Data from: Environmental adaptation contributes to gene polymorphism across the Arabidopsis thaliana genome

The level of within-species polymorphism differs greatly among genes in a genome. Many genomic studies have investigated the relationship between gene polymorphism and factors such as recombination rate or expression pattern. However, the polymorphism of a gene is affected not only by its physical properties or functional constraints, but also by natural selection on organisms in their environments. Specifically, if functionally divergent alleles enable adaptation to different environments, locus-specific polymorphism may be maintained by spatially heterogeneous natural selection. To test this hypothesis and estimate the extent to which environmental selection shapes the pattern of genome-wide polymorphism, we define the ‘environmental relevance’ of a gene as the proportion of genetic variation explained by environmental factors, after controlling for population structure. We found substantial effects of environmental relevance on patterns of polymorphism among genes. In addition, the correlation between environmental relevance and gene polymorphism is positive, consistent with the expectation that balancing selection among heterogeneous environments maintains genetic variation at ecologically important genes. Comparison of the gene ontology annotations shows that genes with high environmental relevance are enriched in unknown function categories. These results suggest an important role for environmental factors in shaping genome-wide patterns of polymorphism and indicate another direction of genomic study.

基因组（genome）中不同基因的种内多态性（within-species polymorphism）水平差异极大。诸多基因组学研究已探讨了基因多态性与重组率（recombination rate）、表达模式（expression pattern）等因素间的关联。然而，基因的多态性不仅受其自身物理属性或功能约束的影响，还会受到生物体所处环境中的自然选择（natural selection）作用的调控。具体而言，若功能分化的等位基因（alleles）能够适应不同环境，那么空间异质性自然选择（spatially heterogeneous natural selection）或许会维持该基因座的特异性多态性。为验证这一假说并评估环境选择塑造全基因组多态性模式的程度，我们将基因的"环境相关性"定义为：在控制种群结构（population structure）的前提下，由环境因素所解释的遗传变异（genetic variation）比例。我们发现，环境相关性对不同基因的多态性模式具有显著影响。此外，环境相关性与基因多态性之间呈正相关，这与异质环境下的平衡选择（balancing selection）能够维持生态重要基因的遗传变异这一预期相符。对基因本体注释（gene ontology annotations）的分析显示，环境相关性较高的基因在功能未知的类别中富集。上述结果表明，环境因素在塑造全基因组多态性模式中发挥着重要作用，同时也为基因组学研究指明了新的方向。