Genomic epidemiology of Lineage 4 Mycobacterium tuberculosis subpopulations in New York City and New Jersey, 1999–2009

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

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