The molecular clock of Mycobacterium tuberculosis

Abstract

19 The molecular clock and its phylogenetic applications to genomic data have changed how we study and 20 understand one of the major human pathogens, Mycobacterium tuberculosis (MTB), the causal agent of 21 tuberculosis. Genome sequences of MTB strains sampled at different times are increasingly used to 22 infer when a particular outbreak begun, when a drug resistant clone appeared and expanded, or when a 23 strain was introduced into a specific region. Despite the growing importance of the molecular clock in 24 tuberculosis research, there is a lack of consensus as to whether MTB displays a clocklike behavior and 25 about its rate of evolution. Here we performed a systematic study of the molecular clock of MTB on a 26 large genomic data set (6,285 strains), covering different epidemiological settings and most of the 27 known global diversity. We found that sampling times below 15-20 years were often insufficient to 28 calibrate the clock of MTB. For data sets where such calibration was possible we obtained a clock rate 29 between 1x10-8 and 5x10-7 nucleotide changes per-site-per-year (0.04 - 2.2 SNPs per-genome-per- 30 year), with substantial differences between clades. These estimates were not strongly dependent on the 31 time of the calibration points as they changed only marginally when we used epidemiological isolates 32 (sampled in the last 40 years) or ancient DNA samples (about 1,000 years old) to calibrate the tree. 33 Additionally, the uncertainty and the discrepancies in the results of different methods were sometimes 34 large, highlighting the importance of using different methods, and of considering carefully their 35 assumptions and limitations. 36 37 Keywords 38 Evolution, Phylogenetics, Pathogen, Bacteria, Molecular clock, Tuberculosis. 39 2 bioRxiv preprint doi: https://doi.org/10.1101/532390; this version posted April 17, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license. 40