Drift and Directional Selection Are the Evolutionary Forces Driving Gene Expression Divergence in Eye and Brain Tissue of Heliconius Butterflies
Drift and Directional Selection Are the Evolutionary Forces Driving Gene Expression Divergence in Eye and Brain Tissue of Heliconius Butterflies
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DOI：
10.1534/genetics.119.302493
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发表时间：
2019-10-01
期刊：
影响因子：
3.3
通讯作者：
Hohna, Sebastian
中科院分区：
文献类型：
--
作者：
Catalan, Ana;Briscoe, Adriana D.;Hohna, Sebastian
在微观和宏观进化时间尺度上研究基因表达进化将扩大我们对基因表达在适应和物种形成中的作用的理解。在这项研究中，我们描述了进化力量对 5 种分化时间与 5-12 MYA 相似的 Heliconius 蝴蝶眼睛和脑组织基因表达水平的影响。我们开发并应用布朗运动 (BM) 和 Ornstein-Uhlenbeck (OU) 模型来识别表达水平通过漂移、稳定选择或谱系特异性转变而进化的基因。我们发现81%的基因是在遗传漂变下进化的。在测试基因表达的分支特异性转变时，我们检测到 368 个（16%）转变事件。显示上调转变的基因比那些显示导致下调的基因具有显着较低的基因表达方差。我们假设定向选择在引起上调的转变中起作用，因为转录成本很高。我们通过模拟进一步发现，OU 模型的参数估计在使用小型系统发育时存在偏差，并且只有在系统发育具有 >= 50 个类群时才变得可靠。因此，我们开发了一种基于 BM 的新统计测试来识别高度保守的基因（即在强稳定选择下进化），该基因占直簇的 3%。总之，我们发现漂移是驱动蝎尾鱼眼睛和脑组织基因表达进化的主要进化力量。然而，在定向选择下进化的基因比例高于在稳定选择下进化的基因，可能反映了视觉和大脑上的物种特异性选择压力，这是满足物种特定要求所必需的。跨物种基因表达模式的表征 - 以及驱动它们的进化力量 - 可以揭示跨物种保持保守的过程，以及以物种特定方式改变的过程......
Investigating gene expression evolution over micro- and macroevolutionary timescales will expand our understanding of the role of gene expression in adaptation and speciation. In this study, we characterized the evolutionary forces acting on gene expression levels in eye and brain tissue of five Heliconius butterflies with divergence times of similar to 5-12 MYA. We developed and applied Brownian motion (BM) and Ornstein-Uhlenbeck (OU) models to identify genes whose expression levels are evolving through drift, stabilizing selection, or a lineage-specific shift. We found that 81% of the genes evolve under genetic drift. When testing for branch-specific shifts in gene expression, we detected 368 (16%) shift events. Genes showing a shift toward upregulation have significantly lower gene expression variance than those genes showing a shift leading toward downregulation. We hypothesize that directional selection is acting in shifts causing upregulation, since transcription is costly. We further uncovered through simulations that parameter estimation of OU models is biased when using small phylogenies and only becomes reliable with phylogenies having >= 50 taxa. Therefore, we developed a new statistical test based on BM to identify highly conserved genes (i.e., evolving under strong stabilizing selection), which comprised 3% of the orthoclusters. In conclusion, we found that drift is the dominant evolutionary force driving gene expression evolution in eye and brain tissue in Heliconius. Nevertheless, the higher proportion of genes evolving under directional than under stabilizing selection might reflect species-specific selective pressures on vision and the brain that are necessary to fulfill species-specific requirements.Characterization of gene expression patterns across species - and the evolutionary forces driving them - can reveal processes that have remained conserved across species, as well as those that have changed in a species- specific manner...