Institut für Populationsgenetik, Vetmeduni Vienna, Wien, Austria.
Vienna Graduate School of Population Genetics, Wien, Austria.
Genome Biol Evol. 2020 Nov 3;12(11):2139-2152. doi: 10.1093/gbe/evaa190.
The P-element, one of the best understood eukaryotic transposable elements, spread in natural Drosophila melanogaster populations in the last century. It invaded American populations first and later spread to the Old World. Inferring this invasion route was made possible by a unique resource available in D. melanogaster: Many strains sampled from different locations over the course of the last century. Here, we test the hypothesis that the invasion route of the P-element may be reconstructed from extant population samples using internal deletions (IDs) as markers. These IDs arise at a high rate when DNA transposons, such as the P-element, are active. We suggest that inferring invasion routes is possible as: 1) the fraction of IDs increases in successively invaded populations, which also explains the striking differences in the ID content between American and European populations, and 2) successively invaded populations end up with similar sets of IDs. This approach allowed us to reconstruct the invasion route of the P-element with reasonable accuracy. Our approach also sheds light on the unknown timing of the invasion in African populations: We suggest that African populations were invaded after American but before European populations. Simulations of TE invasions in spatially distributed populations confirm that IDs may allow us to infer invasion routes. Our approach might be applicable to other DNA transposons in different host species.
P 元素是研究最为透彻的真核转座元件之一,上个世纪在自然的黑腹果蝇种群中扩散。它首先入侵了美洲种群,后来又传播到了旧大陆。通过在黑腹果蝇中可用的独特资源,推断出这种入侵途径成为可能:在过去的一个世纪中,从不同地点采集了许多品系。在这里,我们使用内部缺失 (IDs) 作为标记,检验了 P 元素的入侵途径可以从现存的种群样本中重建的假设。当 DNA 转座子(如 P 元素)活跃时,这些 IDs 会以高频率产生。我们认为,推断入侵途径是可行的,因为:1) 相继入侵的种群中 IDs 的比例增加,这也解释了美洲和欧洲种群之间 ID 含量的显著差异,2) 相继入侵的种群最终具有相似的 ID 集。这种方法使我们能够以合理的准确度重建 P 元素的入侵途径。我们的方法还揭示了非洲种群入侵时间的未知情况:我们认为,非洲种群是在美洲种群之后、欧洲种群之前被入侵的。在空间分布的种群中 TE 入侵的模拟证实,IDs 可能使我们能够推断出入侵途径。我们的方法可能适用于不同宿主物种中的其他 DNA 转座子。