Figure 1

Phylogenetic tree of the Calyptogena clam symbionts with a table showing the presence/absence of mutY and recA. The maximum likelihood tree based on concatenated 16S and 23S rDNA sequences is shown with bootstrap values (> 50%) obtained from the neighbor joining, maximum parsimony and maximum likelihood methods, and with the posterior probabilities obtained in the Bayesian method at each node. The table shows the presence (+) and absence (-) of functional mutY and recA. Abbreviations of the symbionts and accession numbers of the sequences are shown in Table 3. Black triangle (1), Inactivation of recA by deletions (see Figure 2B and Additional file 1, Figure S1), and a substitution mutation of G to A at position 568 to truncate mutY and deletions at positions 797-799 and 974-989 of mutY in Rma (see Additional file 2, Figure S2). Black triangle (2), Inactivation of recA by substitution and deletion mutations in the C. stearnsii symbiont. Black triangle (3), Inactivation of recA by a two-base insertion of "CC" at position 483-484, making a new stop codon, in the C. nautilei symbiont (see Additional file 1, Figure S1). Black triangle (4), Inactivation of recA by a two-base insertion of "CC" at position 483-484, making a new stop codon, in the C. fausta symbiont lineage (see Additional file 1, Figure S1). Black triangle (5), A deletion of almost the same size outside the recA coding region in the recA-amplicon region in the common ancestor of C. fausta and C. pacifica symbionts (Additional file 1, Figure S1: positions 1855-2123 for C. fausta symbiont and 1859-2125 for C. pacifica symbiont). Black triangle (6), Occurrence of large-sized deletions in recA- and mutY-amplicons in the common ancestor of clade I symbionts (Figure 2).