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使用机器学习方法梯度森林为气候不适应的基因组预测提供实验支持。

Experimental support for genomic prediction of climate maladaptation using the machine learning approach Gradient Forests.

机构信息

Appalachian Laboratory, University of Maryland Center for Environmental Science, Frostburg, MD, USA.

Department of Plant Biology, University of Vermont, Burlington, VT, USA.

出版信息

Mol Ecol Resour. 2021 Nov;21(8):2749-2765. doi: 10.1111/1755-0998.13374. Epub 2021 Mar 22.

Abstract

Gradient Forests (GF) is a machine learning algorithm that is gaining in popularity for studying the environmental drivers of genomic variation and for incorporating genomic information into climate change impact assessments. Here we (i) provide the first experimental evaluation of the ability of "genomic offsets" - a metric of climate maladaptation derived from Gradient Forests - to predict organismal responses to environmental change, and (ii) explore the use of GF for identifying candidate SNPs. We used high-throughput sequencing, genome scans, and several methods, including GF, to identify candidate loci associated with climate adaptation in balsam poplar (Populus balsamifera L.). Individuals collected throughout balsam poplar's range also were planted in two common garden experiments. We used GF to relate candidate loci to environmental gradients and predict the expected magnitude of the response (i.e., the genetic offset metric of maladaptation) of populations when transplanted from their "home" environment to the common gardens. We then compared the predicted genetic offsets from different sets of candidate and randomly selected SNPs to measurements of population performance in the common gardens. We found the expected inverse relationship between genetic offset and performance: populations with larger predicted genetic offsets performed worse in the common gardens than populations with smaller offsets. Also, genetic offset better predicted performance than did "naive" climate transfer distances. However, sets of randomly selected SNPs predicted performance slightly better than did candidate SNPs. Our study provides evidence that genetic offsets represent a first order estimate of the degree of expected maladaptation of populations exposed to rapid environmental change and suggests GF may have some promise as a method for identifying candidate SNPs.

摘要

梯度森林 (GF) 是一种机器学习算法,它在研究基因组变异的环境驱动因素以及将基因组信息纳入气候变化影响评估方面越来越受欢迎。在这里,我们 (i) 首次对“基因组偏移”(一种源自梯度森林的气候不适配度量)预测生物体对环境变化的反应能力进行了实验评估,以及 (ii) 探索了使用 GF 来识别候选单核苷酸多态性 (SNP) 的方法。我们使用高通量测序、基因组扫描和几种方法,包括 GF,来识别与银白杨 (Populus balsamifera L.) 适应气候相关的候选基因座。我们还从银白杨的分布范围内收集了个体,并将它们种植在两个共同花园实验中。我们使用 GF 将候选基因座与环境梯度相关联,并预测当从其“家乡”环境移植到共同花园时,种群的预期响应幅度(即不适配的遗传偏移度量)。然后,我们将不同候选和随机选择的 SNP 集的预测遗传偏移与共同花园中种群表现的测量值进行了比较。我们发现遗传偏移与表现之间存在预期的反比关系:与具有较小偏移的种群相比,具有较大预测遗传偏移的种群在共同花园中的表现更差。此外,遗传偏移比“朴素”气候转移距离更好地预测了性能。然而,随机选择的 SNP 集比候选 SNP 集略微更好地预测了性能。我们的研究提供了证据表明,遗传偏移代表了暴露于快速环境变化的种群预期不适配程度的一阶估计,并且表明 GF 可能具有作为识别候选 SNP 的方法的一些前景。

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