2
Linkage Disequilibrium
Montgomery Slatkin
Abstract
Linkage disequilibrium (LD) is the nonrandom association between alleles at
closely linked loci. LD is created by genetic drift and natural selection, and it
decays exponentially with time at a rate proportional to the recombination rate.
This chapter reviews the theory of LD between pairs of loci and the use of LD
for detecting past episodes of selection and for gene mapping.
2.1
Introduction
Although population genetics largely focuses on one locus at a time, much is to
be learned from considering two or more loci together. The reason is that alleles at
different loci are transmitted together, creating the opportunity for correlations that
reflect their common history. This correlation is important for gene mapping, where
the goal is to identify loci that affect a trait, and when considering the effects of
natural selection. Loci that are selected influence nearby neutral loci. Therefore, the
study of sets of loci together can provide more insight into evolutionary processes
and give additional information about gene action than can be obtained by focusing
on each locus separately.
For simplicity, I will start by presenting results for two loci. Assume that the two
loci are on the same pair of homologous chromosomes. If there are two alleles at
each of the two loci (A/a and B/b), there are four combinations, called haplotypes,
on a chromosome, AB, Ab, aB, and ab. These haplotypes can be thought of as the
four kinds of gametes that can be produced by an individual.
M. Slatkin ()
Department of Integrative Biology, University of California, Berkeley, CA, USA
e-mail: slatkin@berkeley.edu
© The Author(s), under exclusive license to Springer Nature Switzerland AG 2021
K. E. Lohmueller, R. Nielsen (eds.), Human Population Genomics,
https://doi.org/10.1007/978-3-030-61646-5_2
31
Linkage Disequilibrium
Montgomery Slatkin
Abstract
Linkage disequilibrium (LD) is the nonrandom association between alleles at
closely linked loci. LD is created by genetic drift and natural selection, and it
decays exponentially with time at a rate proportional to the recombination rate.
This chapter reviews the theory of LD between pairs of loci and the use of LD
for detecting past episodes of selection and for gene mapping.
2.1
Introduction
Although population genetics largely focuses on one locus at a time, much is to
be learned from considering two or more loci together. The reason is that alleles at
different loci are transmitted together, creating the opportunity for correlations that
reflect their common history. This correlation is important for gene mapping, where
the goal is to identify loci that affect a trait, and when considering the effects of
natural selection. Loci that are selected influence nearby neutral loci. Therefore, the
study of sets of loci together can provide more insight into evolutionary processes
and give additional information about gene action than can be obtained by focusing
on each locus separately.
For simplicity, I will start by presenting results for two loci. Assume that the two
loci are on the same pair of homologous chromosomes. If there are two alleles at
each of the two loci (A/a and B/b), there are four combinations, called haplotypes,
on a chromosome, AB, Ab, aB, and ab. These haplotypes can be thought of as the
four kinds of gametes that can be produced by an individual.
M. Slatkin ()
Department of Integrative Biology, University of California, Berkeley, CA, USA
e-mail: slatkin@berkeley.edu
© The Author(s), under exclusive license to Springer Nature Switzerland AG 2021
K. E. Lohmueller, R. Nielsen (eds.), Human Population Genomics,
https://doi.org/10.1007/978-3-030-61646-5_2
31