Local adaptation of Mycobacterium tuberculosis on the Tibetan Plateau

Abstract

During its global dispersal, Mycobacterium tuberculosis (Mtb) has encountered varied geographic environments and host populations. Although local adaptation seems to be a plausible model for describing long-term host-pathogen interactions, genetic evidence for this model is lacking. Here, we analyzed 576 whole-genome sequences of Mtb strains sampled from different regions of high-altitude Tibet. Our results show that, after sequential introduction of a few ancestral strains, the Tibetan Mtb population diversified locally while maintaining strict separation from the Mtb populations on the lower altitude plain regions of China. The current population structure and estimated past population dynamics suggest that the modern Beijing sublineage strains, which expanded over most of China and other global regions, did not show an expansion advantage in Tibet. The mutations in the Tibetan strains showed a higher proportion of A > G/T > C transitions than strains from the plain regions, and genes encoding DNA repair enzymes showed evidence of positive selection. Moreover, the long-term Tibetan exclusive selection for truncating mutations in the thiol-oxidoreductase encoding sseA gene suggests that Mtb was subjected to local selective pressures associated with oxidative stress. Collectively, the population genomics of Mtb strains in the relatively isolated population of Tibet provides genetic evidence that Mtb has adapted to local environments.

Keywords: Mycobacterium tuberculosis; evolution; local adaptation.

Fig. 1.

Genetic structure of Tibetan Mtb population. (A) The numbers of Mtb isolates that were sampled from different municipal regions in Tibet; the blue arrow in the world elevation map refers to the location of the Tibetan Plateau. (B) A maximum likelihood phylogenetic tree of 576 Tibetan Mtb strains; the bar plot in the middle showed the constitutions of different sublineages for each of the 3 y. The branches of the tree were colored according to the sublineages, and the annotated numbers (–6) refer to the Tibetan clades in Fig. 2. (C) Population structure of Mtb strains in 30 provinces of China; the data for other provinces were from a previous countrywide genotyping study (14).

Fig. 2.

Local diversification and origin times of Tibetan Mtb strains. (A) A maximum likelihood phylogenetic tree of 576 Tibetan strains together with 1,159 plain Mtb strains; Tibetan strains are highlighted in green and plain strains in gray. The clades colored in blue represent the plain clades that were selected for comparison with Tibet clades. A total of 12 Tibetan-specific clades are marked, and the pink diamonds indicate the strains that were sampled from plain regions but nested within Tibetan clades. The outer circle marks the global lineages/sublineages. The numbers at each branching site indicate the bootstrap values. (B) Pairwise SNP distances between strains of Tibetan clades and the relative plain clades (gray), and pairwise SNP distances between strains within each Tibetan clade. (C) Pairwise SNP distance between strains from each Tibet municipal region and between different municipal regions. (D) Estimated origin time (median value) for the ancestor strains of each Tibetan clade. (E) A dot plot showing the correlation between origin time and current population size; the gray shading indicates the 95% CI of the linear regression.

Fig. 3.

Bayesian skyline plots of six Tibetan clades. (A–F) Bayesian skyline plots for Tibet 1 to 6 clades; the color ribbons represent the 95% highest posterior density. The dashed green lines highlight the interval when Mtb population appeared to plateau. Effective population size (N_e) refers to the estimated number of breeding individuals in the given population. (G) Comparison of cluster size between clusters from L2.2 and L2.3 sublineages when using 12-SNP distance as the threshold. (H) Comparison of cluster size between clusters from L2.2 and L2.3 sublineages when using 6-SNP distance as the threshold. P values were given by Mann–Whitney U test.

Fig. 4.

Tibetan Mtb strains had higher ratio of A > G/T > C mutations. (A) Comparison of the ratio of A > G/T > C mutations between Tibetan strains and plain strains. (B) The proportion of six mutation types in all mutations from Tibet and plain strains, respectively. (C) Comparison of the ratio of A > G/T > C mutations between each Tibetan clade and the relative plain clade. (D) A bar plot showing the mutational composition for each individual strain from Tibet 1 and plain clades; the dashed white line indicates the mean level of A > G/T > C mutations in the plain group. ****P < 0.0001 and ***P < 0.001; n.s. refers to no significance (given by t test).

Fig. 5.

Local adaptation of Tibetan Mtb strains. (A) Comparison of pNpS ratio for mutations accumulated by Tibetan and plain strains; each dot represents one Mtb isolate. (B) Comparison of pNpS ratio between each Tibetan clade and the relative plain clade. (C) A maximum likelihood phylogenetic tree for Tibet 1 clade with the mutational events of sseA highlighted. Each pink star represents where the relative mutation was accumulated. (D–F) Comparison of pairwise dNdS ratio of Epi, NEpi, Ess, and NEss; Tibet (Post-divers.) refers to the comparison that only considered the mutations accumulated after local diversification. ****P < 0.0001, ***P < 0.001, and ***P < 0.01; n.s. refers to no significance (given by t test).