Figure 1

Best maximum likelihood tree (IQPNNI, WAG, estimated shape parameter α with 8 rate categories + invariable sites) of the RNA polymerase B' subunit (435 aa positions) for members of the halophilic archaea. Bootstrap values were obtained using proML and IQPNNI and are shown in that order. Only those nodes that have a bootstrap value greater than 70% are displayed. Branch lengths are extended by dashed lines such that the taxa representing a particular haloarchaeal genus can be readily associated with the corresponding row in the table, which indicates rhodopsin and nitrate reduction presence/absence within that taxonomic division. The code used in the table to denote the presence/absence of bacteriorhodopsin (BR), halorhodopsin (HR), sensory rhodopsins I and II (SRI and SRII), opsin paralog of unknown function (Op) and nitrate reduction (NO₃) is: G = genome sequence, P = Gene product, S = spectroscopic protein assay, - = Absent. A blank box indicates that information on presence or absence is not available. The groups outlined by shaded boxes represent well-supported clades of haloarchaea. Note that in most cases a single RpoB' sequence is used to represent an entire genus and the representative taxa and accession number can be found in the methods section.