Data from: Selection against recombinant hybrids maintains reproductive isolation in hybridizing Populus species despite F1 fertility and recurrent gene flow

Natural hybrid zones have proven to be precious tools for understanding the origin and maintenance of reproductive isolation (RI) and therefore species. Most available genomic studies of hybrid zones using whole- or partial-genome resequencing approaches have focused on comparisons of the parental source populations involved in genome admixture, rather than exploring fine-scale patterns of chromosomal ancestry across the full admixture gradient present between hybridizing species. We have studied three well-known European ‘replicate’ hybrid zones of Populus alba and P. tremula, two widespread, ecologically divergent forest trees, using up to 432 505 single-nucleotide polymorphisms (SNPs) from restriction site-associated DNA (RAD) sequencing. Estimates of fine-scale chromosomal ancestry, genomic divergence and differentiation across all 19 poplar chromosomes revealed strikingly contrasting results, including an unexpected preponderance of F1 hybrids in the centre of genomic clines on the one hand, and genomically localized, spatially variable shared variants consistent with ancient introgression between the parental species on the other. Genetic ancestry had a significant effect on survivorship of hybrid seedlings in a common garden trial, pointing to selection against early-generation recombinants. Our results indicate a role for selection against recombinant genotypes in maintaining RI in the face of apparent F1 fertility, consistent with the intragenomic ‘coadaptation’ model of barriers to introgression upon secondary contact. Whole-genome resequencing of hybridizing populations will clarify the roles of specific genetic pathways in RI between these model forest trees and may reveal which loci are affected most strongly by its cyclic breakdown.

天然杂交带已被证实为解析生殖隔离（reproductive isolation, RI）乃至物种起源与维持机制的珍贵研究工具。当前多数采用全基因组或局部基因组重测序技术开展的杂交带基因组研究，多聚焦于对比参与基因组混合的亲本源种群，而非探究杂交物种间完整渐渗梯度上的染色体祖先来源精细格局。本研究针对三个经典的欧洲银白杨（*Populus alba*）与欧洲颤杨（*P. tremula*）重复型天然杂交带展开分析，使用基于限制性酶切位点相关DNA（restriction site-associated DNA, RAD）测序获得的至多432505个单核苷酸多态性（single-nucleotide polymorphisms, SNPs）标记。对杨树全部19条染色体的染色体祖先来源、基因组分化与遗传分化进行精细估算后，得到了极具反差的研究结果：一方面，基因组梯度中心区域意外地以F1代杂交种占主导；另一方面，亲本物种间的古老渐渗事件对应着基因组区域特异性、空间分布异质性的共享变异位点。在同质园试验中，遗传祖先类型对杂交幼苗的存活率存在显著影响，表明存在针对早期世代重组型个体的选择淘汰作用。本研究结果显示，尽管F1代杂交种看似可育，但针对重组基因型的选择在维持生殖隔离中发挥了关键作用，这与二次接触时渐渗障碍的基因组内共适应模型相一致。后续对杂交种群开展全基因组重测序研究，将进一步明确这些模式林木间生殖隔离相关特定遗传通路的功能，并揭示哪些基因位点受其周期性瓦解的影响最为显著。