Hundreds of Genes Experienced Convergent Shifts in Selective Pressure in Marine Mammals
Hundreds of Genes Experienced Convergent Shifts in Selective Pressure in Marine Mammals
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DOI：
10.1093/molbev/msw112
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发表时间：
2016-09-01
影响因子：
10.7
通讯作者：
Clark, Nathan L.
中科院分区：
文献类型：
--
作者：
Chikina, Maria;Robinson, Joseph D.;Clark, Nathan L.
哺乳动物物种已经多次向海洋环境过渡，它们的谱系代表了形态和生理特征趋同进化的经典例子之一。然而，它们表型转换的遗传机制还不是很清楚，在分子水平上对收敛的研究也没有定论。虽然过去的研究一直在寻找特定氨基酸位点上的趋同变化，但我们提出了一种替代策略来识别那些在选择压力上经历趋同变化的基因，这些基因在进化速度上的变化特别在海洋谱系中可见。我们通过识别哺乳动物适应海洋环境的三个独立阶段中进化速度的平行变化，在基因水平上提出了广泛趋同的证据。在向水生生物过渡的过程中，所有三个海洋哺乳动物谱系中的数百个基因加速了它们的进化速度。这些海洋加速的基因高度丰富了控制海洋哺乳动物公认的功能适应的途径，包括肌肉生理学、脂肪代谢、感觉系统以及皮肤和结缔组织。这些加速既是皮肤和肺基因的适应性进化，也是味觉和嗅觉基因的功能丧失所致。关于感觉系统，这一发现提供了进一步的证据，表明在海洋哺乳动物中普遍存在味觉和嗅觉减退的现象。我们的分析证明了在全基因组范围内识别具有趋同生物体水平特征的基因的可行性，而不需要事先了解适应，并为研究哺乳动物基因的生理功能提供了一种强有力的方法。
Mammal species have made the transition to the marine environment several times, and their lineages represent one of the classical examples of convergent evolution in morphological and physiological traits. Nevertheless, the genetic mechanisms of their phenotypic transition are poorly understood, and investigations into convergence at the molecular level have been inconclusive. While past studies have searched for convergent changes at specific amino acid sites, we propose an alternative strategy to identify those genes that experienced convergent changes in their selective pressures, visible as changes in evolutionary rate specifically in the marine lineages. We present evidence of widespread convergence at the gene level by identifying parallel shifts in evolutionary rate during three independent episodes of mammalian adaptation to the marine environment. Hundreds of genes accelerated their evolutionary rates in all three marine mammal lineages during their transition to aquatic life. These marine-accelerated genes are highly enriched for pathways that control recognized functional adaptations in marine mammals, including muscle physiology, lipid-metabolism, sensory systems, and skin and connective tissue. The accelerations resulted from both adaptive evolution as seen in skin and lung genes, and loss of function as in gustatory and olfactory genes. In regard to sensory systems, this finding provides further evidence that reduced senses of taste and smell are ubiquitous in marine mammals. Our analysis demonstrates the feasibility of identifying genes underlying convergent organism-level characteristics on a genomewide scale and without prior knowledge of adaptations, and provides a powerful approach for investigating the physiological functions of mammalian genes.