TABLE 2

Nucleotide variation, haplotypic diversity, and neutrality tests in 22 Picea abies loci sequenced across seven populations

Nucleotide diversity
TotalNonsynonymous sitesSilent sitesHaplotype diversityNeutrality tests
GenenLS (singl.)θWtπtaLSθWaπaLSθWsπsNh (SD)He (SD)DaH
col1463,19676 (28)5.413.0388110.260.472263747.444.08360.985 (0.009)−1.57**−5.47
cry529184 (2)0.970.5759541.490.8732100040.418 (0.076)−0.93−4.88
ebs5073016 (8)4.892.2631721.410.25407147.683.86120.481 (0.087)−1.67*
gi487727 (3)2.041.2824321.851.5652152.161.1770.546 (0.073)−1.00−1.21
pat1404203 (1)1.691.9516211.452.3725621.841.7030.396 (0.077)0.35−0.04
phynrI547598 (5)2.331.2258541.500.4317145.143.9480.619 (0.050)−1.270.56
phynrII356892 (1)0.710.2453510.450.1115211.600.7330.165 (0.082)−1.28*0.06
phyo441,77619 (8)2.471.58101651.131.35759144.241.88200.910 (0.027)−1.160.21
phyP497944 (1)1.131.1559910.370.6619333.492.6750.509 (0.073)0.04−0.30
phyP2532735 (2)4.082.0521122.090.5362310.647.2060.440 (0.078)−1.18−1.42
vip3547626 (3)1.730.57*35310.620.1040052.740.9960.234 (0.077)−1.68**0.41
se121414404 (3)2.140.55NDNDNDNDNDNDNDND50.230 (0.086)−1.76**0.23
se129492752 (0)1.641.85NDNDNDNDNDNDNDND30.471 (0.068)0.24−0.73
se1100403466 (0)4.123.958300026365.365.1970.831 (0.031)−0.090.53
se1151494808 (5)3.772.11NDNDNDNDNDNDNDND90.687 (0.076)−1.190.40
se1358494478 (3)4.012.8835542.531.549249.778.0480.684 (0.056)−0.780.32
se1364475524 (1)1.641.3222800032142.832.2850.423 (0.080)−0.440.59
se1368474295 (3)2.661.048712.590.4934042.671.1940.201 (0.048)−1.49−2.98
se13904949513 (4)5.894.8330942.912.88182911.068.25150.922 (0.015)−0.541.33
se1391475034 (1)1.801.02NDNDNDNDNDNDNDND40.304 (0.083)−0.990.46
xy225482096 (3)6.473.425000015568.744.6370.582 (0.074)−1.210.62
xy14204957120 (4)7.866.81*40052.802.311691521.2417.56210.955 (0.011)−0.56−4.22
Total15,836230 (89)7109387288175207
Average4771910.5 (4)3.162.081.300.885.813.999 (8)0.545 (0.254)−0.92−0.74
  • n, sample size; L, length in base pairs; S (singl.), number of segregating sites (number of singletons); Nh (SD), number of haplotypes (standard deviation); He (SD), Nei's haplotypic diversity (standard deviation); D, Tajima's D-statistic; H, Fay and Wu's H-statistic. Indels are excluded from the estimates. Nucleotide diversity estimates (θw and π) are ×103. ND: loci for which no similarity was found in Blast searches were considered only in the calculation of the total nucleotide variation.

  • a Values that are significantly different from the average, i.e., falling outside a 95 (99)% confidence interval obtained from standard coalescent simulations with recombination rate 8.5 × 10−3 for col1 and 5.3 × 10−3 for all other genes (see materials and methods), are indicated by * (**). Tajima's D was nonsignificant when no recombination was assumed.