Data from: Genetic divergence, range expansion and possible homoploid hybrid speciation among pine species in northeast China

Although homoploid hybrid speciation in plants is probably more common than previously realized, there are few well-documented cases of homoploid hybrid origin in conifers. We examined genetic divergence between two currently widespread pines in northeast China, Pinus sylvestris var. mongolica and P. densiflora, and also whether two narrowly distributed pines in the same region, P. funebris and P. takahasii, might have originated from the two widespread species by homoploid hybrid speciation. Our results, based on population genetic analysis of chloroplast (cp), mitochondrial (mt) DNA, and nuclear gene sequence variation, showed that the two widespread species were divergent for both cp- and mtDNA variation, and also for haplotype variation at two of eight nuclear gene loci surveyed. Our analysis further indicated that P. sylvestris var. mongolica and P. densiflora remained allopatric during the most severe Quaternary glacial period that occurred in northeast China, but subsequently exhibited rapid range expansions. Pinus funebris and P. takahasii, were found to contain a mixture of chlorotypes and nuclear haplotypes that distinguish P. sylvestris var. mongolica and P. densiflora, in support of the hypothesis that they possibly originated via homoploid hybrid speciation following secondary contact and hybridization between P. sylvestris var. mongolica and P. densiflora.

尽管植物中的同倍体杂交物种形成（homoploid hybrid speciation）可能比此前学界认知的更为普遍，但针叶树（conifers）中经充分佐证的同倍体杂交起源案例仍屈指可数。本研究针对中国东北地区两种当前广泛分布的松树——樟子松（Pinus sylvestris var. mongolica）与赤松（P. densiflora）开展了遗传分化分析，并探讨了同区域内两种狭域分布的松树：P. funebris与P. takahasii是否可能由这两种广布物种通过同倍体杂交物种形成起源。

本研究基于叶绿体（cp）DNA、线粒体（mt）DNA及核基因序列变异的群体遗传分析，结果显示两种广布物种在叶绿体DNA与线粒体DNA变异层面均存在显著分化，且在所检测的8个核基因位点中的2个位点上存在单倍型（haplotype）变异。进一步分析表明，在中国东北第四纪冰期的最严酷阶段，樟子松与赤松始终处于异域分布状态，随后则经历了快速的分布范围扩张。

研究发现P. funebris与P. takahasii兼具可区分樟子松与赤松的叶绿体型（chlorotypes）与核单倍型组合，这一结果支持了“二者可能是樟子松与赤松二次接触并杂交后，经由同倍体杂交物种形成起源”的假说。