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.

通常，在推断过去种群历史过程的研究中，人们会规避被认为处于选择作用下的基因座（loci），因为它们不符合中性模型的假设。然而，这可能会错失更好地重建部分过去种群历史特征的机会。本研究同时利用离群基因座（outlier loci，即可能受物种间歧化选择影响，或与处于选择作用的基因组区域存在搭便车效应的基因座）和非离群基因座，分析了两种生态动态特征迥异的同域分布欧洲栎类物种——夏栎（Quercus robur）和无梗花栎（Q. petraea）——之间的遗传分化。我们在法国的6个混交林中共采集了855个个体，并利用一组包含262个单核苷酸多态性（SNPs）的标记进行基因分型，该标记组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（coalescent simulation）模型与参数，我们共鉴定出13至74个种间离群基因座。理论上，渐渗（introgression）主要应从定居物种流向入侵物种，因此晚演替物种无梗花栎（Q. petraea）的遗传多样性预期会高于早演替物种夏栎（Q. robur）。值得注意的是，这一预测仅在离群基因座中得到验证，而非离群基因座则未呈现该结果。我们推测，在种间分化程度较高的基因座上，有效种间基因流更低，这更好地保留了由两个物种迥异的生态动态所引发的、过去向无梗花栎定向的不对称渐渗信号。因此，利用处于选择作用下的标记来重建过去种群历史过程的潜力，或许比人们普遍认知的更为广泛。