Figure 4

V1R gene tree. Distance tree produced using 56 codon-aligned V1R sequences (906 nucleotides length) from mouse (musculus V1Rs denoted with "MUS" prefix; spretus V1Rs denoted with "YU" prefix) and rat ("RAT" prefix; dotted boxed clades). Pseudogenes are denoted by "pg" in their names. Musculus-spretus orthologous pairs in which one species encodes an intact V1R and the other species encodes an apparent pseudogene are shaded. Deleted V1Rs in one species but not the other are also shaded. Brackets with asterisks denote the two orthologous gene pairs apparently subject to adaptive selection (dS/dN < 1; see text), and the bracket without asterisk denotes the one orthologous gene pair apparently subject to gene conversion (Fig. 2). From this phylogeny, we infer that the rodent ancestor had five V1R genes: a homolog to rat A16, a homolog to mouse A1, a homolog to mouse A9, a homolog to mouse A7, and a B-like homolog. Bootstrap values (1000 replicas) for nodes <95% are indicated. Dashed lines with arrows show different locations of the MUS.A7, RAT.A2, and RAT.B9 branches in a parsimony bootstrap tree (1000 replicas) (not shown).