Tree of life for the genera of Chinese vascular plants

Chen, Zhiduan; Yang, Tuo; Li, Lin; Lu, Limin; Li, Honglei; Sun, Miao; Liu, Bing; Chen, Min; Niu, Yan-Ting; Ye, Jianfei; Cao, Zhi-Yong; Liu, Hongmei; Wang, Xiaoming; Wang, Wei; Zhang, Jingbo; Meng, Zhen; Cao, Wei; Li, Jianhui; Wu, Songjie; Zhao, Hui-Ling; Liu, Zhong‐Jian; Du, Zhi-Yuan; Wang, Qingfeng; Guo, Jing; Tan, Xinxin; Su, Jun‐Xia; Zhang, Linjing; Yang, Leilei; Liao, Yi-Ying; Li, Minghe; Zhang, Guoqiang; Chung, Shih-Wen; Zhang, Jian; Xiang, Kun; Li, Ruiqi; Soltis, Douglas E.; Soltis, Pamela S.; Zhou, Shiliang; Ran, Jin-Hua; Wang, Xiaoquan; Jin, Xiao‐Hua; Chen, Yousheng; Gao, Tian‐Gang; Li, Jianhua; Zhang, Shouzhou; Lu, Aigang

doi:10.1111/jse.12219

Cited by 94 publications

(104 citation statements)

References 98 publications

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“…The phylogeny based on complete chloroplast genomes using BI and ML methods found that the Apiales are sister to the Dipsacales (Fig. 3A), which agrees with recent phylogenies for this subclass based on other markers (Beaulieu, Tank & Donoghue, 2013; Wikström et al, 2015; Chen et al, 2016; The Angiosperm Phylogeny Group, 2016). However, using the MP method with the same data resulted in a phylogeny with the Asterales sister to the Dipsacales (Fig.…”

Section: Discussionsupporting

confidence: 84%

The complete chloroplast genome sequence ofHelwingia himalaica(Helwingiaceae, Aquifoliales) and a chloroplast phylogenomic analysis of the Campanulidae

Yao

Liu

Tan

et al. 2016

PeerJ

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Complete chloroplast genome sequences have been very useful for understanding phylogenetic relationships in angiosperms at the family level and above, but there are currently large gaps in coverage. We report the chloroplast genome for Helwingia himalaica, the first in the distinctive family Helwingiaceae and only the second genus to be sequenced in the order Aquifoliales. We then combine this with 36 published sequences in the large (c. 35,000 species) subclass Campanulidae in order to investigate relationships at the order and family levels. The Helwingia genome consists of 158,362 bp containing a pair of inverted repeat (IR) regions of 25,996 bp separated by a large single-copy (LSC) region and a small single-copy (SSC) region which are 87,810 and 18,560 bp, respectively. There are 142 known genes, including 94 protein-coding genes, eight ribosomal RNA genes, and 40 tRNA genes. The topology of the phylogenetic relationships between Apiales, Asterales, and Dipsacales differed between analyses based on complete genome sequences and on 36 shared protein-coding genes, showing that further studies of campanulid phylogeny are needed.

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Section: Discussionsupporting

confidence: 84%

The complete chloroplast genome sequence ofHelwingia himalaica(Helwingiaceae, Aquifoliales) and a chloroplast phylogenomic analysis of the Campanulidae

Yao

Liu

Tan

et al. 2016

PeerJ

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“…We combined 328 newly generated sequences (Table S1) with sequences retrieved from GenBank (released December, 2012). The 328 newly generated sequences will be submitted to GenBank together with sequences newly generated in Chen et al () as an integrated contribution of the China Phylogeny Consortium (Chen et al, ). Voucher information for these new sequences and the methods of DNA extraction, gene amplification, and sequencing, as well as primer sequences, are reported in Chen et al ().…”

Section: Methodsmentioning

confidence: 99%

Phylogeny of the Rosidae: A dense taxon sampling analysis

Sun

Naeem

et al. 2016

J of Sytematics Evolution

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125

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Rosidae, a clade of approximately 90 000 species of angiosperms, exhibits remarkable morphological diversity and extraordinary heterogeneity in habitats and life forms. Resolving phylogenetic relationships within Rosidae has been difficult, in large part due to nested radiations and the enormous size of the clade. Current estimates of phylogeny contain areas of poor resolution and/or support, and there have been few attempts to synthesize the available data into a comprehensive view of Rosidae phylogeny. We aim to improve understanding of the phylogeny of Rosidae with a dense sampling scheme using both newly generated sequences and data from GenBank of the chloroplast rbcL, atpB, and matK genes and the mitochondrial matR gene. We combined sequences from 9300 species, representing 2775 genera, 138 families, and 17 orders into a supermatrix. Although 59.26% of the cells in the supermatrix have no data, our results generally agree with previous estimates of Rosidae phylogeny and provide greater resolution and support in several areas of the topology. Several noteworthy phylogenetic relationships are recovered, including some novel relationships. Two families (Euphorbiaceae and Salvadoraceae) and 467 genera are recovered as non-monophyletic in our sampling, suggesting the need for future systematic studies of these groups. Our study shows the value of a botanically informed bioinformatics approach and dense taxonomic sampling for resolving rosid relationships. The resulting tree provides a starting point for large-scale analyses of the evolutionary patterns within Rosidae.Key words: phylogeny, rapid radiation, Rosidae, supermatrix.With approximately 90 000 species (estimated from Hinchliff et al., 2015), 135-140 families, and 17 orders (Soltis et al., 2005;APG III, 2009;APG IV, 2016), Rosidae contains at least one quarter of all angiosperm species and approximately 39% of eudicot species diversity (Magall on et al., 1999;Wang et al., 2009). Molecular dating indicates that Rosidae originated in the Early to Late Cretaceous, between 115 and 93 million years ago (Mya), followed by rapid diversification resulting in the Fabidae and Malvidae crown groups approximately 112 to 91 Mya (Albian to Coniacian) and 109 to 83 Mya (Cenomanian to Santonian), respectively (Wang et al., 2009;Bell et al., 2010), with major lineages diversifying in perhaps as little as 4 to 5 million years (Wang et al., 2009;Soltis et al., 2010). The radiations in Rosidae also represent the rapid rise of angiosperm-dominated forests and associated co-diversification events that have profoundly shaped much of the current terrestrial biodiversity (Wang et al., 2009).This extraordinarily diverse clade exhibits enormous heterogeneity in habitats and life forms, including herbs, shrubs, trees, vines, aquatics, succulents, and parasites. Species of Rosidae generally have bitegmic, crassinucellate ovules, distinguishing them from Asteridae, which are generally characterized by unitegmic, tenuinucellate ovules. Moreover, some members possess novel bio...

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“…To evaluate the effect of evolutionary age of local floras on the biogeographical pattern of sexual systems (i.e., the per-grid proportions of the three sexual systems), we extracted the genus age from the phylogenetic tree of Chinese vascular plants constructed by Chen et al (2016) and calculated the average genus age for each grid cell. Moreover, we also evaluated the relationships between the proportions of sexual systems per grid cell and the phylogenetic diversity of local floras.…”

Section: Genus Age and Phylogenetic Diversitymentioning

confidence: 99%

Drivers of large‐scale geographical variation in sexual systems of woody plants

Wang

Lyu

Shrestha

et al. 2019

Global Ecol Biogeogr

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Aim: Sexual systems strongly influence angiosperm evolution and play important roles in community assembly and species responses to climate change. However, geographical variation in proportions of different sexual systems (dioecy, monoecy and hermaphroditism) in response to changes in climate, life-history traits and evolutionary age remains poorly understood. Here, we map the geographical variation in proportions of different sexual systems and hypothesize that the prevalence of hermaphrodites increases with aridity owing to their advantages in colonizing harsh environments, whereas dioecy is most successful in humid regions with tall-canopy vegetation and old floras. Location: China. Time period: Current. Major taxa studied: Woody angiosperms. Methods: Using data on sexual systems and distributions of 10,449 woody species in China, we estimated the proportions of different sexual systems in local floras (50 km × 50 km grid cells). Spatial linear models, phylogenetic general linear models and structural equation models were used to compare the relative influences of climate, plant height and evolutionary age on geographical variation in proportions of different sexual systems. Results: We found contrasting geographical patterns in the proportions of different sexual systems. The proportions of dioecy and monoecy increased with plant height | 547 WANG et Al.

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Tree of life for the genera of Chinese vascular plants

Cited by 94 publications

References 98 publications

The complete chloroplast genome sequence ofHelwingia himalaica(Helwingiaceae, Aquifoliales) and a chloroplast phylogenomic analysis of the Campanulidae

The complete chloroplast genome sequence ofHelwingia himalaica(Helwingiaceae, Aquifoliales) and a chloroplast phylogenomic analysis of the Campanulidae

Phylogeny of the Rosidae: A dense taxon sampling analysis

Drivers of large‐scale geographical variation in sexual systems of woody plants

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