APPENDIX B

Transition probabilities when the selected mutation is adjacent to the neutral loci

Configuration at end of selection phaseProbability given starting configurationConfiguration at start of neutral phase
00O
00A
0O
0B
00A
0B
O
C
0B
C
00O
00O
0O
00A
0B
00B
0C
00O
00O
00O
• The transition probabilities during the selection phase for each of the three starting configurations are given. Notation is as in appendix a. Note that px refers to the probability of recombination to the wild-type background for the proximal locus, while py refers to the probability of a recombination event between the proximal and the distal locus that moves the distal locus to the wild-type background.