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opencc-zeroMar 2024View details →

Data from: Population structure and species delimitation in the Wehrle's salamander complex

Species are the fundamental unit of biodiversity studies. However, many species complexes are difficult to delimit, especially those characterized by complicated patterns of population structure. Salamanders in the family Plethodontidae often form species by slowly fragmenting across a landscape over space and time. They thus provide many examples of species complexes in which gradual Darwinian evolution has resulted in multiple units of varying degrees of differentiation, including incompletely separated lineages. Here we report on a molecular systematic investigation of woodland salamanders in the Plethodon wehrlei group, which has recently been split from two species into five. To quantify patterns of genetic variation, we collected genetic samples from 24 individuals from 20 populations, including all species and representing a carefully selected subset of previous work. From these samples, we obtained genomic data using anchored hybrid enrichment, which resulted in 319 loci averaging 1300 base pairs in length. Biallelic single nucleotide polymorphisms (SNPs) were randomly selected from 316 of these loci for some analyses. We examined patterns of genetic structure using PCA, DAPC, FEEMS, and STRUCTURE, and found that all of the recognized species formed genetic clusters; however, P. wehrlei and P. punctatus were relatively weakly differentiated, and STRUCTURE identified three separate clusters within P. jacksoni. Species trees inferred using wASTRAL, BPP, and TreeMix all recovered the same topology, with P. dixi sister to the other taxa, which included a northern clade (P. wehrlei, P. punctatus, P. pauleyi) and a southern clade (P. jacksoni, with three separate groups). TreeMix only inferred one gene flow event. We evaluated the candidate species using BPP and the genealogical divergence index (gdi). While BPP delimited all candidate species with strong support (all posterior probabilities = 1.0), the gdi only strongly supported P. dixi and P. pauleyi, both of which have only been recently described. We discuss the difficult problem of species delimitation in groups that form species via range fragmentation. We also provide a vision for future research with the aim of better testing and diagnosing the species diversity within the P. wehrlei group.

opencc-zeroMar 2024View details →

Data from: Range-wide genetic analysis of an endangered bumble bee (Bombus affinis) reveals population structure, isolation by distance, and low colony abundance

Declines in bumblebee species ranges and abundances are documented across multiple continents and have prompted the need for research to aid species recovery and conservation. The rusty patched bumblebee (Bombus affinis) is the first federally-listed bumblebee species in North America. We conducted a range-wide population genetics study of B. affinis from across all extant conservation units to inform conservation efforts. To understand the species' vulnerability and help establish recovery targets, we examined population structure, patterns of genetic diversity, and population differentiation. Additionally, we conducted site-level analysis of colony abundance to inform prioritizing areas for conservation, translocation, and other recovery actions. We find substantial evidence of population structuring along an east-to-west gradient. Putative populations show evidence of isolation by distance, high inbreeding coefficients, and a range wide male diploidy rate of ~15%. Our results suggest the Appalachians represents a genetically distinct cluster with high levels of private alleles and substantial differentiation from the rest of the extant range. Site-level analyses suggest low colony abundance estimates for B. affinis compared to similar datasets of stable, co-occurring species. These results lend genetic support to trends from observational studies suggesting B. affinis has undergone a recent decline and exhibits substantial spatial structure. The low colony abundances observed here suggest caution in overinterpreting the stability of populations even where B. affinis is reliably detected interannually. These results help delineate informed management units, provide context for the potential risks of translocation programs, and can help set clear recovery targets for this and other threatened bumblebee species.

opencc-zeroMar 2024View details →

Data from: Landscape heterogeneity drives population structure in four western bumble bee species

Bumble bees are critical pollinators in wild, agricultural, and urban ecosystems—providing the necessary ecological services for food and crop production. In western North America, mountain ranges have high bumble bee species richness. However, as climate change increases temperatures and restricts montane populations to higher elevational spaces, their ability to disperse and maintain genetic diversity decreases. This genetic isolation could lead to the extirpation of local pollinator communities and an overall loss of pollinators. We analyzed the genetic diversity of four broadly sympatric species of bumble bees across the Rocky and Cascade Mountains of western North America to assess habitat isolation's impact on population genetic structure. We expected species restricted to higher elevation habitats to display higher population structure and less genetic diversity across the landscape. We sampled approximately 150 bees per species from seven to eight sites across each species' range. We genotyped bees with an average of 10 loci and used FST and Bayesian Structure analysis to quantify population differentiation. Using isolation by distance and isolation by resistance analyses, species with both narrow and broad habitat suitability requirements showed evidence of habitat suitability restricting gene flow. Although each species showed varying degrees of genetic structure and gene flow, knowing how habitat heterogeneity drives genetic structure and isolation can help guide conservation efforts and determine focal regions for bumble bee conservation in the face of climate change.

opencc-zeroApr 2024View details →

Data from: Genetic analysis of red deer (Cervus elaphus) administrative management units in a human-dominated landscape - patterns of genetic diversity, population structure and gene flow

Red deer (Cervus elaphus) throughout central Europe are impacted by different anthropogenic activities including habitat fragmentation, selective hunting, and translocations. This has substantial influences on genetic diversity and the long-term conservation of local populations of this species. Here we use genetic samples from 480 red deer individuals to assess the genetic diversity and differentiation of the 12 administrative management units located in Schleswig Holstein, the northernmost federal state in Germany. We applied multiple analytical approaches and show that the history of local populations (i.e., translocations, culling of individuals outside of designated red deer zones, and anthropogenic infrastructures) has led to comparably low levels of genetic diversity. The mean expected heterozygosity was below 0.6 and we observed on average 4.2 alleles across 12 microsatellite loci. Effective population sizes below the recommended level of 50 were estimated for multiple local populations. Our estimates of genetic structure and gene flow show that red deer in northern Germany are best described as a complex network of asymmetrically connected subpopulations, with high genetic exchange among some local populations and reduced connectivity of others. Genetic diversity was also correlated with population densities of neighboring management units. Based on these findings, we suggest that connectivity among existing management units needs to be considered in the practical management of the species, which means that some administrative management units should be managed together, while the effective isolation of other units needs to be mitigated.

opencc-by-4.0Nov 2024View details →

Seismic Reflection Data from the Kentland Impact Structure, Indiana from Robitaille MSc (2024)

This repository contains the correlated and stacked shot gathers and the final unmigrated and migrated files (all in SGY format) collected near the Kentland Crater Impact Structure.  These data are associated with the MSc thesis of Brian Robitaille at Purdue University (2024). See citation below.

opencc-by-4.0Aug 2024View details →

Data and code from "COVID-19 lockdown effects on adolescent brain structure suggest accelerated maturation that is more pronounced in females than in males"

Data and code used to perform analyses published in the research article "COVID-19 lockdown effects on adolescent brain structure suggest accelerated maturation that is more pronounced in females than in males" which is currently in press in the Proceedings of the National Academy of Sciences, USA. (https://doi.org/10.1073/pnas.2403200121).

opencc-by-4.0Dec 2023View details →

Data from: Structured Detection for Simultaneous Super-Resolution and Optical Sectioning in Laser Scanning Microscopy

This repository contains the raw data of the experimental ISM dataset used to make the figures and supplementary figures for the paper entitled Structured Detection for Simultaneous Super-Resolution and Optical Sectioning in Laser Scanning Microscopy.

opencc-by-4.0Nov 2024View details →

Data and Scripts for the Article: Structural Sensitivity of N1s Excitations in N-methylacetamide Solutions

Data and scripts for the article titled: Structural Sensitivity of N1s Excitations in N-methylacetamide Solutions. For further details on the contents, see the "readme.md"-file.

opencc-by-4.0Nov 2021View details →

Supplementary data for structure-conditioned amino-acid couplings

This dataset contains supplementary data for the work "Structure-conditioned amino-acid couplings: how contact geometry affects pairwise sequence preferences" and includes two files: a spreadsheet listing the CASP models used for structure evaluation and an archived directory containing the structure and energy files that make up "DB200K", the main dataset of interaction motifs and their structure-conditioned energies used in the published work. The spreadsheet, "CASP-models.xlsx", lists the CASP round (9, 10, etc.), target name, model ID, and GDT_TS score for each model included in the structure evaluation experiment (see Fig. 7 in the published work). All information was collected from the CASP website, predictioncenter.org. See the "CASP model evaluation" section in the Methods section of the published work for more information. The archived directory, "DB200K.tar.gz", contains the structures and structure-conditioned energies of 200,002 inter-residue contact motifs. Each motif has a structure and set of structure-conditioned energies for each of the three motif sizes considered in the published work: 1x1, 3x3, and 5x5. For each motif of each size, there are two corresponding files, both indexed by the motif size, PDB ID, and position pair (chain and residue numbers according to the PDB file). One file is a PDB file containing the motif's structure and the other is a text-based file listing the 400 structure-conditioned energies of the motif's interacting residue pair. Each of the 400 energies is indexed by the pair of three-letter amino-acid codes it corresponds to. The residue positions in the PDB file match those listed in the energy file. For details on how this database's contacts were selected, see the "Contact database creation" section in the Methods section of the published work; for details on how these energies were computed, see the "Structure-conditioned potentials" section.

opencc-by-4.0Oct 2021View details →

Live-cell fluorescence microscopy data for: Structural Dynamics of the Functional Nonameric Type III Translocase Export Gate

yuan_t3ss_raw_data.zip: Microscopy data types: - Brightfield images - Fluorescence images (514 nm excitation) Microscope: Olympus IX-83 with 1.49NA oil-immersion objective (Olympus UAPON 100x) ET442/514/561 Laser triple band set filtercube (69904, Chroma) Camera: Hamamatsu C9100-13 EM-CCD Camera 80 nm pixel size yuan_t3ss_cell_objects.zip: EPEC and C41 ColiCoords cell objects derived from the raw data. The set contains a total of 24979 individual cells (brightfield, binary, fluorescence and localization datasets for each cell) with corresponding coordinate systems. Code to generate these cell objects from the raw data: https://github.com/Jhsmit/T3SS-paper The data format is .hdf5 and can be read with any HDF5 reader or directly with ColiCoords: https://github.com/Jhsmit/ColiCoords Contact: Jochem Smit

opencc-by-4.0Nov 2021View details →

Data supporting the study "The evolution of surface structure during atmospheric ageing of nano-scale coatings of an organic surfactant aerosol proxy" by Milsom et al.

Reduced neutron reflectometry (NR) data associated with the study "The evolution of surface structure during atmospheric ageing of nano-scale coatings of an organic surfactant aerosol proxy" by Milsom et al.. One folder contains the raw data for fitted parameters obtained from NR curves and supporting figure 3 in the study. The other contains a set of sub-folders which have reduced NR data along with python scripts which were used to create and fit the interfacial model to the data. Fitting bounds for each parameter are found in these scripts.

opencc-zeroDec 2021View details →

Bone structural data for the Denver Longitudinal Growth Study

Long bone structural dimensions have been shown to be responsive to mechanical loadings during life. Thus, they can be used to track behavioral changes as well as changes in body size during ontogeny. Radiographic measurements of long bone structural properties (lengths, cross-sectional geometric properties, articular breadths) were carried out for a sample of 20 children who had participated in the Denver Growth Study. An average of 36 longitudinal time points for each individual, taken at 6-month intervals between early infancy and late adolescence, were included. Anthropometric and muscle area dimensions were also available. The data have been previously used in a range of studies, including growth changes in bone strength, adaptation to bipedalism, and body size prediction in juveniles.

opencc-zeroDec 2021View details →

Model and data for: Economical defense of resources structures territorial space use in a cooperative carnivore

Manuscript Abstract: Ecologists have long sought to understand space use and mechanisms underlying patterns observed in nature. We developed an optimality landscape and mechanistic territory model to understand mechanisms driving space use and compared model predictions to empirical reality. We demonstrate our approach using gray wolves (Canis lupus). In the model, simulated animals selected territories to economically acquire resources by selecting patches with greatest value, accounting for benefits, costs, and tradeoffs of defending and using space on the optimality landscape. Our approach successfully predicted and explained first- and second-order space use of wolves, including the population's distribution, territories of individual packs, and influences of prey density, competitor density, human-caused mortality risk, and seasonality. It accomplished this using simple behavioral rules and limited data to inform the optimality landscape. Results contribute evidence that economical territory selection is a mechanistic bridge between space use and animal distribution on the landscape. This approach and resulting gains in knowledge enable predicting effects of a wide range of environmental conditions, contributing to both basic ecological understanding of natural systems and conservation. We expect this approach will demonstrate applicability across diverse habitats and species, and that its foundation can help continue to advance understanding of spatial behavior. Model & Data Abstract: In support of the above manuscript, all model files and data to re-create the analyses for the manuscript are included on Dryad. The model can be run in NetLogo (installation file included), using the associated input files to build the Montana landscape for wolves. Expertise in NetLogo is strongly recommended for using this model. Output files are likewise included along with code to create each plot in the manuscript and SI. Software files for the model and code to create each plot in the manuscript are located at Zenodo: https://doi.org/10.5281/zenodo.5802243.

opencc-zeroDec 2021View details →

Data from: Microbial metabolic activity in two basins of the Gulf of Mexico influenced by mesoscale structures

Information on microbial metabolic activity is essential for quantifying carbon and energy flows through marine food webs. We quantified community (Rcom) and prokaryotic (Rpro) respiration rates, bacterial production (BP), bacterial abundance (BA), and bacterial growth efficiencies (BGE) in the Perdido and Coatzacoalcos basins of the Gulf of Mexico (GOM) during summer and winter conditions in 2016. Our results showed seasonal, regional, and mesoscale eddy influences on those metabolic variables. Rpro accounted for more than 60% of total respiration in both regions, being three times higher in stations influenced by a cyclonic eddy (CE) in September (24.1 μM O2 d-1) than in stations affected by an anticyclonic eddy in March (7.2 μM O2 d-1) within the Coatzacoalcos basin where the eddy-trapping mechanism advected biomass-enriched waters from the Bay of Campeche. The eddy-stirring mechanism produced horizontal and vertical dipole patterns of metabolic variables increasing up to one order of magnitude Rcom and Rpro while decreasing BGE to 25-fold from the southeastern to the northwestern edges in CEs. This finding indicates that dissolved organic matter is more actively taken up to build bacterial biomass on the eastern edge of CEs in the GOM, while respiration rates increase on the western edges. Satellite integrated primary production was coupled with surface respiration rates at CEs and no eddies. Bacterial production was mainly regulated by CEs and was about 50% higher in the Coatzacoalcos basin (~0.03–0.14 µmol C L-1 d-1). BP increased in zones with high respiration rates, suggesting that Rcom is associated with heterotrophic prokaryote activity in both basins. Bacterial growth efficiency was lower than 25% within the upper 500 m during both cruises, but the highest values were quantified in the euphotic zone and during the September cruise. Metabolic variables integrated over the water column showed that 40–80% of the activity occurred between the base of the euphotic zone and 150 m depth. Our findings contribute to a better understanding of the metabolic activity of the microbial communities in two regions of the GOM influenced by mesoscale eddies.

Raw diffraction data for structure of SARS-CoV-2 main protease with Z31792168 (PDB: 7QT5)

Raw diffraction data for SARS-CoV-2 main protease in complex with Z31792168 collected as part of an room-temperature crystallographic ligand screening experiments on beamline i24 at Diamond Light Source.

Raw diffraction data for structure of SARS-CoV-2 main protease with Z4439011520 (PDB: 7QT7)

Raw diffraction data for SARS-CoV-2 main protease in complex with Z4439011520 collected as part of an room-temperature crystallographic ligand screening experiments on beamline i24 at Diamond Light Source.

Raw diffraction data for structure of SARS-CoV-2 main protease with Z1367324110 (PDB: 7QT6)

Raw diffraction data for SARS-CoV-2 main protease in complex with Z1367324110 (SMILES:CN1CCCC=2C=CC(=CC12)S(=O)(=O)N) collected as part of an room-temperature crystallographic ligand screening experiments on beamline i24 at Diamond Light Source.

Raw diffraction data for structure of SARS-CoV-2 main protease with Z4439011584 (PDB: 7QT9)

Raw diffraction data for SARS-CoV-2 main protease in complex with Z4439011584 collected as part of an room-temperature crystallographic ligand screening experiments on beamline i24 at Diamond Light Source.

opencc-by-4.0Apr 2022View details →

Cross-spectra used in "Detailed S-wave velocity structure of sediment and crust off Sanriku, Japan by a new analysis method for distributed acoustic sensing data using a seafloor cable and seismic interferometry"

Cross-spectra used in "Detailed S-wave velocity structure of sediment and crust off Sanriku, Japan, derived from distributed acoustic sensing data collected using a seafloor cable with seismic interferometry", by Shun Fukushima, Masanao Shinohara, Kiwamu Nishida, Akiko Takeo, Tomoaki Yamada, and Kiyoshi Yomogida  For more information, please contact Shun Fukushima (s-fuku@eri.u-tokyo.ac.jp)