How Population Growth Affects Linkage Disequilibrium
Alan R. Rogers

Abstract

The "LD curve" relates the linkage disequilibrium (LD) between pairs of nucleotide sites to the distance that separates them along the chromosome. The shape of this curve reflects natural selection, admixture between populations, and the history of population size. The present article derives new results about the last of these effects. When a population expands in size, the LD curve grows steeper, and this effect is especially pronounced following a bottleneck in population size. When a population shrinks, the LD curve rises but remains relatively flat. As LD converges toward a new equilibrium, its time path may not be monotonic. Following an episode of growth, for example, it declines to a low value before rising toward the new equilibrium. These changes happen at different rates for different LD statistics. They are especially slow for estimates of σ2d, which therefore allow inferences about ancient population history. For the human population of Europe, these results suggest a history of population growth.

  • Received November 10, 2013.
  • Accepted May 28, 2014.