Unrooted NJ tree of RubisCO/RLP lineages. To construct this tree, a total of 193 sequences were aligned with MEGA 3.1 () and evaluated by ProtTest (), and the tree was then constructed using the equal-input model with a gamma rate distribution of 1.554. The total numbers of sequences considered in each lineage were 35 for I-A, 16 for I-B, 9 for I-C, 22 for I-D, 20 for II, 10 for III-1, 4 for III-2, 20 for IV-NonPhoto, 2 for IV-EnvOnly, 14 for IV-Photo, 16 for IV-DeepYkrW, 12 for IV-YkrW, and 5 for IV-GOS. The width of the arrows is directly proportional to the number of sequences considered for each clade. For a complete list of sequences and sources, see Table S1 in the supplemental material. The scale bar represents a difference of 0.5 substitutions per site. Bootstrap values for nodes are shown in Fig. . Single-sequence abbreviations and sequence identifiers are as follows: IV-Arc.ful-DSM 4304, *Archaeoglobus fulgidus* strain DSM4304 (GenBank accession number NP_070416); Met.bur-DSM6242, *Methanococcoides burtonii* strain DSM6242 (accession number ZP_00563653); Met.hun-JF-1, *Methanospirillum hungatei* strain JF-1 (accession number YP_503739); Met.the-PT, *Methanosaeta thermophila* strain PT (accession number ZP_01153096).

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