Sequences of Pitcairnia flammea

Geographic isolation and reduced population sizes can lead to local extinction, low efficacy of selection, and decreased speciation. However, population differentiation is an essential step of biological diversification. In allopatric speciation, geographically isolated populations differentiate and persist until the evolution of reproductive isolation and ecological divergence complete the speciation process. Pitcairnia flammea allow us to study the evolutionary consequences of habitat fragmentation on naturally disjoint rock outcrop species from the Brazilian Atlantic Rainforest (BAF). Our main results showed low to moderate genetic diversity within populations, and deep population structuring caused by limited gene flow, low connectivity, genetic drift and inbreeding of long-term isolation and persistence of rock outcrops populations throughout Quaternary climatic oscillations. Bayesian phylogenetic and model-based clustering analyses found no clear northern and southern phylogeographic structure commonly reported for many BAF organisms. Although, we found two main lineages diverging by approximately 2 Mya during the early Pleistocene, species delimitation analysis assigned most of the populations as independent evolving entities, suggesting an important role of disjoint rock outcrops in promoting high endemism in this rich biome. Lastly, we detected limited gene flow in sympatric populations although some hybridization and introgression were observed, suggesting a continuous of speciation processes in this species complex. Our data not only inform us about the extensive differentiation and limited gene flow found among Pitcairnia flammea species complex, they also contain information about the mechanisms that shape the genetic architecture of small and fragmented populations of isolated rock outcrop of recently radiated plants.地理隔离（Geographic isolation）与种群规模缩减可引发局地灭绝、自然选择效能下降以及物种形成速率降低。然而，种群分化是生物多样化的关键环节。在异域物种形成（Allopatric speciation）过程中，地理隔离的种群持续分化并存续，直至生殖隔离与生态分化的演化完成物种形成进程。火红凤梨（Pitcairnia flammea）为我们研究巴西大西洋雨林（Brazilian Atlantic Rainforest, BAF）自然隔离的岩石露头物种的生境破碎化演化效应提供了理想研究对象。我们的主要研究结果显示，种群内部存在中低水平的遗传多样性，而有限的基因流、低下的种群连通性、遗传漂变，以及第四纪气候震荡期间岩石露头种群长期隔离与存续引发的近交，共同塑造了深度的种群遗传结构。贝叶斯系统发育分析与基于模型的聚类分析发现，该类群并未呈现多数BAF生物所普遍报道的南北谱系地理结构。尽管我们检测到两个主要谱系在更新世早期分化，分化时间约为200万年前，但物种界定分析将多数种群归类为独立演化单元，这表明隔离的岩石露头在推动这一丰富生物群区的高度特有性方面发挥了重要作用。最后，我们在同域种群中检测到有限的基因流，尽管同时观测到部分杂交与基因渐渗现象，这暗示该物种复合群正处于持续的物种形成过程中。本研究数据不仅揭示了火红凤梨物种复合群中广泛存在的种群分化与有限基因流，还阐明了塑造新近辐射演化的隔离岩石露头小型破碎种群遗传架构的潜在机制。