The birth of new genes is a major molecular innovation driving phenotypic diversity across all domains of life. Although repurposing of existing protein-coding material by duplication is considered the main process of new gene formation, recent studies have discovered thousands of transcriptionally active sequences as a rich source of new genes. However, differential loss rates have to be assumed to reconcile the high birth rates of these incipient de novo genes with the dominance of ancient gene families in individual genomes. Here, we test this rapid turnover hypothesis in the context of the nematode model organism Pristionchus pacificus. We extended the existing species-level phylogenomic framework by sequencing the genomes of six divergent P. pacificus strains. We used these data to study the evolutionary dynamics of different age classes and categories of origin at a population level. Contrasting de novo candidates with new families that arose by duplication and divergence from known genes, we find that de novo candidates are typically shorter, show less expression, and are overrepresented on the sex chromosome. Although the contribution of de novo candidates increases toward young age classes, multiple comparisons within the same age class showed significantly higher attrition in de novo candidates than in known genes. Similarly, young genes remain under weak evolutionary constraints with de novo candidates representing the fastest evolving subcategory. Altogether, this study provides empirical evidence for the rapid turnover hypothesis and highlights the importance of the evolutionary timescale when quantifying the contribution of different mechanisms toward new gene formation.

中文翻译：

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多个 Pristionchus pacificus 基因组揭示了 de novo 候选基因和重复基因之间不同的进化动力学

新基因的诞生是一项重大的分子创新，推动了生命各个领域的表型多样性。尽管通过复制重新利用现有蛋白质编码材料被认为是新基因形成的主要过程，但最近的研究发现数以千计的转录活性序列是新基因的丰富来源。然而，必须假设不同的损失率来协调这些早期新生基因的高出生率与古代基因家族在个体基因组中的主导地位。在这里，我们在线虫模式生物Pristionchus pacificus的背景下测试这种快速周转假设。我们通过对六种不同的P. pacificus的基因组进行测序来扩展现有的物种级系统发育框架菌株。我们使用这些数据来研究人口水平上不同年龄段和起源类别的进化动态。将新候选基因与已知基因的复制和分歧产生的新家族进行对比，我们发现新候选基因通常更短、表达更少，并且在性染色体上的比例过高。尽管 de novo 候选者的贡献对年轻年龄组有所增加，但同一年龄组内的多重比较显示 de novo 候选者的流失率明显高于已知基因。同样，年轻基因仍然处于弱进化约束之下，新候选基因代表了进化最快的子类别。共，