Table 2.

Pairwise divergences and relative rate tests among duplicated genes in allopolyploid (A_T, D_T) cotton and their orthologous counterparts (A, D) from progenitor diploid genomes

Locus	Length, nt	Distance† between sequences and relative rate test results‡
		A vs. AT	D vs. DT	A vs. D	AT vs. DT	AT v. Gk	DT vs. Gk
A1286	294	0.0034	0.0069	0.0139	0.0174	0.0544	0.0583
A1341	624	0.0033	0.0082	0.0318	0.0267	0.0384	0.0364
A1520	957	0.0011	0.0044	0.0087	0.0077	0.0703	0.0749
A1550	1448	0.0104	0.0131	0.0240	0.0235	0.0552	0.0545
A1623	840	0.0048	0.0195	0.0171	0.0246	0.0362	0.0438
A1625	1061	0.0051	0.0144	0.0276	0.0325	0.0327	0.0364
A1713	702	0.0080	0.0047	0.0176	0.0158	0.0475	0.0512
A1751	807	0.0025	0.0000	0.0125	0.0150	0.0329	0.0304
A1834	882	0.0037	0.0061	0.0249§	0.0261§	—§	—§
G1121	749	0.0054	0.0040	0.0176	0.0148	0.0325	0.0312
G1134	546	0.0000	0.0018	0.0074	0.0093	0.0414	0.0402
G1262	888	0.0045	0.0057	0.0194	0.0206	0.0372	0.0372
AdhA	951	0.0096	0.0140	0.0184	0.0249	0.0325	0.0315
AdhC	1680	0.0097	0.0273	0.0478*(D)	0.0494**(DT)	0.0510	0.0794
CelA1	1096	0.0037	0.0102	0.0168	0.0178*+(DT)	0.0320	0.0429
CelA2	1180	0.0206	0.0051	0.0286†(A)	0.0367**†(AT)	0.0529	0.0332
Total	14,705	0.0068	0.0105*(DT)	0.0224	0.0249	0.0442	0.0464

^† Jukes–Cantor transformations using all nucleotide sites. 

^‡  Significance levels using the Tajima 1D rate test (42) and G. kirkii (Gk) as the reference taxon are indicated by single (P ≤ 0.05) and double (P ≤ 0.01) asterisks (for all nucleotide sites) and plus symbols (for nonsynonymous sites); the taxon with the faster rate is shown parenthetically. 

^§ Relative rate tests and pairwise comparisons could not be conducted, because outgroup sequences were unavailable.