Table 2.

Mutational behaviors

Mutation type	No. of mutations	WT	cac1Δ cac3Δ	pif1Δ	pol32Δ	tsa1Δ	msh2Δ	rad27Δ	mec1Δ tel1Δ	clb5Δ	mre11Δ
Parallel lines		4	4	4	4	4	4	4	8	4	4
Bottlenecks		100	75	100	100	100	100	100	25	100	75
SNPs	Transition
	A:T→G:C	6	9	7	12	60	229	26	4	21	6
	G:C→A:T	13	9	13	9	194	461	36	4	34	14
	Transversion
	A:T→T:A	6	5	7	6	58	41	28	0	17	7
	G:C→T:A	8	7	36	10	68	191	42	6	32	12
	A:T→C:G	4	1	2	2	65	22	17	5	18	6
	G:C→C:G	4	9	10	8	66	21	26	5	34	3
	Total number of mutations	41 [8–14]	40 [8–14]	75 [12–26]	47 [9–15]	512* [50-227]	965* [153–473]	175* [33–54]	24 [1–5]	156* [32–53]	49 [9–14]
	Mutation rate	0.36	0.47	0.65	0.41	4.47	8.42	1.53	0.42	1.36	0.57
	Relative increase	1	1	2	1	12	23	4	1	4	2
Small InDels (−11 to +3 bp)	Number of mutations	0	0	2 [0–1]	3 [0–2]	11 [2–4]	703 [133–215]	174 [25–54]	0	7 [1–2]	4 [1–2]
	Relative increase	1	1	>2	>3	>11	>703	>174	1	>7	>5
Intermediate-sized SVs (50 bp to 5 kb)	Number of mutations	0	0	1	6 [1–3]	10 [2–3]	4 [1–4]	57 [12–18]	0	0	1
	Relative increase	1	1	>1	>6	>10	>4	>57	1	1	>1
Large SVs (>5 kb)	Number of mutations	0	0	0	0	2 [0–1]	6	10 [1–3]	14 [1–3]	6 [0–3]	2 [0–1]
	Relative increase	1	1	1	1	>2	>6	>10	>28	>6	>3
Aneuploid chromosomes	Number of mutations	0	0	0	0	1	1	0	12 [1–2]	12 [1–6]	3 [0–1]
	Relative increase	1	1	1	1	>1	>1	1	>24	>12	>4
Total number of mutations		41	40	78	56	536	1,679	416	50	181	59
Relative increase		1	1	2	1	13	41	10	2	4	2

The number of parallel lines for each strain and the number of bottlenecks per strain are indicated (Fig. 1). For each mutation type and strain, the total number of mutations accumulated is indicated. The number of mutations observed in the two most variant lines is provided within brackets. Base substitution mutation rates were calculated as follows: total number of mutations identified/number of parallel lines/number of bottlenecks/25 (estimated number of generation per midsize colonies)/1.15 × 10⁷ (total number of nucleotides in the attainable S. cerevisiae genome). For example, in the WT strain, 41/4/100/25/1.15 × 10⁷ = 0.36 × 10⁻⁹. The relative increase over the WT strain is also provided. Aneuploidies correspond to the number of additional chromosome copies that accumulated in the total set of lines. The list of mutations per line per mutant is reported in Datasets S1–S10.

^*Statistical analysis: based on the Wilcoxon Mann–Whitney test the number of SNPs accumulated in the clb5Δ, msh2Δ rad27Δ, and tsa1Δ mutant lines is significantly higher compared with WT lines (P = 0.028).