Centre for Biological Timing, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, UK; Division of Neuroscience, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, UK.
Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA; School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia.
Curr Biol. 2023 Aug 7;33(15):3289-3298.e6. doi: 10.1016/j.cub.2023.06.068. Epub 2023 Jul 21.
Patterns of diel activity-how animals allocate their activity throughout the 24-h daily cycle-play key roles in shaping the internal physiology of an animal and its relationship with the external environment. Although shifts in diel activity patterns have occurred numerous times over the course of vertebrate evolution, the genomic correlates of such transitions remain unknown. Here, we use the African striped mouse (Rhabdomys pumilio), a species that transitioned from the ancestrally nocturnal diel niche of its close relatives to a diurnal one, to define patterns of naturally occurring molecular variation in diel niche traits. First, to facilitate genomic analyses, we generate a chromosome-level genome assembly of the striped mouse. Next, using transcriptomics, we show that the switch to daytime activity in this species is associated with a realignment of daily rhythms in peripheral tissues with respect to the light:dark cycle and the central circadian clock. To uncover selection pressures associated with this temporal niche shift, we perform comparative genomic analyses with closely related rodent species and find evidence of relaxation of purifying selection on striped mouse genes in the rod phototransduction pathway. In agreement with this, electroretinogram measurements demonstrate that striped mice have functional differences in dim-light visual responses compared with nocturnal rodents. Taken together, our results show that striped mice have undergone a drastic change in circadian organization and provide evidence that the visual system has been a major target of selection as this species transitioned to a novel temporal niche.
昼夜活动模式——动物如何在 24 小时的日常周期内分配其活动——在塑造动物的内部生理和与外部环境的关系方面起着关键作用。尽管在脊椎动物进化过程中，昼夜活动模式发生了多次转变，但这种转变的基因组相关性仍然未知。在这里，我们使用非洲条纹鼠（Rhabdomys pumilio），一种从其近亲的祖传夜行昼夜生态位转变为昼行昼夜生态位的物种，来定义昼夜生态位特征中自然发生的分子变异模式。首先，为了促进基因组分析，我们生成了条纹鼠的染色体水平基因组组装。接下来，通过转录组学，我们表明该物种向日间活动的转变与外周组织的昼夜节律与中央生物钟的重新调整有关。为了揭示与这种时间生态位转变相关的选择压力，我们与密切相关的啮齿动物物种进行了比较基因组分析，并发现条纹鼠在光感受器转导途径中的基因受到净化选择放松的证据。与此一致的是，视网膜电图测量表明，与夜间啮齿动物相比，条纹鼠在弱光视觉反应中存在功能差异。总之，我们的研究结果表明，条纹鼠的昼夜节律组织发生了剧烈变化，并提供了证据表明，随着该物种向新的时间生态位转变，视觉系统已成为选择的主要目标。
