Table 3 Genetic diversity (π), haplotype diversity (H), Watterson (θ), and Tajima’s D of X. fastidiosa subsp. fastidiosa (California US and Costa Rica) and X. fastidiosa subsp. pauca (Italy, Costa Rica, and Brazil) with and without recombinant regions
From: Impacts of local population history and ecology on the evolution of a globally dispersed pathogen
Population | With recombination | Without recombination | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
SNPs | Core (nt) | Nucleotide diversity (π) | Haplotype diversity (H) | Watterson’s estimator (θ) | Tajima’s D | SNPs | Core (nt) | Nucleotide diversity (π) | Haplotype diversity (H) | Watterson’s estimator (θ) | Tajima’s D | |
X. fastidiosa subsp. fastidiosa | ||||||||||||
 California (141) | 452 | 1,401,004 | 2.81x10e−05 | 6.87x10e−07 | 5.85x10e−05 | −1.712 | 334 | 957,139 | 4.59x10e−05 | 9.87x10e−07 | 6.35x10e−05 | −0.912 |
 Costa Rica (12) | 14,573 | 3.18x10e−03 | 7.14x10e−07 | 3.44x10e−03 | −0.37 | 10,024 | 3.19x10e− 03 | 1.04x10e− 06 | 3.47x10e− 03 | −0.385 | ||
 South East US (9) | 1206 | 2.97x10e−04 | 7.14x10e−07 | 3.17x10e− 03 | −0.33 | 942 | 3.32x10e−04 | 1.04x10e− 06 | 3.62x10e− 04 | −0.441 | ||
 Spain (3) | 3 | 1.43x10e−06 | 7.14x10e−07 | 1.42x10e− 06 | * | 2 | 1.39x10e−06 | 1.04x10e−06 | 3.39x10e− 06 | * | ||
 Taiwan (2) | 6 | 4.28x10e−06 | 7.14x10e−07 | 4.28x10e− 06 | * | 4 | 4.18x10e−06 | 1.04x10e−06 | 4.18x10e− 06 | * | ||
X. fastidiosa subsp. pauca | ||||||||||||
 Italy (78) | 16 | 510,568 | 1.12x10e−06 | 5.01x10e− 07 | 6.45x10e− 06 | −3.022 | 9 | 261,720 | 1.04x10e− 06 | 4.09x10e− 07 | 7.07x10e− 06 | −2.234 |
 Brazil (15) | 4291 | 3.02x10e−03 | 1.90x10e−06 | 2.58x10e− 03 | 0.592 | 2158 | 2.95x10e−03 | 3.53x10e−06 | 2.54x10e−03 | 0.731 | ||
 Costa Rica (3) | 3 | 3.92x10e−06 | 1.96x10e− 06 | 3.92x10e− 06 | * | 2 | 5.09x10e−06 | 3.82x10e− 06 | 5.09x10e− 06 | * | ||