Common genetic variations associated with the persistence of immunity following childhood immunisation
Contributors: Daniel O'Connor
... Genotyping data of common genetic variations associated with the persistence of immunity following childhood immunisation
Integrating bioacoustics, DNA barcoding and niche modeling for frog conservation – the threatened balloon frogs of Sri Lanka: audio, 16S & maps
Contributors: Madhava Meegaskumbura, Nayana Wijayathilaka, Gayani Senevirathne
... This data is associated with the following paper: Integrating bioacoustics, DNA barcoding and niche modeling for frog conservation – the threatened balloon frogs of Sri Lanka: audio, 16S & maps.
Data for: Is subterranean lifestyle reversible? Independent and recent large-scale dispersal into surface waters by two species of the groundwater amphipod genus Niphargus
Contributors: Denis Copilas-Ciocianu, Adam Petrusek, Péter Borza, Cene Fiser
... The folder contains: - concatenated alignment of COI, 28S and H3 markers - phylogenetic trees obtained in BEAST and RAxML - COI and ITS alignments for Niphargus hrabei and N. valachicus. - .kml files displaying the dispersal history of both species (can be visualized with Google Earth)
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Contributors: Thomas Cooke
... Data files and scripts (R and Python) for generating Figures 1-3 from Cooke et al (2017) "Genetic Mapping and Biochemical Basis of Yellow Feather Pigmentation in Budgerigars". See README files for details.
Data for: The role of post-collisional strike-slip tectonics in the geological evolution of the late Neoproterozoic volcano-sedimentary Guaratubinha Basin, southern Brazil
Contributors: Leonardo Mairink Barão, Fernando F Vesely, Luís Gustavo de Castro, Barbara Trzaskos, Ferreira Francisco Jose Fonseca, Eleonora Maria Gouvea Vasconcellos, Tiago C. Barbosa
... This is the work related to Guaratubinha Basin on Southern of Brazil
Contributors: Ivan Denisov, Andrey Zimin, Петр Иванович Белобров
... The dataset includes the results of ab initio computations of ground state wavefunctions of diamondoids C78H64 , C123H100 and C211H140 at the DFT R-B3LYP/6-31G(d,p) level of theory. Input files for computation pipeline are also provided. You can encode (7z) and view GAMESS output files using VMD software. You will see three distinct classes of collective orbitals: collective bonding states resembling modulated particle in a box solutions; surface-localized non-bonding conductive Tamm states and subsurface-localized bonding states for nonuniformly compressed nanodiamond (s > 0). The collective states despite their importance are rarely used to describe the electron structure of dielectric materials. The nature of the unrelated to impurities unpaired spins found experimentally in the nanodiamond is still under discussion. We propose the explanation of their nature in terms of the collective electron states. The existence of the unpaired spins is supposed to result from the spin-density fluctuation effects significant on the nanoscale collective and spread subsurface states. Find more in the article: Ivan A. Denisov, Andrey A. Zimin, Leslie A. Bursill, Peter I. Belobrov. Nanodiamond collective electron states and their localization // Journal of Siberian Federal University. Mathematics & Physics. 2014. Vol. 7, № 1. P. 35–45.
Data from: Widespread selection and gene flow shape the genomic landscape during a radiation of monkeyflowers
Contributors: Stankowski, Sean, Chase, Madeline A., Fuiten, Allison M., Rodrigues, Murillo F., Ralph, Peter L., Streisfeld, Matthew A.
... Speciation genomic studies aim to interpret patterns of genome-wide variation in light of the processes that give rise to new species. However, interpreting the genomic ‘landscape’ of speciation is difficult, because many evolutionary processes can impact levels of variation. Facilitated by the first chromosome-level assembly for the group, we use whole-genome sequencing and simulations to shed light on the processes that have shaped the genomic landscape during a radiation of monkeyflowers. After inferring the phylogenetic relationships among the nine taxa in this radiation, we show that highly similar diversity (π) and differentiation (FST) landscapes have emerged across the group. Variation in these landscapes was strongly predicted by the local density of functional elements and the recombination rate, suggesting that the landscapes have been shaped by widespread natural selection. Using the varying divergence times between pairs of taxa, we show that the correlations between FST and genome features arose almost immediately after a population split and have become stronger over time. Simulations of genomic landscape evolution suggest that background selection (i.e., selection against deleterious mutations) alone is too subtle to generate the observed patterns, but scenarios that involve positive selection and genetic incompatibilities are plausible alternative explanations. Finally, tests for introgression among these taxa reveal widespread evidence of heterogeneous selection against gene flow during this radiation. Combined with previous evidence for adaptation in this system, we conclude that the correlation in FST among these taxa informs us about the processes contributing to adaptation and speciation during a rapid radiation.
Data from: Genome analysis reveals genetic admixture and signature of selection for productivity and environmental traits in Iraqi cattle
Contributors: Alshawi, Akil Farouk, Essa, Abdulameer, Al-Bayatti, Sahar, Hanotte, Olivier
... The Near East cattle are adapted to different agro-ecological zones including desert areas, mountains habitats as well as humid regions along the Tigris and Euphrates rivers system. The region was one of the earliest and most significant areas of cattle husbandry. Currently four main breeds of Iraqi cattle are recognized. Among these, the Jenoubi is found in the southern more humid part of Iraq while the Rustaqi is found in the middle and drier region of the country. Despite their importance, Iraqi cattle have up to now been poorly characterized at genome level. Here, we report at genome-wide level the diversity and signature of positive selection in these two breeds. Thirty-five unrelated Jenoubi cattle, sampled in the Maysan and Basra regions, and 60 Rustaqi cattle, from around Baghdad and Babylon, were genotyped using the Illumina Bovine HD BeadChip (700K). Genetic population structure and diversity level were studied using principal component analysis (PCA), expected heterozygosity (He), observed heterozygosity (Ho) and admixture. Signatures of selection were studied using Extended Haplotype Homozygosity (EHH) (iHS and Rsb) and inter-population Wright’s Fst. The results of PCA and admixture analysis, including European taurine, Asian indicine, African indicine and taurine indicate that the two breeds are crossbreed zebu x taurine, with more zebu background in Jenoubi cattle compared to Rustaqi. The Rustaqi has the greatest mean heterozygosity (He = 0.37) among all breeds. iHS and Rsb signature of selection analyses identify 68 candidate genes under positive selection in the two Iraqi breeds, while Fst analysis identifies 220 candidate genes including genes related to the innate and acquired immunity responses, different environmental selection pressures (e.g. tick resistance, heat stress) and genes of commercial interest (e.g. marbling score).
Contributors: Burford Reiskind, Martha O., Labadie, Paul E, Bargielowski, Irka, Lounibos, L. Philip, Reiskind, Michael H.
... While few species introduced into a new environment become invasive, those that do provide critical information on ecological mechanisms that determine invasions success and the evolutionary responses that follow invasion. Aedes albopictus (the Asian tiger mosquito) was introduced into the naturalized range of Aedes aegypti (the yellow fever mosquito) in the USA in the mid-1980s, resulting in the displacement of A. aegypti in much of the southeastern USA. The rapid displacement was likely due to the superior competitive ability of A. albopictus as larvae and asymmetric mating interference competition, in which male A. albopictus mate with and sterilize A. aegypti females, a process called “satyrization”. The goal of this study was to examine the genomic responses of a resident species to an invasive species in which the mechanism of character displacement is understood. We used double-digest restriction enzyme DNA sequencing (ddRADseq) to analyze outlier loci between selected and control lines of laboratory-reared A. aegypti females from two populations (Tucson, AZ and Key West, Florida, USA), and individual females classified as either “resisted” or “mated with” A. albopictus males via mating trials of wild-derived females from four populations in Florida. We found significant outlier loci in comparing selected and control lines and between mated and non-mated A. aegypti females in the laboratory and wild-derived populations, respectively. We found overlap in specific outlier loci between different source populations that support consistent genomic signatures of selection within A. aegypti. Our results point to regions of the A. aegypti genome and potential candidate genes that may be involved in mating behavior, and specifically in avoiding interspecific mating choices.
Contributors: Kruczkiewicz, Peter
... Salmonella In Silico Typing Resource (SISTR) sistr_cmd version 1.0.2 serotyping databases File structure tree for sistr_cmd data folder: . |-- [4.0K] antigens | |-- [1.0M] fliC.fasta | |-- [210K] fljB.fasta | |-- [126K] wzx.fasta | `-- [ 60K] wzy.fasta |-- [4.0K] cgmlst | |-- [7.4M] cgmlst-centroid.fasta | |-- [ 96M] cgmlst-full.fasta | |-- [134M] cgmlst-profiles.hdf | `-- [ 803] README.md |-- [1.1M] genomes-to-serovar.txt |-- [1.0M] genomes-to-subspecies.txt |-- [118K] Salmonella-serotype_serogroup_antigen_table-WHO_2007.csv `-- [ 92M] sistr.msh 2 directories, 12 files Description of files: genomes-to-serovar.txt: Each genome id to serovar designation delimited by tab character for the 52,790 Salmonella genomes. genomes-to-subspecies.txt: Each genome id to subspecies designation delimited by tab character for the 52,790 Salmonella genomes. Salmonella-serotype_serogroup_antigen_table-WHO_2007.csv: Serovar and antigenic formula information table used by `sistr_cmd` for looking up serovar designations from antigen results sistr.msh: Mash sketch file of 11840 Salmonella genomes for Mash-based serotyping antigens: for antigen gene search-based serotyping fliC.fasta: fliC gene alleles for H1-antigen typing fljB.fasta: fljB gene alleles for H2-antigen typing wzx.fasta: wzx gene alleles for O-antigen typing wzy.fasta: wzy gene alleles for O-antigen typing cgmlst for core-genome multilocus sequence typing (cgMLST) and cgMLST-based serotyping cgmlst-profiles.hdf: HDF5 file with cgMLST allelic profiles of 52,790 Salmonella genomes read in with Pandas, i.e. pd.read_hdf(CGMLST_PROFILES_PATH, key='cgmlst') cgmlst-centroid.fasta: "Centroid" or representative alleles of 52,790 Salmonella genomes for rapid NCBI BLAST+ blastn searching. Centroid alleles were defined from the full set of alleles for the 52,790 Salmonella genomes as the alleles for each locus: group alleles by length group length grouped alleles by ends (28bp at allele start and end; 28 is word size of blastn megablast) hierarchical clustering of length+end grouped alleles flat clusters at 2.5% distance within each cluster, pick allele with least distance to others in cluster cgmlst-full.fasta: alleles for the 52,790 Salmonella genomes