Data from: Ecological genomics of mutualism decline in nitrogen-fixing bacteria

Anthropogenic changes can influence mutualism evolution; however, the
genomic regions underpinning mutualism that are most affected by
environmental change are generally unknown, even in well-studied model
mutualisms like the interaction between legumes and their nitrogen
(N)-fixing rhizobia. Such genomic information can shed light on the agents
and targets of selection maintaining cooperation in nature. We recently
demonstrated that N-fertilization has caused an evolutionary decline in
mutualistic partner quality in the rhizobia that form symbiosis with
clover. Here population genomic analyses of N-fertilized versus control
rhizobium populations indicate that evolutionary differentiation at a key
symbiosis gene region on the symbiotic plasmid (pSym) contributes to
partner quality decline. Moreover patterns of genetic variation at
selected loci were consistent with recent positive selection within
N-fertilized environments, suggesting that N-rich environments might
select for less-beneficial rhizobia. By studying the molecular population
genomics of a natural bacterial population within a long-term ecological
field experiment, we find that: 1) the N environment is indeed a potent
selective force mediating mutualism evolution in this symbiosis, 2)
natural variation in rhizobium partner quality is mediated in part by key
symbiosis genes on the symbiotic plasmid, and 3) differentiation at
selected genes occurred in the context of otherwise recombining genomes,
resembling eukaryotic models of adaptation.