The biota of Antarctica is amazingly rich and highly endemic. The phylogenetics of notothenioid fishes has been extensively investigated through analyses of morphological characters, DNA sequences from mitochondrial genes, and single copy nuclear genes. These phylogenetic analyses have produced reasonably similar phylogenetic trees of notothenioids, however a number of phylogenetic questions remain. The nototheniid clade Trematomus is an example of a group where phylogenetic relationships remain unresolved. In this paper we revisit the phylogenetic relationships of Trematomus using both increased taxon sampling and an expanded dataset which includes DNA sequences from two mitochondrial genes (ND2 and 16S rRNA) and one single-copy nuclear gene (RPS7). The Bayesian phylogeny resulting from the analysis of the combined mitochondrial and nuclear gene datasets was well resolved and contained more interspecific nodes supported with significant Bayesian posteriors than either the mitochondrial or nuclear gene phylogenies alone. This demonstrates that the addition of nuclear gene sequence data to mitochondrial data can enhance phylogenetic resolution and increase node support. Additionally, the results of the combined mitochondrial and nuclear Bayesian analyses provide further support for the inclusion of species previously classified as Pagothenia and Cryothenia in Trematomus.

Bacterial ribosomal protein S7 initiates the folding of the 3′ major domain of 16S ribosomal RNA by binding to its lower half. The X-ray structure of protein S7 from thermophilic bacteria was recently solved and found to be a modular structure, consisting of an α-helical domain with a β-ribbon extension. To gain further insights into its interaction with rRNA, we cloned the S7 gene from Escherichia coli K12 into a pET expression vector and introduced 4 deletions and 12 amino acid substitutions in the protein sequence. The binding of each mutant to the lower half of the 3′ major domain of 16S rRNA was assessed by filtration on nitrocellulose membranes. Deletion of the N-terminal 17 residues or deletion of the β hairpins (residues 72–89) severely decreased S7 affinity for the rRNA. Truncation of the C-terminal portion (residues 138–178), which includes part of the terminal α-helix, significantly affected S7 binding, whereas a shorter truncation (residues 148–178) only marginally influenced its binding. Severe effects were also observed with several strategic point mutations located throughout the protein, including Q8A and F17G in the N-terminal region, and K35Q, G54S, K113Q, and M115G in loops connecting the α-helices. Our results are consistent with the occurrence of several sites of contact between S7 and the 16S rRNA, in line with its role in the folding of the 3′ major domain.