Biodiversity Science ›› 2014, Vol. 22 ›› Issue (1): 21-39.doi: 10.3724/SP.J.1003.2014.13189

Special Issue: From Genome to Diversity

• Orginal Article • Previous Article     Next Article

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:2014-02-10
  • Ma Hong E-mail:hongma@fudan.edu.cn

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

Fig. 1

The relationships of major lineages of angiosperms. Except for three basal orders, all angiosperms formed a monophyletic group composed of five major lineages: Chloranthaceae, magnoliids, monocots, Ceratophyllaceae and eudicots. However, their relationships are not clear. Among monocots, Acorales is the basal order and commelinids (shown as triangle in this figure) with four orders are the core groups. The relationships among four magnoliid orders have been clarified. In eudicots, Ranunculales is sister to all other eudicots and Gunnerales is sister to all other core eudicots, which formed a monophyletic group known as Pentapetalae. Rosids and asterids are core groups of Pentapetalae, but there are many uncertain relationships in Pentapetalae. In rosids, it is still uncertain whether the sister group of the COM clade is the nitrogen-fixing clade or malvids."

Fig. 2

The relationships within rosids, asterids, monocots and magnoliids, respectively. (a) Rosids contain three clades: malvids, COM and the nitrogen-fixing clade, but whether the sister group of the COM clade is the nitrogen-fixing clade or malvids remains unclear. (b) Asterids are composed of euasterid I, euasterid II and two basal orders: Ericales and Cornales. The relationships among euasterids I are not clear. Garryales and Aquifoliales were respectively regarded as the basal group of euasterids I and II; however, new evidence based on nuclear genes suggested that these two together formed a sister group of other euasterids I. (c) Commelinids is the core group of monocots, and Acorales is the basal order. The relationships among commelinids are not clear. (d) In magnollids, Magnoliales and Laurales are sister groups, and Canellales and Piperales are sister groups."

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