Fig. 5

Strain-level diversity differs between SDPs, and strains segregate into different bees. a Proportion of metagenomic reads mapping to core genes in reference database genomes within each SDP of the phylotype Gilliamella. Each vertical bar in the heatmap corresponds to a single sample. The phylogenetic tree is the same as in Fig. 2. Node labels indicate geographic origin of genomes (CH: Switzerland, USA: United States of America, NO: Norway). b The upper part of the panel shows the percentage of polymorphic sites per SDP/phylotype within samples (the center line displays the median, the boxes correspond to the 25th and 75th percentiles, and whiskers extend to the most extreme data-points that are within the 1.5 interquartile range of the box), and the total fraction across the study is indicated by red diamonds. The lower part of the panel shows the total mapped coverage for each SDP/phylotype on the reduced database, across the study. c For the 10 SDPs/phylotypes with the highest representation across samples, the cumulative fraction of variable sites relative to the number of sampled bees is shown. Ten random sampling orders were done per SDP/phylotype, where the blue curve represents the smoothed conditional mean (loess, span = 0.2), and data for individual sampling orders are shown as grey circles