Extended Date Figure 2. Microdiversity within the SAR11 populations.

a, Recruitment plot of metagenomic reads from the ETNP OMZ 300 m sample, against scaffolds from SAG E4. Notice that the recruited reads vary in identities from 100 down to 85%, indicating the presence of closely affiliated clades, as well as extensive microdiversity within the same clade (i.e., reads sharing >95% identity) b, Phylogenetic reconstruction of reference RpoB protein sequences from SAR11 genomes, and placement of identified RpoB metagenomic sequences (denoted with the cross symbols). The alignment length was 1406 columns with 5.9% gaps or undetermined sites. The presence of multiple divergent rpoB reads within the same subclade (predominantly for subclades IIa.A and Ic) suggests high abundance but also extensive microdiversity within those populations (rather than clonal populations).