111) substrate. Unlike previous studies that involved Pt overlayers on hematite, the present hematite films were grown on a stable Pt buffer layer and displayed structural changes as a function of thickness. These structural differences (the presence of a ferrimagnetic phase in the thinner film) significantly affected the magnetotransport properties of the bilayers. We observed a sign change of the SMR from positive to negative when the thickness of hematite increased from 6 nm to 15 nm. For α-Fe2O3(15 nm)/Pt, we demonstrated room-temperature switching of the Néel order with rectangular, nondecaying switching characteristics. Such structures open the way to extending magnetotransport studies to more complex systems with double asymmetric metal/hematite/Pt interfaces.

opencc-by-4.0Aug 2022View details →

structural variants data

The origin data are used to replicate our work. The topic is "Accuracy assessment of structural variation calling methods for breast cancer gene panel in the absence of gold standard".

opencc-by-4.0Jul 2023View details →

Basic Functions of the Numerical Structure of Scientific Data

Thematic meanings of numerical definitions of subject data in various fields of science lead to manipulation of digital codes of known physical, chemical, biological, genetic and other quantities. In principle, each scientific justification contains, to one degree or another, a quantitative, qualitative characteristic of comparison or content. Thus, the language of natural numbers, like mathematical operations, can be accompanied by any definition in any terminology. In this text, the author does not use well-known terms related to the main scientific areas. In this text, the numbers speak for themselves. Any combination of orders or compositions of complex numerical structures presented in this text has its own logical meaning. Any paradox of numerical combinations is an algorithm of real values of numbers.

Data from: Virus community structuring is shaped by habitat heterogeneity and resource utilisation strategies

After decades of disconcerted research, we still recognise large gaps in the understanding of mechanisms that govern disease dynamics in complex biological communities. To determine how spatial structuring of plant communities caused by anthropic disturbance affects resource utilisation traits of viruses, we combine high-throughput, network, and metacommunity approaches. We find that the disturbance gradient corresponded to network modules and habitat specificity exhibited by a majority of viruses. Communities were connected through key hub species of either generalist viruses or high potential host reservoirs. Spatial dependencies were evident in regression models of species richness and correlations between metacommunity structure and both host range and transmission mode at finer spatial resolutions. We propose that virus community assembly is influenced by variation in niche opportunities. Distinctions in virus community composition caused by resource compartmentalisation can be used to track ecological traits important in forecasting transmission risk.

Data from: Genomic diversity and geographical structure of the Pyrenean desman

The Pyrenean desman (Galemys pyrenaicus) is a small semi-aquatic mammal endemic to the Iberian Peninsula. The species has recently experienced a strong decline and some of its populations are severely threatened with extinction. To help in the preservation of this species, it is critical to understand its genetic structure and main evolutionary units, as these may have specific local adaptations and could be of great conservation value. Sequencing reduced representation libraries (ddRAD) from 26 specimens selected from across its entire range, we obtained around 45,000 loci per specimen and 1185 single nucleotide polymorphisms. Heterozygosity varied substantially among individuals from different areas. Interestingly, specimens from the southeastern Pyrenees had some of the lowest proportions of heterozygous positions inferred from genome-wide data in mammals so far. In addition, we estimated a tree reflecting genomic divergence, performed a principal component analysis, and carried out a Bayesian analysis of the population structure. Combined evidence supported the existence of five distinct genomic clusters largely coincident with the main mountain ranges where the species occurs, with few specimens presenting relevant admixture levels. There was good correspondence between these populations and the mitochondrial lineages detected in a previous study, yet substantial differences in some areas demonstrate the importance of performing genomic analysis to reveal the whole population history. Although the analysis of further specimens is necessary to better characterize the distribution of the different evolutionary units, the distinctive geographical structure of this species revealed by the genomic data should be considered in future conservation plans.

opencc-by-4.0Jul 2023View details →

Data files for 'Tan et al., (2023). Structural heterogeneity-controlled rupture process of the 2021 Mw 7.1 Fukushima, Japan earthquake revealed by joint inversion of seismic and geodetic data'

slip model.dat: rupture model of the 2021 Mw 7.1 Fukushima earthquake In 'slip model.dat', each row contains the moment rate function of each sub-fault. The numbers of the sub-faults are given in the first two columns.

Data from: Philopatry influences the genetic population structure of the blacktip shark (Carcharhinus limbatus) at multiple spatial scales

Understanding how interactions among microevolutionary forces generate genetic population structure of exploited species is vital to the implementation of management policies that facilitate population persistence. Philopatry displayed by many coastal shark species can impact gene flow and facilitate selection, and thus has direct implications for the spatial scales of management plans. Here, genetic structure of the blacktip shark (Carcharhinus limbatus) was examined using a mixed-marker approach based on mitochondrial control region sequences and 4,339 SNP-containing loci generated using ddRAD-Seq. Genetic variation was assessed among young-of-the-year sampled in 11 sites in waters of the United States in the western North Atlantic Ocean, including the Gulf of Mexico. Spatial and environmental analyses detected 68 nuclear loci putatively under selection, enabling separate assessments of neutral and adaptive genetic structure. Both mitochondrial and neutral SNP data indicated three genetically distinct units – the Atlantic, eastern Gulf, and western Gulf – that align with regional stocks and suggest regional philopatry by males and females. Heterogeneity at loci putatively under selection, associated with temperature and salinity, was observed among sites within Gulf units, suggesting local adaptation. Furthermore, five pairs of siblings were identified in the same site across timescales corresponding with female reproductive cycles. This indicates that females re-used a site for parturition, which has the potential to facilitate the sorting of adaptive variation among neighboring sites. The results demonstrate differential impacts of microevolutionary forces at varying spatial scales and highlight the importance of conserving essential habitats to maintain sources of adaptive variation that may buffer species against environmental change.

Data for: Lipid biomarkers recording marine microbial community structure changes through the Frasnian‐Famennian mass extinction event

This dataset contains data for a research article published on Geobiology. The article is entitled " Lipid biomarkers recording marine microbial community structure changes through the Frasnian‐Famennian mass extinction event". This study aims to reconstruct changes in the marine microbial community structure through the Late Devonian Frasnian‐Famennian (F‐F) transition. We performed a multiproxy investigation on a drill core of the Upper Devonian New Albany Shale from the Illinois Basin (western Kentucky, USA). Detailed information regarding the data collection, analysis, and interpretation can be found in the following paper: Chen J., Hogancamp N., Lu M., Ikejiri T., Malina N., Ojeda A., Sun Y., Lu Y. 2023. Lipid Biomarkers Recording Marine Microbial Community Structure Changes Through the Frasnian‐Famennian Mass Extinction Event. Geobiology <a href="https://doi.org/10.1111/gbi.12568">https://doi.org/10.1111/gbi.12568</a>

Macrocystis pyrifera before (2008) and after (2018-19) microsatellite data in Structure format

Given the impacts of climate change and other anthropogenic stressors on marine systems, there is a need to accurately predict how species respond to changing environments and disturbance regimes. The use of genetic tools to monitor temporal trends in populations gives ecologists the ability to estimate changes in genetic diversity and effective population size that may be undetectable by traditional census methods. Although multiple studies have used temporal genetic analysis, they usually involve commercially important species, and rarely sample before and after disturbance. In this study, we run a temporal analysis of giant kelp, Macrocystis pyrifera, genetic diversity over the scope of 10 years (2008-2018) using the same microsatellite marker panel to assess the genetic consequences of disturbance in several populations of giant kelp (Macrocystis pyrifera) in the Southern California Bight. The study is a rare pre- and post-disturbance microsatellite analysis that included declines to giant kelp caused by the 2015/16 El Nino Southern Oscillation event. We used canopy biomass estimated by remote sensing (Landsat) to quantify the extent of disturbance to kelp beds, and sea surface temperature data to understand how kelp was pushed towards its temperature limits during this period. Despite prolonged periods with decreased canopy at several sites, no changes in genetic structure and allelic richness were observed. We argue that giant kelp in the region is best described as a "patchy population" system where true extinctions are rare. We discuss how deep refugia of subsurface sporophytes and cryptic microscopic life stages could have kept genetic diversity through disturbance. Given the increasing effects of climate change and uncertainty in modeling impacts of species with cryptic life history stages, we suggest further investigation to reveal the role such stages play in species resilience. Genetic monitoring studies of sites selected by remote census demographic and climate surveys should be continued in the future given the predicted impacts of climate change.

Data from: The effect of initial vortex asymmetric structure on tropical cyclone intensity change in response to an imposed environmental vertical wind shear

Previous studies have investigated how the environmental vertical wind shear (VWS) may trigger the asymmetric structure in an initially axisymmetric tropical cyclone (TC) vortex and how TC intensity changes in response. In this study, the possible effect of the initial vortex asymmetric structure on the TC intensity change in response to an imposed environmental VWS is investigated based on idealized full-physics model simulations. Results show that the effect of the asymmetric structure in the initial TC vortex can either enhance or suppress the initial weakening of the TC in response to the imposed environmental VWS. When the initial asymmetric structure is in phase of the VWS-induced asymmetric structure, the TC weakening will be enhanced and vice versa. Our finding calls for realistic representation of initial TC asymmetric structure in numerical weather prediction models and observations to better resolve the asymmetric structure in TCs.

opencc-by-4.0Aug 2023View details →

Data set for "Electrical detection of the flat band dispersion in van der Waals field-effect structures"

Data set for "Electrical detection of the flat band dispersion in van der Waals field-effect structures" paper published in doi:10.1038/s41565-023-01489-x

Data from: Phylogenetic, population structure, and population demographic analyses reveal that Vicia sepium in Japan is native and not introduced

Vicia sepium (bush vetch) is a perennial legume widely distributed throughout the Eurasian continent. However, its distribution in Japan is limited to Mt. Ibuki and small parts of central and southern Hokkaido. Therefore, each Japanese V. sepium lineage has been considered to have been introduced separately from Europe. Here, we examined whether the species was introduced or not on the basis of cpDNA sequences and genome-wide SNPs from Japanese and overseas samples. Both the cpDNA haplotype network and the nuclear DNA phylogenetic tree showed that Japanese V. sepium is monophyletic. Furthermore, although the nuclear DNA phylogenetic tree also showed that each lineage is clearly monophyletic, genetic admixture of the genetic cluster dominated in the Hokkaido lineage was also detected in the Mt. Ibuki lineage. Population divergence analysis showed that the two lineages diverged during the last glacial period. The Mt. Ibuki lineage showed a sudden population decline 300–400 years ago, indicating that some anthropogenic activity might be involved, while the Hokkaido lineage showed a gradual population decline from 5,000 years ago. Consequently, these two lineages show low current genetic diversity compared with overseas lineages. These results show that the Japanese V. sepium is not introduced but is native.

opencc-by-4.0Aug 2023View details →

biogasoutcomesmalawi: Data for 61 semi-structured interviews with biogas owners in Malawi

This dataset consists of 61 semi-structured interviews with biogas owners in the Southern Region of Malawi. Interviews were conducted over multiple visits to sites over the course of a two-year period between June 2021 and October 2022.

opencc-by-4.0Aug 2023View details →

Data for the manuscript "Bridged Nucleic Acid ASOs over Locked Nucleic Acid ASOs and their impact on the structure and stability of ASO/RNA duplexes"

The dataset contains: DFT and MD Data for the manuscript "Bridged Nucleic Acid ASOs over Locked Nucleic Acid ASOs and their impact on the structure and stability of ASO/RNA duplexes".

opencc-by-4.0Sep 2023View details →

Data for submitted manuscript "Connections between Sub-cloud Coherent Structures and the Life Cycle of Shallow Cumulus Clouds: Evidence from Large Eddy Simulation"

This is the dataset for a submitted manuscript "Connections between Sub-cloud Coherent Structures and the Life Cycle of Shallow Cumulus Clouds: Evidence from Large Eddy Simulation" for peer review. The NetCDF file includes masked objects for sub-cloud coherent structures and cloud for tracking.

openother-openSep 2023View details →

OMaraLab/OCT1_2023: Structural Basis of Promiscuous Substrate Transport in Organic Cation Transporter 1 - MD DATA

Molecular dynamics trajectory data relating to Structural Basis of Promiscuous Substrate Transport in Organic Cation Transporter 1, by Yi C. Zeng, Meghna Sobti, Ada Quinn, Nicola J. Smith, Simon H. J. Brown, Jamie I. Vandenberg, Renae M. Ryan, Megan L. O'Mara & Alastair G. Stewart.

opencc-zeroSep 2023View details →

Data from: Divergence in the internal genital morphology of females is correlated with divergence in male intromittent structures among populations of a millipede

Our understanding of genital evolution comes largely from studies of male genitalia. Females have received far less attention because of the difficulties inherent in quantifying the shapes of their internal genital structures. Here we combine advances in micro-computed tomography with a new landmark free method of quantifying three-dimensional trait shape, to document patterns of divergence in female genital shape, and the correlated divergence of male genitalia among populations of the millipede Antichiropus variabilis. We used single nucleotide polymorphisms to estimate levels of neutral genetic divergence among seven populations of millipede. Genetic divergence was high and correlated with geographic distance. Comparing phenotypic divergence in genital shape to neutral genetic divergence, we found that genital shape for both females and males has diverged more than would be expected from random drift, consistent with a pattern of directional selection. While there was significant covariation between female and male genital shape across populations, the magnitude of divergence in genital shape between the sexes was not correlated. Our results demonstrate the utility of using three-dimensional scanning technologies to examine female genital traits and add to a small but growing number of studies showing that like male genitalia, female genitalia can be under strong directional selection.