目的:探索物种如何分化对于理解物种形成的驱动因素至关重要。地理分离和生态选择等因素,杂交,多倍体化和交配系统的转变都是植物物种形成的主要机制,但是他们对分歧的贡献很少被人们理解。在这里,我们在两种植物中测试这些机制,龙胆和G.hoae,目的是了解青藏高原(QTP)最近的异域物种差异。
方法:我们进行了贝叶斯聚类,系统发育分析和使用561,302个核基因组SNP的杂交估计。我们进行了冗余分析,并鉴定和注释了物种特异性SNP(ssSNP),以探索气候偏好与遗传差异之间的关联。我们还使用流式细胞术估计了基因组大小,以测试被忽视的多倍体。
结果:基因组证据证实,甘草和甘草是密切相关但不同的物种,而基因组大小估计显示,在没有多倍体的情况下发生了分歧。G.hoae的平均Fis值明显高于G.lhassica。基于基因组SNP的群体聚类没有显示最近杂交的特征,然而,每个物种的特征是与同源物杂交的独特历史,形成了基因组广泛的变异。拉西亚已经捕获了叶绿体,并经历了与不同的龙胆物种的渗入,而G.hoae经历了与相关分类群的反复杂交。物种分布模型表明在最后一个间冰期范围重叠,而冗余分析表明,降水和温度是解释物种分离的主要气候差异。该物种相差2,993个ssSNP,基因组注释显示与胁迫抗性有关的基因中的错义变异。
结论:这项研究表明,这些物种在QTP中的独特性是由杂交组合驱动的,地理隔离,交配系统差异和不同气候偏好的演变。
Exploring how species diverge is vital for understanding the drivers of speciation. Factors such as geographical separation and ecological selection, hybridization, polyploidization and shifts in mating system are all major mechanisms of plant speciation, but their contributions to divergence are rarely well understood. Here we test these mechanisms in two plant species, Gentiana lhassica and G. hoae, with the goal of understanding recent allopatric species divergence on the Qinghai-Tibet Plateau (QTP).
We performed Bayesian clustering, phylogenetic analysis and estimates of hybridization using 561 302 nuclear genomic single nucleotide polymorphisms (SNPs). We performed redundancy analysis, and identified and annotated species-specific SNPs (ssSNPs) to explore the association between climatic preference and genetic divergence. We also estimated genome sizes using flow cytometry to test for overlooked polyploidy.
Genomic evidence confirms that G. lhassica and G. hoae are closely related but distinct species, while genome size estimates show divergence occurred without polyploidy. Gentiana hoae has significantly higher average FIS values than G. lhassica. Population clustering based on genomic SNPs shows no signature of recent hybridization, but each species is characterized by a distinct history of hybridization with congeners that has shaped genome-wide variation. Gentiana lhassica has captured the chloroplast and experienced introgression with a divergent gentian species, while G. hoae has experienced recurrent hybridization with related taxa. Species distribution modelling suggested range overlap in the Last Interglacial Period, while redundancy analysis showed that precipitation and temperature are the major climatic differences explaining the separation of the species. The species differ by 2993 ssSNPs, with genome annotation showing missense variants in genes involved in stress resistance.
This study suggests that the distinctiveness of these species on the QTP is driven by a combination of hybridization, geographical isolation, mating system differences and evolution of divergent climatic preferences.