Phylogenomic Insights into Deep Phylogeny of Angiosperms Based on Broad Nuclear Gene Sampling
------------------------------------------------------------------------------------------------Plant Commutations 2020/3/7
The vast majority (∼99.95%) of angiosperms form a clade called Mesangiospermae, which is subdivided into five major groups: eudicots, monocots, magnoliids, Chloranthales, and Ceratophyllales.
大部分被子植物形成核心被子植物的一枝，分成真双子叶植物（eudicots），单子叶植物（monocots），木兰类（magnoliids），金粟兰目（Chloranthales）和金鱼藻目（Ceratophyllales）。（本人翻译水平有限，如有错误欢迎指正）
Eudicots and monocots are the two largest and most diverse clades of Mesangiospermae, accounting for ∼75% and ∼20% of angiosperm species (http://www.theplantlist.org/). Magnoliids, with over 10 000 species, form the third major clade, and comprise four orders: Canellales, Laurales, Magnoliales, and Piperales (Cantino et al., 2007). The other two Mesangiospermae groups, Chloranthales and Ceratophyllales, are relatively small lineages, but are evolutionarily significant with macrofossil records dating back to the Early Cretaceous (Friis et al., 2010). Chloranthales encompass four genera and about 77 extant species, and Ceratophyllales comprise four species of the single extant genus Ceratophyllum (Maarten et al., 2016).
真双子叶植物大约占核心被子植物的75%，单子叶植物大约占核心被子植物的20%。木兰类有超过10000个物种，包括白樟目（Canellales）, 樟目（Laurales）, 木兰目（Magnoliales）, 和胡椒目（ Piperales）。金粟兰目包括四个属，含77个现存物种。金鱼藻目现存一个属，含四个种。
Previous analyses based on plastid genes suggest that a clade comprising Chloranthales + magnoliids is sister to monocots + (Ceratophyllales + eudicots) (Figure 1A; Moore et al., 2007, Soltis et al., 2011, Ruhfel et al., 2014, Gitzendanner et al., 2018). Despite sampling nearly 3000 chloroplast genomes across the angiosperm phylogeny, Li et al. (2019) have shown that the relationships among Mesangiospermae remained poorly resolved and that the rapid radiations may have occurred during the early evolutionary history of Mesangiospermae. Analyses based on mitochondrial genes recover different relationships within Mesangiospermae, with eudicots + monocots forming the sister group to magnoliids, and these three lineages being the sister group to Ceratophyllales + Chloranthales (Figure 1B; Qiu et al., 2010). Endress and Doyle (2009) combined plastid and morphological data, and recovered eudicots + (monocots + magnoliids) as sister to the clade including Ceratophyllales and Chloranthales (Figure 1C). The relationships among these clades remain discrepancies in different analyses using nuclear datasets. Zeng et al. (2014) analyzed 59 low-copy nuclear genes of 60 angiosperms, and suggested that a clade comprising Chloranthales + Ceratophyllales is closely related to eudicots, with magnoliids and monocots as successive sister groups (Figure 1D). Wickett et al. (2014) used large number of nuclear genes (674 or fewer genes) to estimate the relationships among land plants and recovered a similar angiosperm topology to that reported by Zeng et al. (2014), but included few angiosperms (37 species) and did not sample Ceratophyllales. Puttick et al. (2018) used expanded data from Wickett et al. (2014) with optimized phylogenetic analyses, and found a close relationship between eudicots and Chloranthales + magnoliids, with monocots being the sister lineage to these three groups (Figure 1E). Recently Leebens-Mack et al. (2019) showed that the deep-branching relationships of angiosperm remain unresolved even using thousands of transcriptomes of green plants. Overall, despite being a widely studied topic, the relationships along the backbone of angiosperm phylogeny remain elusive.
这五大类的进化关系不断被讨论，但一直没有定论。本文章也研究了这个问题。
Our phylogenomic analyses recovered full support for Amborella being sister to all other extant angiosperms, followed successively by Nymphaeales（睡莲目） and Austrobaileyales（木兰藤目） (ANA grade:Amborella/Nymphaeales/Austrobaileyales), in agreement with previous studies (e.g., The Amborella Genome Project, 2013, Wickett et al., 2014, Zeng et al., 2014, Zhong and Betancur-R, 2017, Gitzendanner et al., 2018, Leebens-Mack et al., 2019, Li et al., 2019, Zhang et al., 2020).
incomplete lineage sorting（ILS）经常遇到这个词，一直没太理解，看看读了这篇文章能否加深我的理解。
radiation 这个词在进化中又是什么意义呢？
