Quantifying bacterial evolution in the wild : A birthday problem for Campylobacter lineages

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Calland , J K , Pascoe , B , Bayliss , S C , Mourkas , E , Berthenet , E , Thorpe , H A , Hitchings , M D , Feil , E J , Corander , J , Blaser , M J , Falush , D & Sheppard , S K 2021 , ' Quantifying bacterial evolution in the wild : A birthday problem for Campylobacter lineages ' , PLoS Genetics , vol. 17 , no. 9 , 1009829 . https://doi.org/10.1371/journal.pgen.1009829

Title: Quantifying bacterial evolution in the wild : A birthday problem for Campylobacter lineages
Author: Calland, Jessica K.; Pascoe, Ben; Bayliss, Sion C.; Mourkas, Evangelos; Berthenet, Elvire; Thorpe, Harry A.; Hitchings, Matthew D.; Feil, Edward J.; Corander, Jukka; Blaser, Martin J.; Falush, Daniel; Sheppard, Samuel K.
Contributor organization: Department of Mathematics and Statistics
Helsinki Institute for Information Technology
Biostatistics Helsinki
Jukka Corander / Principal Investigator
Date: 2021-09
Language: eng
Number of pages: 23
Belongs to series: PLoS Genetics
ISSN: 1553-7404
DOI: https://doi.org/10.1371/journal.pgen.1009829
URI: http://hdl.handle.net/10138/340200
Abstract: Measuring molecular evolution in bacteria typically requires estimation of the rate at which nucleotide changes accumulate in strains sampled at different times that share a common ancestor. This approach has been useful for dating ecological and evolutionary events that coincide with the emergence of important lineages, such as outbreak strains and obligate human pathogens. However, in multi-host (niche) transmission scenarios, where the pathogen is essentially an opportunistic environmental organism, sampling is often sporadic and rarely reflects the overall population, particularly when concentrated on clinical isolates. This means that approaches that assume recent common ancestry are not applicable. Here we present a new approach to estimate the molecular clock rate in Campylobacter that draws on the popular probability conundrum known as the 'birthday problem'. Using large genomic datasets and comparative genomic approaches, we use isolate pairs that share recent common ancestry to estimate the rate of nucleotide change for the population. Identifying synonymous and non-synonymous nucleotide changes, both within and outside of recombined regions of the genome, we quantify clock-like diversification to estimate synonymous rates of nucleotide change for the common pathogenic bacteria Campylobacter colt (2.4 x 10(-6) s/s/y) and Campylobacter jejuni (3.4 x 10(-6) s/s/y). Finally, using estimated total rates of nucleotide change, we infer the number of effective lineages within the sample time frame-analogous to a shared birthday-and assess the rate of turnover of lineages in our sample set over short evolutionary timescales. This provides a generalizable approach to calibrating rates in populations of environmental bacteria and shows that multiple lineages are maintained, implying that large-scale clonal sweeps may take hundreds of years or more in these species.
1181 Ecology, evolutionary biology
11832 Microbiology and virology
Peer reviewed: Yes
Rights: cc_by
Usage restriction: openAccess
Self-archived version: publishedVersion

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