Data from: Adaptation with gene flow across the landscape in a dune sunflower

AbstractIsolation by adaptation increases divergence at neutral loci when natural selection against immigrants reduces the rate of gene flow between different habitats. This can occur early in the process of adaptive divergence and is a key feature of ecological speciation. Despite the ability of isolation by distance and other forms of landscape resistance to produce similar patterns of neutral divergence within species, few studies have used landscape genetics to control for these other forces. We have studied the divergence of Helianthus petiolaris ecotypes living in active sand dunes and adjacent non-dune habitat, using landscape genetics approaches, such as circuit theory and multiple regression of distance matrices, in addition to coalescent modelling. Divergence between habitats was significant, but not strong, and was shaped by isolation by distance. We expected that increased resistance due to patchy and unfavourable habitat in the dunes would contribute to divergence. Instead, we found that landscape resistance models with lower resistance in the dunes performed well as predictors of genetic distances among subpopulations. Nevertheless, habitat class remained a strong predictor of genetic distance when controlling for isolation by resistance and isolation by distance. We also measured environmental variables at each site and confirmed that specific variables, especially soil nitrogen and vegetation cover, explained a greater proportion of variance in genetic distance than did landscape or the habitat classification alone. Asymmetry in effective population sizes and numbers of migrants per generation was detected using coalescent modelling with Bayesian inference, which is consistent with incipient ecological speciation being driven by the dune habitat., Usage notesPopulation_datagsd_main_15l.strugsd_migrate_12l

摘要：当针对迁入个体的自然选择降低了不同生境间的基因流（gene flow）速率时，适应性隔离（isolation by adaptation）会提升中性基因座（neutral loci）的分化水平。这一过程可发生在适应性分化（adaptive divergence）的早期阶段，是生态物种形成（ecological speciation）的核心特征。尽管距离隔离（isolation by distance）与其他类型的景观阻力（landscape resistance）同样可在物种种内产生中性分化模式，但鲜有研究借助景观遗传学（landscape genetics）方法对这些干扰因素进行控制。我们针对栖息于活动沙丘与相邻非沙丘生境的沙地向日葵（Helianthus petiolaris）生态型（ecotype）开展了研究，除溯祖建模（coalescent modelling）外，还采用了电路理论、距离矩阵多元回归等景观遗传学分析手段。生境间的分化显著但并不强烈，且受到距离隔离的塑造。我们曾推测，沙丘内地块破碎且不适宜的生境所带来的更高阻力，会推动分化进程。但实际结果却显示，以沙丘内更低阻力构建的景观阻力模型，可较好地预测亚种群间的遗传距离。尽管如此，在控制阻力隔离（isolation by resistance）与距离隔离的影响后，生境类型仍是遗传距离的强预测因子。我们还测定了每个样点的环境变量，证实相较于单纯的景观因素或生境分类，特定环境变量——尤其是土壤氮含量与植被覆盖度——可解释遗传距离中更大比例的变异。通过贝叶斯推断（Bayesian inference）的溯祖建模，我们检测到有效种群大小与每代迁入者数量存在不对称性，这与由沙丘生境驱动的初期生态物种形成（incipient ecological speciation）结论相符。使用说明：Population_datagsd_main_15l.strugsd_migrate_12l