Figure 2.

Instantaneous population contraction with a subsequent neutral fixation. A mutant (green star) appeared t_m generations ago and has just fixed neutrally in a diploid population that experienced a contraction t_c generations ago. We represent the population as a set of ${2N}_c$ 2-locus haplotypes that are painted so that the gene copies present at t = 0 can be traced back to t = t_m. Due to recombination, haplotype i carries a red gene copy at the linked locus at t = 0. Correspondingly, the coalescence time T^(l) of the haplotypes i and j at the linked locus (black tree) is larger than t_m. On the other hand, the coalescence time T^(f) at the focal locus (green tree) is smaller than t_m because at this locus all gene copies descend from the same haplotype (due to the fixation of the focal mutation).