Table 2.
Genetic diversity and neutrality test statistics by lineage (L1-L4)
| Lineage | N | S | π | D T | D FL | F FL | R 2 | H FW | Hn FW |
|---|---|---|---|---|---|---|---|---|---|
| L1 | 7 | 2238 | 1.7E-4 | −1.157 | −0.9802 (−1.7817*) |
−1.0910 (−1.9267*) |
0.0812** | 457.62 | 1.180 |
| L2 | 9 | 2240 | 1.3E-4 | −1.627 | −1.66780 (−2.3468**) |
−1.8172 (−2.5742**) |
0.0795** | 162.92 | 0.430 |
| L1/L2/L3 | 19 | 6249 | 2.7E-4 | −1.622 | −2.1420* (−2.9363**) |
−2.2253* (−2.9868**) |
0.0631** | 635.80 | 0.671 |
| L4 | 47 | 4892 | 1.1E-4 | −2.205* | −4.3046** (−5.3287**) |
−4.1559** (−4.8682**) |
0.0334** | 304.47 | 0.490 |
| L4: NYC | 21 | 2262 | 8.9E-5 | −1.649 | −2.5102* (−3.3684 *) |
−2.6277* (−3.4054 *) |
0.0593** | 230.01 | 0.7874 |
| L4: S75 | 9 | 149 | 1.5E-5 | −0.498 | 0.07218 (0.45497) |
−0.07462 (0.22079) |
0.1297 | −29.14 | −1.125 |
N, number of ingroup sequences; S, number of segregating sites; π, nucleotide diversity; k, average number of nucleotide differences; D T, Tajima’s D; R 2 , Ramos-Onsins and Rozas’ R 2, D FL and F FL, Fu and Li’s D and F (calculated with M. bovis as an outgroup); H FW, Fay and Wu’s H; Hn FW, Fay and Wu’s normalized H. Statistical significance was assess with 10,000 coalescent simulations (50,000 simulations for R 2). *P < 0.05, **P < 0.005