Signatures of kin selection in a natural population of the bacteria Bacillus subtilis

Abstract

Laboratory experiments have suggested that bacteria perform a range of cooperative behaviors, which are favored because they are directed toward relatives (kin selection). However, there is a lack of evidence for cooperation and kin selection in natural bacterial populations. Molecular population genetics offers a promising method to study natural populations because the theory predicts that kin selection will lead to relaxed selection, which will result in increased polymorphism and divergence at cooperative genes. Examining a natural population of Bacillus subtilis, we found consistent evidence that putatively cooperative traits have higher polymorphism and greater divergence than putatively private traits expressed at the same rate. In addition, we were able to eliminate alternative explanations for these patterns and found more deleterious mutations in genes controlling putatively cooperative traits. Overall, our results suggest that cooperation is favored by kin selection, with an average relatedness of r = .79 between interacting individuals.

SOCfinder: a genomic tool for identifying social genes in bacteria

“…aeruginosa and B. subtilis have supported the predictions from kin selection [32, 33]. However, these studies used the artisanal approach to identify cooperative and private genes.…”

“…The artisanal method, based on the results of examining behaviours with laboratory experiments represents the relative gold standard in terms of accuracy. It is for this reason that we used it previously when carrying out population genetic analyses, where any incorrect assignments would have introduced noise that could have concealed underlying patterns [32, 33]. However, this approach is labour intensive, produces a limited number of genes, and is restricted to species where there has been considerable experimental work, such as P.…”

“…We followed the approach used in our previous research of analysing signatures of selection on genes whose expression is controlled by quorum-sensing [32, 33]. Population genetic theory predicts that, in non-clonal populations (genetic relatedness r <1) that traits favoured by kin selection for cooperation will exhibit increased polymorphism and divergence, relative to traits that provide private benefits [71–75].…”

“…Population genetic theory predicts that, in non-clonal populations (genetic relatedness r <1) that traits favoured by kin selection for cooperation will exhibit increased polymorphism and divergence, relative to traits that provide private benefits [71–75]. To make our results directly comparable to the ‘artisan’ categorisation of genes from our previous studies [32, 33], we compared traits which are likely to be co-expressed at the same time [32, 33]. We do this by examining genes controlled by the quorum sensing network.…”

“…For example, do species where interacting individuals are more likely to be clonally related have more cooperative genes [26]? Alternatively, population genetic approaches can be used to test for ‘signatures’ (footprints) of selection for cooperation, to test if putatively cooperative behaviours really are cooperative in natural populations [32, 33]. Other possibilities include comparisons between populations, between species with different lifestyles, or between genes that can undergo different rates of horizontal transfer [31].…”