scholarly journals A Fine-Scale Linkage-Disequilibrium Measure Based on Length of Haplotype Sharing

2006 ◽  
Vol 78 (4) ◽  
pp. 615-628 ◽  
Author(s):  
Yan Wang ◽  
Lue Ping Zhao ◽  
Sandrine Dudoit
Keyword(s):  
Linkage Disequilibrium ◽  
Fine Scale ◽  
Haplotype Sharing ◽  
Linkage Disequilibrium Measure

Haplotype Sharing Tests of Linkage Disequilibrium in a Hutterite Asthma Data Set

2001 ◽  
Vol 21 (S1) ◽  
pp. S308-S311 ◽  
Author(s):  
Douglas F. Levinson ◽  
Ilja Nolte ◽  
Gerard J. te Meerman
Keyword(s):  
Linkage Disequilibrium ◽  
Haplotype Sharing ◽  
Data Set

Fine-Scale Mapping of a Novel Dementia Gene, PLOSL, by Linkage Disequilibrium

Genomics ◽  
1998 ◽  
Vol 54 (2) ◽  
pp. 307-315 ◽  
Author(s):  
P. Pekkarinen ◽  
M. Kestilä ◽  
J. Paloneva ◽  
J. Terwilliger ◽  
T. Varilo ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Fine Scale ◽  
Fine Scale Mapping

scholarly journals Linkage disequilibrium under polysomic inheritance

2020 ◽  
Author(s):  
Kang Huang ◽  
Derek W. Dunn ◽  
Wenkai Li ◽  
Dan Wang ◽  
Baoguo Li
Keyword(s):  
Linkage Disequilibrium ◽  
Equilibrium State ◽  
Genetic Drift ◽  
Recombination Rate ◽  
Mating Systems ◽  
Correlation Coefficients ◽  
Effective Population ◽  
Under Five ◽  
Polysomic Inheritance ◽  
Linkage Disequilibrium Measure

AbstractThe influence of genetic drift on linkage disequilibrium in finite populations has been extensively studied in diploids. However, to date the effects of ploidy on LD has not been extensively studied. We here extend the linkage disequilibrium measure D and Burrow’s Δ statistic to include polysomic inheritance, as well as their corresponding squared correlation coefficients r2 and , where the former is for phased genotypes and the latter for unphased genotypes. Weir & Hill’s double non-identity framework is also extended to include polysomic inheritance, and the expressions of double non-identity coefficients are derived under five mating systems. On this basis, the approximated expectations of estimated r2 and at equilibrium state, d2 and δ2, are derived under five mating systems. We assess the behaviors of the estimated r2 and and the influence of the recombination rate on d2 or δ2, simulate the application of estimating effective population size, and evaluate the statistical performance of the method of estimating.

scholarly journals A STUDY OF LINKAGE DISEQUILIBRIUM IN BRITISH POPULATIONS OF DROSOPHILA SUBOBSCURA

Genetics ◽  
1979 ◽  
Vol 92 (3) ◽  
pp. 983-994 ◽  
Author(s):  
B Charlesworth ◽  
D Charlesworth ◽  
M Loukas
Keyword(s):  
Linkage Disequilibrium ◽  
Geographical Variation ◽  
Direct Evidence ◽  
Drosophila Subobscura ◽  
Broad Agreement ◽  
Enzyme Loci ◽  
Linkage Disequilibrium Measure ◽  
High Degree ◽  
Individual Enzyme ◽  
Very High

ABSTRACT Data have been obtained concerning the genetic content of samples of O chromosomes from three British populations, and J chromosomes from one population, of Drosophila subobscura. Some improvements to the genetic map of the O and J chromosomes have been made. Allele frequencies at the loci studied do not show much geographical variation, except where associations with geographically varying gene arrangements distort the picture. Striking nonrandom associations between alleles at three enzyme loci and closely linked O chromosome gene arrangements are present. Some historical explanation for these associations cannot at present be ruled out, but it is clear that a very high degree of genetic differentiation must exist between different gene arrangements in this species. There is no convincing direct evidence for linkage disequilibrium between pairs of enzyme loci, although there is a significant association between close linkage and a high value of the linkage disequilibrium measure. This suggests that there may be disequilibria between closely linked enzyme loci that are too small to be individually detectable. These results are in broad agreement with those reported by workers on other Drosophila species. At present there appears to be no evidence to support the concept that selection is sufficiently strong at individual enzyme loci to produce a high degree of nonrandom associations. (FRANKLIN and LEWONTIN 1970).

scholarly journals Broad-scale puma connectivity could restore genomic diversity to fine-scale coastal populations

2021 ◽  
Author(s):  
Kyle D Gustafson ◽  
Roderick B Gagne ◽  
Michael R Buchalski ◽  
T Winston Vickers ◽  
Seth PD Riley ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Linkage Disequilibrium ◽  
Puma Concolor ◽  
Genomic Diversity ◽  
Strong Linkage Disequilibrium ◽  
Fine Scale ◽  
High Genetic Diversity ◽  
Population Genomic ◽  
Genome Wide ◽  
Genetic Clusters

Urbanization is decreasing wildlife habitat and connectivity worldwide, including for apex predators, such as the puma (Puma concolor). Puma populations along California's central and southern coastal habitats have experienced rapid fragmentation from development, leading to calls for demographic and genetic management. To address urgent conservation genomic concerns, we used double-digest restriction-site associated DNA (ddRAD) sequencing to analyze 16,285 genome-wide single-nucleotide polymorphisms (SNPs) from 401 broadly sampled pumas. Our analyses indicated support for 4–10 geographically nested, broad- to fine-scale genetic clusters. At the broadest scale, the 4 genetic clusters had high genetic diversity and exhibited low linkage disequilibrium, indicating pumas have retained statewide genomic diversity. However, multiple lines of evidence indicated substructure, including 10 fine-scale genetic clusters, some of which exhibited allelic fixation and linkage disequilibrium. Fragmented populations along the Southern Coast and Central Coast had particularly low genetic diversity and strong linkage disequilibrium, indicating genetic drift and close inbreeding. Our results demonstrate that genetically at-risk populations are typically nested within a broader-scale group of interconnected populations that collectively retains high genetic diversity and heterogeneous fixations. Thus, extant variation at the broader scale has potential to restore diversity to local populations if management actions can enhance vital gene flow and recombine locally sequestered genetic diversity. These state- and genome-wide results are critically important for science-based conservation and management practices. Our broad- and fine-scale population genomic analysis highlights the information that can be gained from population genomic studies aiming to provide guidance for fragmented population conservation management.

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