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57 results for “Linkage disequilibrium”
Data from: Linkage disequilibrium network analysis (LDna) gives a global view of chromosomal inversions, local adaptation and geographic structure
Recent advances in sequencing allow population-genomic data to be generated for virtually any species. However, approaches to analyse such data lag behind the ability to generate it, particularly in nonmodel species. Linkage disequilibrium (LD, the nonrandom association of alleles from different loci) is a highly sensitive indicator of many evolutionary phenomena including chromosomal inversions, local adaptation and geographical structure. Here, we present linkage disequilibrium network analysis (LDna), which accesses information on LD shared between multiple loci genomewide. In LD networks, vertices represent loci, and connections between vertices represent the LD between them. We analysed such networks in two test cases: a new restriction-site-associated DNA sequence (RAD-seq) data set for Anopheles baimaii, a Southeast Asian malaria vector; and a well-characterized single nucleotide polymorphism (SNP) data set from 21 three-spined stickleback individuals. In each case, we readily identified five distinct LD network clusters (single-outlier clusters, SOCs), each comprising many loci connected by high LD. In A. baimaii, further population-genetic analyses supported the inference that each SOC corresponds to a large inversion, consistent with previous cytological studies. For sticklebacks, we inferred that each SOC was associated with a distinct evolutionary phenomenon: two chromosomal inversions, local adaptation, population-demographic history and geographic structure. LDna is thus a useful exploratory tool, able to give a global overview of LD associated with diverse evolutionary phenomena and identify loci potentially involved. LDna does not require a linkage map or reference genome, so it is applicable to any population-genomic data set, making it especially valuable for nonmodel species.
The evolutionary patterns of barley pericentromeric chromosome regions, as shaped by linkage disequilibrium and domestication
<p>The distribution of recombination events along large cereal chromosomes is uneven and generally restricted to gene-rich telomeric ends. In order to understand how the lack of recombination affects diversity in the large pericentromeric regions, we assembled and analysed deep exome capture data from a panel of 879 cultivars, landraces, and wild barleys, sampled from across their eco-geographical ranges. We defined and compared variant data across the pericentromeric and non-pericentromeric regions, observing a clear partitioning of diversity both within and between chromosomes and germplasm groups. Dramatically reduced diversity was found in the pericentromeres of both cultivars and landraces when compared to wild barley. We observed a mixture of completely and partially differentiated SNPs between domesticated and wild genepools, suggesting the former were derived from multiple wild ancestors. Patterns of genome-wide linkage disequilibrium, haplotype block size and number, and variant frequency within blocks showed clear contrasts among individual chromosomes and between cultivars and wild barleys. While most cultivar chromosomes shared a single major pericentromeric haplotype, chromosome 7H clearly differentiated 2-row and 6-row types associated with different geographical origins. Within the pericentromeric regions we identified 22,387 non-synonymous SNPs, of which 92 were fixed for alternative alleles in cultivar versus wild accessions. Surprisingly, only 29 SNPs found exclusively in the cultivars were predicted to be ‘highly deleterious’. GO terms associated with the pericentromeric regions revealed housekeeping genes to be over-represented. Overall, our data reveal an unconventional pericentromeric genetic landscape among distinct barley gene pools with different evolutionary processes driving domestication and diversification.</p>
Data from: Linkage disequilibrium and inversion-typing of the Drosophila melanogaster Genome Reference Panel
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Data from: Linkage disequilibrium clustering-based approach for association mapping with tightly linked genome-wide data
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Data from: Linkage disequilibrium network analysis (LDna) gives a global view of chromosomal inversions, local adaptation and geographic structure
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Data from: Patterns of linkage disequilibrium and long range hitchhiking in evolving experimental Drosophila melanogaster populations
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Data from: Commercial chicken breeds exhibit highly divergent patterns of linkage disequilibrium
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Data from: An evaluation of the methods to estimate effective population size from measures of linkage disequilibrium
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Data from: Physical linkage and mate preference generate linkage disequilibrium for behavioral isolation in two parapatric crickets
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Data from: Linkage disequilibrium and effective population size when generations overlap
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Data from: Estimations of linkage disequilibrium, effective population size and ROH-based inbreeding coefficients in Spanish Churra sheep using imputed high-density SNP genotypes
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Data from: An evaluation of a novel estimator of linkage disequilibrium
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Effective population size, extended linkage disequilibrium and signatures of selection in the rare dog breed Lundehund
GEO Series GSE66677. Canis lupus familiaris. 28 samples. Type: Genome variation profiling by SNP array; SNP genotyping by SNP array.
Data from: Diversity and linkage disequilibrium in farmed Tasmanian Atlantic salmon
Farmed Atlantic salmon (Salmo salar) is a globally important production species, including in Australia where breeding and selection has been in progress since the 1960s. The recent development of SNP genotyping platforms means genome-wide association and genomic prediction can now be implemented to speed genetic gain. As a precursor, this study collected genotypes at 218 132 SNPs in 777 fish from a Tasmanian breeding population to assess levels of genetic diversity, the strength of linkage disequilibrium (LD) and imputation accuracy. Genetic diversity in Tasmanian Atlantic salmon was lower than observed within European populations when compared using four diversity metrics. The distribution of allele frequencies also showed a clear difference, with the Tasmanian animals carrying an excess of low minor allele frequency variants. The strength of observed LD was high at short distances (<25 kb) and remained above background for marker pairs separated by large chromosomal distances (hundreds of kb), in sharp contrast to the European Atlantic salmon tested. Genotypes were used to evaluate the accuracy of imputation from low density (0.5 to 5 K) up to increased density SNP sets (78 K). This revealed high imputation accuracies (0.89–0.97), suggesting that the use of low density SNP sets will be a successful approach for genomic prediction in this population. The long-range LD, comparatively low genetic diversity and high imputation accuracy in Tasmanian salmon is consistent with known aspects of their population history, which involved a small founding population and an absence of subsequent introgression. The findings of this study represent an important first step towards the design of methods to apply genomics in this economically important population.
Data from: Estimating contemporary effective population size in non-model species using linkage disequilibrium across thousands of loci
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Data from: Genetic substructure and admixture as important factors in linkage disequilibrium-based estimation of effective number of breeders in recovering wildlife populations
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Data from: Diversity and linkage disequilibrium in farmed Tasmanian Atlantic salmon
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