膜蕨科植物rbcL基因的适应性进化和共进化分析

Adaptive evolution and coevolution of the rbcL gene in Hymenophyllaceae

膜蕨科植物是薄囊蕨类中种类最多的科,主要分布在潮湿的热带地区,拥有陆生、附生、半附生和攀生等多种生态型。为进一步了解膜蕨科植物辐射式物种分化的分子适应机制,该研究在时间框架下采用位点模型对膜蕨科植物rbc L基因的进化式样进行分析。结果表明:共鉴定出6个氨基酸正选择位点(125I、227L、231A、258F、304S和351L),其中位点304S位于环六上,对维持Rubisco功能有重要作用。此外,还计算了Rubisco大亚基内部氨基酸位点之间的共进化关系,共检测出39组(35个氨基酸)共进化位点,其中位点在α螺旋上的占46%,在β折叠上的占14%。膜蕨科植物rbc L基因这种复杂的进化式样可能与其起源较早有关。鉴于此,基于UCLD分子钟模型对膜蕨科植物的分化时间进行了估计,结果显示膜蕨科植物首次发生分歧的时间在三叠纪早期,瓶蕨属和膜蕨属的分歧时间分别发生在侏罗纪早期和白垩纪晚期,并且得出陆生生态型是其它生态型进化的基础,推测最近几次最热事件可能对物种分化的形成产生一定的作用。该研究结果对认识膜蕨科植物如何应对被子植物兴起所导致的陆地生态系统改变具重要意义。

Hymenophyllaceae is the most rich speices family of leptosporangiate ferns. It mainly distributed in the humid tropics,possessing terrestrial,epiphytic,hemepiphytic and climbing ecotypes. To further understand the molecular adaptation linked to fern radiation,evolutionary patterns of the rbc L sequences in the family Hymenophyllaceae were examined using random-site models along with the estimated time-scale of Hymenophyllaceous phylogeny. By comparing Modles M1 a / M2 a and M7 / M8 under random-site modles,six amino acid sites（ 125 I,227L,231 A,258F,304 S and 351L） were found to be positively selected,in which the site 304 S was located in the D-loop six,playing an important role in keeping Rubisco function. We also used CAPS v1.0（ coevolution analysis using protein sequences） to study the evolutionary relationship between the amino sites within the Rubisco large subunit. Thirty-nine groups of coevolutionary sites were detected（ totally thirty-five amino sites）,of which 46% were located in the α-helix,14% in the β-sheet. This complex evolutionary patterns may be related to its earlier origin. In view of this, the phylogenetic tree was reconstructed. The results showed that the initial divergence whin Hymenophyllaceae occurred in the early Triassic. Thedivergence within Trichomanes and Hymenophyllum occurred in the early Jurassic and Cretaceous,seperatelly. The results also indicated that the ancestral state for the Hymenophyllaceae was terrestrial,suggesting possible roles played by the Thermal Maximum recently. These results provide new insights for how Hymenophyllaceae ferns response to the terrestrial ecosystem changes caused by the rise angiosperms.