Supplementary Table S2. Genetic diversity of local M. tuberculosis Beijing genotype populations. N, number of SDLV branches /other branches

Transcription

1 Evolutionary History and Ongoing Transmission of Phylogenetic Sublineages of Mycobacterium tuberculosis Genotype in China Qing-qin Yin, Hai-can Liu, Wei-wei Jiao, Qin-jing Li, Rui Han, Jian-ling Tian, Zhi-guang Liu, Xiu-qin Zhao, Ying-jia Li, Kang-lin Wan, A-dong Shen, Igor Mokrousov Supplementary Table S2. Genetic diversity of local M. tuberculosis genotype populations. Province, region H, mean diversity of 24 loci N, number of SDLV branches /other branches Cumulative index of diversity, H/N /10= /19= Manchuria /8= /11= /8= Distance from *, km /8= *Distance between Bijie (the largest city in ) and the largest city of the respective province/region, calculated using:

2 (A) Supplementary Figure S1. Minimum spanning tree of 24-VNTR loci with highlighted regions of strain isolation. 15 North Center South X BJ JL 11 JL Shx FJ Guangxi Sichuan 1 AH FJ HeN HN AH FJ Shx GS FJ 7 HQ AH T 9 Jiangsu BJ HeN 8 UY HeN AH FJ

3 (B) AH BJ CQ FJ GS JL SC UY T BJ TJ HeN SC 19 AH HN 18 Shanxi Qinghai UY GS im Liaoning JL HeN 27 BJ SC 28

4 GZ T FJ GX (C)

5 (A) : Early ancient Ancient Modern Supplementary Figure S2. Minimum spanning tree of 24-VNTR loci with highlighted genotype sublineages. 15 Shaan BJ JL JL Shx FJ 1 AH FJ HeN HN AH FJ Shx 6 UY HeN AH FJ GS FJ HQ AH T 9 Jiangsu BJ HeN Guangxi Sichuan

6 (B) 17 : Early ancient Ancient Modern 16 HeN SC AH BJ CQ FJ GS JL SC Shanxi UY T AH HN BJ TJ Qinghai UY GS im JL HeN Liaoning (A0): Central Asian/Russian clone (B0/W148): Russian epidemic clone BJ SC 28 Shaa

7 GZ T FJ GX (C) : Early ancient Ancient Modern

8 (A) Adult Child Supplementary Figure S3. Minimum spanning tree of 24-VNTR loci with highlighted age group (adult/child) BJ JL JL Shx FJ 1 AH FJ HeN HN AH FJ Shx Guangxi Sichuan GS FJ UY HeN AH FJ 7 8 HQ AH T 9 Jiangsu BJ HeN 14

9 (B) Adult Child BJ TJ HeN SC 19 AH HN 18 AH BJ CQ FJ GS JL SC UY T Shanxi Qinghai 25 UY GS im Liaoning JL HeN 27 BJ SC 26 28

10 GZ T FJ GX (C) Adult Child

11 (A) CC-1 modern Supplementary Figure S4. Minimum spanning tree of 24-VNTR loci with highlighted drug resistance profile. 15 CC-14 modern Shaa pre-xdr, XDR MDR, polyresistant Monoresistant Susceptible No data 1 AH FJ HeN HN 2 14 Guangxi Sichuan CC-11 modern 12 BJ JL 11 JL Shx FJ UY HeN AH FJ 7 8 HQ AH T AH FJ Shx CC-6 modern JiangsuBJ HeN 10 GS FJ

12 (B) 17 CC-18 modern 16 HeN SC AH HN 18 AH BJ CQ FJ GS JL SC UY T Shanxi CC-A ancient 20 BJ TJ Qinghai 25 UY GS im JL HeN Liaoning 27 BJ SC CC-27/28 ancient Shaa

13 32 29 FJ GX GZ T CC-B ancient CC-29 ancient CC-D ancient CC-C ancient CC-32 Early ancient (C)

14 Supplementary Figure S5. UPGMA dendrogram of 24-MIRU-VNTR profiles of M. tuberculosis genotype isolates from adult TB patients in China. Number code designates sublineages: 1 - early ancient, 2 - ancient, 3 - modern. Mlva15-9 code was assigned by MIRU-VNTRplus.org. 24-loci order according to their order in genome.

15 Supplementary Figure S6. UPGMA dendrogram of 24-MIRU-VNTR profiles of M. tuberculosis genotype isolates from children TB patients in China. Number code designates sublineages: 1 - early ancient, 2 - ancient, 3 - modern. Mlva15-9 code was assigned by MIRU-VNTRplus.org. 24-loci order according to their order in genome.