Supplementary data tables from Convergent copy number increase of genes associated with freshwater colonization in fishes

Copy number variation (CNV) can cause phenotypic changes. However, in contrast to amino acid substitutions and cis-regulatory changes, little is known about the functional categories of genes in which CNV is important for adaptation to novel environments. It is also unclear whether the same genes repeatedly change the copy numbers for adapting to similar environments. Here, we investigate CNV associated with freshwater colonization in fishes, which was observed multiple times across different lineages. Using 48 ray-finned fishes across diverse orders, we identified 23 genes whose copy number increases were associated with freshwater colonization. These genes showed enrichment for peptide receptor activity, hexosyltransferase activity and unsaturated fatty acid metabolism. We further revealed that three of the genes showed copy number increases in freshwater populations compared to marine ancestral populations of the stickleback genus Gasterosteus. These results indicate that copy number increases of genes involved in fatty acid metabolism (FADS2), immune function (PSMB81) and thyroid hormone metabolism (UGT2) may be important for freshwater colonization at both the inter-order macroevolutionary scale and at the intra-genus microevolutionary scale. Further analysis across diverse taxa will help to understand the role of CNV in the adaptation to novel environments.This article is part of the theme issue ‘Genetic basis of adaptation and speciation: from loci to causative mutations’.

拷贝数变异（Copy number variation, CNV）可引发表型改变。然而，与氨基酸替换和顺式调控变异不同，学界对于拷贝数变异在适应新环境中具有重要作用的基因功能类别仍知之甚少。此外，学界也尚未明确，是否同一类基因会通过反复改变拷贝数以适应相似的环境。本研究聚焦鱼类淡水定植相关的拷贝数变异——该现象在不同演化支中已被多次观测到。我们选取覆盖多个目级类群的48种辐鳍鱼进行分析，鉴定出23个拷贝数增加与淡水定植显著相关的基因。这些基因显著富集于肽受体活性、己糖基转移酶活性以及不饱和脂肪酸代谢通路。进一步分析发现，在刺鱼属（Gasterosteus）的海洋祖先种群与淡水种群的对比中，有3个基因的拷贝数出现了显著增加。本研究结果表明，参与脂肪酸代谢的FADS2、免疫功能相关的PSMB81以及甲状腺激素代谢相关的UGT2，其拷贝数增加在跨目的宏观演化尺度以及属内微观演化尺度上，均可能对鱼类淡水定植起到关键作用。后续针对多样类群的深入分析，将有助于进一步阐明拷贝数变异在生物适应新环境过程中的作用机制。本文隶属于专题专栏“适应与物种形成的遗传基础：从基因座到致病变异”。