Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA.
Department of Biology, Pennsylvania State University, University Park, PA.
Mol Biol Evol. 2017 Dec 1;34(12):3089-3098. doi: 10.1093/molbev/msx230.
Gene duplication is thought to play a major role in phenotypic evolution. Yet the forces involved in the functional divergence of young duplicate genes remain unclear. Here, we use population-genetic inference to elucidate the role of natural selection in the functional evolution of young duplicate genes in Drosophila melanogaster. We find that negative selection acts on young duplicates with ancestral functions, and positive selection on those with novel functions, suggesting that natural selection may determine whether and how young duplicate genes are retained. Moreover, evidence of natural selection is strongest in protein-coding regions and 3' UTRs of young duplicates, indicating that selection may primarily target encoded proteins and regulatory sequences specific to 3' UTRs. Further analysis reveals that natural selection acts immediately after duplication and weakens over time, possibly explaining the observed bias toward the acquisition of new functions by young, rather than old, duplicate gene copies. Last, we find an enrichment of testis-related functions in young duplicates that underwent recent positive selection, but not in young duplicates that did not undergo recent positive selection, or in old duplicates that either did or did not undergo recent positive selection. Thus, our findings reveal that natural selection is a key player in the functional evolution of young duplicate genes, acts rapidly and in a region-specific manner, and may underlie the origin of novel testis-specific phenotypes in Drosophila.
基因复制被认为在表型进化中起着重要作用。然而，涉及年轻重复基因功能分化的力量仍不清楚。在这里，我们使用群体遗传学推断来阐明自然选择在黑腹果蝇年轻重复基因功能进化中的作用。我们发现，具有祖先功能的年轻重复基因受到负选择，而具有新功能的年轻重复基因受到正选择，这表明自然选择可能决定年轻重复基因是否以及如何被保留。此外，自然选择的证据在年轻重复基因的编码区和 3'UTR 中最强，表明选择可能主要针对编码蛋白和特定于 3'UTR 的调节序列。进一步的分析表明，自然选择在复制后立即发生，并随着时间的推移而减弱，这可能解释了观察到的年轻而非年老重复基因拷贝获得新功能的偏向。最后，我们发现，在最近经历正选择的年轻重复基因中，富集了与睾丸相关的功能，但在最近没有经历正选择的年轻重复基因中，或者在最近经历或没有经历正选择的年老重复基因中，没有这种富集。因此，我们的研究结果表明，自然选择是年轻重复基因功能进化的关键因素，它快速而特异性地起作用，可能是果蝇中新的睾丸特异性表型起源的基础。
