Figure 1

Microdiversity and diversity in gene content. Environmental surveys, using PCR amplification and sequencing of marker genes such as 16S rRNA or more rapidly evolving protein-coding genes and intergenic spacers, often reveal microdiverse clusters of strains with closely related sequences. The diagram shows a hypothetical phylogenetic tree compiled from such sequences, with each cluster indicated by a set of circles of the same color. Such a pattern of clustering by sequence might be expected if there were process other than random divergence and extinction of lineages at play (see Figure 2), and has been attributed [11,23,24] to an ecotype speciation process (see text). In this context, a microdiverse cluster might generally be a species. Comparisons of sequenced genomes for multiple strains of many designated species, and of genome sizes from isolates of others, show, however, that gene content can vary by up to 30% among different lineages of strains, even when the 'species' marker genes are identical in sequence [25]. The different sizes of the circles represent on an exaggerated scale the diversity in genome size in closely related strains found by such studies.