Eukaryotic genomes frequently acquire new protein-coding genes which may significantly impact an organism’s fitness. Novel genes can be created, for example, by duplication of large genomic regions or de novo, from previously non-coding DNA. Either way, creation of a novel transcript is an essential early step during novel gene emergence. Most studies on the gain-and-loss dynamics of novel genes so far have compared genomes between species, constraining analyses to genes that have remained fixed over long time scales. However, the importance of novel genes for rapid adaptation among populations has recently been shown. Therefore, since little is known about the evolutionary dynamics of transcripts across natural populations, we here study transcriptomes from several tissues and nine geographically distinct populations of an ecological model species, the three-spined stickleback. Our findings suggest that novel genes typically start out as transcripts with low expression and high tissue specificity. Early expression regulation appears to be mediated by gene-body methylation. Although most new and narrowly expressed genes are rapidly lost, those that survive and subsequently spread through populations tend to gain broader and higher expression levels. The properties of the encoded proteins, such as disorder and aggregation propensity, hardly change. Correspondingly, young novel genes are not preferentially under positive selection but older novel genes more often overlap with F ST outlier regions. Taken together, expression of the surviving novel genes is rapidly regulated, probably via epigenetic mechanisms, while structural properties of encoded proteins are non-debilitating and might only change much later.

中文翻译：

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三刺棘鱼种群中新基因的进化

真核基因组经常获得新的蛋白质编码基因，这可能会显着影响生物体的健康。例如，可以通过从以前的非编码 DNA 复制大基因组区域或从头复制来创建新基因。无论哪种方式，新转录本的创建都是新基因出现过程中必不可少的早期步骤。迄今为止，大多数关于新基因得失动态的研究都比较了物种之间的基因组，将分析限制在长时间保持固定的基因上。然而，最近已经显示出新基因对种群间快速适应的重要性。因此，由于对跨自然种群的转录本的进化动态知之甚少，我们在这里研究了生态模型物种三刺棘鱼的几个组织和九个地理上不同的种群的转录组。我们的研究结果表明，新基因通常以低表达和高组织特异性的转录物开始。早期表达调控似乎是由基因体甲基化介导的。尽管大多数新的和窄表达的基因会迅速丢失，但那些存活下来并随后在人群中传播的基因往往会获得更广泛和更高的表达水平。编码蛋白质的特性，如无序和聚集倾向，几乎不会改变。相应地，年轻的新基因不优先处于正选择下，但较老的新基因更常与 F ST 离群区域重叠。综合起来，