Table 3.
Estimates of nucleotide and indel diversity for the knox-I and HB-3 genes of P. abies
| Gene | Coding region | Noncoding region | Silent sitesa | Total | |
|---|---|---|---|---|---|
| Synonymous | Nonsynonymous | ||||
| KN1 (n = 46)b | |||||
| No of sitesc | 244.2 | 889.8 | 1121 | 1365.2 | 2255 |
| SNPs (singletons)d | 10 (7) | 3 (2) | 35 (14) | 45 (21) | 48 (23*) |
| Indels (size)e | 0 | 0 | 3 (Σ = 56 bp: 54, 1, 1) | 3 (Σ = 56 bp: 54, 1, 1) | 3 (Σ = 56 bp: 54, 1, 1) |
| π | 0.00395 | 0.00019 | 0.00438 | 0.00430 | 0.00264 |
| θ | 0.00932 | 0.00077 | 0.00748 | 0.00782 | 0.00496 |
| KN2 (n = 46) | |||||
| No of sites | 247.9 | 889.1 | 2351 | 2598.9 | 3488 |
| SNPs (singletons) | 5 (2) | 5 (2) | 34 (18) | 39 (20) | 44 (22***) |
| Indels (size) | 0 | 0 | 9 (Σ = 49 bp: 25, 11, 5, 2 × 2, 4 × 1) | 9 (Σ = 49 bp: 25, 11, 5, 2 × 2, 4 × 1) | 9 (Σ = 49 bp: 25, 11, 5, 2 × 2, 4 × 1) |
| π | 0.00536 | 0.00088 | 0.00193 | 0.00226 | 0.00191 |
| θ | 0.00459 | 0.00128 | 0.00336 | 0.00348 | 0.00291 |
| KN3 (n = 46) | |||||
| No of sites | 275.0 | 982.0 | 842 | 1117.0 | 2099 |
| SNPs (singletons) | 6 (4) | 3 (3) | 16 (8) | 22 (12) | 25 (15**) |
| Indels (size) | 0 | 1 (3 bp) | 5 (Σ = 7 bp: 2, 2, 3 × 1) | 5 (Σ = 7 bp: 2, 2, 3 × 1) | 6 (Σ = 10 bp: 3, 2, 2, 3 × 1) |
| π | 0.00140 | 0.00013 | 0.00150 | 0.00148 | 0.00085 |
| θ | 0.00496 | 0.00070 | 0.00436 | 0.00451 | 0.00272 |
| KN4 (n = 46) | |||||
| No of sites | 246.5 | 938.5 | 1402 | 1648.5 | 2587 |
| SNPs (singletons) | 2 | 5 (2) | 39 (10) | 41 (10) | 46 (12) |
| Indels (size) | 0 | 0 | 5 (Σ = 13 bp: 5, 4, 2, 2 × 1) | 5 (Σ = 13 bp: 5, 4, 2, 2 × 1) | 5 (Σ = 13 bp: 5, 4, 2, 2 × 1) |
| π | 0.00069 | 0.00100 | 0.00587 | 0.00509 | 0.00359 |
| θ | 0.00185 | 0.00121 | 0.00639 | 0.00570 | 0.00406 |
| HB-3 (n = 46) | |||||
| No of sites | 611.2 | 1914.8 | 3360 | 3971.2 | 5886 |
| SNP (singletons) | 8 (5) | 1 (1) | 63 (28) | 71 (33) | 72 (34*) |
| Indel (size) | 0 | 0 | 7 (Σ = 11 bp: 4, 2,1, 1, 3 × 1) | 7 (Σ = 11 bp: 4, 2,1, 1, 3 × 1) | 7 (Σ = 11 bp: 4, 2,1, 1, 3 × 1) |
| π | 0.00102 | 0.00002 | 0.00182 | 0.00170 | 0.00115 |
| θ | 0.00298 | 0.00012 | 0.00428 | 0.00408 | 0.00279 |
| Total (n = 230) | |||||
| No of sites | 1624.7 | 5614.3 | 9076 | 10700.7 | 16315 |
| SNPs (singletons) | 31 (18) | 17 (10) | 187 (78) | 218 (96) | 235 (106) |
| Indels (total size) | 0 | 1 (3 bp) | 29 (136 bp) | 29 (136 bp) | 30 (139 bp) |
| Weighted average | |||||
| π | 0.00214 | 0.00037 | 0.00276 | 0.00267 | 0.00186 |
| θ | 0.00434 | 0.00069 | 0.00477 | 0.00470 | 0.00331 |
aSilent sites include synonymous and noncoding sites
b n is the number of sequences in the sample
cThe number of sequenced sites includes gaps induced by indels
dThe total number of substitutions with the number of singletons indicated in parentheses
eThe total number of indels with the size of indels indicated in parentheses and indels corresponding to singletons in italics
* P < 0.05, ** P < 0.01, *** P < 0.001 corresponding to the P value for obtaining a number of SNP singletons (under the neutral coalescent process) equal or higher than that observed