Chikina Maria, Robinson Joseph D, Clark Nathan L
Department of Computational and Systems Biology, University of Pittsburgh
Department of Molecular and Cell Biology, University of California Berkeley.
Mol Biol Evol. 2016 Sep;33(9):2182-92. doi: 10.1093/molbev/msw112. Epub 2016 Jun 21.
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 genome-wide scale and without prior knowledge of adaptations, and provides a powerful approach for investigating the physiological functions of mammalian genes.
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，它们表型转变的遗传机制却知之甚少，对分子水平上趋同现象的研究尚无定论。过去的研究一直在特定氨基酸位点寻找趋同变化，而我们提出了一种替代策略，以识别那些在选择压力方面经历了趋同变化的基因，这种变化在海洋谱系中表现为进化速率的改变。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率的平行变化，提供了基因水平上广泛趋同的证据。在向水生生活过渡期间，数百个基因在所有三个海洋哺乳动物谱系中加速了它们的进化速率。这些海洋加速基因在控制海洋哺乳动物公认功能适应的途径中高度富集，包括肌肉生理学、脂质代谢、感觉系统以及皮肤和结缔组织。加速既源于皮肤和肺部基因中所见的适应性进化，也源于味觉和嗅觉基因中的功能丧失。关于感觉系统，这一发现进一步证明了味觉和嗅觉减退在海洋哺乳动物中普遍存在。我们的分析证明了在全基因组范围内识别趋同生物体水平特征背后的基因的可行性，且无需事先了解适应性情况，并为研究哺乳动物基因的生理功能提供了一种强大的方法。
