生物多样性 ›› 2014, Vol. 22 ›› Issue (1): 21-39.doi: 10.3724/SP.J.1003.2014.13189

所属专题: 基因组和生物多样性

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被子植物系统发育深层关系研究: 进展与挑战

曾丽萍, 张宁, 马红*()   

  1. 复旦大学生命科学院, 遗传工程国家重点实验室, 植物科学研究所, 进化生物学中心, 上海 200433
  • 收稿日期:2013-08-16 接受日期:2013-12-07 出版日期:2014-01-20
  • 通讯作者: 马红 E-mail:hongma@fudan.edu.cn
  • 基金项目:
    植物适应逆境中转录调控的分子进化机制(91131007)

Advances and challenges in resolving the angiosperm phylogeny

Liping Zeng, Ning Zhang, Hong Ma*()   

  1. State Key Laboratory of Genetic Engineering and Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200433
  • Received:2013-08-16 Accepted:2013-12-07 Online:2014-01-20
  • Contact: Ma Hong E-mail:hongma@fudan.edu.cn

被子植物系统发育学是研究被子植物及其各类群间亲缘关系与进化历史的学科。从20世纪90年代起, 核苷酸和氨基酸序列等分子数据开始被广泛运用于被子植物系统发育研究, 经过20多年的发展, 从使用单个或联合少数几个细胞器基因, 到近期应用整个叶绿体基因组来重建被子植物的系统发育关系, 目、科水平上的被子植物系统发育框架已被广泛接受。在这个框架中, 基部类群、主要的5个分支(即真双子叶植物、单子叶植物、木兰类、金粟兰目和金鱼藻目)、每个分支所包含的目以及几个大分支包括的核心类群等都具有高度支持。与此同时, 细胞器基因还存在一些固有的问题, 例如单亲遗传、系统发育信息量有限等, 因此近年来双亲遗传的核基因在被子植物系统发育研究中的重要性逐渐得到关注, 并在不同分类阶元的研究中都取得了一定进展。但是, 被子植物系统发育中仍然存在一些难以确定的关系, 例如被子植物5个分支之间的关系、真双子叶植物内部某些类群的位置等。本文简述了20多年来被子植物系统发育深层关系的主要研究进展, 讨论了被子植物系统发育学常用的细胞器基因和核基因的选用, 已经确定和尚未确定系统发育位置的主要类群, 以及研究中尚存在的问题和可能的解决方法。

关键词: 亲缘与进化关系, 分子系统发育, 细胞器基因, 核基因, 系统发育基因组学

Angiosperm phylogenetics investigates the evolutionary history and relationships of angiosperms based on the construction of phylogenetic trees. Since the 1990s, nucleotide or amino acid sequences have been widely used for this and angiosperm phylogenetic analysis has advanced from using single or a combination of a few organellar genes to whole plastid genome sequences, resulting in the widely accepted modern molecular systematics of angiosperms. The current framework of the angiosperm phylogeny includes highly supported basal angiosperm relationships, five major clades (eudicots, monocots, magnoliids, Chloranthales, and Ceratophyllales), orders grouped within these clades, and core groups in the monocots or eudicots. However, organellar genes have some limitations; these involve uniparental inheritance in most instances and a relatively low percentage of phylogenetic informative sites. Thus, they are unable to resolve some relationships even when whole plastid genome sequences are used. Therefore, the utility of biparentally inherited nuclear genes with more information about evolutionary history, has gradually received more attention. Nevertheless, there are still some plant groups that are difficult to place in the angiosperm phylogeny, such as those involving the relative positions of the five major groups as well as those of several orders of eudicots. In this review, we discuss the applications, advantages and disadvantages of marker genes, the deep relationships that have been resolved in angiosperm phylogeny, groups with uncertain positions, and the challenges that remain in resolving an accurate phylogeny for angiosperms.

Key words: evolutionary relationships, molecular phylogeny, organellar genes, nuclear genes, phylogenomics

图1

被子植物各大类群关系图。除了位于最基部的3个目之外, 其余所有被子植物形成单系群。这个单系群由5个类群组成: 金粟兰目、木兰类、单子叶植物、金鱼藻目和真双子叶植物, 但是这5个分支的关系没有被确定, 因此五者的关系在树上以梳子结构来表示。单子叶植物中, 菖蒲目被认为是最基部的类群; 鸭跖草分支则是其核心类群, 包含4个目, 在树上以三角形表示。木兰类4个目的关系已经确定。毛茛目被认为位于真双子叶植物的最基部; 而在核心真双子叶植物中, 洋二仙草目被认为位于最基部, 其他的类群形成一个被称为Pentaperalae的单系群, 蔷薇类和菊类是其核心类群, 但是Pentaperalae内部各个类群的关系并没有被最终确定。蔷薇类中, COM分支与固氮分支还是锦葵类形成姊妹群仍然有争议。"

图2

蔷薇类植物、菊类植物、单子叶植物和木兰类植物内部关系图。(a)蔷薇类主要包含3个高支持率的分支, 即锦葵类植物、COM分支和固氮分支, 但是COM分支的姊妹群是固氮分支还是锦葵类植物仍然有争议, 因此在图中以梳齿结构显示。(b)菊类植物主要分为真菊I类和II类, 杜鹃花目和山茱萸目位于其基部; 真菊I类内部的关系尚不清楚; 绞木目和冬青目曾被认为分别位于真菊I类和II类的基部, 但最近来自核基因的研究结果表明二者以姊妹群形式位于真菊I类的基部。(c)单子叶类植物的核心类群是鸭跖草分支, 但该分支内部几个目的关系并不是很清楚; 菖蒲目是单子叶植物的最基部类群。(d)木兰类植物中, 木兰目与樟目、白桂皮目与胡椒目互为姊妹群。"

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