Find research datasets worth reusing

opencc-by-4.0May 2023View details →

Supplementary data and summary statistics - Genetic influences on circulating retinol and its relationship to human health

Summary statistics from the circulating retinol GWAS See - GWAS_summary_stats_README.txt for details of these files and the header names. METSIM+INTERVAL meta-analyses have a sample size of 17268. The full meta-analysis that includes ATBC+PLCO has a sample size of 22274. Please cite the following if you use any of these data - Reay, W.R. et al. Genetic influences on circulating retinol and its relationship to human health. Nature Communications (2024). By downloading these summary statistics, investigators agree to the following: <ol> <li>Investigators acknowledge that these data are provided on an “as-is” basis, without warranty of any type, expressed or implied, including but not limited to any warranty as to their performance, merchantability, or fitness for any particular purpose.</li> <li>Investigators will not cross-post these data or make them available elsewhere – this website is the definitive source for these data without express written permission from the study corresponding authors.</li> <li>Investigators will never attempt to identify any participant who contributed to these data.</li> <li>Any commercial or for-profit use of these data is forbidden unless express permission is sought from the study corresponding authors.</li> <li>Investigators will cite the associated manuscript when using these data.</li> </ol> Supplementary data from the circulating retinol GWAS phenome-wide Mendelian randomisation study 1. MR_retinol_as_exp - full output from the MR-pheWAS using circulating retinol as the exposure

opencc-by-4.0Sep 2023View details →

A scalable, accurate, and universal analysis framework using individual-level allele frequency for large-scale genetic association studies in an admixed population

Inclusion of individuals with diverse or admixed genetic ancestries is crucial to discover novel findings that may be missed by genomics analyses rooted solely in Caucasian population. Here, we present an analysis framework, SPAmix, which is scalable to a large-scale biobank data analysis including hundreds of thousands of admixed individuals and is universally applicable to various types of complex traits including binary trait, quantitative trait, time-to-event trait, longitudinal traits, etc. For each genetic variant, SPAmix uses genotype data and genetic principal components (PCs) to estimate individual-level allele frequency, which is subsequently used to calibrate p values via a retrospective analysis. A hybrid strategy including saddlepoint approximation (SPA) can greatly increase the accuracy to analyze rare genetic variants, especially if the phenotypic distribution is unbalanced or extremely unbalanced. Compared to Tractor, SPAmix does not require local ancestry information and can be straightforwardly applicable to a multi-way admixed population. Meanwhile, SPAmix can also be extended to SPAmixlocal in which the local ancestry can be incorporated if available. In addition, we propose SPAmixCCT to combine the p values of SPAmix and SPAmixlocal via Cauchy combination (CCT). SPAmixlocal performs close to Tractor when analyzing quantitative traits and is more accurate when analyzing binary traits with an unbalanced case-control ratio. And SPAmixCCT is an optimal unified approach for various cross-ancestry genetic architectures. Extensive simulation studies and real data analyses of 369,314 UK Biobank individuals from multiple ancestries demonstrated that SPAmix is scalable and can discover novel hits while controlling type I error rates well.

opencc-by-4.0Aug 2023View details →

Evaluation of buckwheat genetic resources in Slovenia within the ECOBREED project

Publication and supplementary data: Data related to the publication in Fagopyrum 40 (2):67-76: field evaluation data (seed weight, plant height, protein content) and concentrations of phenolic compounds and antioxidant capacity of 17 buckwheat genetic resources and 6 commercial varieties tested in two years (2020 & 2021) in Slovenia.

opencc-by-4.0Sep 2023View details →

Genetic diversity, population structure, and linkage disequilibrium among tropical quality protein maize (QPM) lines assessed with high-density SNP markers

The study of genetic diversity (GD), population structure, and linkage disequilibrium (LD) provides a better understanding of the genetic relationships between individuals in a population which can be utilized in crop research and improvement. Genotyping-by-sequencing (GBS) was used to detect and genotype single nucleotide polymorphisms (SNPs) in a collection of 74 quality protein maize (QPM) lines and further to characterize their genetic diversity, population structure, and linkage disequilibrium. A total of 235,214 high-quality SNPs were used for different genetic analyses except for structure analysis where 11,950 SNPs were used. Analysis of molecular variance (AMOVA) based on these SNPs revealed high genetic heterozygosity among the five populations with 1% of the total genetic variation present among the subpopulations and 99% of the variation among individuals within the populations.  Population structure analysis using Bayesian-based clustering revealed that the 74 lines could be clustered into four groups. However, neighbor-joining trees indicate the lines are grouped into three major clusters.  Further analysis using principal component analyses (PCA) clustered the genotypes into five groups which are concordant with the groups based on pedigree information. Higher genetic diversity was detected in population 1 with a GD value of 0.484 and the lowest in population 5 (0.396) and overall, with a mean of 0.434. The LD pattern in the quality protein maize was investigated and we observed a relatively rapid LD decay of 3.53kb and 10.66kb at r2 =0.2 and r2= 0.1, respectively. Our findings provide important information for future Linkage mapping studies, genome-wide association analyses, and marker-assisted selective breeding of maize as well as genomic prediction-based selection in tropical germplasm.

opencc-by-4.0May 2019View details →

Genetic variants (chr. 6) from Old World Schistosoma mansoni exomes

Variant calling file (VCF) produced from exome libraries of Schistosoma mansoni (bloodfluke) samples from the Old Wold (West Africa (Senegal, Niger), East Africa (Tanzania), and Middle East (Oman)). One sample form the New World (Caribbean (HR9)) was added for comparison. The variants were called on the 3 Mb of chromosome 6 centered on the SmSULT-OR gene. This gene is involved in resistance to the drug oxamniquine  (OXA). The aim of the related article was to investigate the origin of OXA resistant mutations in the New Wolrd by identifying sequence variation in SmSULT-OR in S. mansoni from the Old World, where OXA has seen minimal usage.

openCC (other)Dec 2021View details →

State Water Project, Genetic Determination of Population of Origin 2011-2021

Central Valley Chinook Salmon populations differ in their Endangered Species Act listing status. It is often difficult to distinguish individuals from the different Evolutionarily Significant Units. As such, many of the salmon monitoring and evaluation efforts in the Central Valley and San Francisco Bay-Delta are hampered by uncertainty about population (stock) identification and proportional effects of management actions (Dekar et al. 2013; IEP 2019). Studies have identified that the current identification method (length-at-date models) of juvenile Chinook salmon (Fisher 1992) captured in the watershed vary in their accuracy, particularly for spring-run (NMFS 2013; Harvey et al. 2014; Merz et al. 2014). The inaccuracy of the size-based methods is likely due to differences in fish distribution during early rearing, habitat-specific growth rates, and inter-annual variability in temperatures and food availability that lead to overlap in size ranges among stocks. The primary objective of this project was the genetic classification (to race; Evolutionary Significant Unit) of Chinook Salmon captured from State Water Project and Central Valley Project fish protection facilities and Interagency Ecological Program monitoring programs. The population-of-origin was determined for sampled fish by comparing their genotypes to reference genetic baselines. Genetic methods, having less statistical uncertainty that size-based models for population identification, were intended to directly target (and reduce) one source of uncertainty in the estimation of loss (take) from water diversions (operations) and develop the information necessary for understanding stock-specific distribution, habitat utilization, abundance, and life history variation. This project supports recommendations from the Interagency Ecological Program’s Salmon and Sturgeon Assessment of Indicators by Life Stage and Interagency Ecological Program Science Agenda efforts to improve Central Valley salmonid monitoring

openCC (other)Jul 2020View details →

Large-scale longitudinal gradients of genetic diversity: a meta-analysis across six phyla in the Mediterranean basins

Predicting patterns of variation in biodiversity across the globe is a fundamental issue in ecology and evolution. Diversity within species, that is, genetic diversity, is of prime importance for understanding past and present evolutionary patterns, and highlighting areas where conservation might be a priority. However, most studies on spatial patterns of genetic diversity have not considered longitude as a potentially important ecological driver of these patterns. Therefore, we carried out a meta-analysis to examine the longitudinal patterns of genetic diversity in the Mediterranean Basin. Using published literature and a systematic review/meta-analysis framework, we collected data on the genetic diversity of species whose populations occur in the Mediterranean basin. We then calculated a coefficient of correlation between within‐population genetic diversity indices and longitude, and estimated the role of biological, ecological, biogeographic, and marker type factors on the strength and magnitude of this correlation in six phylla. The results of this study were published in the paper titled Large‐scale longitudinal gradients of genetic diversity: a meta‐analysis across six phyla in the Mediterranean basin (Conord et al. 2012).

openOpenFeb 1998View details →

Soil physical and chemical properties based on genetic horizon from 4 replicate pits placed around the replicate LTER control plots sampled in 1988 and 1989.

Dataset contains the following soil properties for each genetic horizon - site, Soil pit, upper and lower boundary (cm), Mg meq/100gm, Ca meq/100gm, K meq/100gm, CEC meq/100gm, pH, %C, %sand, %silt, %clay, Total %N, Total %P, % organic matter, Mn meq/100gm, Available-P ppm, %CO3, bulk density gm/cm3, Volume wt gm/m2.

openCustomJan 2020View details →

MCR LTER: Genetics: Settlement dynamics in the three-spot damselfish, Dascyllus trimaculatus

These data describe the genetics of recruiting Dascyllus trimaculatus. We first placed two rows of 8 anemones in a region (the west side of the bay of Opunohu) previously devoid of anemones. Anemones are 10 meters apart, the two rows are 100 meters apart. The row close to the reef crest is called crest , or OUT, row, the row away from the crest and close to the boat channel is called channel, or IN, row. The project started with the placement of the anemones in the fall of 2000. Since then, we regularly clear the anemones of Dascyllus and then collect newly settled fishes every morning. These fishes are later typed by sequencing the mitochondrial control region. Fishes are labeled as follows: DTR IN 01010205. This is a Dascyllus Trimaculatus collected on the channel row, first anemone, on January 2nd 2005. Anemones are numbered 1 to 8, from west to east. These data are published in Bernardi, G., R. Beldade, S.J. Holbrook and R.J. Schmitt. 2012. Full-sibs in cohorts of newly settled coral reef fishes. PloS One 7(9):e44953.

openCustomApr 2012View details →

MCR LTER: Genetics: Settlement dynamics in the clownfish, Amphiprion chrysopterus

These data describe the genetics of recruiting Amphiprion chrysopterus. Our goal is to score every single clownfish from the island of Moorea (we believe that the total population in Moorea is of approximately 300-500 individuals). Individuals are characterized using microsatellites, thus the data are presented as a matrix of alleles corresponding to a set of microsatellite loci. Ultimately, we want to determine the level of self-recruitment in Moorea by estimating the number of offspring which recruit on Moorea and that are derived from Moorea parents. These data are published in DOI: 10.1098/rspb.2011.2433 Beldade, R., S.J. Holbrook, R.J. Schmitt, S. Planes, D. Malone and G. Bernardi. In Press. Larger female fish contribute disproportionately more to self-replenishment. Proceedings of the Royal Society of London. Series B, Biological Sciences.

openCC (other)Jul 2021View details →

Descriptive data file for information regarding microbial genetic research in the environs of Plum Island Sound watersheds, PIE LTER, Massachusetts.

This is a descriptive, tabular dataset of publications related to microbial or genomic research conducted within PIE. Assession numbers for genetic sequences generated from PIE samples are provided where available, followed by a very brief description of analysis type and study objectives. Sampling locations within PIE, sampling dates, and habitat type (sea water, fresh water, sediment, marsh) are also given. Environmental data are included in some publications and are listed here (if brief) or availability is described. Links to sequence archives are given in Methods.

opencc-zeroJan 2020View details →

Geographical gradients of genetic diversity and differentiation among the southernmost marginal populations of Abies sachalinensis revealed by EST-SSR polymorphism

Research Highlights: We detected the longitudinal gradients of genetic diversity parameters, such as the number of alleles, effective number of alleles, heterozygosity, and inbreeding coefficient, and found that these might be attributable to climatic conditions, such as temperature and snow depth. Background and Objectives: Genetic diversity among local populations of a plant species at its distributional margin has long been of interest in ecological genetics. Populations at the distribution center grow well in favorable conditions, but those at the range margins are exposed to unfavorable environments, and the environmental conditions at establishment sites might reflect the genetic diversity of local populations. This is known as the central-marginal hypothesis in which marginal populations show lower genetic variation and higher differentiation than do central populations. In addition, genetic variation in a local population is influenced by phylogenetic constraints and the population history of selection under environmental constraints. In this study, we investigated this hypothesis in relation to Abies sachalinensis, a major conifer species in Hokkaido. Materials and methods: A total of 1,189 trees from 25 natural populations were analyzed using 19 EST-SSR loci. Results: The eastern populations; namely, those in the species distribution center, showed greater genetic diversity than did the western peripheral populations. Another important finding is that the southwestern marginal populations were highly differentiated from the other populations. Conclusions: These differences might be due to genetic drift in the small and isolated populations at the range margin. Therefore, our results indicated that the central-marginal hypothesis held true for the southernmost A. sachalinensis populations in Hokkaido.

opencc-by-4.0Apr 2019View details →

Fig. 3 in Genetic diversity and population structure of Brycon nattereri (Characiformes: Bryconidae): a Neotropical fish under threat of extinction

Fig. 3. Haplotype network based on partial sequencing of the D-loop region (mtDNA) of 92 individuals of Brycon nattereri from the Laranjinha River. Circle sizes are pro- portional to haplotype frequency.

opencc-by-4.0Mar 2020View details →

Genetic insights into recolonization processes of Mediterranean octocorals

Marine ecosystems are strongly impacted by the consequences of human activities, such as climate change and habitat destruction or artificialization. In the Mediterranean Sea, sessile benthic species, and particularly octocorals, have been affected by mass mortality events linked with temperature anomalies. The future evolution of octocorals facing global change will depend on their recolonization abilities facing local extirpation or important modification of their habitat. We studied these processes in Mediterranean octocorals in two situations: the colonization of artificial substrates (wrecks) by the red gorgonian Paramuricea clavata, and the recolonization following mortality events in the yellow gorgonian Eunicella cavolini. With microsatellite markers, we analyzed the genetic diversity of these populations and their differentiation from other neighboring populations. For P. clavata the populations on artificial substrates were not or lowly differentiated from the closest populations on natural substrates, and with similar levels of genetic diversity. Artificial substrates can then be considered as an interesting substitute for natural substrates for this species. For E. cavolini we did not detect any variation in diversity nor relatedness following recuperation after mortality events. In both cases our results suggest input from different populations in recolonization process, which helps in maintaining genetic diversity. These results are useful for the management of these species and of associated ecosystems. The data are presented in two files, one for each species, at the Genepop format (https://kimura.univ-montp2.fr/~rousset/Genepop.htm). Some alleles have been recoded and do not correspond to the original PCR size so this dataset can not be used with methods based on allele size.

opencc-by-4.0Apr 2020View details →

Number of genes per function within mobile genetic elements in Martinez Arbas, Narayanasamy et. al. (2020)

This repository contains a set of tables separated by COG functional categories and the type of mobile genetic element, i.e. phage or plasmid. Each table contains predicted gene functions for each COG category and information on protospacer-containing contigs (PSCCs) and non-PSCCs This repository is related to the work published in Martinez Arbas, Narayanasamy et. al. (2020).

opencc-by-4.0Dec 2019View details →

Influence of Paleolithic Range Contraction, Admixture and Long-Distance Dispersal on Genetic Gradients of Modern Humans in Asia

Each folder is identified according to the scenario, and contains another folder with the input files (files *.txt, *.par, *.sam, *.asc) to simulate it, the corresponding simulated genetic data (files *.arp) and the derived PC maps (files *.png). A file with the locations of the samples is also included (coord.txt). * Pure Paleolithic expansion *  The folder “Paleo” contains the input files (INFILES), the genetic data and the corresponding PC maps simulated under the scenario of a pure Paleolithic expansion, ignoring the range contraction induced by the LGM and LDD events. * Pure Paleolithic expansion considering the range contraction induced by the LGM *  The folder “Paleo_REC” contains the input files (INFILES), the genetic data and the corresponding PC maps simulated under the scenario of a pure Paleolithic expansion suffering the range contraction induced by the LGM.  * Pure Paleolithic expansion considering long-distance dispersal (LDD) events *  The folder “Paleo_LDD” contains the input files (INFILES), the genetic data  and the corresponding PC maps simulated under the scenario of a pure Paleolithic expansion considering LDD events.  * Paleolithic expansion followed by two Neolithic expansions (IR=0) from Middle East and East Asia considering the range contraction induced by the LGM *  The folder “Paleo2NeoIR0_REC” contains the input files (INFILES), the genetic data and the corresponding PC maps simulated under the scenario of a Paleolithic expansion followed by two Neolithic expansions (IR=0) from Middle East and later from East Asia suffering the range contraction induced by the LGM.  * Paleolithic expansion followed by two Neolithic expansions (IR=0) from Middle East and East Asia considering LDD events *  The folder “Paleo2NeoIR0_LDD” contains the input files (INFILES), the genetic data and the corresponding PC maps simulated under the scenario of a Paleolithic expansion followed by two Neolithic expansions from Middle East and later from East Asia considering LDD events.  * Paleolithic expansion followed by a single Neolithic expansion (IR=0) from Middle East considering the range contraction induced by the LGM *  The folder “Paleo_MiddleEastNeoIR0_REC” contains the input files (INFILES), the genetic data and the corresponding PC maps simulated under the scenario of a Paleolithic expansion followed by a single Neolithic expansions (IR=0) from Middle East suffering the range contraction induced by the LGM.  * Paleolithic expansion followed by a single Neolithic expansion (IR=0) from East Asia considering the range contraction induced by the LGM *  The folder “Paleo_EastAsiaNeoIR0_REC” contains the input files (INFILES) and the corresponding PC maps simulated under the scenario of a Paleolithic expansion followed by a single Neolithic expansion (IR=0) from East Asia suffering the range contraction induced by the LGM.  * Paleolithic expansion followed by a single Neolithic expansion (IR=0) from Middle East considering LDD events *  The folder “Paleo_MiddleEastNeoIR0_REC” contains the input files  (INFILES), the genetic data and the corresponding PC maps simulated under the scenario of a Paleolithic expansion followed by a single Neolithic expansions (IR=0) from Middle East considering LDD events.  * Paleolithic expansion followed by a single Neolithic expansion (IR=0) from East Asia considering LDD events *  The folder “Paleo_EastAsiaNeoIR0_REC” contains the input files (INFILES) the genetic data and the corresponding PC maps simulated under the scenario of a Paleolithic expansion followed by a single Neolithic expansion (IR=0) from East Asia considering LDD events.  * Paleolithic expansion followed by a single Neolithic expansion (IR=0.04) from Middle East considering the range contraction induced by the LGM *  The folder “Paleo_MiddleEastNeoIR004_REC” contains the input files (INFILES), the genetic data and the corresponding PC maps simulated under the scenario of a Paleolithic expansion followed by a single Neolithic expansion (IR=0.04) from East Asia suffering the range contraction induced by the LGM.  * Paleolithic expansion followed by a single Neolithic expansion (IR=0.04) from East Asia considering the range contraction induced by the LGM *  The folder “Paleo_EastAsiaNeoIR0_REC” contains the input files (INFILES), the genetic data  and the corresponding PC maps simulated under the scenario of a Paleolithic expansion followed by a single Neolithic expansions (IR=0.04) from East Asia suffering the range contraction induced by the LGM.  * Paleolithic expansion followed by a single Neolithic expansion (IR=0.04) from Middle East considering LDD events *  The folder “Paleo_MiddleEastNeoIR004_REC” contains the input files (INFILES), the genetic data and the corresponding PC maps simulated under the scenario of a Paleolithic expansion followed by a single Neolithic expansion (IR=0.04) from East Asia considering LDD events.  * Paleolithic expansion followed by a single Neolithic expansion (IR=0.04) from East Asia considering LDD events *  The folder “Paleo_EastAsiaNeoIR0_REC” contains the input files  (INFILES), the genetic data and the corresponding PC maps simulated under the scenario of a Paleolithic expansion followed by a single Neolithic expansions (IR=0.04) from East Asia considering LDD events.

Appendix. List of the 28S and 16S rRNA sequences recovered from GenBank. 28S = 28S rRNA GenBank accession number; 16S = 16S rRNA GenBank accession number. in Genetic and morphological evidence for cryptic species in Macrobrachium australe and resurrection of M. ustulatum (Crustacea, Palaemonidae)

Appendix. List of the 28S and 16S rRNA sequences recovered from GenBank. 28S = 28S rRNA GenBank accession number; 16S = 16S rRNA GenBank accession number.

Fig. 5 in Genetic and morphological evidence for cryptic species in Macrobrachium australe and resurrection of M. ustulatum (Crustacea, Palaemonidae)

Fig. 5. Macrobrachium ustulatus (Nobili, 1899). – A–B, E. MNHN-IU-2013-13202. A. Cephalothorax. B. Epistome. E. Major second pereiopod finger. – C, G. MNHN-IU-2013-13201. C. Fourth thoracic sternite. G. Minor second pereiopod finger. – D, F. MNHN-IU-2013-13203. D. Major second pereiopod. F. Minor second pereiopod. Scale bars: A, E, G = 2 mm; B–C = 1 mm; D, F = 4 mm.

Fig. 3 in Genetic and morphological evidence for cryptic species in Macrobrachium australe and resurrection of M. ustulatum (Crustacea, Palaemonidae)

Fig. 3. Macrobrachium australe (Guérin-Méneville, 1838 in Guérin-Méneville 1829–1838), MNHN- IU-2013-13198. A. Cephalothorax. B. Epistome. C. Fourth thoracic sternite. D. Major second pereiopod. E. Major second pereiopod finger. F. Minor second pereiopod. G. Minor second pereiopod finger. Scale bars: A, E, G = 2 mm; B–C = 1 mm; D, F = 4 mm.

Fig. 1 in Genetic and morphological evidence for cryptic species in Macrobrachium australe and resurrection of M. ustulatum (Crustacea, Palaemonidae)

Fig. 1. Map of the Indo-Pacific showing localities where Macrobrachium australe (Guérin-Méneville, 1838 in Guérin-Méneville 1829–1838) (black area) and M. ustulatum (Nobili, 1899) (red area) were collected and/or recorded. Capitalized locality names correspond to the 7 localities sampled for this study. Non-capitalized locality names correspond to the localities reported from the literature. Stars shows the type localities of the synonyms of M. australe (black stars) and M. ustulatum (red star).