PTERV1 Phylogenetic Tree

<p>Portions of the <i>gag</i> and <i>env</i> genes (about 823 bp) were resequenced from 101 PTERV1 elements from common chimpanzee (<i>n</i> = 42), gorilla (<i>n</i> = 25), rhesus macaque (<i>n</i> = 14), and olive baboon (<i>n</i> = 20). A neighbor-joining phylogenetic tree shows a monophyletic origin for the gorilla and chimpanzee endogenous retroviruses but a polyphyletic origin among the Old World monkey species. Bootstrap support (<i>n</i> = 10,000 replicates) for individual branches are underlined. Although the retroviral insertions have occurred after speciation, retroviral sequences show greater divergence than expected for a non-coding nuclear DNA element (see <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030110#st004" target="_blank">Table S4</a>). <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030110#st008" target="_blank">Table S8</a> provides a clone key for number designation. Phylogenetic trees showing the <i>gag, env,</i> and LTR segments separately are presented in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030110#sg006" target="_blank">Figure S6</a>. Sequences 11 and 30 (red) are mapped to one of the 12 ambiguous overlapping loci described in the text (see <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030110#st003" target="_blank">Table S3</a>). They do not cluster in this phylogenetic tree, which indicates that they are unlikely to be true orthologs.