Supplementary Tables S2 detailing differential expression of transcripts between Winter Skate populations from Adaptive phenotypic response to climate enabled by epigenetics in a K-strategy species, the fish Leucoraja ocellata (Rajidae)

The relative importance of genetic versus epigenetic changes in adaptive evolution is a hotly debated topic, with studies showing that some species appear to be able to adapt rapidly without significant genetic change. Epigenetic mechanisms may be particularly important for the evolutionary potential of species with long maturation times and low reproductive potential ('K-strategists'), particularly when faced with rapidly changing environmental conditions. Here we study the transcriptome of two populations of the winter skate (Leucoraja ocellata), a typical 'K-strategist', in Atlantic Canada; an endemic population in southern Gulf of St. Lawrence and a large population on the Scotian Shelf. The endemic population has been able to adapt to a 10 degrees Celsius higher water temperatures over short evolutionary time (7000 years), dramatically reducing its body size (by 45%) significantly below the minimum maturation size of Scotian Shelf and other populations of winter skate, as well as exhibiting other adaptations in life history and physiology. We demonstrate that the adaptive response to selection has an epigenetic basis, cataloguing 3653 changes in gene expression that may have enabled this species to rapidly respond to the novel environment. We argue that the epigenetic augmentation of species evolutionary potential (its regulation though gene expression) can enable K-strategists to survive and adapt to different environments, and this mechanism may be particularly important for the persistence of sharks, skates and rays in the light of future climate change.适应性进化中，遗传变化与表观遗传变化的相对重要性是一个广受热议的议题。诸多研究表明，部分物种可在未发生显著遗传改变的情况下快速完成适应。表观遗传机制对于成熟周期长、繁殖能力低的K策略者（K-strategists）的进化潜力可能尤为关键，尤其是在面临快速变化的环境条件时。本研究对加拿大大西洋海域的两个冬季鳐（Leucoraja ocellata）种群的转录组展开分析，该物种为典型的K策略者：分别是圣劳伦斯湾南部的特有种群与斯科舍陆架的大型种群。该特有种群可在短短7000年的进化时间内，适应比原环境高10摄氏度的水温，其体型较斯科舍陆架及其他冬季鳐种群的最小性成熟体型显著缩小了45%，同时在生活史与生理特征上也呈现出其他适应性变化。本研究证实，该物种对选择压力的适应性响应具有表观遗传基础，共鉴定出3653个基因表达变化，这些变化或助力该物种快速响应全新环境。我们认为，通过基因表达调控实现的表观遗传增强，可提升K策略者的进化潜力，帮助其在不同环境中存活并完成适应；这一机制在未来气候变化背景下，对于鲨鱼、鳐类与魟类的存续或尤为关键。