An-Ming Lu

PHYLOGENETIC RELATIONSHIPS IN FAGALES BASED ON DNA SEQUENCES FROM THREE GENOMES

Nucleotide sequences of six regions from three plant genomes—trnL‐F, matK, rbcL, atpB (plastid), matR (mtDNA), and 18S rDNA (nuclear)—were used to analyze inter‐ and infrafamilial relationships of Fagales. All 31 extant genera representing eight families of the order were sampled. Congruence among data sets was assessed using the partition homogeneity test, and five different combined data sets were analyzed using maximum parsimony and the Bayesian approach. At the familial level, the same phylogenetic relationships were inferred from five different analyses of these data. Nothofagus, followed by Fagaceae, are subsequent sisters to the rest of the order. Fagaceae are then sister to the core “higher” hamamelids, which consist of two main subclades, one being Myricaceae (Rhoipteleaceae (Juglandaceae)) and the other Casuarinaceae (Ticodendraceae (Betulaceae)). The combined data sets provide the best‐supported estimate of evolutionary relationships within Fagales. Our results suggest that the combination of different sequences from several species within the same genus representing a terminal taxon has little influence on phylogenetic accuracy. Inclusion of taxa with some missing data in combined data sets also does not have a major impact on the topology.

Tree of life for the genera of Chinese vascular plants

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.

Discovery of vessels in Tetracentron (Trochodendraceae) and its systematic significance

Through SEM observation, we found that there are vessels as well as tracheids in the secondary wood of Tetracentron sinense Oliv. The vessel elements are as narrow and as long as or slightly shorter than the tracheids and generally have 1 to 3 very long, or sometimes relatively short and oblique end-wall perforation plates; such perforation plates are also present on the lateralwalls. The perforation plates of the vessels include scalariform and reticulate-scalariform types, with various degrees of membrane remnants present in the end walls.

Organogenesis of the inflorescence and flowers in Platycarya strobilacea (Juglandaceae)

The reproductive structures of the monotypic genus Platycarya (Juglandaceae), in particular the nature of the fruit wings, have been interpreted variously. We investigated organogenesis of inflorescence and flowers with scanning electron microscopy (SEM). This is the first SEM study to show the whole developmental process of male, female, and bisexual flowers in a member of the Fagales. In staminate and bisexual flowers, only a subtending bract is present, while bracteole and perianth are absent. Four to 10 stamen primordia of different sizes are arranged as an irregular circle or two semicircles. With further development of the stamens, the receptacle, which is fused to the base of the bract, enlarges, and the whorled arrangement of stamens becomes less and less distinct. In pistillate flowers, the transversely ellipsoidal floral primordium develops a central depression. Two bracteoles are initiated in the lateral position of the floral primordium. Soon, the inconspicuous circular perianth primordium appears around the central depression, and two carpels are initiated bordering the central depression opposite to the bracteoles. The perianth is highly reduced and fused with the ovary wall from the initial stage. Each wing of the fruit of Platycarya strobilacea is formed by a combination of one bracteole and the lateral lobe of the perianth.

Global versus Chinese perspectives on the phylogeny of the N‐fixing clade

There has been increasing interest in integrating a regional tree of life with community assembly rules in the ecological research. This raises questions regarding the impacts of taxon sampling strategies at the regional versus global scales on the topology. To address this concern, we constructed two trees for the nitrogen‐fixing clade: (i) a genus‐level global tree including 1023 genera; and (ii) a regional tree comprising 303 genera, with taxon sampling limited to China. We used the supermatrix approach and performed maximum likelihood analyses on combined matK, rbcL, and trnL‐F plastid sequences. We found that the topology of the global and the regional tree of the N‐fixing clade were generally congruent. However, whereas relationships among the four orders obtained with the global tree agreed with the accepted topology obtained in focused analyses with more genes, the regional topology obtained different relationships, albeit weakly supported. At a finer scale, the phylogenetic position of the family Myricaceae was found to be sensitive to sampling density. We expect that internal support throughout the phylogeny could be improved with denser taxon sampling. The taxon sampling approach (global vs. regional) did not have a major impact on fine‐level branching patterns of the N‐fixing clade. Thus, a well‐resolved phylogeny with relatively dense taxon sampling strategy at the regional scale appears, in this case, to be a good representation of the overall phylogenetic pattern and could be used in ecological research. Otherwise, the regional tree should be adjusted according to the correspondingly reliable global tree.

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