Scotti Ivan, Lalagüe Hadrien, Oddou-Muratorio Sylvie, Scotti-Saintagne Caroline, Ruiz Daniels Rose, Grivet Delphine, Lefevre François, Cubry Philippe, Fady Bruno, González-Martínez Santiago C, Roig Anne, Lesur-Kupin Isabelle, Bagnoli Francesca, Guerin Vanina, Plomion Christophe, Rozenberg Philippe, Vendramin Giovanni G
INRAE, URFM, Avignon, France.
UMR EcoFoG, AgroParisTech, CIRAD, CNRS, INRAE, Université des Antilles, Université de Guyane, Campus Agronomique, Kourou, France.
Mol Ecol. 2023 Jan;32(2):393-411. doi: 10.1111/mec.16750. Epub 2022 Nov 14.
Microgeographical adaptation occurs when the effects of directional selection persist despite gene flow. Traits and genetic loci under selection can then show adaptive divergence, against the backdrop of little differentiation at other traits or loci. How common such events are and how strong the selection is that underlies them remain open questions. Here, we discovered and analysed microgeographical patterns of genomic divergence in four European and Mediterranean conifers with widely differing life-history traits and ecological requirements (Abies alba MIll., Cedrus atlantica [Endl.] Manetti, Pinus halepensis Mill. and Pinus pinaster Aiton) by screening pairs from geographically close forest stands sampled along steep ecological gradients. We inferred patterns of genomic divergence by applying a combination of divergence outlier detection methods, demographic modelling, Approximate Bayesian Computation inferences and genomic annotation to genomic data. Surprisingly for such small geographical scales, we showed that selection is strong in all species but generally affects different loci in each. A clear signature of selection was systematically detected on a fraction of the genome, of the order of 0.1%-1% of the loci depending on the species. The novel modelling method we designed for estimating selection coefficients showed that the microgeographical selection coefficient scaled by population size (Ns) was 2-30. Our results convincingly suggest that selection maintains within-population diversity at microgeographical scales in spatially heterogeneous environments. Such genetic diversity is likely to be a major reservoir of adaptive potential, helping populations to adapt under fluctuating environmental conditions.
当定向选择的效应在存在基因流的情况下仍然持续时,就会发生微地理适应。在这种情况下,受到选择的性状和基因座会出现适应性分化,而其他性状或基因座的分化程度则很小。这类事件有多普遍,以及其背后的选择强度如何,仍是悬而未决的问题。在这里,我们通过筛选沿陡峭生态梯度采样的地理上相邻的林分中的配对样本,发现并分析了四种具有广泛不同生活史特征和生态需求的欧洲和地中海针叶树(欧洲冷杉、大西洋雪松、地中海松和海岸松)的基因组分化微地理模式。我们通过将分化异常值检测方法、种群动态建模、近似贝叶斯计算推断和基因组注释相结合,应用于基因组数据,来推断基因组分化模式。令人惊讶的是,在如此小的地理尺度上,我们发现所有物种中的选择作用都很强,但通常影响每个物种中的不同基因座。在基因组的一部分上系统地检测到了明显的选择特征,根据物种不同,这部分基因座占比约为0.1%-1%。我们设计的用于估计选择系数的新建模方法表明,按种群大小(Ns)缩放的微地理选择系数为2-30。我们的结果令人信服地表明,在空间异质环境中,选择在微地理尺度上维持了种群内的多样性。这种遗传多样性很可能是适应性潜力的主要储备,有助于种群在波动的环境条件下适应。