Detecting the molecular basis of local adaptation and identifying selective drivers is still challenging in nonmodel species. The use of purely population genetic approaches is limited by some characteristics of genetic systems, such as pleiotropy and polygenic control, and parallel evidence from phenotypic‐based experimental comparisons is required. In long‐lived organisms, the detection of selective pressures might also be precluded by evolutionary lag times in response to the environment. Here, we used the English yew to showcase an example of a multiscale integrative approach in a nonmodel species with limited plant and genomic resources. We combined information from two independent sources, phenotypes in a common environment and genomic data in natural populations, to investigate the signature of selection. Growth differences among populations in a common environment, and phenological patterns of both shoot elongation and male strobili maturation, were associated with climate clines, providing evidence for local adaptation and guiding us in the selection of populations for genomic analyses. We used information on over 25,000 SNPs from c. 1,200 genes to infer the demographic history and to test for molecular signatures of selection at different levels: SNP, gene, and biological pathway. Our results confirmed an overall demographic history of population decline, but we also found evidence for putative local adaptation at the molecular level. We identified or confirmed several candidate genes for positive and negative selection in forest trees, including the pseudo‐response regulator 7 (PRR7), an essential component of the circadian clock in plants. In addition, we successfully tested an approach to detect polygenic adaptation in biological pathways, allowing us to identify the flavonoid biosynthesis pathway as a candidate stress‐response pathway that deserves further attention in other plants. Finally, our study contributes to the emerging view that explaining contemporary standing genetic variation requires considering adaptation to past climates, especially for long‐lived trees.

中文翻译：

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检测非模式树种选择的多尺度方法：尽管红豆杉种群数量下降，但广泛适应。

在非模式物种中，检测局部适应的分子基础并识别选择性驱动因素仍然具有挑战性。纯粹群体遗传方法的使用受到遗传系统的某些特征的限制，例如多效性和多基因控制，并且需要来自基于表型的实验比较的平行证据。在长寿的生物体中，对环境的反应的进化滞后时间也可能阻碍选择压力的检测。在这里，我们使用英国红豆杉展示了在植物和基因组资源有限的非模型物种中采用多尺度综合方法的示例。我们结合了来自两个独立来源的信息，即共同环境中的表型和自然群体中的基因组数据，以研究选择的特征。共同环境中种群之间的生长差异以及芽伸长和雄性球果成熟的物候模式与气候变化相关，为当地适应提供了证据，并指导我们选择用于基因组分析的种群。我们使用了c. 25,000多个SNP的信息。1,200 个基因，用于推断人口统计历史并测试不同级别选择的分子特征：SNP、基因和生物途径。我们的结果证实了人口下降的总体人口历史，但我们也在分子水平上发现了推定的局部适应的证据。我们鉴定或确认了森林树木中正选择和负选择的几个候选基因，包括伪反应调节因子 7 (PRR7)，它是植物生物钟的重要组成部分。此外，我们成功测试了一种检测生物途径中多基因适应的方法，使我们能够将类黄酮生物合成途径确定为候选应激反应途径，值得在其他植物中进一步关注。最后，我们的研究促进了一种新的观点，即解释当代的遗传变异需要考虑对过去气候的适应，特别是对于长寿的树木。