Data from: Outlier loci highlight the direction of introgression in oaks

Loci considered to be under selection are generally avoided in attempts to infer past demographic processes as they do not fit neutral model assumptions. However, opportunities to better reconstruct some aspects of past demography might thus be missed. Here we examined genetic differentiation between two sympatric European oak species with contrasting ecological dynamics (Quercus robur and Q. petraea) with both outlier (i.e. loci possibly affected by divergent selection between species or by hitchhiking effects with genomic regions under selection) and non-outlier loci. We sampled 855 individuals in six mixed forests in France and genotyped them with a set of 262 SNPs enriched with markers showing high interspecific differentiation, resulting in accurate species delimitation. We identified between 13 and 74 interspecific outlier loci, depending on the coalescent simulation models and parameters used. Greater genetic diversity was predicted in Q. petraea (a late successional species) than in Q. robur (an early successional species) as introgression should theoretically occur predominantly from the resident species to the invading species. Remarkably, this prediction was verified with outlier loci but not with non-outlier loci. We suggest that the lower effective interspecific gene flow at loci showing high interspecific divergence has better preserved the signal of past asymmetric introgression towards Q. petraea caused by the species’ contrasting dynamics. Using markers under selection to reconstruct past demographic processes could therefore have broader potential than generally recognized.

被认为处于选择作用下的基因座通常在推断过往种群历史过程的研究中被规避，因其不符合中性模型假设。然而，这一做法可能会错失更好地重构部分种群历史特征的机会。本研究针对两种生态动态截然不同的同域分布欧洲栎类物种——夏栎（*Quercus robur*）与无梗花栎（*Quercus petraea*）——的遗传分化展开分析，同时纳入异常位点（即可能受物种间分化选择影响，或与受选择基因组区域存在遗传搭车效应的基因座）与非异常位点两类标记。我们在法国的6个混交林分中采集了855个个体，使用一组经筛选的262个单核苷酸多态性（Single Nucleotide Polymorphism, SNP）标记进行基因分型，该组标记额外富集了种间分化程度较高的位点，从而实现了精准的物种界定。根据所采用的溯祖模拟模型与参数的不同，我们共鉴定出13至74个种间异常位点。此前的理论预测显示，作为晚期演替物种的无梗花栎（*Q. petraea*）的遗传多样性高于早演替物种夏栎（*Q. robur*），因为理论上基因渐渗主要发生在定居物种向入侵物种的方向。值得注意的是，这一预测仅在异常位点组中得到验证，而非异常位点组则未呈现该结果。我们推测，在种间分化程度较高的基因座上，更低的有效种间基因流更好地保留了由物种生态动态差异引发的、指向无梗花栎的不对称基因渐渗信号。因此，利用受选择标记重构过往种群历史过程的应用潜力，或许比当前普遍认知的更为广泛。