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opencc-by-nc-4.0Feb 2017View details →

Raw Genotyping data from: Variation in recombination rate and its genetic determinism in sheep populations from combining multiple genomewide datasets

Data supporting : Variation in recombination rate and its genetic determinism in sheep populations from combining multiple genomewide datasets Morgane Petit, Jean-Michel Astruc, Julien Sarry, Laurence Drouilhet, Stephane Fabre, Carole Moreno, Bertrand Servin http://doi.org/10.1534/genetics.117.300123 Abstract Recombination is a complex biological process that results from a cascade of multiple events during meiosis. Understanding the genetic determinism of recombination can help to understand if and how these events are interacting. To tackle this question, we studied the patterns of recombination in sheep, using multiple approaches and datasets. We constructed male recombination maps in a dairy breed from the south of France (the Lacaune breed) at a fine scale by combining meiotic recombination rates from a large pedigree genotyped with a 50K SNP array and historical recombination rates from a sample of unrelated individuals genotyped with a 600K SNP array. This analysis revealed recombination patterns in sheep similar to other mammals but also genome regions that have likely been affected by directional and diversifying selection. We estimated the average recombination rate of Lacaune sheep at 1.5 cM/Mb, identified about 50,000 crossover hotspots on the genome and found a high correlation between historical and meiotic recombination rate estimates. A genome-wide association study revealed two major loci affecting inter-individual variation in recombination rate in Lacaune, including the RNF212 and HEI10 genes and possibly 2 other loci of smaller effects including  the KCNJ15  and FSHR genes. Finally, we compared our results to those obtained previously in a distantly related population of domestic sheep, the Soay. This comparison revealed that Soay and Lacaune males have a very similar distribution of recombination along the genome and that the two datasets can be combined to create more precise male meiotic recombination maps in sheep. Despite their similar recombination maps, we show that Soay and Lacaune males exhibit different heritabilities and QTL effects for inter-individual variation in genome-wide recombination rates.   Data files are provided in Plink format ( https://www.cog-genomics.org/plink2 ).

opencc-by-sa-4.0Jun 2017View details →

Statistical Data of Vienna's population

Statistical analysis of the population of Vienna by districts from 2001 to 2015. Input Data is taken from https://www.data.gv.at/katalog/dataset/stadt-wien_viebevlkerungseit1869wien/resource/f55512e6-81ef-4fa9-a01f-19f9c5f838c2. The source code for experiment which produces the data provided here can be found on https://bitbucket.org/BerwanY/dp3 The csv-files of the districts population are containing the years as labels and the population for every year in the first row. The overview of vienna's population csv-file contains as first label 'YEAR', where the other label are the districts. So every row contains the population data of every district for one year. The csv-files are named as follows: <ul> <li>For districts: 'district_DISTRICTNUMBER.csv'</li> <li>Overview: 'district_all.csv'</li> </ul> , where DISTRICTNUMBER is replaced with the corresponding code of the district.

opencc-by-4.0Dec 2021View details →

GSTRIDE: A database of frailty and functional assessments with inertial gait data from elderly fallers and non-fallers populations

The GSTRIDE database contains relevant metrics and motion data of elder people for the assessment of their health status. The data correspond to 163 patients, 45 men and 118 women, between 70 and 98 years old with an average Body Mass Index (BMI) of 26.1±5.0 kg/m2 and a cognitive deterioration status index between 1 and 7, according to the Global Deterioration Scale (GDS) scale. In this way, we ensure variability among the volunteers in terms of socio-demographic and anatomic parameters and their functional and cognitive capacities. The database files are stored in CSV format to ease their usability with common data processing software. We provide socio-demographic data, anatomical, functional and cognitive variables, and the outcome measurements from test commonly performed for the evaluation of elder people. The evaluation tests carried out to obtain these data are the Gait Speed Test (4-metre), the Hand Grip Strength, the Short Physical Performance Battery (SPPB), the Timed up and go (TUG) and the Short Falls Efficacy Scale International (FES-I). We also include the outcomes of the GDS questionnaire, the Frailty assessment and the information about falls during the last year prior to the tests. These data are complemented with the gait parameters of a walking test recorded by an Inertial Measurement Unit (IMU) placed on the foot. Inertial data from foot-mounted IMUs (acceleration (m/s2), angular velocity (rad/s) and timestamps (s)) are included in the database in .csv files for each participant. The current version includes a new gait analysis processing conducted following the methodology described in [1]. The complete gait analysis is included for each participant and trial in .csv files, including the gait parameters estimated for all individual steps and the gait segmentation events. The gait parameters included are: cycle duration (CD) (s), cadence (steps/min), stride length (SL) (m), path length 3D (%SL), path length 2D (%SL), stride velocity (m/s), percentage of swing (%CD), percentage of stance (%CD), percentage of stance subphases (loading, foot-flat, and pushing) (%stance), heel strike pitch (degrees), toe-off pitch (degrees), peak angle velocity (degrees/s), turning angle (degrees), and heel range of motion (ROM) (degrees).  GSTRIDE is specially focused on, but not limited to, the study of faller and non-faller elder people. The main aim of this dataset is the availability of study these different populations. By including the results of the health evaluation tests and questionnaires and the inertial and spatio-temporal data, researchers can analyze different techniques for the identification of fallers. Moreover, this database allows the analysis of cognitive deterioration and frailty parameters of patients by the research community. [1] L. Ruiz-Ruiz, J. J. García-Domínguez and A. R. Jiménez, "A Novel Foot-Forward Segmentation Algorithm for Improving IMU-Based Gait Analysis," in IEEE Transactions on Instrumentation and Measurement, vol. 73, pp. 1-13, 2024, Art no. 4010513, doi: 10.1109/TIM.2024.3449951.

opencc-by-4.0Oct 2023View details →

An observed population of intermediate-mass helium stars that have been stripped in binaries - theoretical, computational and observational data

This Zenodo repository contains the observational and computational data presented in the manuscript "An observed population of intermediate-mass helium stars stripped in binaries" by Drout, Götberg, Ludwig, Groh, de Mink, O'Grady and Smith.We organize the data as follows:<ul><li>The stacked spectra presented in Figures S16-S21 are located in stacked_spectra.tar.gz, which contains a text file for each star. The text files have three columns that correspond to wavelength in Angstrom, normalized counts, and errors, respectively.  </li><li>The spectral model grid computed based on binary evolutionary model output and presented in detail in the Supplementary information section S1.2.1, is labeled with names starting S121. The file S121_evol_based_006_absolute_magnitudes.txt contains the absolute AB magnitudes for the models in UV and optical filters. The .tar.gz S121_evol_based_006_spectra.tar.gz contains files with the full spectral energy distribution and normalized spectra of each model. The .tar.gz S121_evol_based_006_complete_models.tar.gz contains the full CMFGEN models.  </li><li>For the stellar atmosphere model grid presented in Supplementary material section S1.2.2, we refer to the Zenodo repository 10.5281/zenodo.7976200, which is made available in association with the second paper in our series. We note that we used a subset of that grid in the article associated with this Zenodo repository. We refer to section S1.2.2 for more details.  </li><li>The spectral models demonstrating the mass loss rate variations in Supplementary information section S1.2.3 are presented here with names starting with S123. There is one file containing the absolute magnitudes (S123_mdot_variation_absolute_magnitudes.txt), the S123_mdot_variation_spectra.tar.gz contains the spectral energy distributions and normalized spectra for each of the models, and the S123_mdot_variation_complete_models.tar.gz contains the full CMFGEN models.  </li><li>The spectral model grid computed based on main-sequence evolutionary model output and presented in detail in the Supplementary information section S1.3.1, is labeled with names starting S131. The file S131_MS_evol_based_006_absolute_magnitudes.tar.gz contains three files with the absolute AB magnitudes for the models in the UV and optical filters, each file corresponding to either 20%, 60%, or 90% through the main-sequence evolution and labeled f20, f60, and f90, respectively. S131_MS_evol_based_006_spectra.tar.gz contains three folders labeled f20, f60 and f90, which each contains the SEDs (in Flambda and ABmag) and normalized spectra for the corresponding models. The files S131_MS_evol_based_006_complete_models_fX0.tar.gz contain the complete CMFGEN models.  </li><li>The custom index files we use for astrometry.net in section S3.1.1 are located in the zip file called S311_astrometry_index_files.zip. This information was used to recalculate the astrometry on the Swift UVOT images of the Magellanic Clouds.  </li><li>To make Figure 2B, we calculated the equivalent widths for a set of models assuming a signal-to-noise ratio of 35. This procedure is described in Section S3.7.2. In Figure2B_Model_EWs.zip, we provide three files that each contain these modeled equivalent widths for (1) stripped star models, (2) OB star models, and (3) composite models.   </li><li>To make Figure S7 (see also Sections S1.2.3 and S2.2), which is similar to Figure 2B, but presents the effects of varying the wind mass loss of stripped stars, we used a similar set of modeled equivalent widths as when we produced Figure 2B. These modeled equivalent widths are provided in FigureS7_Model_EWs.zip.   </li><li>To make Figure 3, we calculated equivalent widths for the model grid described in Section S1.2.2 and the TLUSTY OB star grids (see Section S1.3.2) assuming a signal-to-noise ratio of 100. These model equivalent widths are provided in the file called Figure3_Model_EWs.zip. </li></ul>

opencc-by-4.0Oct 2023View details →

Georeferenced data for the study Environmental suitability throughout the late Quaternary explains population genetic diversity

Data filtered from GBIF (datasetKey: 50c9509d-22c7-4a22-a47d-8c48425ef4a7)  Contains 150 records of the Sciurus aberti squirrel filtered in latitudinal windows of 5 degrees from 20 to 45 degrees N.

opencc-zeroDec 2022View details →

Data for: Multi-generational fitness effects of natural immigration indicate strong heterosis and epistatic breakdown in a wild bird population

The fitness of immigrants and their descendants produced within recipient populations fundamentally underpins the genetic and population dynamic consequences of immigration. Immigrants can in principle induce contrasting genetic effects on fitness across generations, reflecting multi-faceted additive, dominance, and epistatic effects. Yet, full multi-generational and sex-specific fitness effects of regular immigration have not been quantified within naturally structured systems, precluding inference on underlying genetic architectures and population outcomes. We used four decades of song sparrow (Melospiza melodia) life-history and pedigree data to quantify fitness of natural immigrants, natives, and their F1, F2, and backcross descendants, and test for evidence of non-additive genetic effects. Values of key fitness components (including adult lifetime reproductive success and zygote survival) of F1 offspring of immigrant-native matings substantially exceeded their parent mean, indicating strong heterosis. Meanwhile, F2 offspring of F1-F1 matings had notably low values, indicating surprisingly strong epistatic breakdown. Further, magnitudes of effects varied among fitness components, and differed between females and males descendants. These results demonstrate that strong non-additive genetic effects on fitness can arise within weakly structured and fragmented populations experiencing frequent natural immigration. Such effects will substantially affect the net degree of effective gene flow and resulting local genetic introgression and adaptation.

opencc-by-4.0Nov 2023View details →

Supporting data for: Vocal fingerprinting reveals a substantially smaller global population of the Critically Endangered cao vit gibbon (Nomascus nasutus) than previously thought

These data were used in the publication "Vocal fingerprinting reveals a substantially smaller global population of the Critically Endangered cao vit gibbon (Nomascus nasutus) than previously thought", currently in review. The acoustic measurements provided in the file were input to the clustering analyses detailed in the paper. Each row corresponds to a single male song phrase. The columns include:<ul><li>GroupID - the name of the gibbon group, based on manual identification of the song phrase</li><li>MFCC[1-88] - Mel-frequency cepstral coefficients as detailed in the paper</li><li>Delta[89-176] - Delta-cepstral coefficients as detailed in the paper</li><li>Duration - the length of the song phrase (in seconds)</li><li>Freq 5% (Hz) and Freq 95% (Hz) - 5th and 95th percentile frequencies, respectively</li><li>Cao and Vit - the number of "cao" and "vit" components, respectively, present in the song phrase</li><li>CutFileName - the file name of the extracted song phrase (which also acts as a unique identifier)</li><li>Representative - whether the given song phrase was 'representative' ("Yes" or "No") of a typical phrase for that male (as defined by the modal number of 'cao' and 'vit' components for males)</li></ul>All columns (except GroupID, CutFileName and Representative) have been standardised (i.e. centred to the mean and scaled according to the standard deviation).

opencc-by-4.0Aug 2020View details →

FIG. 1 in Analysis of Genomic Sequence Data Reveals the Origin and Evolutionary Separation of Hawaiian Hoary Bat Populations

FIG. 1.—Map of the Hawaiian Islands with collection sitesfor Hawaiian hoary bat tissues used inthis study. Sites with n> 1 are denoted with an asterisk.

opencc-by-4.0Aug 2020View details →

FIG. 2 in Analysis of Genomic Sequence Data Reveals the Origin and Evolutionary Separation of Hawaiian Hoary Bat Populations

FIG. 2.—PCA result plot showing clustering of individual bats from four Hawaiian Islands using 21,808,031 SNPs. Sample information included in supplementary table S4, Supplementary Material online.

opencc-by-4.0Aug 2020View details →

FIG. 4 in Analysis of Genomic Sequence Data Reveals the Origin and Evolutionary Separation of Hawaiian Hoary Bat Populations

FIG. 4.—SNAPP-based phylogenetic tree inference. (A) The maximum clade credibility or consensus tree, showing approximate divergence of hoary bats across the Hawaiian archipelago. The axis on the bottom of the figure corresponds to million years before present (Ma), using the emergence of Hawai'i (~0.43 Ma) as a calibration point (95% confidence intervals were given in square brackets). (B) The drawing of all sampled trees showing all ingroup nodes were supported by maximum posterior probabilities (1.00).

opencc-zeroJan 2024View details →

Data for: Effective population size mediates the impact of pollination services on pollen limitation

Inadequate pollen receipt limits flowering plant reproduction worldwide. Ecological causes of pollen limitation ('PL'), like pollinator scarcity and low plant abundance, have been a primary focus of research. The genetic diversity of plant populations could impact both quantity and quality components of PL in concert with ecological factors, yet empirical examples are lacking. We evaluated joint effects of ecological factors (flower abundance, pollinator visitation) and genetic effective population size (NE) on PL across 13 populations of a common herb. We used a histological approach with 5504 styles from 1137 flowers to separate quantity and quality components of PL, and link these to reproductive output. NE and pollinator visitation interacted to shape PL, but NE had stronger direct effects. Effectively smaller populations experienced stronger quantity PL, and controlled crosses in a pollinator-free environment revealed that pollen quantity was an intrinsic population-level attribute that increased with NE. Pollinator visitation enhanced pollen quality, but only in effectively larger populations. Quantity and quality PL negatively impacted fruit and seed set, respectively. Results highlight that PL is dictated by plant population genetic diversity in addition to commonly evaluated ecological factors. Efforts to support pollinators will only enhance plant reproduction in genetically diverse plant populations.

opencc-zeroFeb 2024View details →

Data and R code used in: Plant geographic distribution influences chemical defenses in native and introduced Plantago lanceolata populations

Plants growing outside their native range may be confronted by new regimes of herbivory, but how this affects plant chemical defense profiles has rarely been studied. Using Plantago lanceolata as a model species, we investigated whether introduced populations show significant differences from native populations in several growth and chemical defense traits. Plantago lanceolata (ribwort plantain) is an herbaceous plant species native to Europe and Western Asia that has been introduced to numerous countries worldwide. We sampled seeds from nine native and ten introduced populations that covered a broad geographic and environmental range and performed a common garden experiment in a greenhouse, in which we infested half of the plants in each population with caterpillars of the generalist herbivore Spodoptera littoralis. We then measured size-related and resource-allocation traits as well as the levels of constitutive and induced chemical defense compounds in roots and shoots of P. lanceolata. When we considered the environmental characteristics of the site of origin, our results revealed that populations from introduced ranges were characterized by an increase of chemical defense compounds without compromising plant biomass. The concentrations of iridoid glycosides and verbascoside, the major anti-herbivore defense compounds of P. lanceolata, were higher in introduced populations than in native populations. In addition, introduced populations exhibited greater rates of herbivore-induced volatile organic compound emission and diversity, and similar chemical diversity based on untargeted analyses of leaf methanol extracts. In general, the geographic origin of the populations had a significant influence on morphological and chemical plant traits, suggesting that P. lanceolata populations are not only adapted to different environments in their native range but also in their introduced range.

Data and code for: Nonlinear life table response analysis: Decomposing nonlinear and nonadditive population growth responses to changes in environmental drivers

Life table response experiments (LTREs) decompose differences in population growth rate between environments into separate contributions from each underlying demographic rate. However, most LTRE analyses make the unrealistic assumption that the relationships between demographic rates and environmental drivers are linear and independent, which may result in diminished accuracy when these assumptions are violated. In this study, we compare the relative efficacy of linear and second-order LTRE analyses in capturing changes in population growth rate caused by environmental driver changes. To explore this question, we analyze demographic data collected for three long-lived plant species: Ardisia escallonioides (Pascarella & Horvitz, 1998), Silene acaulis, and Bistorta vivipara (Doak & Morris, 2010). This repository includes data files containing vital rate (survival, growth, reproduction) observations or models for our three case studies, as well as an R script in which we use these demographic data to calculate linear and second-order LTRE approximations of changes in population growth rate for each system and generate the figures we present in our paper.

Data for: Harvest and decimation affect genetic drift and the effective population size in wild reindeer

Harvesting and culling are methods used to monitor and manage wildlife diseases. An important consequence of these practices is a change in the genetic dynamics of affected populations that may threaten their long-term viability. The effective population size (Ne) is a fundamental parameter for describing such changes as it determines the amount of genetic drift in a population. Here, we estimate Ne of a harvested wild reindeer population in Norway. Then we use simulations to investigate the genetic consequences of management efforts for handling a recent spread of chronic wasting disease, including increased adult male harvest and population decimation. The Ne/N ratio in this population was found to be 0.124 at the end of the study period, compared to 0.239 in the preceding 14-year period. The difference was caused by increased harvest rates with a high proportion of adult males (older than 2.5 years) being shot (15.2 % in 2005-2018 and 44.8 % in 2021). Increased harvest rates decreased Ne in the simulations, but less sex-biased harvest strategies had a lower negative impact. For harvest strategies that yield stable population dynamics, shifting the harvest from calves to adult males and females increased Ne. Population decimation always resulted in decreased genetic variation in the population, with higher loss of heterozygosity and rare alleles with more severe decimation or longer periods of low population size. A very high proportion of males in the harvest had the most severe consequences for the loss of genetic variation. This study clearly shows how the effects of harvest strategies and changes in population size interact to determine the genetic drift of a managed population. The long-term genetic viability of wildlife populations subject to disease will also depend on the population impacts of the disease and how these interact with management actions.

Simulated Herbarium data for testing the accuracy with which specimen data can predict the timing and duration of population-level flowering displays

This dataset provides code and example data for simulating specimen collections of flowering plants across North America, and for developing phenological predictions of population-level flowering onset and termination for these data. It further presents code for assessing the accuracy of these predictions relaticve to known (simulated) population-level flowering dates at the location of each collection.

Data from: Do pheromones contribute to the persistence of asexual populations in a facultatively parthenogenetic stick insect?

Facultative parthenogenesis is a form of reproduction in which females can either lay unfertilised eggs that typically develop into female offspring only, or mate and lay fertilised eggs that develop into male and female offspring. Facultative parthenogens often occur in mixed-sex populations where reproduction is mostly sexual, and all-female populations where reproduction is asexual. How all-female populations avoid invasion by males remains unknown. Here, we investigated the role of volatile and non-volatile (cuticular hydrocarbons, CHCs) pheromones in the persistence of all-female populations in the facultatively parthenogenetic stick insect, Megacrania batesii. We found that M. batesii exhibits slight sexual dimorphism in antenna morphology, and behavioural assays provided little evidence that males could locate females solely by volatile pheromones. However, CHC profiles differed substantially between different types of females. Analysis of CHC structure and abundance indicated a clear genetic difference between females from all-female versus mixed-sex populations, as well as a maternal effect of female parthenogenesis versus sexual development. Together, our results suggest that males might rely more on close-range chemical cues to differentiate females, and chemical communication could play a role in the persistence of all-female populations.

opencc-by-4.0Mar 2024View details →

Data from: Unexpected stability in faunal population abundances following an estuary-wide collapse of oysters

Data describing the number and lengths of fish and macroinvertebrates sampled from long-term fisheries independent sampling in Florida’s coastal waters. Original data were collected by the Florida Fish and Wildlife Conservation Commission (FWC) Fish and Wildlife Research Institute (FWRI).

opencc-zeroApr 2024View details →

Data from: Feather corticosterone is lower in translocated and historical populations of the endangered Laysan duck (Anas laysanensis)

Identifying reliable bioindicators of population status is a central goal of conservation physiology. Physiological stress measures are often used as metrics of individual health and can assist in managing endangered species if linked to fitness traits. We analysed feather corticosterone, a cumulative physiological stress metric, of individuals from historical, translocated, and source populations of an endangered endemic Hawaiian bird, the Laysan duck (Anas laysanensis). We hypothesised that feather corticosterone would reflect the improved reproduction and survival rates observed in populations translocated to Midway and Kure Atolls from Laysan Island. We also predicted less physiological stress in historical Laysan birds collected before ecological conditions deteriorated and the population bottleneck. All hypotheses were supported: we found lower feather corticosterone in the translocated populations and historical samples than in those from recent Laysan samples. This suggests that current Laysan birds are experiencing greater physiological stress than historical Laysan and recently translocated birds. Our initial analysis suggests that feather corticosterone may be an indicator of population status and could be used as a non-invasive physiological monitoring tool for this species with further validation. Furthermore, these preliminary results, combined with published demographic data, suggest that current Laysan conditions may not be optimal for this species.

opencc-zeroApr 2024View details →

Scholarly Wikidata: Population and Exploration of Conference Data in Wikidata using LLMs

This dataset provides the input data and intermediate results of the paper titled "Scholarly Wikidata: Population and Exploration of Conference Data in Wikidata using Large Language Models and Semantic Web Techniques". It contains the following resources. <ul> <li>conference proceedings front matter links - these links can be used to download the pdf files of the conference proceeding front matters that include information about the number of submitted and accepted papers that can be used to calculate acceptance rates, names of all conference organization committee members, list of programme committee and senior programme member names for each track with other interesting facts such as the main topics of the submitted papers and emerging topics according to the editors, etc.</li> <li>web crawl of conference websites - this contains a set of crawled content from each conference website in both HTML and text formats. Each file contains web pages from a specific conference along with the page URL, page title, and page content. Information such as important dates (deadlines) and other announcements can be extracted from the content of the web sites. </li> <li>papers and paper-authors list for each conference in a given conference series - this contains the paper list along with their corresponding authors for each conference series extracted from DBLP. </li> <li>OpenRefine projects - this contains examples of open refile projects that were used to perform entity linking and reconciliation as well as the schemas that was used to map the tabular data columns to Wikidata properties, and qualifiers and cell values to Wikidata entities.</li> <li>evaluation benchmark - this contains the outputs of LLM generations for the tasks (a) extracting the number of submitted and accepted papers per each track at a given conference, (b) extraction of organizers with their roles for each conference, (c) extraction of programme committee members with track and their role (member, SPC member), and (d) extraction of important dates or deadlines for each activity (submission, notification, etc.) in each track. </li> </ul> The corresponding source code is available at the <a href="https://github.com/scholarly-wikidata/scholarly-wikidata/">scholary-data repo</a>.