Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, SA, Australia.
Institute for Applied Ecology, University of Canberra, Canberra, ACT, Australia.
Mol Ecol. 2017 Dec;26(24):6841-6856. doi: 10.1111/mec.14432. Epub 2017 Dec 2.
Understanding whether small populations with low genetic diversity can respond to rapid environmental change via phenotypic plasticity is an outstanding research question in biology. RNA sequencing (RNA-seq) has recently provided the opportunity to examine variation in gene expression, a surrogate for phenotypic variation, in nonmodel species. We used a comparative RNA-seq approach to assess expression variation within and among adaptively divergent populations of a threatened freshwater fish, Nannoperca australis, found across a steep hydroclimatic gradient in the Murray-Darling Basin, Australia. These populations evolved under contrasting selective environments (e.g., dry/hot lowland; wet/cold upland) and represent opposite ends of the species' spectrum of genetic diversity and population size. We tested the hypothesis that environmental variation among isolated populations has driven the evolution of divergent expression at ecologically important genes using differential expression (DE) analysis and an anova-based comparative phylogenetic expression variance and evolution model framework based on 27,425 de novo assembled transcripts. Additionally, we tested whether gene expression variance within populations was correlated with levels of standing genetic diversity. We identified 290 DE candidate transcripts, 33 transcripts with evidence for high expression plasticity, and 50 candidates for divergent selection on gene expression after accounting for phylogenetic structure. Variance in gene expression appeared unrelated to levels of genetic diversity. Functional annotation of the candidate transcripts revealed that variation in water quality is an important factor influencing expression variation for N. australis. Our findings suggest that gene expression variation can contribute to the evolutionary potential of small populations.
理解小种群是否可以通过表型可塑性对快速环境变化做出反应，这是生物学中一个悬而未决的研究问题。RNA 测序（RNA-seq）最近为研究非模式物种的基因表达变异（表型变异的替代物）提供了机会。我们使用比较 RNA-seq 方法评估了澳大利亚墨累-达令盆地陡峭的水文气候梯度上受威胁的淡水鱼类 Nannoperca australis 适应性分化种群内和种群间的表达变异。这些种群在不同的选择环境中进化（例如，干燥/炎热的低地；潮湿/寒冷的高地），代表了该物种遗传多样性和种群大小范围的两个极端。我们使用差异表达（DE）分析和基于 anova 的比较系统发育表达方差和进化模型框架检验了环境变异在孤立种群中驱动生态重要基因分化表达进化的假设，该框架基于 27425 个从头组装的转录本。此外，我们还测试了种群内基因表达方差是否与遗传多样性水平相关。在考虑系统发育结构后，我们确定了 290 个候选 DE 转录本、33 个具有高表达可塑性证据的转录本和 50 个候选基因表达分化选择的转录本。基因表达的方差似乎与遗传多样性水平无关。候选转录本的功能注释表明，水质变化是影响 N. australis 表达变异的一个重要因素。我们的研究结果表明，基因表达变异可以为小种群的进化潜力做出贡献。
