Petrov D A, Hartl D L
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA.
Mol Biol Evol. 1998 Mar;15(3):293-302. doi: 10.1093/oxfordjournals.molbev.a025926.
We recently proposed that patterns of evolution of non-LTR retrotransposable elements can be used to study patterns of spontaneous mutation. Transposition of non-LTR retrotransposable elements commonly results in creation of 5' truncated, "dead-on-arrival" copies. These inactive copies are effectively pseudogenes and, according to the neutral theory, their molecular evolution ought to reflect rates and patterns of spontaneous mutation. Maximum parsimony can be used to separate the evolution of active lineages of a non-LTR element from the fate of the "dead-on-arrival" insertions and to directly assess the relative frequencies of different types of spontaneous mutations. We applied this approach using a non-LTR element, Helena, in the Drosophila virilis group and have demonstrated a surprisingly high incidence of large deletions and the virtual absence of insertions. Based on these results, we suggested that Drosophila in general may exhibit a high rate of spontaneous large deletions and have hypothesized that such a high rate of DNA loss may help to explain the puzzling dearth of bona fide pseudogenes in Drosophila. We also speculated that variation in the rate of spontaneous deletion may contribute to the divergence of genome size in different taxa by affecting the amount of superfluous "junk" DNA such as, for example, pseudogenes or long introns. In this paper, we extend our analysis to the D. melanogaster subgroup, which last shared a common ancestor with the D. virilis group approximately 40 MYA. In a different region of the same transposable element, Helena, we demonstrate that inactive copies accumulate deletions in species of the D. melanogaster subgroup at a rate very similar to that of the D. virilis group. These results strongly suggest that the high rate of DNA loss is a general feature of Drosophila and not a peculiar property of a particular stretch of DNA in a particular species group.
我们最近提出，非LTR反转录转座元件的进化模式可用于研究自发突变模式。非LTR反转录转座元件的转座通常会导致产生5'端截短的“到达即死亡”拷贝。这些无活性的拷贝实际上就是假基因，根据中性理论，它们的分子进化应该反映自发突变的速率和模式。最大简约法可用于区分非LTR元件活性谱系的进化与“到达即死亡”插入的命运，并直接评估不同类型自发突变的相对频率。我们在果蝇属的粗壮果蝇组中使用非LTR元件海伦娜应用了这种方法，结果表明大缺失的发生率惊人地高，而插入几乎不存在。基于这些结果，我们认为果蝇总体上可能表现出较高的自发大缺失率，并推测如此高的DNA丢失率可能有助于解释果蝇中真正假基因令人困惑的缺乏现象。我们还推测，自发缺失率的变化可能通过影响多余“垃圾”DNA（如假基因或长内含子）的数量，导致不同分类群基因组大小的差异。在本文中，我们将分析扩展到黑腹果蝇亚组，该亚组与粗壮果蝇组大约在4000万年前有共同祖先。在同一个转座元件海伦娜的不同区域，我们证明黑腹果蝇亚组物种中的无活性拷贝以与粗壮果蝇组非常相似的速率积累缺失。这些结果强烈表明，DNA高丢失率是果蝇的一个普遍特征，而不是特定物种组中特定DNA片段的特殊性质。
