ddRAD of Microlepia

Natural hybridization is common in nature and plays a crucial role in driving biodiversity. Despite its significance, the understanding of hybridization in ferns remains inadequate. Therefore, it is imperative to study fern hybridization to gain a more comprehensive understanding of fern biodiversity. Our study delves into the role of hybridization in shaping fern species, employing Microlepia matthewii as a case study to investigate its origins of hybridization. We performed simplified genome sequencing on M. matthewii and its potential parent species, identifying nuclear and chloroplast SNPs. Initially, nuclear SNPs were employed to construct the three cluster analysis: phylogenetic tree, principal component analysis, and population structure analysis. Subsequently, to confirm whether the observed genetic mixture pattern resulted from hybridization, we utilized two methods: ABBA-BABA statistical values in the D-suite program and gene frequency covariance in the Treemix software to detect gene flow. Finally, we employed chloroplast SNPs to construct a phylogenetic tree, tracing the maternal origin. The analysis of the nuclear SNP cluster revealed that M. matthewii possesses a genetic composition that is a combination of M. hancei and M. calvescens. Furthermore, the analysis provided strong evidence of significant gene flow signatures from the parental species to the hybrid, as indicated by the two gene flow analyses. The samples of M. matthewii cluster separately with M. hancei or M. calvescens on the chloroplast systematic tree. However, the parentage ratio significantly differs from 1:1, suggesting that M. matthewii is a bidirectional and asymmetrical hybrid offspring of M. hancei and M. calvescens.自然杂交在自然界中普遍存在，对驱动生物多样性形成发挥着至关重要的作用。尽管其意义重大，但学界对蕨类植物杂交现象的认知仍存在不足。因此，开展蕨类杂交研究以全面解析蕨类生物多样性，实属必要。本研究以粗毛鳞盖蕨（Microlepia matthewii）为案例物种，探究其杂交起源，深入剖析杂交在塑造蕨类物种中的作用。研究对粗毛鳞盖蕨及其潜在亲本物种开展简化基因组测序，鉴定得到核单核苷酸多态性（nuclear Single Nucleotide Polymorphisms, SNPs）与叶绿体单核苷酸多态性（chloroplast Single Nucleotide Polymorphisms, SNPs）。首先利用核SNPs开展三类聚类分析：系统发育树（phylogenetic tree）构建、主成分分析（principal component analysis）与群体结构分析（population structure analysis）。随后，为验证观测到的遗传混合模式是否由杂交导致，本研究借助两种方法检测基因流（gene flow）：D-suite程序中的ABBA-BABA统计值，以及Treemix软件中的基因频率协方差。最后，利用叶绿体SNPs构建系统发育树，追溯其母本起源。核SNPs聚类分析结果显示，粗毛鳞盖蕨的遗传组成为汉密尔鳞盖蕨（M. hancei）与鳞盖蕨（M. calvescens）的遗传组合。此外，两项基因流分析均显示，亲本物种向该杂交种存在显著的基因流信号，这为该结论提供了强有力的证据支持。在叶绿体系统发育树中，粗毛鳞盖蕨的样本分别与汉密尔鳞盖蕨或鳞盖蕨聚类，但亲本贡献比例显著偏离1:1，表明粗毛鳞盖蕨是汉密尔鳞盖蕨与鳞盖蕨双向不对称的杂交后代。