Data from: Plasticity in gene transcription explains the differential performance of two invasive fish species

Phenotypic plasticity buffers organisms from environmental change and is hypothesized to aid the initial establishment of non-indigenous species in novel environments and post-establishment range expansion. The genetic mechanisms that underpin phenotypically plastic traits are generally poorly characterized; however, there is strong evidence that modulation of gene transcription is an important component of these responses. Here we use RNA sequencing to examine the transcriptional basis of temperature tolerance for round and tubenose goby, two non-indigenous fish species that differ dramatically in the extent of their Great Lakes invasions despite similar invasion dates. We used generalized linear models of read count data to compare gene transcription responses of organisms exposed to increased and decreased water temperature from those at ambient conditions. We identify greater response in the magnitude of transcriptional changes for the more successful round goby compared with the less successful tubenose goby. Round goby transcriptional responses reflect alteration of biological function consistent with adaptive responses to maintain or regain homeostatic function in other species. In contrast, tubenose goby transcription patterns indicate a response to stressful conditions, but the pattern of change in biological functions do not match those expected for a return to homeostatic status. Transcriptional plasticity plays an important role in the acute thermal tolerance for these species; however, the impaired response to stress we demonstrate in the tubenose goby may contribute to their limited invasion success relative to the round goby. Transcriptional profiling allows the simultaneous assessment of the magnitude of transcriptional response as well as the biological functions involved in the response to environmental stress and is thus a valuable approach for evaluating invasion potential.

表型可塑性（phenotypic plasticity）可使生物缓冲环境变化带来的压力，且有假说认为其可助力非本土物种在新环境中完成初始定殖，并促进定殖后的分布范围扩张。调控表型可塑性性状的遗传机制目前尚缺乏充分解析；不过已有大量证据表明，基因转录调控是这类适应性响应的重要组成部分。本研究利用RNA测序（RNA sequencing）技术，针对圆吻虎鱼（round goby）与管鼻虎鱼（tubenose goby）这两种非本土鱼类，探究其温度耐受的转录调控基础：二者入侵起始年代相近，但在北美五大湖（Great Lakes）的入侵扩张程度差异悬殊。我们基于读段计数数据构建广义线性模型（generalized linear models），对比了暴露于升温和降温水环境的个体与处于常温环境个体的基因转录响应差异。研究发现，相较于入侵成效较弱的管鼻虎鱼，成功度更高的圆吻虎鱼的转录变化幅度更为显著。圆吻虎鱼的转录响应体现出生物学功能的重塑，这与其他物种中为维持或重建内稳态的适应性响应特征相符。与之相反，管鼻虎鱼的转录模式仅反映出对胁迫环境的响应，但其生物学功能的变化模式并不符合恢复内稳态的预期特征。转录可塑性对这两种鱼类的急性温度耐受具有关键作用；不过相较于圆吻虎鱼，本研究证实管鼻虎鱼存在受损的胁迫响应能力，这或为其入侵范围受限的重要诱因。转录组分析（transcriptional profiling）可同时评估转录响应的幅度，以及参与环境胁迫响应的生物学功能，因此是评估物种入侵潜力的有效研究手段。