scholarly journals Assessment of Linkage Disequilibrium by the Decay of Haplotype Sharing, with Application to Fine-Scale Genetic Mapping

1999 ◽  
Vol 65 (3) ◽  
pp. 858-875 ◽  
Author(s):  
Mary Sara McPeek ◽  
Andrew Strahs
Keyword(s):  
Linkage Disequilibrium ◽  
Genetic Mapping ◽  
Fine Scale ◽  
Haplotype Sharing

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

scholarly journals Comparative Genetic Mapping and Discovery of Linkage Disequilibrium Across Linkage Groups in White Clover (Trifolium repensL.)

2012 ◽  
Vol 2 (5) ◽  
pp. 607-617 ◽  
Author(s):  
Sachiko N. Isobe ◽  
Hiroshi Hisano ◽  
Shusei Sato ◽  
Hideki Hirakawa ◽  
Kenji Okumura ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Genetic Mapping ◽  
White Clover ◽  
Linkage Groups ◽  
Comparative Genetic Mapping

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 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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