TABLE 2.

Ratios of correction to lineage substitutions for duplicated genes

Block no.	Gene pair	CAI	C	L	N	C/L
7	NHP6B-NHP6A	Low	3	26	5
7	YMC2-YMC1	Low	9	132	10
7	TKL2-TKL1	Low	26	320	18
7	TEF2-TEF1	High	44	0	0	High
8	SSE2-SSE1	Medium	26	252	25
8	SMY2-YPL105C	Low	28	504	32
8	YBR177C-YPL095C	Low	19	243	27
8	RPS6B-RPS6A	High	12	0	0	High
8	SMP1-RLM1	Low	6	74	4
8	YBR183W-YPL087W	Low	18	203	9
8	RPS9B-RPS9A	High	17	2	2	High
8	RPL21A-RPL21B	High	4	14	1	Low
8	YBR197C-YPL077C	Low	7	163	10
8	KTR4-KTR6	Low	15	426	9
8	KTR3-KTR6	Low	10	343	11
10	RPS14A-RPS14B	High	8	0	0	High
12	ARF2-ARF1	Low	9	19	2
12	RPL35B-RPL35A	High	13	1	0	High
12	PPH21-PPH22	Low	87	20	6	High
12	LYS21-LYS20	Low	116	37	3	High
15	BDF2-BDF1	Low	20	482	19
15	RPS29B-RPS29A	High	2	8	1	Low
19	PPZ2-PPZ1	Low	29	335	28
19	YDR438W-YML018C	Low	15	251	8
19	YDR450W-RPS18B	High	1	4	2	Low
19	YDR451C-YOX1	Low	19	240	9
26	RPS26B-RPS26A	High	4	12	0	Low
26	PMD1-MDS3	Low	62	935	64
29	YGR221C-YHR149C	Low	18	431	20
29	YGR230W-SPO12	Low	6	77	9
29	KEL2-KEL1	Low	36	499	34
29	YAP1802-YAP1801	Low	27	387	20
29	YGR243W-YHR162W	Low	4	64	5
29	SOL4-SOL3	Low	16	147	13
29	ENO1-ENO2	High	48	14	7	High
29	GND2-GND1	Medium	20	100	14
30	YGR004W-YLR324W	Low	14	365	14
30	STF2-YLR327C	Low	2	37	4
30	YGR010W-YLR328W	Low	17	175	11
30	RPS25A-RPS25B	High	2	3	0	Low
30	ORM1-YLR350W	Low	8	109	5
30	BUD9-BUD8	Low	15	210	24
30	YGR043C-TAL1	Medium	13	164	8
30	SCM4-YLR356W	Low	6	158	4
30	RSC1-RSC2	Low	26	553	33
30	ROM1-ROM2	Low	54	673	46
30	YGR071C-YLR373C	Low	35	671	31
32	YGL139W-YPL221W	Low	33	371	26
32	RPL1B-RPL1A	High	29	1	0	High
32	PCL10-PCL8	Low	21	324	14
32	YGL133W-YPL216W	Low	50	724	50
33	YGL084C-YPL189W	Low	35	273	33
33	YGL082W-YPL191C	Low	18	217	13
33	RPL7A-RPL7B	High	37	5	1	High
33	AFT1-YPL202C	Low	9	388	10
33	PUS2-PUS1	Low	19	266	14
34	RPL11B-RPL11A	High	30	7	0	High
34	DBF2-DBF20	Low	23	215	18
34	ASK10-YPR115W	Low	46	628	44
34	CLB1-CLB2	Low	13	100	17
34	CLB6-CLB5	Low	14	220	22
34	RPS23A-RPS23B	High	5	0	3	High
34	MEP1-MEP3	Low	16	188	21
34	ASN2-ASN1	Low	45	112	20
34	YGR131W-NCE102	Low	7	95	8
34	YGR136W-YPR154W	Low	12	88	8
34	YGR141W-YPR157W	Low	26	230	21
34	SKN1-KRE6	Low	43	290	31
35	YHL017W-PTM1	Low	6	176	7
35	YHL012W-UGP1	Low	17	365	8
35	LAG1-YKL008C	Low	12	126	15
35	RPL14B-RPL14A	High	13	5	0	High
35	YHR001W-YKR003W	Low	18	180	24
37	YHR115C-YNL116W	Low	25	228	18
37	TOM72-TOM70	Low	25	385	24
37	EPT1-CPT1	Low	15	215	13
37	YHR131C-YNL144C	Low	32	477	36
37	YHR133C-YNL156C	Low	6	220	9
37	YCK1-YCK2	Low	25	243	22
37	SPS100-YGP1	Medium	12	212	10
37	RPL42B-RPL42A	High	3	2	0	High
38	UBP7-UBP11	Low	29	426	28
38	YIL151C-YKR096W	Low	57	637	52
38	RPL40A-RPL40B	High	0	8	3	Low
39	TPM2-TPM1	Low	5	86	4
39	RPL16A-RPL16B	High	5	14	3	Low
39	FKH1-FKH2	Low	23	291	17
39	SIM1-SUN4	Low	5	11	4
39	YIL121W-YNL065W	Low	21	390	17
39	YIL120W-YNL065W	Low	21	406	19
39	POR2-POR1	Low	17	153	9
39	YIL113W-MSG5	Low	11	100	10
39	COX5B-COX5A	Low	9	51	3
39	SEC24-YNL049C	Low	41	449	29
39	YIL105C-YNL047C	Low	29	373	28
39	PRK1-ARK1	Low	24	336	15
40	RPL17B-RPL17A	High	5	14	1	Low
40	HAL5-KKQ8	Low	31	459	32
40	TPK1-TPK3	Low	22	162	13
40	CIS3-PIR3	High	5	99	9
41	YUR1-KTR2	Low	25	212	13
41	TIF2-TIF1	High	58	1	0	High
41	GLG2-GLG1	Low	22	261	20
41	RPS21B-RPS21A	High	5	2	5	High
41	LCB3-LBP2	Low	14	133	9
41	MRS3-MRS4	Low	7	140	9
41	TRK1-TRK2	Low	42	456	35
41	NCA3-UTH1	Low	22	147	9
41	YJL112W-CAF4	Low	27	423	18
41	GZF3-DAL80	Low	7	169	7
41	YJL105W-YKR029C	Low	15	459	13
41	CHS6-YKR027W	Low	22	408	23
41	SAP185-SAP190	Low	46	594	36
41	YJL084C-YKR021W	Low	39	623	30
41	YJL083W-IRS4	Low	0	2	0
41	YJL082W-YKR018C	Low	32	354	35
44	CNA1-CNA2	Low	25	258	22
44	RPS1A-RPS1B	High	5	30	3	Low
44	SIR3-ORC1	Low	30	743	30
44	RPL6B-RPL6A	High	6	14	3	Low
44	FPR4-FPR3	Low	10	188	15
44	HMG2-HMG1	Low	47	575	41
45	YLR266C-YRR1	Low	38	505	38
45	YLR270W-YOR173W	Low	12	179	10
45	BRR5-YOR179C	Low	9	90	13
45	RPS30A-RPS30B	High	7	0	0	High
45	GSP1-GSP2	Medium	4	47	4
45	EXG1-SPR1	Low	17	197	10
47	YMR222C-YOR280C	Low	8	151	13
47	RPS10B-RPS10A	High	3	10	0	Low
47	YMR233W-YOR295W	Low	11	168	14
47	YMR237W-BUD7	Low	32	342	22
47	RPL20A-RPL20B	High	12	10	0	High
47	ZRC1-COT1	Low	14	223	18
47	FAA4-FAA1	Low	51	307	35
48	MMT1-MMT2	Low	16	245	18
48	YMR180C-CET1	Low	14	229	15
48	YMR181C-YPL229W	Low	6	120	5
48	RGM1-YPL230W	Low	14	117	9
48	SSO2-SSO1	Low	10	119	12
48	YMR192W-YPL249C	Low	26	500	24
48	RPL36A-RPL36B	High	3	11	1	Low
48	YMR195W-YPL250C	Low	6	85	2
48	CIK1-VIK1	Low	21	484	26
48	CLN1-CLN2	Low	12	284	14
49	MCK1-YOL128C	Low	15	305	13
49	RPS19B-RPS19A	High	8	4	0	High
49	TRF5-TRF4	Low	21	331	22
49	CLA4-SKM1	Low	30	369	25
49	MSB3-MSB4	Low	21	294	25
49	RFC3-RFC4	Low	12	172	7
51	DED1-DBP1	Low	20	291	18
51	YOR222W-YPL134C	Low	12	163	4
51	YOR226C-YPL135W	Low	5	65	5
51	YOR227W-YPL137C	Low	60	707	42
51	YOR229W-UME1	Low	12	322	12
51	WTM1-UME1	Low	15	308	11
51	MKK1-MKK2	Low	28	260	24
51	KIN4-YPL141C	Low	27	482	35
51	RPL33B-RPL33A	High	2	7	2	Low
51	HES1-KES1	Low	18	197	12
IV:VIII	STP1-STP2	Low	24	319	17
IV:VIII	RPL27B-RPL27A	High	4	19	0	Low
VII:VII	TIF4631-TIF4632	Low	35	492	29
VII:VII	RPL24B-RPL24A	High	15	2	4	High
VII:X	RNR4-RNR2	Medium	25	215	3
VII:X	BUB1-MAD3	Low	20	351	24
VII:X	TDH3-TDH2	High	10	0	7	High
VIII:X	RPS4B-RPS4A	High	26	1	0	High

“Block no.” is from Wolfe and colleagues (http://acer.gen.tcd.ie/~khwolfe/yeast/nova/). Blocks were analyzed only if they contained at least one gene pair of high CAI (see below), and gene pairs in such blocks were analyzed only if two different homologs could be found in S. bayanus (i.e., analysis was carried out only when it was possible to make the four-way alignment). CAI was considered “high” if both of the cerevisiae genes had a CAI >0.80; CAI was considered “medium” if at least one of the cerevisiae genes had a CAI >0.45 but at least one was <0.80; otherwise, CAI was considered “low.” C is the number of correction substitutions in the four-way alignment; L, the number of lineage substitutions in the four-way alignment; N, the number of noise substitutions in the four-way alignment. For all gene pairs with high CAI, the C/L ratio is noted as “high” (>1) or “low” (<1). With two exceptions, all gene pairs with a low CAI had low C/L ratios, and so are not noted. The two exceptions are noted by italics. Correction, lineage, and noise-type substitutions are defined in Figures 4 and 5 and Table 1.