Find research datasets worth reusing

Data from: Climate and vegetation structure shape ant communities along elevational gradients on the Colorado Plateau

Aim: Terrestrial animal communities are largely shaped by vegetation and climate. With climate also shaping vegetation, can we attribute animal patterns solely to climate? To understand this, we compare the relative and interactive effects of climate and vegetation on an animal community. Our study observes ant community changes along climatic gradients (i.e. elevational gradients) within different habitat types (i.e. open and forest). We compare the explanatory powers and effect sizes of climate and vegetation variables on ant communities and describe what drives elevational distributions of ant species. Location: Colorado Plateau, southwestern United States Taxon: Formicidae Methods: We sampled ants and vegetation along two elevational gradients spanning 1132m with average annual temperature and precipitation differences of 5.7C° and 645 mm, respectively. Regression analysis and structural equation modeling was then used to test the relative effects of climate and vegetation variables on ant communities. Results: Climate variables had the strongest correlations and the largest effect sizes on ant communities, while vegetation composition, richness, and primary productivity were relatively small. Precipitation was the strongest predictor for most ant community metrics. Ant richness and abundance had a negative relationship with precipitation in forested habitats, and positive in open habitats. Main conclusions: Our results show strong direct climate effects on ants with little or no effects of vegetation composition or primary productivity, but contrasting patterns between vegetation type (i.e. forested vs open) with precipitation. This indicates vegetation structure can modulate climate responses of ant communities. Our study demonstrates climate-animal relationships may vary among vegetation types which can impact both findings from elevational studies and how communities will react to changes in climate.

opencc-by-4.0Jul 2021View details →

Data for "A method for intuitively extracting macromolecular dynamics from structural disorder"

Analyses associated with the manuscript "A method for intuitively extracting macromolecular dynamics from structural disorder".

Data from: BIOVERA-Tree: tree diversity, community composition, forest structure and functional traits along gradients of forest-use intensity and elevation in Veracruz, Mexico

Here, we describe BIOVERA-Tree, a database on tree diversity, community composition, forest structure, and functional traits collected in 120 forest plots distributed along an extensive elevational gradient in Veracruz State, Mexico. BIOVERA-Tree includes information on forest structure from three levels of forest-use intensity, namely old-growth, degraded, and secondary forest, replicated across eight elevations from sea-level to near the tree line at 3500 m and on size and location of 4549 tree individuals with a diameter at breast height ≥ 5 cm belonging to 216 species, 154 genera, and 80 families. We also report measurements of eight functional traits, namely wood density for 143 species, maximum height for 216 species and leaf traits including: specific leaf area, lamina density, leaf thickness, chlorophyll content, and leaf area for 148 species and leaf dry matter content for 145 species.

Data from: Distribution and biogeography of Sanguina snow algae: fine-scale sequence analyses reveal previously unknown population structure

It has been previously suggested that snow algal species within the genus Sanguina (S. nivaloides and S. aurantia) show no population structure despite being found globally (S. nivaloides) or throughout the Northern Hemisphere (S. aurantia). However, systematic biogeographic research into global distributions is lacking due to few genetic and no genomic resources for these snow algae. Here, using all publicly available and previously unpublished Sanguina sequences of the Internal Transcribed Spacer 2 region, we investigate if this purported lack of population structure within Sanguina species is supported by additional evidence. Using a minimum entropy decomposition (MED) approach to examine fine-scale genetic population structure, we find that these snow algae populations are largely distinct regionally and have some interesting biogeographic structuring. This is in opposition to the currently accepted idea that Sanguina species lack any observable population structure across their vast ranges and highlights the utility of fine-scale (sub-OTU) analytical tools to delineate geographic and genetic population structure. This work extends the known range of S. aurantia and emphasizes the need for development of genetic and genomic tools for additional studies on snow algae biogeography.

Nonrandom missing data can bias PCA inference of population genetic structure

Population genetic studies in non-model systems increasingly use next-generation sequencing to obtain more loci, but such methods also generate more missing data that may affect downstream analyses. Here we focus on the Principal Component Analysis (PCA) which has been widely used to explore and visualize population structure with mean-imputed missing data. We simulated data of different population models with various total missingness (1%, 10%, 20%) introduced either randomly or biased among individuals or populations. We found that individuals biased with missing data would be dragged away from their real population clusters to the origin of PCA plots, making them indistinguishable from true admixed individuals and potentially leading to misinterpreted population structure. We also generated empirical data of the big brown bat (Eptesicus fuscus) using restriction site-associated DNA sequencing (RADseq). We filtered three data sets with 19.12%, 9.87%, and 1.35% total missingness, all showing nonrandom missing data with biased individuals dragged towards the PCA origin, consistent with results from simulations. We highlight the importance of considering missing data effects on PCA in non-model systems where nonrandom missing data are common due to varying sample quality. To help detect missing data effects, we suggest to 1) plot PCA with a color gradient showing per sample missingness, 2) interpret samples close to the PCA origin with extra caution, 3) explore filtering parameters with and without the missingness-biased samples, and 4) use complementary analyses (e.g., model-based methods) to cross-validate PCA results and help interpret population structure.

opencc-by-4.0Sep 2021View details →

Source Data for the publication "From crystallographic data to solution structure of photoreceptors: the case of AppA BLUF domain"

This dataset contains the raw data for the results shown in the paper, all in excel format, one sheet per file: <ul> <li> chemical_shifts.xlsx - Chemical shifts of FMN and residues (on optimized frames) </li> <li> excitation_energies.xlsx - Excitation energies of FMN (on optimized frames) </li> <li> Distance_H3.xlsx - Distance between ASN-OD1 and FMN-H3 (on optimized frames) </li> <li> CO_freq_QMMM_MD.xlsx - Average C=O frequencies and relevant distances for each QM/MM MD.   </li> </ul>

opencc-zeroSep 2021View details →

Diversity patterns and community structure of the macrofauna along the beach-inland transition zone of small tropical islands: supporting raw data and code

Biodiversity follows distinct and observable patterns. Where to systems meet, biodiversity is often increased, due to overlapping occurrence ranges and the presence of specialized species that can tolerate the dynamic conditions of the transition zones. One of the most pronounced transition zones occurs at shores, where oceans and terrestrial habitat collide, forming the shore-inland transition zone. The relevance of this transition zone in shaping a system's community structure is particularly pronounced on small islands due to their high shore-to-inland-area ratio. However, the community structure of insular faunas along this transition zone is unknown. Here, we investigated the diversity patterns along the beach-inland transition zone of small islands and tested the hypothesis that species diversity increases towards the transition zone where beach and interior habitat meet. By measuring environmental parameters, resource availability, and macrofauna diversity along transects running across the beach-inland transition zone, we show that a gradual change in species composition from beach to the inland exists, but neither taxa richness, Shannon diversity, nor overall abundance change significantly. These findings give important insight into insular community structure at the transition zone from sea to land that are relevant to better understand the dynamic and unique characteristics of insular ecosystems.

opencc-by-4.0Jan 2019View details →

Data sets associated with "Deep structure of the lunar South Pole–Aitken basin"

These grid files contain the data used in Figures 2 and 3 of the submitted manuscript, "Deep structure of the lunar South Pole–Aitken basin". Although the data are global, note that they are not meant to be used outside of the South Pole–Aitken basin.

opencc-zeroOct 2021View details →

Microsatellites data set: Correlated population genetic structure in a three-tiered host-parasite system: the potential for coevolution and adaptive divergence

Three subspecies of Northern Bahamian Rock Iguanas, Cyclura cychlura, are currently recognized: C. c. cychlura,restricted to Andros Island, and C. c. figginsi and C. c. inornata, native to the Exuma Island chain. Populations on Andros are genetically distinct from Exuma Island populations, yet genetic divergence among populations in the Exumas is inconsistent with the two currently recognized subspecies from those islands. The potential consequences of this discrepancy might include the recognition of a single subspecies throughout the Exumas rather than two. That inference also ignores evidence that populations of C. cychlura are potentially adaptively divergent. We compared patterns of population relatedness in a three-tiered host-parasite system: C. cychlura iguanas, their ticks (genus Amblyomma, preferentially parasitizing these reptiles), and Rickettsia spp. endosymbionts (within tick ectoparasites). Our results indicate that while C. c. cychlura on Andros is consistently supported as a separate clade, patterns of relatedness among populations of C. c. figginsi and C. c. inornata within the Exuma Island chain are more complex. The distribution of the hosts, different tick species, and Rickettsia spp., supports the evolutionary independence of C. c. inornata. Further, these patterns are also consistent with two independent evolutionarily significant units within C. c. figginsi. Our findings suggest coevolutionary relationships between the reptile hosts, their ectoparasites, and rickettsial organisms, suggesting local adaptation. This work also speaks to the limitations of using neutral molecular markers from a single focal taxon as the sole currency for recognizing evolutionary novelty in populations of endangered species.

opencc-by-4.0Oct 2021View details →

Codes and data regarding "Temporal dissipative structures in optical Kerr resonators with transient loss fluctuation"

Here we upload codes and figure data relate to the article "Temporal dissipative structures in optical Kerr resonators with transient loss fluctuation" that was published on Optics Express (<a href="https://doi.org/10.1364/OE.439212">https://doi.org/10.1364/OE.439212</a>) Please note that the codes have been tested using Matlab in the version of 2019a. The ".opj" and ".opju" files in the folder "Figure_data" can be opened via <a href="https://www.originlab.com/viewer/">the Origin viewer</a> (a free app published by Originlab)

opencc-by-4.0Oct 2021View details →

Raw data for "Multi-Length Scale Structure of 2D/3D Dion–Jacobson Hybrid Perovskites Based on an Aromatic Diammonium Spacer"

Raw solid-state NMR data (Bruker format), and optical and XRD data (Microsoft Excel format).

opencc-by-4.0Oct 2021View details →

Data set of 1) plant abundance in the herb layer and 2) Shrub and tree composition and structure following forest management along a chronosequence

In each site (1200 m²), three circular plots (400 m²) were established (total of 198 plots). Data presented here for 1) plant of the herb layer and 2) shrub and tree are grouped by site (addition of three plots).  In the herb layer, total plant species identity and abundance (percentage cover) were sampled in each plot using eight circular micro-plots of 4 m². Data were collected in 2016 and 2017, between June and August. To minimize seasonal variability and allow detection of early spring species, plants (identity and abundance) in the herb layer were measured twice (once in June to early-July, and once in late-July to August). For tree, in each plot, species identity, diameter at breast height (DBH, 1.3 m) and locations of each tree > 9.1 cm DBH were determined. In each plot, species identity and DBH of shrubs and small trees (DBH range: 1.1 to 9.1 cm) were measured in three circular micro-plots of 25 m². Data that were related to the shrub-canopy layer included all trees and shrubs with DBH > 1.1 cm. Here, in each site, forest composition and structure is represented by different combinations of DBH classes (1.1-4 cm, 4-9.1 cm, 9.1-20 cm, 20-35 cm, >35 cm) and species. Plant community composition and abundance were assessed in unmanaged forests (sites of old-growth forest > 100 years, with dominant and co-dominant trees older than 200 years, and no obvious sign of past harvesting), and in even-aged and uneven-aged managed forests along a chronosequence (< 5 years, 15 years, 30 years after forest harvesting).

opencc-by-4.0Dec 2022View details →

Substrate-Binding Guides Individual Melibiose Permeases MelB to Structurally Soften and to Destabilize Cytoplasmic Middle-Loop C3. Blaimschein et al.: Data sets

Data sets used in the manuscript 'Substrate-Binding Guides Individual Melibiose Permeases MelB to Structurally Soften and to Destabilize Cytoplasmic Middle-Loop C3' by Blaimschein et al. The analysis scripts can be found at https://doi.org/10.5281/zenodo.7268838

opencc-by-4.0May 2022View details →

Structural data for "Structural and rheological evolution of brittle fault zones in mafic crust: Implications for the strength of oceanic transform faults"

Structural data for "Structural and rheological evolution of brittle fault zones in mafic crust: Implications for the strength of oceanic transform faults"

openNov 2022View details →

Data from: Chromosome-scale reference genome and RAD-based genetic map of yellow starthistle (Centaurea solstitialis) reveal putative structural variation and QTLs associated with invader traits

The data directory here includes all of the data and scripts necessary to recreate the results and plots for the manuscript titled "Chromosome-scale reference genome and RAD-based genetic map of yellow starthistle (Centaurea solstitialis) reveal putative structural variation and QTLs associated with invader traits". These data include a genetic map, QTL analysis, paleolog analysis, gene synteny analysis,  and assembly validation for yellow starthistle (Centaurea solstitialis).

Datasets related to paper "Crustal structure and fault geometries of the Garhwal Himalaya, India: Insight from new high-resolution gravity data modeling and PSO inversion"

The files include Satellite gravity data, topography and earthquake data used in the paper "Crustal structure and fault geometries of the Garhwal Himalaya, India: Insight from new high-resolution gravity data modeling and PSO inversion" by Chamoli A., Rana S., Dwivedi D., Pandey A.K.. This has been submitted to Journal of Geophysical Research: Solid Earth. Restrictions applied to the availability of the land gravity data set.

Structural control within flawed rock specimens under external loading as visualized through repeating nucleation on multiple sites by acoustic emission (AE) [DATA]

Data for article: Structural control within flawed rock specimens under external loading as visualized through repeating nucleation on multiple sites by acoustic emission (AE).

Data Sets for: Complete Description of the LaCl3-NaCl Melt Structure and the Concept of a Spacer Salt that Causes Structural Heterogeneity

Data Sets for published figures and sample input files for PIM and AIMD simulations in paper <a href="https://doi.org/10.1021/jacs.2c09987">https://doi.org/10.1021/jacs.2c09987</a>   Complete Description of the LaCl3–NaCl Melt Structure and the Concept of a Spacer Salt That Causes Structural Heterogeneity Matthew S. Emerson, Shobha Sharma, Santanu Roy*, Vyacheslav S. Bryantsev*, Alexander S. Ivanov*, Ruchi Gakhar*, Michael E. Woods, Leighanne C. Gallington, Sheng Dai, Dmitry S. Maltsev, and Claudio J. Margulis*

West Spitsbergen Fold and Thrust Belt: a digital educational data package for teaching structural geology

The following digital educational data package is provided as part of the submission of the publication Horota et al. (2022) West Spitsbergen Fold and Thrust Belt: a digital educational data package for teaching structural geology, considered for publication in the Journal of Structural Geology. The dataset contains a QGIS, ArcGIS Pro and a Petrel projects with all the associated data.