Data from: Tracking the progression of speciation: variable patterns of introgression across the genome provide insights on the species delimitation between progenitor-derivative spruces (Picea mariana × P. rubens)

The genic species concept implies that while most of the genome can be exchanged somewhat freely between species through introgression, some genomic regions remain impermeable to interspecific gene flow. Hence, interspecific differences can be maintained despite ongoing gene exchange within contact zones. This study assessed the heterogeneous patterns of introgression at gene loci across the hybrid zone of an incipient progenitor–derivative species pair, Picea mariana (black spruce) and Picea rubens (red spruce). The spruce taxa likely diverged in geographic isolation during the Pleistocene and came into secondary contact during late Holocene. A total of 300 SNPs distributed across the 12 linkage groups (LG) of black spruce were genotyped for 385 individual trees from 33 populations distributed across the allopatric zone of each species and within the zone of sympatry. An integrative framework combining three population genomic approaches was used to scan the genomes, revealing heterogeneous patterns of introgression. A total of 23 SNPs scattered over 10 LG were considered impermeable to introgression and putatively under diverging selection. These loci revealed the existence of impermeable genomic regions forming the species boundary and are thus indicative of ongoing speciation between these two genetic lineages. Another 238 SNPs reflected selectively neutral diffusion across the porous species barrier. Finally, 39 highly permeable SNPs suggested ancestral polymorphism along with balancing selection. The heterogeneous patterns of introgression across the genome indicated that the speciation process between black spruce and red spruce is young and incomplete, albeit some interspecific differences are maintained, allowing ongoing species divergence even in sympatry. The approach developed in this study can be used to track the progression of ongoing speciation processes.

基因物种概念（genic species concept）指出，尽管多数基因组可通过基因渐渗（introgression）在物种间较为自由地交换，但部分基因组区域对种间基因流仍保持不可渗透特性。因此，即便在接触区内持续发生基因交流，物种间的差异仍得以维持。本研究针对初期祖源-衍生物种种对——黑云杉（Picea mariana）与红云杉（Picea rubens）的杂交带，评估了基因位点上的异质性渐渗模式。该云杉类群可能在更新世时期经历地理隔离分化，并在全新世晚期发生二次接触。研究对分布于两个物种的异域分布区及同域分布区内的33个种群的385株个体树木进行了基因分型，共获得分布于黑云杉12个连锁群（LG）上的300个单核苷酸多态性位点（SNPs）。研究结合三种种群基因组学方法构建整合分析框架以扫描基因组，揭示了异质性的渐渗模式：其中23个分散于10个连锁群上的SNPs被认为对渐渗具有不可渗透性，且可能处于趋异选择作用之下。这些位点表明存在构成物种边界的不可渗透基因组区域，从而印证了这两个遗传谱系间正在进行的物种形成过程。另有238个SNPs表现为跨多孔性物种屏障的选择中性扩散模式；剩余39个高可渗透性SNPs则提示存在伴随平衡选择的祖先多态性。全基因组范围内的异质性渐渗模式表明，黑云杉与红云杉间的物种形成过程尚处于年轻且未完成的阶段，尽管部分种间差异得以维持，但即便在同域分布区内，物种分化仍在持续进行。本研究开发的分析方法可用于追踪正在进行的物种形成过程的进展。