Novel multilocus measure of linkage disequilibrium to estimate past effective population size

Hayes, Ben J., Visscher, Peter M., McPartlan, Helen C. and Goddard, Mike E. (2003) Novel multilocus measure of linkage disequilibrium to estimate past effective population size. Genome Research, 13 4: 635-643. doi:10.1101/gr.387103


Author Hayes, Ben J.
Visscher, Peter M.
McPartlan, Helen C.
Goddard, Mike E.
Title Novel multilocus measure of linkage disequilibrium to estimate past effective population size
Journal name Genome Research   Check publisher's open access policy
ISSN 1088-9051
1549-5469
Publication date 2003-04-01
Sub-type Article (original research)
DOI 10.1101/gr.387103
Open Access Status Not yet assessed
Volume 13
Issue 4
Start page 635
End page 643
Total pages 9
Place of publication Cold Spring Harbor, NY, United States
Publisher Cold Spring Harbor Laboratory Press
Language eng
Formatted abstract
Linkage disequilibrium (LD) between densely spaced, polymorphic genetic markers in humans and other species contains information about historical population size. Inferring past population size is of interest both from an evolutionary perspective (e.g., testing the "out of Africa" hypothesis of human evolution) and to improve models for mapping of disease and quantitative trait genes. We propose a novel multilocus measure of LD, the chromosome segment homozygosity (CSH). CSH is defined for a specific chromosome segment, up to the full length of the chromosome. In computer simulations CSH was generally less variable than the r2 measure of LD, and variability of CSH decreased as the number of markers in the chromosome segment was increased. The essence and utility of our novel measure is that CSH over long distances reflects recent effective population size (N), whereas CSH over small distances reflects the effective size in the more distant past. We illustrate the utility of CSH by calculating CSH from human and dairy cattle SNP and microsatellite marker data, and predicting N at various times in the past for each species. Results indicated an exponentially increasing N in humans and a declining N in dairy cattle. CSH is a valuable statistic for inferring population histories from haplotype data, and has implications for mapping of disease loci.
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: Queensland Alliance for Agriculture and Food Innovation
 
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