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“Science Daily 的報導指出用反轉病毒解釋人類進化樹碰到了巨大麻煩。” 這篇文章並沒有這麼說，你誤解了文章的意思。
“1。首先那些RNA片段的插入點在各猿類中遠不是同一個位置。” 正因為並不是所有的ERV出現在不同物種的同一個位置 (我沒有講清楚），所以不是所有的ERV都能被用作標記。PERV就不能用作標記。
“2。這些插入的RNA--DNA片段並非垃圾基因，而是新物種的重要基因組成部分。” 我講的不是很清楚，更準確的說法是ERV本身沒有功能，可是當嵌入宿主的染色體，ERV
有時能影響宿主基因的表達，或者引發recombination。我說的ERV (K-HERV) 非常穩定，是由於它對宿主的基因沒有影響。
“3。病毒譜系分析發現人類進化樹遠不是JTY所說的那麼清晰。” 雖然ERV很複雜，但是K-HERV的進化樹規律非常清晰。
PERV沒有同位嵌入的現象 （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.），正好說明這個ERV並不是在靈長類的祖先身上出現的 （This undermines the notion that an ancient infection invaded an ancestral primate lineage）。這是一個特殊的ERV,其形成機理有待研究（在被你省略掉的一段話里）。這才是這篇文章的意思。
(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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