Fig. 2.

Schematic of different lineage dynamics that contribute to LD. a) Separate mutations: A and B mutations arise on independent wildtype backgrounds and are both still segregating at the time of observation (blue region). b) Recent nested mutations: a double mutant (AB) is produced by a single-mutant background (A) in the recent past, and both haplotypes are still segregating at the time of observation. c) Older nested mutations: a double mutant is produced by a larger single-mutant lineage in the distant past, but drifts back down to lower frequencies by the time of observation. d) Recombination produces double-mutant lineages from single-mutant lineages, and vice versa.