Eveno Emmanuelle, Collada Carmen, Guevara M Angeles, Léger Valérie, Soto Alvaro, Díaz Luis, Léger Patrick, González-Martínez Santiago C, Cervera M Teresa, Plomion Christophe, Garnier-Géré Pauline H
Institut National de Recherche Agronomique, Unité Mixte de Recherche 1202 Biodiversity Genes & Communities, Cestas, France.
Mol Biol Evol. 2008 Feb;25(2):417-37. doi: 10.1093/molbev/msm272. Epub 2007 Dec 7.
The importance of natural selection for shaping adaptive trait differentiation among natural populations of allogamous tree species has long been recognized. Determining the molecular basis of local adaptation remains largely unresolved, and the respective roles of selection and demography in shaping population structure are actively debated. Using a multilocus scan that aims to detect outliers from simulated neutral expectations, we analyzed patterns of nucleotide diversity and genetic differentiation at 11 polymorphic candidate genes for drought stress tolerance in phenotypically contrasted Pinus pinaster Ait. populations across its geographical range. We compared 3 coalescent-based methods: 2 frequentist-like, including 1 approach specifically developed for biallelic single nucleotide polymorphisms (SNPs) here and 1 Bayesian. Five genes showed outlier patterns that were robust across methods at the haplotype level for 2 of them. Two genes presented higher F(ST) values than expected (PR-AGP4 and erd3), suggesting that they could have been affected by the action of diversifying selection among populations. In contrast, 3 genes presented lower F(ST) values than expected (dhn-1, dhn2, and lp3-1), which could represent signatures of homogenizing selection among populations. A smaller proportion of outliers were detected at the SNP level suggesting the potential functional significance of particular combinations of sites in drought-response candidate genes. The Bayesian method appeared robust to low sample sizes, flexible to assumptions regarding migration rates, and powerful for detecting selection at the haplotype level, but the frequentist-like method adapted to SNPs was more efficient for the identification of outlier SNPs showing low differentiation. Population-specific effects estimated in the Bayesian method also revealed populations with lower immigration rates, which could have led to favorable situations for local adaptation. Outlier patterns are discussed in relation to the different genes' putative involvement in drought tolerance responses, from published results in transcriptomics and association mapping in P. pinaster and other related species. These genes clearly constitute relevant candidates for future association studies in P. pinaster.
异花授粉树种自然种群中，自然选择对于塑造适应性性状分化的重要性早已得到认可。确定局部适应性的分子基础在很大程度上仍未得到解决，并且选择和种群统计学在塑造种群结构中的各自作用仍在激烈争论中。我们使用旨在从模拟中性预期中检测异常值的多位点扫描，分析了表型对比的海岸松（Pinus pinaster Ait.）在其地理范围内不同种群中11个耐旱性多态候选基因的核苷酸多样性和遗传分化模式。我们比较了3种基于合并的方法：2种类似频率论的方法，其中1种是专门为此处的双等位基因单核苷酸多态性（SNP）开发的方法，另1种是贝叶斯方法。5个基因表现出异常模式，其中2个基因在单倍型水平上的模式在各种方法中都很稳健。2个基因呈现出比预期更高的F(ST)值（PR - AGP4和erd3），表明它们可能受到了种群间多样化选择作用的影响。相反，3个基因呈现出比预期更低的F(ST)值（dhn - 1、dhn2和lp3 - 1），这可能代表了种群间同质化选择的特征。在SNP水平上检测到的异常值比例较小，表明干旱响应候选基因中特定位点组合可能具有潜在的功能意义。贝叶斯方法似乎对低样本量具有稳健性，对迁移率假设具有灵活性，并且在检测单倍型水平的选择方面很强大，但适用于SNP的类似频率论方法在识别显示低分化的异常SNP方面更有效。贝叶斯方法估计的种群特异性效应还揭示了移民率较低的种群，这可能导致有利于局部适应的情况。结合海岸松和其他相关物种转录组学及关联图谱的已发表结果，讨论了与不同基因在耐旱反应中假定参与情况相关的异常模式。这些基因显然构成了未来海岸松关联研究的相关候选基因。
