Estimating the relative roles of recombination and point mutation in the generation of single locus variants in Campylobacter jejuni and Campylobacter coli
Yu, S and Fearnhead, P and Holland, BR and Biggs, P and Maiden, M and French, N, Estimating the relative roles of recombination and point mutation in the generation of single locus variants in Campylobacter jejuni and Campylobacter coli, Journal of Molecular Evolution, 74, (5-6) pp. 273-280. ISSN 0022-2844 (2012) [Refereed Article]
Single locus variants (SLVs) are bacterial sequence types that differ at only one of the seven canonical multilocus sequence typing (MLST) loci. Estimating the relative roles of recombination and point mutation in the generation of new alleles that lead to SLVs is helpful in understanding how organisms evolve. The relative rates of recombination and mutation for Campylobacter jejuni and Campylobacter coli were estimated at seven different housekeeping loci from publically available MLST data. The probability of recombination generating a new allele that leads to an SLV is estimated to be roughly seven times more than that of mutation for C. jejuni, but for C. coli recombination and mutation were estimated to have a similar contribution to the generation of SLVs. The majority of nucleotide differences (98% for C. jejuni and 85% for C. coli) between strains that make up an SLV are attributable to recombination. These estimates are much larger than estimates of the relative rate of recombination to mutation calculated from more distantly related isolates using MLST data. One explanation for this is that purifying selection plays an important role in the evolution of Campylobacter. A simulation study was performed to test the performance of our method under a range of biologically realistic parameters. We found that our method performed well when the recombination tract length was longer than 3 kb. For situations in which recombination may occur with shorter tract lengths, our estimates are likely to be an underestimate of the ratio of recombination to mutation, and of the importance of recombination for creating diversity in closely related isolates. A parametric bootstrap method was applied to calculate the uncertainty of these estimates.
single locus variant, MLST, purifying selection, evolution of Campylobacter, mutation, recombination