The versatility of Bradyrhizobium
A recent paper by Matt Parker  documents the relationship between symbiosis gene diversity and core gene diversity in Bradyrhizobium isolated from many different legume hosts in the Eastern USA. The pattern of relatedness of symbiosis genes is quite different from that of core genes. I have lost count of the number of papers that have reported a similar observation; the first, as far as I know, was our own work in 1988 . Such a commonplace finding would not be enough to justify publication in a highly selective journal like Molecular Ecology. The great thing about Matt’s paper is that he sets new high standards in terms of data analysis. The phylogenetic incongruence between symbiosis and core gene trees is analysed quantitatively, and levels of polymorphism, linkage disequilibrium and signals of selection are calculated and compared. Matt concludes that novel symbiosis variants are often strongly advantageous, but that adaptation to specific symbiotic niches has relatively little effect on the core genome. As he points out, this pattern, frequently observed in rhizobia, casts doubts on Fred Cohan’s ecotype model of bacterial speciation . Matt’s paper is carefully argued and features colourful phylogenies. I recommend it.
 Parker, M.A. (2012) Legumes select symbiosis island sequence variants in Bradyrhizobium. Molecular Ecology 21: 1769-1778. http://dx.doi.org/10.1111/j.1365-294X.2012.05497.x
 Young, J.P.W., and Wexler, M. (1988) Sym plasmid and chromosomal genotypes are correlated in field populations of Rhizobium leguminosarum. Journal of General Microbiology 134: 2731-2739. http://dx.doi.org/10.1099/00221287-134-10-2731
 Cohan, F.M., and Perry, E.B. (2007) A systematics for discovering the fundamental units of bacterial diversity. Current Biology 17: R373-R386. http://dx.doi.org/10.1016/j.cub.2007.03.032