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...

We reconstructed a phylogenetic tree of Chinese vascular plants (Tracheophyta) using sequences of the chloroplast genes atpB, matK, ndhF, and rbcL and mitochondrial matR. We produced a matrix comprising 6098 species and including 13 695 DNA sequences, of which 1803 were newly generated. Our taxonomic sampling spanned 3114 genera representing 323 families of Chinese vascular plants, covering more than 93% of all genera known from China. The comprehensive large phylogeny supports most relationships among and within families recognized by recent molecular phylogenetic studies for lycophytes, ferns (monilophytes), gymnosperms, and angiosperms. For angiosperms, most families in Angiosperm Phylogeny Group IV are supported as monophyletic, except for a paraphyletic Dipterocarpaceae and Santalaceae. The infrafamilial relationships of several large families and monophyly of some large genera are well supported by our dense taxonomic sampling. Our results showed that two species of Eberhardtia are sister to a clade formed by all other taxa of Sapotaceae, except Sarcosperma. We have made our phylogeny of Chinese vascular plants publically available for the creation of subtrees via SoTree (http://www.darwintree.cn/flora/index.shtml), an automated phylogeny assembly tool for ecologists.

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Capparaceae (Brassicales) as traditionally circumscribed is heterogeneous, and several genera have been segregated from it based on molecular and/or morphological data. However, Borthwickia and Stixis, two Southeast Asian endemic genera of Capparaceae with controversial positions, have not previously been evaluated in a molecular phylogenetic study. Here, we used four plastid DNA regions (matK, ndhF, rbcL, trnL–trnF) and pollen data to determine their phylogenetic relationships within core Brassicales. Our results showed that neither Borthwickia nor Stixis is a member of Capparaceae. The two genera, together with Forchhammeria, Gyrostemonaceae, Resedaceae, and Tirania, formed a clade with strong support. Stixis is closely related to Tirania, a relationship that is also supported by morphological characters, such as six sepals and three–or four–locular ovaries. Most interestingly, Borthwickia was resolved as sister to the Forchhammeria–Resedaceae–Stixis–Tirania clade with moderate to strong support. However, Borthwickia differs markedly from its sister group in having opposite leaves, one indistinct stigma, more than four carpels and locules, a linear ovary with ridges, and pollen grains with perforate exine sculpturing. Thus, we describe a new family, Borthwickiaceae, for the genus.