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15,277 results for “GENETICS”
Tectona grandis: Narrow Genetic Base? A New Perspective on the Genetic Variability of Teak
Teak (Tectona grandis Linn. f.) is considered one of the most expensive hardwoods in the world. The dispersion of the species over the years has taken the teak beyond its origin centers and little is known about the genetic origin and genetic variability. This study aimed to investigate the genetic diversity and population structure existing in a teak germplasm bank collection in Brazil. DNA was extracted from young leaves and each sample were genotyped by whole genome sequencing at 8x of coverage, the sequencing were aligned using the genome at NCBI, and SNPcalls and quality control were made. To study the population structure of the genotypes, Bayesian variational inference was used via fastStructure, the phylogenetic tree was based on the modified Euclidean distance and the clustering by the UPGMA hierarchical method. Genetic diversity was analyzed based on the pairwise genetic divergence (Fst) of Weir and Cockerham. Genotyping by sequencing resulted in a database of approximately 1.4 million of variations SNPs were used for analysis. It was possible to identify four subpopulations with genetic variability between and within the subpopulations, so this study made it possible to confirm the existence of genetic variability in teak, contrary to what was expected.
Trans-eQTL effects on risk of type 1 diabetes: a test of the sparse effector (omnigenic) hypothesis of complex trait genetics (supplementary data)
<p>This repository contains summary-level data generated by performing <a href="https://github.com/molepi-precmed/trans-qtls">Genomewide aggregated trans- effects (GATE) analysis</a> in case-control study of Type 1 Diabetes (T1D).</p>
Genetic diversity and sperm characteristics are not associated in two bluethroat (Luscinia svecica) populations
<p>Individual heterozygosity may influence the expression of fitness-related traits, via genome-wide or local genetic effects. Earlier studies have shown negative relationships between heterozygosity and sperm variation, predominantly in captive, highly inbred populations. Little is known about the possible influence of variation in heterozygosity on sperm traits in wild, outbred populations. We studied two populations of the bluethroat, one from the widely distributed northern subspecies (<em>Luscinia</em>. <em>s</em>. <em>svecica</em>) and the other from the smaller, more patchily distributed subspecies breeding along the French coast of Brittany (<em>L. s. namnetum</em>). The two subspecies differed significantly in body size, plumage colour, sperm traits and the degree of genetic diversity. However, there was no evidence that sperm traits (total length and motility) were influenced by the degree of heterozygosity at the individual level. In contrast, we found that male body size was positively related to heterozygosity across both populations, indicating a possible relationship between overall genetic diversity and general vigour or ability to obtain food. We conclude that sperm traits are unrelated to levels of heterozygosity in the studied outbred and weakly genetically depauperate bluethroat populations.</p>
Obuasi case study data: Performance of neutral SNP barcodes to determine genetic diversity and structure of Plasmodium falciparum in Africa
<p>A small number of informative biallelic single nucleotide polymorphisms (SNPs) have been proposed to be an economical method to fast-track the genotyping and relatedness analysis of <em>Plasmodium</em> <em>falciparum</em> in malaria-endemic areas. Whilst used successfully in low-transmission areas where infections are monoclonal and highly related, we present the first study to evaluate the performance of these 24- and 96-SNP molecular barcodes in African countries characterised by moderate-to-high transmission. Using haplotypes generated from the MalariaGEN <em>P. falciparum</em> Community Project version 6 database, 52.3% of infections were multiclonal, generating high frequencies of mixed-allele calls (MACs) per isolate. Both multiclonality and low heterozygosity of SNPs impeded haplotype construction for analyses of relatedness. Although fewer SNPs provided usable data, these SNP barcodes weakly identified genetic differentiation across large geographic distances. However, both minor and major alleles' frequencies were temporally unstable. We conclude that these standardised SNP barcodes are vulnerable to ascertainment bias. While large numbers of SNPs acquired by whole-genome sequencing and computational methods to construct haplotypes present a way forward, these approaches may not be practical or cost-effective for surveillance on large scales in malaria-endemic areas. </p>
The genetics of immune and infection phenotypes in wild mice, Mus musculus domesticus
<p><span>Wild animals are under constant threat from a wide range of micro- and macroparasites in their environment. Animals make immune responses against parasites, and these are important in affecting the dynamics of parasite populations. Individual animals vary in their anti-parasite immune responses. Genetic polymorphism of immune-related loci contributes to inter-individual differences in immune responses, but most of what we know in this regard comes from studies of humans or laboratory animals; there are very few such studies of wild animals naturally infected with parasites. Here we have investigated the effect of Single Nucleotide Polymorphisms (SNPs) in immune-related loci (the MHC, and loci coding for cytokines and Toll-like receptors) on a wide range of immune and infection phenotypes in UK wild house mice, <em>Mus musculus domesticus</em>. We found strong associations between SNPs in various MHC and cytokine-coding loci on both immune measures (antibody concentration and cytokine production) and on infection phenotypes (infection with mites, worms and viruses). Our study provides a comprehensive view of how polymorphism of immune-related loci affects immune and infection phenotypes in naturally infected wild rodent populations.</span></p>
Figure 2 in Expanding Population Edge Craniometrics and Genetics Provide Insights into Dispersal of Commensal Rats through Nusa Tenggara, Indonesia
Figure 2. Sampling locations for skulls included in the craniometric analysis.
Figure 1. A in Genetic Relationships of Long-nosed Potoroos Potorous tridactylus (Kerr, 1792) from the Bass Strait Islands, with Notes on the Subspecies Potorous tridactylus benormi Courtney, 1963
Figure 1. A map of Bass Strait and the Bass Strait Islands.
Data from: Maintenance and expansion of genetic and trait variation following domestication in a clonal crop: Enset tGBS individual genotype data
<p class="MsoNormal">Clonal propagation enables favourable crop genotypes to be rapidly selected and multiplied. However, the absence of sexual propagation can lead to low genetic diversity and accumulation of deleterious mutations, which may eventually render crops less resilient to pathogens or environmental change. To better understand this trade-off, we characterise the domestication and contemporary genetic diversity of Enset (<em>Ensete ventricosum</em>), an indigenous African relative of bananas (<em>Musa</em>) and principal starch staple for 20 million Ethiopians. Wild enset is strictly sexually outcrossing, but in cultivation is propagated clonally and associated with diversification and specialisation into hundreds of named landraces. We applied tGBS sequencing to generate genome-wide genotypes for 192 accessions from across enset's cultivated distribution, and surveyed 1340 farmers on enset agronomic traits. Overall, reduced heterozygosity in the domesticated lineage was consistent with a domestication bottleneck that retained 37% of wild diversity. However, an excess of putatively deleterious missense mutations at low frequency present as heterozygotes suggested accumulation of mutational load in clonal domesticated lineages. Our evidence indicates that the major domesticated lineages initially arose through historic sexual recombination associated with a domestication bottleneck, followed by amplification of favourable genotypes through an extended period of clonal propagation. Among domesticated lineages we found significant phylogenetic signal for multiple farmer-identified food, nutrition and disease resistance traits and little evidence of contemporary recombination. Development of future-climate adapted genotypes may require crop breeding, but outcrossing risks exposing deleterious alleles as homozygotes. This trade-off may partly explain the ubiquity and persistence of clonal propagation over recent centuries of comparative climate stability.</p>
Local coexistence and genetic isolation of three pollinator species on the same fig tree species
Molecular tools increasingly reveal cryptic lineages and species that were previously unnoticed by traditional taxonomy. The discovery of cryptic species in sympatry prompts the question of how they coexist in the apparent absence of ecological divergence. However, this assumes first that the molecular taxonomy used to identify cryptic lineages delimits species boundaries accurately. This issue is important, because many diversity studies rely heavily or solely on data from mitochondrial DNA sequences for species delimitation, and several factors may lead to poor identification of species boundaries. We used a multilocus population genetics approach to show that three mtDNA-defined cryptic lineages of the fig wasp Pleistodontes imperialis Saunders, which pollinate Port Jackson figs (Ficus rubiginosa) in north-eastern Australia, represent reproductively isolated species. These species coexist locally, with about 13% of figs (where mating occurs) containing wasps from two or three species. However, there was no evidence for gene flow between them. Confirmed cases of coexisting cryptic species provide excellent opportunities for future studies of the ecological and evolutionary forces shaping both species coexistence and fig/pollinator coevolution.
Habitat differences influence genetic impacts of human land use on the American beech (Fagus grandifolia)
Natural reforestation after regional forest clearance is a globally common land-use sequence. The genetic recovery of tree populations in these recolonized forests may depend on the biogeographic setting of the landscape, for instance whether they are in the core or in the marginal part of the species' range. Using data from 501 individuals genotyped across 7 microsatellites, we investigated whether regional differences in habitat quality affected the recovery of genetic variation in a wind-pollinated tree species, American beech (Fagus grandifolia) in Massachusetts. We compared populations in forests that were recolonized following agricultural abandonment to those in remnant forests that have only been logged in both central inland and marginal coastal regions. Across all populations in our entire study region, recolonized forests showed limited reduction of genetic diversity as only observed heterozygosity was significantly reduced in these forests (H O = 0.520 and 0.590, respectively). Within inland region, this pattern was observed, whereas in the coast, recolonized populations exhibited no reduction in all genetic diversity estimates. However, genetic differentiation among recolonized populations in marginal coastal habitat increased (F st logged = 0.072; F st secondary = 0.249), with populations showing strong genetic structure, in contrast to inland region. These results indicate that the magnitude of recovery of genetic variation in recolonized populations can vary at different habitats.
Genetic diversity varies with species traits and latitude in predatory soil arthropods (Myriapoda: Chilopoda)
<p><strong>Aim</strong></p> <p>To investigate the drivers of intra-specific genetic diversity in centipedes, a group of ancient predatory soil arthropods.</p> <p><strong>Location</strong></p> <p>Asia, Australasia and Europe</p> <p><strong>Time period</strong></p> <p>Present</p> <p><strong>Major taxa studied</strong></p> <p>Centipedes (Class: Chilopoda)</p> <p><strong>Methods</strong></p> <p>We assembled a database of 1245 mitochondrial cytochrome c oxidase subunit I sequences representing 128 centipede species from all five orders of Chilopoda. This sequence dataset was used to estimate genetic diversity for centipede species and compare its distribution with estimates from other arthropod groups. We studied the variation in centipede genetic diversity with species traits and biogeography using a beta regression framework, controlling for the effect of shared evolutionary history within a family.</p> <p><strong>Results</strong></p> <p>A wide variation in genetic diversity across centipede species (0 to 0.1713) falls towards the higher end of values among arthropods. Overall, 27.57% of the variation in mitochondrial COI genetic diversity in centipedes was explained by a combination of predictors related to life history and biogeography. Genetic diversity decreased with body size and latitudinal position of sampled localities, was greater in species showing maternal care and increased with geographic distance among conspecifics.</p> <p><strong>Main conclusions</strong></p> <p>Centipedes fall towards the higher end of genetic diversity among arthropods, which may be related to their long evolutionary history and low dispersal ability. In centipedes, the negative association of body size with genetic diversity may be mediated by its influence on local abundance or the influence of ecological strategy on long-term population history. Species with maternal care had higher genetic diversity, which goes against expectations and needs further scrutiny. Hemispheric differences in genetic diversity can be due to historic climatic stability and lower seasonality in the southern hemisphere. Overall, we find that despite the differences in mean genetic diversity among animals, similar processes related to life history strategy and biogeography are associated with the variation within them.</p>
Unmasking hidden genetic, vocal, and size variation in the Masked Flowerpiercer along the Andes supports two species separated by Northern Peruvian Low
<p>Genetic divergence among isolated populations is not always reflected in phenotypic differentiation. We investigated the genetic and phenotypic differentiation in <em>Diglossa cyanea</em> (Thraupidae; Masked Flowerpiercer), a widely distributed species in the tropical Andes. We found strong evidence for two main lineages separated by the Marañón River valley in the Northern Peruvian Low (NPL). These two lineages show a deep sequence divergence in mitochondrial DNA (mtDNA; ~6.7% uncorrected <em>p</em>-distance, n = 122), spectral frequency and song structure (with exclusive final whistles in southern populations, n = 88), and wing length (the northern populations are smaller, n = 364). The two divergent <em>D. cyanea</em> mitochondrial lineages were not sister to each other, suggesting a possible paraphyly with respect to <em>D. caerulescens</em> (Bluish Flowerpiercer) that remains to be tested with nuclear genomic data. No genetic variation, size difference or song structure was observed within the extensive range of the southern group (from the NPL to central Bolivia) or within all sampled northern populations (from the NPL to Venezuela). These vocal differences appear to have consequences for song discrimination, and species recognition, according to a previously published playback experiment study. We propose that the southern taxon be elevated to species rank as <em>D. melanopis</em>, a monotypic species (with the proposed name Whistling Masked-Flowerpiercer). In turn, we provide a redefinition of <em>D. cyanea</em> (Warbling Masked-Flowerpiercer), which is now restricted to the northern half of the tropical Andes as a polytypic species with three subspecies (<em>tovarensis</em>, <em>obscura</em>, and <em>cyanea</em>). Based on our results, the subspecies <em>dispar </em>should be treated as a junior synonym of <em>cyanea</em>. Our study highlights the need to continue amassing complementary datasets from field observations, experiments, and collection-based assessments to better characterize the evolutionary history, biogeography, bioacoustics, and taxonomy of Neotropical montane birds.</p>
Data from: Gut microbiome dysbiosis is associated with host genetics in the Norwegian Lundehund
<p class="MsoNormal"><span>A group of diseases have been shown to correlate with a phenomenon called microbiome dysbiosis, where the bacterial species composition of the gut becomes abnormal. The gut microbiome of an animal is influenced by many factors including diet, exposures to bacteria during post-gestational growth, lifestyle, and disease status. Studies also show that host genetics can affect microbiome composition. We sought to test whether host genetic background is associated with gut microbiome composition in the Norwegian Lundehund dog, a highly inbred breed with an effective population size of 13 individuals. The Lundehund has a high rate of a protein-losing enteropathy in the small intestine that is often reported as Lundehund syndrome, which negatively affects longevity and life-quality. An outcrossing project with the Buhund, Norrbottenspets and Icelandic sheepdog was recently established to reintroduce genetic diversity to the Lundehund and improve its health. To assess whether there was an association between host genetic diversity and the microbiome composition, we sampled the fecal microbiomes of 75 dogs of the parental (Lundehund), F1 (Lundehund x Buhund), and F2 (F1 x Lundehund) generations. We found significant variation in microbiome composition from the parental Lundehund generation compared to the outcross progeny. The variation observed in purebred Lundehunds corresponded to dysbiosis as seen by a highly variable microbiome composition with an elevated Firmicutes to Bacteroidetes ratio and an increase in the prevalence of <em>Streptococcus bovis/Streptococcus equinus </em>complex, a known pathobiont that can cause several diseases. We tracked several other environmental factors including diet, the presence of a cat in the household, living on a farm and the use of probiotics, but we did not find evidence of an effect of these on microbiome composition and alpha diversity. In conclusion, we found an association between host genetics and gut microbiome composition, which in turn may be associated with the high incidence of Lundehund syndrome in the purebred parental dogs.</span></p>
Patterns of genetic variation and morphology support the recognition of five species in the Gaultheria leucocarpa Blume (Ericaceae) group from mainland China
<p><em>Gaultheria</em> <em>leucocarpa</em> and its varieties form a clade of aromatic shrubs that is widely distributed in subtropical and East Asian tropical regions. The group is taxonomically difficult and is in need of thorough taxonomic investigation. This study focused on taxonomic delimitation within the <em>G. leucocarpa </em>group from mainland China. Field surveys covering the distributional range of <em>G. leucocarpa</em> in mainland China were conducted, wherein four populations from Yunnan and one from Hunan were found bearing visibly morphological and habitat differences. A 63-species phylogenetic tree of <em>Gaultheria</em> based on one nuclear and three chloroplast markers that included samples from the <em>G. leucocarpa</em> group was reconstructed with maximum likelihood to clarify the monophyly of the <em>G. leucocarpa</em> group. Taxonomic relationships among populations of the <em>G. leucocarpa</em> group were investigated with morphology and population genetics, the latter by using two chloroplast genes and two low-copy nuclear genes. Based on the sum of morphological and genetic analyses, we described three species of <em>Gaultheria</em> as new to science, clarified the taxonomic status of <em>G. leucocarpa</em> var. <em>pingbienensis</em>, elevating it to the species level, and resurrected <em>G</em>. <em>crenulata</em> and treated the varieties <em>G. leucocarpa </em>var<em>. crenulata</em>, and <em>G. leucocarpa </em>var<em>. yunnanensis</em> as synonyms of this species. We provide a key to the five species now recognized, along with descriptions and photographs.</p>
Data from: Ecological genetics of local adaptation in Arabidopsis: an 8-year field experiment
<p>There is considerable evidence for local adaptation in nature, yet important questions remain regarding its genetic basis. How many loci are involved? What are their effect sizes? What is the relative importance of conditional neutrality vs. genetic trade-offs? Here we address these questions in the self-pollinating, annual plant <em>Arabidopsis thaliana</em>. We used 400 recombinant inbred lines (RIL) derived from two locally adapted populations in Italy and Sweden, grew the RILs and parents at the parental locations, and mapped quantitative trait loci (QTL) for mean fitness (fruits/seedling planted). We previously published results from the first three years of the study, and here add five additional years, providing a unique opportunity to assess how temporal variation in selection might affect QTL detection and classification. We found ten adaptive and one maladaptive QTL in Italy, and six adaptive and four maladaptive QTL in Sweden. The discovery of maladaptive QTL at both sites suggests that even locally adapted populations are not always at their genotypic optimum. Mean effect sizes for adaptive QTL, 0.97 and 0.55 fruits in Italy and Sweden respectively, were large relative to the mean fitness of the RILs (approximately 8 fruits/seedling planted at both sites). Both genetic trade-offs (four cases) and conditional neutrality (seven cases) contribute to local adaptation in this system. The eight-year dataset provided greater power to detect QTL and to estimate their locations compared to our previous three-year study, identifying one new genetic trade-off and reclassifying one QTL from genetic trade-off to conditionally neutral.</p>
Code and source data for the paper: "Heat over heritability: increasing body size in response to global warming is not stabilized by genetic effects in Bechstein's bats"
<p>The first two script include code for the model building testing different fixed effect strucutes.</p> <p>The next two script includes all code for the descriptive analysis, all figures, as well as the animal models that compare heritabilty between the different environments (Q1-Q4) as well as between the birth environments differentials of mothers and daughters.</p> <p>Data contain the pedigree ('pedigree_Model_cod.csv'), further information ('pedigree_information_cod.csv) and weather data ('Weather_summer.csv')</p>
Integrative multi-ancestry genetic analysis of gene regulation in coronary arteries prioritizes disease risk loci
<p>All full-sample files contain results generated in coronary artery tissue from 138 American adults. Subset analyses utilized 80 individuals selected from the original 138. Scripts accompanying some of these data in downstream analyses can be viewed on our Github, which also contains a link to the current version of our accompanying manuscript: https://github.com/MillerLab-CPHG/CAD_QTL</p> <p>Full summary statistics for eQTL associations using mixQTL (https://github.com/hakyimlab/mixqtl/wiki) by chromosome are located in UVA_coronary_mixQTL_sumstats_by_chromosome.zip</p> <p>Full summary statistics for eQTL associations using mixQTL in the subset of 100% European-ancestry study sample members by chromosome are located in Hodonsky_mixQTL_Euro_sumstats.zip</p> <p>Full summary statistics for eQTL associations using mixQTL in the genetically diverse downsampled subset by chromosome are located in Hodonsky_mixQTL_downsample_sumstats.zip</p> <p>Full summary statistics for nominal pass for all genes identified as significant in the permutation pass using QTLtools (https://qtltools.github.io/qtltools/) adjusting for local ancestry by gene by chromosome are located in Local_ancestry_UVA_coronary_QTLtools_nominal_sumstats.zip</p> <p>Full summary statistics for sQTL associations with splice junctions using QTLtools by gene are located in sQTL_results_UVA_coronary_full_sumstats.zip</p>
Spatial Mapping and Host Linking of Mobile Genetic Elements in Complex Microbiomes - Mapping MGEs in oral plaque biofilms at high specificity
<p>We stained for the GFP gene in samples that contained mixtures of plaque and GFP-transformed E. coli. We mapped mefE, an AMR gene located on a plasmid and encoding an antibiotic efflux pump, in the plaque metagenomic data of volunteer A but not volunteer B. To test the efficacy of gel embedding and clearing, we used orthogonal FISH probes, designed to not target any sequence in the plaque. We identified a T7-like prophage via metagenomic analysis and developed probes targeting its capsB gene, which encodes the minor capsid protein. We identified a highly prevalent prophage of the class Caudoviricetes with a large terminase gene, termL, and were able to design a large set of FISH probes to stain in three different colors simultaneously. We identified three non-plasmid AMR genes within metagenome assembled genomes: patA, patB, and adeF.</p>
Spatial Mapping and Host Linking of Mobile Genetic Elements in Complex Microbiomes - Optimization of single molecule MGE FISH
<p>We used <em>Escherichia coli </em>transformed with pJKR-H-tetR plasmids encoding an inducible <em>GFP</em> gene as a model system to assess and optimize MGE-FISH on a confocal microscope. We designed FISH probes for the non-coding strand of the <em>GFP</em> gene, used non-transformed <em>E. coli </em>as a negative control, and tested six different FISH protocols.<strong> </strong></p>
Spatial Mapping and Host Linking of Mobile Genetic Elements in Complex Microbiomes - Combined taxonomic mapping and MGE mapping
<p>We used rRNA FISH to stain five common oral genera, <em>Veillonella, Streptococcus, Corynebacterium, Lautropia, </em>and <em>Neisseria</em>, each with a different fluorophore, and we used MGE-FISH to stain the <em>termL</em> gene of an active prophage with a sixth fluorophore. </p> <p>We chose a target panel of 18 genera that are highly abundant and prevalent in human plaque and designed a HiPR-FISH probe panel using a 5-fluorophore combinatorial barcoding scheme. Using MGE-FISH, we stained a plasmid carrying mefE, subunit of a major-facilitator-superfamily antibiotic efflux pump. </p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.