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

Area of Science:

• Microbial genomics
• Evolutionary biology
• Population genetics

Background:

• Estimating bacterial molecular evolution rates typically relies on samples with recent common ancestry.
• This method is insufficient for multi-host pathogens with sporadic sampling, like environmental bacteria.
• Campylobacter species are significant human pathogens with complex transmission dynamics.

Purpose of the Study:

• To develop a new approach for estimating molecular clock rates in bacteria with multi-host transmission.
• To apply this method to Campylobacter coli and Campylobacter jejuni to determine their nucleotide substitution rates.
• To infer lineage turnover and dynamics in bacterial populations over short evolutionary timescales.

Main Methods:

• Utilized a novel approach inspired by the 'birthday problem' probability conundrum.
• Employed large genomic datasets and comparative genomics to analyze isolate pairs with recent common ancestry.
• Differentiated between synonymous and non-synonymous nucleotide changes within and outside recombined genomic regions.

Main Results:

• Estimated synonymous nucleotide substitution rates for Campylobacter coli (2.4 x 10^-6 s/s/y) and Campylobacter jejuni (3.4 x 10^-6 s/s/y).
• Inferred the number of effective lineages and assessed lineage turnover rates over short evolutionary periods.
• Demonstrated that multiple lineages are maintained in these bacterial populations.

Conclusions:

• The developed method offers a generalizable approach for calibrating molecular clock rates in environmental bacteria.
• Findings suggest that large-scale clonal sweeps in Campylobacter species may occur over hundreds of years or longer.
• The study highlights the persistence of multiple lineages, challenging assumptions of rapid clonal expansion in these pathogens.