The Tree of Life: China project

The knowledge of evolutionary relationships is fundamental to all disciplines of biology, yielding novel and profound insights across plant sciences, from comparative genomics, molecular evolution, and plant development, to the study of adaptation, speciation, community assembly, and ecosystem functioning (Forest et al., 2007; Donoghue, 2008; Gehrke & Linder, 2011). Phylogeny (the Tree of Life, TOL) has become the foundation of evolutionary biology. It is accurate to say “Evolutionary biology makes much more sense in the light of phylogeny”, as a corollary to Dobzhansky’s (1973) famous statement “Nothing in biologymakes sense except in the light of evolution.” China harbors 31 362 species, 3328 genera, and 312 families of vascular plants (Wu et al., 1994–2013) and has the richest flora of the Northern Hemisphere (Wu et al., 2003). A well-resolved phylogeny of vascular plants of China has many potential uses in various areas of biology—ecology, conservation genetics, and agriculture—as well as stimulates new research at the interface of evolutionary ecology, phylogenetics, and biogeography, thus clarifying processes that shaped patterns of distribution and diversity of such a rich flora of the Northern Hemisphere (Qian & Ricklefs, 2000; Wang et al., 2009; L opezPujol et al., 2011). Understanding the phylogeny of vascular plants andphylogenetic diversity at this scalewill help elucidate fundamental processes underlying plant/animal associations and the assembly of entire ecosystems, and help manage the impact of global challenges to biodiversity and the maintenance of natural resources to humankind. In June 2007, an international symposium on the TOL was held in Beijing, China. Journal of Systematics and Evolution (JSE) organized and published the symposium special issue: Patterns of Evolution and the Tree of Life (JSE vol. 46, no. 3, 2008). Since then, the Chinese botanical community has continued to make contributions to TOL studies. The present special issue aims to present recent progress in reconstructing TOL of the vascular plant genera in China, including the assembly of DNA materials, establishment of co-operation, data generation, tree reconstruction, on how to use the China TOL as a framework to further examine the origin and evolution of major clades in vascular plants, and the floristic relationship between China and other regions of the world as all vascular plants share a common ancestor (Wen et al., 2010; Xiang et al., 2015). This special issue consists of 11 papers all related to the “giant” phylogeny of the Chinese vascular plants. Chen et al. (2016) sampled 6098 species representing 3114 genera of vascular plants and five genera of bryophytes as out-groups to reconstruct the TOL of the Chinese vascular plants at the generic level. To facilitate further application of such a largescale phylogeny to other biology fields, the SoTree software was introduced to enable the efficient generation of the phylogenetic trees by providing sub-datasets with interested species lists for studies concerning the origin, ecology, and biogeography of the local flora in China. Using DNA sequences of three plastid genes, Liu (2016) presents a phylogenetic analysis of 259 genera of pteridophytes, which provided evidence documenting the impact of Ren-Chang Ching’s integrative classification of pteridophytes. Ten out of 11 orders in Ching’s system are consistent with the modern DNA-based phylogeny, whereas four new orders were introduced to avoid paraphyletic orders in the leptosporangiate ferns. Wang et al. (2016) integrated Leefructus mirus—one of the earliest eudicot macrofossils—in an exhaustive morphological dataset of extant Ranunculales to improve our understanding of the diversification of this lineage in eudicots. As a result of the integration of this fossil, the authors recovered that basal eudicots experienced an accelerated diversification during the onset of the angiosperm radiation in the Early Cretaceous. Du et al. (2016) sampled 139 genera (in 43 families) representing most families of the aquatic plants worldwide. Their results suggested that aquatic habitats were colonized at least three times during the early radiation of angiosperms, namely by Nymphaeales, Ceratophyllales, and the monocots. Three of the papers address the phylogeny of angiosperms at the ordinal level or above. Special attention is given to the rosids (Rosidae) because the clade contributes not only onequarter of the extant diversity of angiosperms, including considerable economically important crops and most dominant forest trees, but is also recognized as amajor contributor to the angiosperm diversity of China. Using a supermatrix approach, Sun et al. (2016) resolved the phylogeny of Rosidae world-wide with a dense sampling scheme (four genes, a total of 9300 taxa representing 2775 genera, 138 families, and 17 orders). They discovered several novel relationships and recognized two families and 467 genera as non-monophyletic. As part of the rosids, the N-fixing clade is one of the largest clades of the angiosperms, containing over 1300 genera, approximately 30 000 species, which are important components of extant temperate and tropical forest. Li et al. (2016a) constructed the most comprehensive and robust global tree of the N-fixing clade to date with a supermatrix to compare with the local tree from the TOL of the Chinese vascular plants. Topologies of the global tree and the local tree are generally congruent and most of the internal supports are greatly improved with dense sampling. Yang et al. (2016) used eight chloroplast markers and one mitochondrial gene, and assembled a matrix of 11 951 characters of 649 genera, covering ca. 54% of the genera of Gentianales, to reconstruct the phylogeny of Gentianales. Topologies of the global Gentianales tree and the Chinese Gentianales tree are largely JSE Journal of Systematics and Evolution