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“Science Daily 的报导指出用反转病毒解释人类进化树碰到了巨大麻烦。” 这篇文章并没有这么说，你误解了文章的意思。
“1。首先那些RNA片段的插入点在各猿类中远不是同一个位置。” 正因为并不是所有的ERV出现在不同物种的同一个位置 (我没有讲清楚），所以不是所有的ERV都能被用作标记。PERV就不能用作标记。
“2。这些插入的RNA--DNA片段并非垃圾基因，而是新物种的重要基因组成部分。” 我讲的不是很清楚，更准确的说法是ERV本身没有功能，可是当嵌入宿主的染色体，ERV
有时能影响宿主基因的表达，或者引发recombination。我说的ERV (K-HERV) 非常稳定，是由于它对宿主的基因没有影响。
“3。病毒谱系分析发现人类进化树远不是JTY所说的那么清晰。” 虽然ERV很复杂，但是K-HERV的进化树规律非常清晰。
PERV没有同位嵌入的现象 （The authors compared the sites of viral integration in each of these primates and found that few if any of these insertion sites were shared among the primates.），正好说明这个ERV并不是在灵长类的祖先身上出现的 （This undermines the notion that an ancient infection invaded an ancestral primate lineage）。这是一个特殊的ERV,其形成机理有待研究（在被你省略掉的一段话里）。这才是这篇文章的意思。
(ZT)
In a new study, Evan Eichler and colleagues scanned finished chimpanzee genome sequence for endogenous retroviral elements, and found one (called PTERV1) that does not occur in humans. Searching the genomes of a subset of apes and monkeys revealed that the retrovirus had integrated into the germline of African great apes and Old World monkeys—but did not infect humans and Asian apes (orangutan, siamang, and gibbon). This undermines the notion that an ancient infection invaded an ancestral primate lineage, since great apes (including humans) share a common ancestor with Old World monkeys.
Eichler and colleagues found over 100 copies of PTERV1 in each African ape (chimp and gorilla) and Old World monkey (baboon and macaque) species. The authors compared the sites of viral integration in each of these primates and found that few if any of these insertion sites were shared among the primates. It appears therefore that the sequences have not been conserved from a common ancestor, but are specific to each lineage.
As for how this retroviral infection bypassed orangutans and humans, the authors offer a number of possible scenarios ...A better understanding of the evolutionary history and population genetics of great apes will help identify the most likely scenarios. And knowing how these retroviral elements infiltrated some apes while sparing others could provide valuable insights into the process of evolution itself.
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