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141 results for “population genetics analysis”
A scalable, accurate, and universal analysis framework using individual-level allele frequency for large-scale genetic association studies in an admixed population
<p>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 SPAmix<sub>local</sub> in which the local ancestry can be incorporated if available. In addition, we propose SPAmix<sub>CCT</sub> to combine the p values of SPAmix and SPAmix<sub>local</sub> via Cauchy combination (CCT). SPAmix<sub>local</sub> performs close to Tractor when analyzing quantitative traits and is more accurate when analyzing binary traits with an unbalanced case-control ratio. And SPAmix<sub>CCT </sub>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.</p>
Construction of a SNP fingerprinting database and population genetic analysis of 329 cauliflower cultivars
<p>The VCF file contains the information of 1662 SNP sites of 820 cauliflower inbred lines that were filtered according to a series of stringent conditions.</p>
Fig. 2 in Optimisation Of Dna Extraction And Rapd-Pcr Amplification For Population Genetic Analysis Of Daphnia Cucullata Sars, 1862 (Crustacea: Cladocera)
Fig. 2. RAPD fingerprints results from different samples of Daphnia cucullata with primers OPA-03 and OPA-05 (M- marker, 1-11 runners- different samples of Daphnia cucullata; 12- control) using RAPD-PCR 10 × Taq buffer with (NH4)2SO4.
Fig.1 in Optimisation Of Dna Extraction And Rapd-Pcr Amplification For Population Genetic Analysis Of Daphnia Cucullata Sars, 1862 (Crustacea: Cladocera)
Fig.1. RAPD fingerprints results from different samples of Daphnia cucullata with primers OPA-03 and OPA-05 (M- marker, 1-16 runners- different samples of Daphnia cucullata; 17- control) using RAPD-PCR 10 × Taq buffer with KCl.
Fig. 2 in Genetic diversity and population structure of endangered Neofinetia falcata (Orchidaceae) in South Korea based on microsatellite analysis
Fig. 2. Structure analyses for putative genetic clusters of N. falcata. A: Graphs of ΔK values to determine the ideal number of groups present in the accessions of N. falcata. B: Estimated genetic structure of the 3 populations of brinjal based on STRUCTURE analysis K = 2 and K = 3.
Figure 2 in High genetic distinctiveness of wild and farm fox (Vulpes vulpes L.) populations in Poland: evidence from mitochondrial DNA analysis
Figure 2. Neighbor-joining haplotype network based on frequencies showing relationships between concatenated MT-CO1 and MTATP6 sequences of fur farm and wild red foxes.
Figure 1 in High genetic distinctiveness of wild and farm fox (Vulpes vulpes L.) populations in Poland: evidence from mitochondrial DNA analysis
Figure 1. Distribution of sampling sites of wild and fur-farm red foxes in Poland: light gray areas represent the provinces from which samples of wild foxes were taken; the darker gray area indicated with a black circle shows the location of investigated fox farms; the numbers represent fox fur-farms in particular voivodeships.
Figure. Phylogram showing phylogenetic relationships estimated using maximum likelihood analysis of 16S rRNA and COXI gene revealed the grouping of Orthochirus iranus, O. farzanpay, O. stockwelli, O. zagrosensis, O. innesi (JQ514244.1 Morocco), and O. bicolor (KT716038.1 India), with the outgroup species Androctonus crassicauda (FJ217732). in A study of genetic diversity among different population of Orthochirus sp. based on cytochrome C oxidase subunit I and 16srRNA sequencing
Figure. Phylogram showing phylogenetic relationships estimated using maximum likelihood analysis of 16S rRNA and COXI gene revealed the grouping of Orthochirus iranus, O. farzanpay, O. stockwelli, O. zagrosensis, O. innesi (JQ514244.1 Morocco), and O. bicolor (KT716038.1 India), with the outgroup species Androctonus crassicauda (FJ217732).
Fig. 2. Principal Component Analysis plot showing the 42 in Evidence of genetic connectivity between fragmented pig populations in a tropical urban city-state
Fig. 2. Principal Component Analysis plot showing the 42 individuals from the Central Catchment Nature Reserve (CCNR) and the Northeast differentiated by sex and age class. Individuals exhibiting genetic admixture are labelled. Percentage variation accounted for by each principal component is indicated in brackets.
Fig. S1. Principal Component Analysis plot showing 28 in Evidence of genetic connectivity between fragmented pig populations in a tropical urban city-state
Fig. S1. Principal Component Analysis plot showing 28 out of 42 individuals from the Central Catchment Nature Reserve (CCNR) and the Northeast with kinship values <0.2. Individuals are differentiated by sex and age class. Individuals exhibiting genetic admixture are labelled. Percentage variation accounted for by each principal component is indicated in brackets.
Fig. 3 in A multi-approach analysis of the genetic diversity in populations of Astyanax aff. bimaculatus Linnaeus, 1758 (Teleostei: Characidae) from Northeastern Brazil
Fig. 3. Giemsa-stained karyotypes of Astyanax aff. bimaculatus (2n = 50, FN = 96) from sites A (a), B (b) and C (c). In (d), a somatic metaphase after silver nitrate staining in a specimen from Contas River, showing four positive signals (arrows). The bar equals 5µm.
Fig. 2 in A multi-approach analysis of the genetic diversity in populations of Astyanax aff. bimaculatus Linnaeus, 1758 (Teleostei: Characidae) from Northeastern Brazil
Fig. 2. Partial view of collection sites of Astyanax aff. bimaculatus in the State of Bahia, Brazil: (a) Contas River, upstream Pedra Dam, Porto Alegre County – site A, (b) Contas River, downstream Pedra Dam, city of Jequié – site B, and (c) Mineiro stream, Recôncavo Sul Basin, city of Itamari – site C. In (d), view of Pedra Dam reservoir in Middle Contas River, city of Jequié.
Fig. 1 in A multi-approach analysis of the genetic diversity in populations of Astyanax aff. bimaculatus Linnaeus, 1758 (Teleostei: Characidae) from Northeastern Brazil
Fig. 1. Map of the studied area in the State of Bahia, Brazil, showing the hydrographic system and collection sites of Astyanax aff. bimaculatus: (a) site A - Contas River, upstream of Pedra Dam, Porto Alegre County (b) site B - Contas River, downstream of Pedra Dam, city of Jequié (Contas River Basin), (c) site C - Mineiro stream, city of Itamari (Recôncavo Sul Basin) and (*) location of Pedra Dam in Contas River. A specimen of Astyanax aff. bimaculatus is illustrated in detail (total length = 6.65 cm).
Data from: Genetic effects of anthropogenic habitat fragmentation on remnant animal and plant populations: a meta-analysis
Open the record for dataset details and reuse information.
Data from: Population analysis reveals genetic structure of an invasive agricultural thrips pest related to invasion of greenhouses and suitable climatic space
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Data of "Investigating the potential for genetic improvement of nitrogen and phosphorus efficiency of in a Swiss Large White pigs population using chemical analysis"
<p>Data for article 'Investigating the Potential for Genetic Improvement of Nitrogen and Phosphorus Efficiency in a Swiss Large White Pig Population using Chemical Analysis' (DOI: 10.1111/JBG.12472). Dataset of 294 Swiss Large White pigs for which phenotypes of nitrogen efficiency, phosphorus efficiency (both determined by chemical analysis of N and P content of empty body and carcass as well as the feed ingested over the experiment phase), average daily gain and gain:feed ratio are available. We also provide the pedigree that was used to estimate genetic parameters in animal models and a description of the variables (metadata).</p>
Mixed-stock analysis using Rapture genotyping to evaluate stock-specific exploitation of a walleye population despite weak genetic structure
<p>Mixed-stock analyses using genetic markers have informed fisheries management in cases where strong genetic differentiation occurs among local spawning populations, yet many fisheries are supported by multiple spawning stocks that are weakly differentiated. Freshwater fisheries exemplify this problem, with many harvested populations supported by multiple stocks of young evolutionary age and that are isolated across small spatial scales. As a result, attempts to conduct genetic mixed-stock analyses of inland fisheries have often been unsuccessful. Advances in genomic sequencing now offer the ability to discriminate among populations with weak population structure, by providing the necessary resolution to conduct mixed-stock assignment among previously indistinguishable stocks. We demonstrate the use of genomic data to conduct a mixed-stock analysis of Lake Erie's commercial and recreational walleye (<em>Sander vitreus</em>) fisheries and estimate the relative harvest of weakly differentiated stocks. We used RAD-capture (Rapture) to sequence and genotype individuals at 12,081 loci that had been previously determined to be capable of discriminating between western and eastern basin stocks (mean pairwise F<sub>ST</sub> = 0.001) with 95% reassignment accuracy. An outcome not possible in the past with microsatellite markers. Genetic assignment of 1,075 fish harvested from recreational and commercial fisheries in the eastern basin indicated that western basin stocks supported the majority of the harvest during peak harvest (July – September). Composition of harvest changed seasonally, with eastern basin fish comprising much of the early season harvest (May – June). Clear spatial structure in stock-specific harvest existed; more easterly sites contained more individuals of east basin origin than did westerly sites. Our study provides important stock contribution estimates for Lake Erie fishery management and demonstrates the power of genomic data to facilitate mixed-stock analysis in exploited fish populations with weak population structure or limited existing genetic resources.</p>
Does genetic diversity protect host populations from parasites? A meta-analysis across natural and agricultural systems
<p>If parasites transmit more readily between closely related hosts, then parasite burdens should decrease with increased genetic diversity of host populations. This important hypothesis is often accepted at face value - notorious epidemics of crop monocultures testify to the vulnerability of host populations that have been purged of diversity. Yet the relationship between genetic diversity and parasitism likely varies across contexts, differing between crop and non-crop hosts and between experimental and natural host populations. Here, we used a meta-analytic approach to ask if host diversity confers protection against parasites over the range of contexts in which it has been tested.</p> <p>We synthesized the results of 102 studies, comprising 2,004 effect sizes representing a diversity of approaches and host-parasite systems. Our results validate a protective effect of genetic diversity, while revealing significant variation in its strength across biological and empirical contexts. In experimental host populations, genetic diversity reduces parasitism by ~20% for non-crop hosts and by ~50% for crop hosts. In contrast, observational studies of natural host populations show no consistent relationship between genetic diversity and parasitism, with both strong negative and positive correlations reported. This result supports the idea that, if parasites preferentially attack close relatives, the correlation of genetic diversity with parasitism could be positive or negative depending upon the potential for host populations to evolve in response to parasite selection. Taken together, these results reinforce genetic diversity as a priority for both conservation and agriculture and emphasize the challenges inherent to drawing comparisons between controlled experimental populations and dynamic natural populations.</p>
Supplementary Material for Frontiers Plant Genetics and Genomics 'Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality'
<p>Authors</p> <p>Zhian N. Kamvar, Jonah C. Brooks, and Niklaus J. Grünwald</p>
Data from: Range-wide genetic analysis of an endangered bumble bee (Bombus affinis) reveals population structure, isolation by distance, and low colony abundance
<p>Declines in bumblebee species ranges and abundances are documented across multiple continents and have prompted the need for research to aid species recovery and conservation. The rusty patched bumblebee (<em>Bombus affinis</em>) is the first federally-listed bumblebee species in North America. We conducted a range-wide population genetics study of <em>B. affinis</em> from across all extant conservation units to inform conservation efforts. To understand the species' vulnerability and help establish recovery targets, we examined population structure, patterns of genetic diversity, and population differentiation. Additionally, we conducted site-level analysis of colony abundance to inform prioritizing areas for conservation, translocation, and other recovery actions. We find substantial evidence of population structuring along an east-to-west gradient. Putative populations show evidence of isolation by distance, high inbreeding coefficients, and a range wide male diploidy rate of ~15%. Our results suggest the Appalachians represents a genetically distinct cluster with high levels of private alleles and substantial differentiation from the rest of the extant range. Site-level analyses suggest low colony abundance estimates for <em>B. affinis</em> compared to similar datasets of stable, co-occurring species. These results lend genetic support to trends from observational studies suggesting B. affinis has undergone a recent decline and exhibits substantial spatial structure. The low colony abundances observed here suggest caution in overinterpreting the stability of populations even where <em>B. affinis</em> is reliably detected interannually. These results help delineate informed management units, provide context for the potential risks of translocation programs, and can help set clear recovery targets for this and other threatened bumblebee species.</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.