Detecting the genomic and transcriptomic imprints of environmental change in a marine fish species through space and time

在过去的几十年里，全球生态系统面临着前所未有的环境变化，给生物群落带来了可怕的后果。虽然许多物种被认为正在衰退，但一些物种似乎能够忍受环境变化，这可能是通过快速的进化适应。然而，这种进化变化的总体相关性和遗传机制尚未得到很好的理解。本研究利用波罗的海和北海的一种鱼类elelpout Zoarces viviparus的独特的30年时间序列种群数据，通过空间和时间探索暴露于环境变化的种群的表型、转录组和基因组反应。作为德国范围内生物监测计划的一部分，这些样本是根据高度标准化的协议收集的，并储存在超低温下。由此产生的良好保存使我们能够同时分析种群的时间基因组和转录组变化。我们将首先分析整个鱼类范围内的种群基因组，以确定其遗传结构和适应自然环境梯度（即盐度和温度）的特征。基于这一背景，并使用种群基因组时间序列，我们将测试这一假设，即鱼类在过去30年里已经适应了不断变化的环境条件。我们将通过详细的表型评估和沿着种群时间序列和水族馆实验改变基因表达模式的调查来补充我们的种群基因组分析。我们的工作承诺前所未有的实时洞察种群对全球变化的表型，转录组和基因组反应，并将为未来的海洋生物多样性保护提供重要信息。

Global ecosystems have been exposed to unprecedented environmental change in the past decades, with dire consequences for biological communities. While many species are assumed to decline, some seemingly tolerate environmental change, possibly by rapid evolutionary adaptation. However, the overall relevance and genetic mechanisms of such evolutionary change are not well understood. Here we propose to use a unique 30-year time series population dataset of the eelpout Zoarces viviparus, a fish species from the Baltic and Northern Seas, to explore phenotypic, transcriptomic and genomic responses of populations exposed to environmental change through space and time. The samples were collected according to a highly standardized protocol and stored at ultra-low temperatures as part of a Germany-wide biomonitoring program. The resulting excellent preservation allows us to analyze temporal genomic and transcriptomic changes of populations in parallel. We will first analyze population genomes from across the fish’s range to identify its genetic structure and signatures of adaptation to natural environmental gradients, namely, salinity and temperature. Based on this background and using population genomic time series, we will then test the hypothesis that the fish have adapted to changing environmental conditions in the past 3 decades. We will complement our population genomic analyses with detailed phenotypic assessments and investigations of changing gene expression patterns along the population time series and in an aquarium experiment. Our work promises unprecedented real-time insights into phenotypic, transcriptomic and genomic responses of populations to global change, and will be of great relevance to inform future conservation of marine biodiversity.