Constructing primate phylogenies front ancient retrovirus sequences
Constructing primate phylogenies front ancient retrovirus sequences
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DOI：
10.1073/pnas.96.18.10254
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发表时间：
1999-08-31
影响因子：
11.1
通讯作者：
Coffin, JM
中科院分区：
文献类型：
--
作者：
Johnson, WE;Coffin, JM
现代人的基因组中充满了数以千计的内源性逆转录病毒(HERV)，这些病毒是古代病毒感染灵长类血统的前病毒残留物。大多数HERV是无功能的、选择性中性的基因座。这一事实，再加上它们在灵长类基因组中的绝对丰富，使HERV成为开发作为系统发育标记的理想选择。内源性逆转录病毒(ERV)以两种方式提供系统发育信息：(I)通过比较整合位点的多态性和(Ii)通过进化、前病毒、核苷酸序列的同源比较。在这项研究中，树是由几个ERV基因座的非编码长末端重复序列(LTRs)构建的。由于ERV的两个LTrs在整合时是相同的，但独立进化，每个ERV基因座可以根据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，树形拓扑对转换事件高度敏感，允许容易地检测重组所涉及的序列以及对此类事件的校正。尽管其他动物物种含有丰富的ERV序列，但本研究中HERV的具体使用允许将树木与东半球灵长类动物的系统发育标准进行比较。HERV，以及其他物种的ERV，构成了研究逆转录病毒科及其动物宿主进化史的独特而丰富的资源。
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.