Low-copy nuclear sequence data confirm complex patterns of farina evolution in notholaenid ferns (Pteridaceae)
Low-copy nuclear sequence data confirm complex patterns of farina evolution in notholaenid ferns (Pteridaceae)
复制标题
低拷贝核序列数据证实了蕨类植物（蕨科）中淀粉进化的复杂模式
DOI：
10.1016/j.ympev.2019.05.016
复制
发表时间：
2019
影响因子：
4.1
通讯作者：
Rothfels, Carl J.
中科院分区：
文献类型：
--
作者：
Kao, Tzu-Tong;Pryer, Kathleen M.;Freund, Forrest D.;Windham, Michael D.;Rothfels, Carl J.
Notholaenids是一种不寻常的蕨类植物，它们已经适应了墨西哥和美国西南部的沙漠，并在其中多样化。大约有40个物种，这一组是注意到的是耐干燥和具有“粉”-粉末状渗出物的亲脂性黄酮苷元-这发生在配子体和孢子体阶段的生活史。最新的notholaenids基于质体标记的界限令人惊讶地表明，一些形态特征，包括花粉的表达，是homoplasious。在一个引人注目的趋同案例中，Notholaena standleyi似乎与coreNotholaena有远亲关系，有几个以前与Notholaenanested没有联系的分类群。这种冲突可能是由于适应性趋同导致的形态同源性，或者，质体同源性本身可能是误导的，由于不完整的谱系分类，杂交或其他因素而偏离了真正的物种树。在这项研究中，我们提出了一个物种的notholaenid蕨类植物，使用四个低拷贝的核基因座和连接数据从三个质体基因座。共61个个体（49 notholaenids和12个外群类群）进行了采样，其中包括37个公认的notholaenid物种中的31个。使用PacBio测序和PURCbioinformatics pipeline检索同源基因/等位基因核序列。首先使用最大似然法和贝叶斯推断法对每个数据集进行单独分析，并使用 *BEAST推断物种的亲缘关系。虽然我们观察到几个核和质体的同源性之间的不一致，我们的主要结果与以前的推断的基础上质体的数据是广泛一致的。通过绘制我们的共识系统发育树上的淀粉和他们的生化组成的存在下，我们证实，字符确实是同质的，有复杂的进化历史。与其他研究充分的蕨类植物属相比，notholaenid分支中公认的物种之间的杂交似乎相对罕见。
Notholaenids are an unusual group of ferns that have adapted to, and diversified within, the deserts of Mexico and the southwestern United States. With approximately 40 species, this group is noted for being desiccation-tolerant and having “farina”—powdery exudates of lipophilic flavonoid aglycones—that occur on both the gametophytic and sporophytic phases of their life cycle. The most recent circumscription of notholaenids based on plastid markers surprisingly suggests that several morphological characters, including the expression of farina, are homoplasious. In a striking case of convergence,Notholaena standleyiappears to be distantly related to coreNotholaena, with several taxa not before associated withNotholaenanested between them. Such conflicts can be due to morphological homoplasy resulting from adaptive convergence or, alternatively, the plastid phylogeny itself might be misleading, diverging from the true species tree due to incomplete lineage sorting, hybridization, or other factors. In this study, we present a species phylogeny for notholaenid ferns, using four low-copy nuclear loci and concatenated data from three plastid loci. A total of 61 individuals (49 notholaenids and 12 outgroup taxa) were sampled, including 31 out of 37 recognized notholaenid species. The homeologous/allelic nuclear sequences were retrieved using PacBio sequencing and the PURCbioinformatics pipeline. Each dataset was first analyzed individually using maximum likelihood and Bayesian inference, and the species phylogeny was inferred using *BEAST. Although we observed several incongruences between the nuclear and plastid phylogenies, our principal results are broadly congruent with previous inferences based on plastid data. By mapping the presence of farina and their biochemical constitutions on our consensus phylogenetic tree, we confirmed that the characters are indeed homoplastic and have complex evolutionary histories. Hybridization among recognized species of the notholaenid clade appears to be relatively rare compared to that observed in other well-studied fern genera.