Johnson W E, Coffin J M
Department of Molecular Microbiology, Tufts University School of Medicine, Boston, MA 02111, USA.
Proc Natl Acad Sci U S A. 1999 Aug 31;96(18):10254-60. doi: 10.1073/pnas.96.18.10254.
The genomes of modern humans are riddled with thousands of endogenous retroviruses (HERVs), the proviral remnants of ancient viral infections of the primate lineage. Most HERVs are nonfunctional, selectively neutral loci. This fact, coupled with their sheer abundance in primate genomes, makes HERVs ideal for exploitation as phylogenetic markers. Endogenous retroviruses (ERVs) provide phylogenetic information in two ways: (i) by comparison of integration site polymorphism and (ii) by orthologous comparison of evolving, proviral, nucleotide sequence. In this study, trees are constructed with the noncoding long terminal repeats (LTRs) of several ERV loci. Because the two LTRs of an ERV are identical at the time of integration but evolve independently, each ERV locus can provide two estimates of species phylogeny based on molecular evolution of the same ancestral sequence. Moreover, tree topology is highly sensitive to conversion events, allowing for easy detection of sequences involved in recombination as well as correction for such events. Although other animal species are rich in ERV sequences, the specific use of HERVs in this study allows comparison of trees to a well established phylogenetic standard, that of the Old World primates. HERVs, and by extension the ERVs of other species, constitute a unique and plentiful resource for studying the evolutionary history of the Retroviridae and their animal hosts.
现代人类的基因组中充斥着数以千计的内源性逆转录病毒（HERV），它们是灵长类谱系古代病毒感染的前病毒残余物。大多数HERV是无功能的、选择性中性位点。这一事实，再加上它们在灵长类基因组中的丰富数量，使得HERV成为作为系统发育标记进行利用的理想选择。内源性逆转录病毒（ERV）通过两种方式提供系统发育信息：（i）通过整合位点多态性的比较，以及（ii）通过对不断进化的前病毒核苷酸序列进行直系同源比较。在本研究中，利用几个ERV位点的非编码长末端重复序列（LTR）构建树。由于ERV的两个LTR在整合时是相同的，但会独立进化，每个ERV位点可以基于同一祖先序列的分子进化提供两种物种系统发育的估计。此外，树的拓扑结构对转换事件高度敏感，便于检测参与重组的序列以及对此类事件进行校正。虽然其他动物物种富含ERV序列，但本研究中对HERV的特定使用使得能够将树与一个完善的系统发育标准——旧世界灵长类的标准进行比较。HERV，以及由此延伸的其他物种的ERV，构成了研究逆转录病毒科及其动物宿主进化历史的独特而丰富的资源。
