Figure 4.

Evolutionary relationships of the eutherian mammalian TRGJ genes. The TRGJ coding sequences of all mammalian species were included in the tree. A chicken (Galgal) TRGJ gene was used as outgroup [66]. Multiple alignments of the gene sequences were carried out using the MUSCLE program [111]. The evolutionary analyses were conducted in MEGA7 [112]. We used the neighbor-joining (NJ) method to reconstruct the phylogenetic tree [113]. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (100 replicates) is shown next to the branches [114]. The trees are drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic trees. The evolutionary distances were computed using the p-distance method [115] and the units are the number of base differences per site. The analysis involved 67 nucleotide sequences. All positions containing gaps and missing data were eliminated. There were a total of 39 positions in the final dataset. The C-proximal TRGJ genes are shown in red; the C-distal TRGJ genes are shown in blue. The TRGJ genes occupying the middle position of the J cluster formed by three genes within each own TRG locus are marked with a black circle. The IMGT six-letter standardized abbreviations for species (Homsap (human), Musmus (mouse), Felcat (cat), Bostau (bovine), Oviari (sheep), Camdro (dromedary), Turtru (dolphin), Orycun (rabbit)) and nine-letter standardized abbreviation for subspecies (Canlupfam, dog) taxa are used.