TY - JOUR
T1 - On the utility of linkage disequilibrium as a statistic for identifying targets of positive selection in nonequilibrium populations
AU - Jensen, Jeffrey D.
AU - Thornton, Kevin R.
AU - Bustamante, Carlos D.
AU - Aquadro, Charles F.
PY - 2007/8
Y1 - 2007/8
N2 - A critically important challenge in empirical population genetics is distinguishing neutral nonequilibrium processes from selective forces that produce similar patterns of variation. We here examine the extent to which linkage disequilibrium (i.e., nonrandom associations between markers) improves this discrimination. We show that patterns of linkage disequilibrium recently proposed to be unique to hitchhiking models are replicated under nonequilibrium neutral models. We also demonstrate that jointly considering spatial patterns of association among variants alongside the site-frequency spectrum is nonetheless of value. Through a comparison of models of equilibrium neutrality, nonequilibrium neutrality, equilibrium hitchhiking, nonequilibrium hitchhiking, and recurrent hitchhiking, we evaluate a linkage disequilibrium (LD) statistic (ωmax) that appears to have power to identify regions recently shaped by positive selection. Most notably, for demographic parameters relevant to non-African populations of Drosophila melanogaster, we demonstrate that selected loci are distinguishable from neutral loci using this statistic.
AB - A critically important challenge in empirical population genetics is distinguishing neutral nonequilibrium processes from selective forces that produce similar patterns of variation. We here examine the extent to which linkage disequilibrium (i.e., nonrandom associations between markers) improves this discrimination. We show that patterns of linkage disequilibrium recently proposed to be unique to hitchhiking models are replicated under nonequilibrium neutral models. We also demonstrate that jointly considering spatial patterns of association among variants alongside the site-frequency spectrum is nonetheless of value. Through a comparison of models of equilibrium neutrality, nonequilibrium neutrality, equilibrium hitchhiking, nonequilibrium hitchhiking, and recurrent hitchhiking, we evaluate a linkage disequilibrium (LD) statistic (ωmax) that appears to have power to identify regions recently shaped by positive selection. Most notably, for demographic parameters relevant to non-African populations of Drosophila melanogaster, we demonstrate that selected loci are distinguishable from neutral loci using this statistic.
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U2 - 10.1534/genetics.106.069450
DO - 10.1534/genetics.106.069450
M3 - Article
C2 - 17565955
AN - SCOPUS:34548395446
SN - 0016-6731
VL - 176
SP - 2371
EP - 2379
JO - Genetics
JF - Genetics
IS - 4
ER -