Constructing primate phylogenies front ancient retrovirus sequences

The genomes of modern humans are riddled with thousands of endogenous retro viruses (HERVs), the proviral remnants of ancient viral infections of the p rimate lineage. Most HERVs are nonfunctional, selectively neutral loci. Thi s fact, coupled with their sheer abundance in primate genomes, makes HERVs ideal for exploitation as phylogenetic markers. Endogenous retroviruses (ER Vs) provide phylogenetic information in two ways: (i) by comparison of inte gration site polymorphism and (ii) by orthologous comparison of evolving, p roviral, nucleotide sequence. In this study, trees are constructed with the noncoding long terminal repeats (LTRs) of several ERV loci. Because the tw o LTRs of an ERV are identical at the time of integration but evolve indepe ndently, each ERV locus can provide two estimates of species phylogeny base d on molecular evolution of the same ancestral sequence. Moreover, tree top ology is highly sensitive to conversion events, allowing for easy detection of sequences involved in recombination as well as correction for such even ts. Although other animal species are rich in ERV sequences, the specific u se of HERVs in this study allows comparison of trees to a well established phylogenetic standard, that of the Old World primates. HERVs, and by extens ion the ERVs of other species, constitute a unique and plentiful resource f or studying the evolutionary history of the Retroviridae and their animal h osts.