Fig. 5. Dominant Dewar Creek populations belonging to the Aquificae, Kryptonia, and Deinococcus-Thermus phyla.

A Lineage-specific conserved marker trees (same 56 markers used in above bacteria/archaea tree), where all available marker sequences were used for each phylum; sequences were depreplicated based on RNA Polymerase clustering at 100, 100, and 90% similarity for the Aquificae, Kryptonia, and Deinococcus-Thermus sequences, respectively. Dereplication was performed to remove redundancy and generate a representative set of marker sequences for each phylum. Dewar Creek genomes were also dereplicated, but at 100% RNA Polymerase identity where larger bubbles indicate an increase in the number of genomes for a given RNA Polymerase gene cluster. B SNP trees where variant positions were identified based on whole genome alignments. Tip colors correspond to hierBAPs Bayesian clustering results. A permanova analysis was performed to compare tree topologies with hierBAPs clustering, identifying inconsistences within Hydrogenobacter sp. (p < 0.05), but not Kryptonia sp. or Thermus antranikianii species (p > 0.05). C SNP linkage disequilibrium (LD) curves demonstrating evidence for more recent recombination within the Hydrogenobacter sp. The red dotted line represents the distance where the LD curve crosses an R² threshold of 0.5, i.e., the distance in base pairs where 50% of the SNP pairs are no longer correlated. A smaller distance at an R² of 0.5 indicates a higher rate of recombination.