Data from: Bioclimatic, ecological, and phenotypic intermediacy and high genetic admixture in a natural hybrid of octoploid strawberries

PREMISE OF THE STUDY: Hybrid zones provide ‘natural laboratories’ for understanding the processes of selection, reinforcement and speciation. We sought to gain insight into the degree of introgression and the extent of ecological/phenotypic intermediacy in the natural hybrid strawberry, Fragaria × ananassa subsp. cuneifolia. METHODS: We used whole plastome sequencing to identify parental species-specific (Fragaria chiloensis and F. virginiana) chloroplast SNPs, and combined the use of these with nuclear microsatellite markers to genetically characterize the hybrid zone. We assessed the potential role of selection in the observed geographic patterns by bioclimatically characterizing the niche of the hybrid populations and phenotypically characterizing hybrid individuals of known genomic constitution. KEY RESULTS: Significant admixture and little overall maternal bias in chloroplast or nuclear genomes suggest a high degree of inter-fertility among the parental and hybrid species and point to a long history of backcrossing and genetic mixing in the hybrid zone. Even though hybrids were phenotypically intermediate to the parental species there was still a discernible fingerprint of the parental genotype within hybrid individuals. Thus, while the pattern of introgression observed suggests geographic limitations to gene flow, it may be reinforced by selection for specific parental traits in the bioclimatically-intermediate habitat occupied by the hybrid. CONCLUSION: This work uncovered the genetic complexity underlying the hybrid zone of the wild relatives of the cultivated strawberry. It lays the foundation for experimental dissection of the causes of genomic introgression and nuclear-cytoplasmic disassociation, and understanding other parts of the Fragaria evolutionary history.

研究背景：杂交带是解析选择作用、生殖隔离强化与物种形成过程的"天然实验室"。本研究旨在探究天然杂交草莓——凤梨草莓楔叶亚种（Fragaria × ananassa subsp. cuneifolia）的基因渐渗程度，以及其生态/表型中间型的分布范围。
研究方法：本研究通过全质体基因组测序，鉴定得到智利草莓（Fragaria chiloensis）与弗吉尼亚草莓（F. virginiana）这两个亲本物种的特异性叶绿体单核苷酸多态性（chloroplast SNPs）；结合该标记与核微卫星标记，对该杂交带开展遗传特征分析。此外，通过生物气候学特征解析杂交种群的生态位，并对已知基因组构成的杂交个体进行表型特征分析，以此评估选择作用在观测到的地理格局中的潜在作用。
主要结果：叶绿体与核基因组均呈现显著的遗传混合，且整体母系偏好较弱，这表明亲本与杂交物种间具有较高的种间可育性，同时也暗示该杂交带存在长期的回交与遗传混合历史。尽管杂交个体的表型介于两个亲本物种之间，但在其基因组中仍可识别出亲本基因型的特征印记。综上，尽管观测到的基因渐渗模式提示基因流存在地理限制，但该过程或可通过杂交种群所处的生物气候中间型生境中，针对特定亲本性状的选择作用得到强化。
结论：本研究揭示了栽培草莓野生近缘种杂交带背后的遗传复杂性，为解析基因组渐渗与核质分离的成因提供了实验基础，同时也为理解草莓属（Fragaria）的其他进化历史环节提供了参考。