Data from: The life cycle of Drosophila orphan genes

Orphans are genes restricted to a single phylogenetic lineage and emerge at high rates. While this predicts an accumulation of genes, the gene number has remained remarkably constant through evolution. This paradox has not yet been resolved. Because orphan genes have been mainly analyzed over long evolutionary time scales, orphan loss has remained unexplored. Here we study the patterns of orphan turnover among close relatives in the Drosophila obscura group. We show that orphans are not only emerging at a high rate, but that they are also rapidly lost. Interestingly, recently emerged orphans are more likely to be lost than older ones. Furthermore, highly expressed orphans with a strong male-bias are more likely to be retained. Since both lost and retained orphans show similar evolutionary signatures of functional conservation, we propose that orphan loss is not driven by high rates of sequence evolution, but reflects lineage specific functional requirements.

孤儿基因（orphan genes）是指仅局限于单个系统发育谱系的基因，且其产生速率极高。该现象本应推动基因总量的积累，但进化过程中基因数量却始终保持惊人的恒定，这一进化悖论至今尚未得到合理解释。由于此前针对孤儿基因的研究多基于漫长的进化时间尺度，孤儿基因的丢失现象长期未被深入探究。
本研究聚焦暗果蝇种组（Drosophila obscura group）的近缘物种，解析了孤儿基因的周转模式。研究发现，孤儿基因不仅产生速率居高，同时也会快速发生丢失。值得注意的是，新近产生的孤儿基因相较于古老孤儿基因更易出现丢失事件。此外，表达量较高且具有显著雄性偏好性的孤儿基因更易被保留。
鉴于发生丢失与得以保留的孤儿基因均表现出相似的功能保守性进化特征，本研究提出，孤儿基因的丢失并非由序列进化速率过快所驱动，而是反映了谱系特异性的功能需求。