Subtropical evergreen broadleaved forests (EBLFs) inhabit large areas of East Asia. Although paleovegetation reconstructions have revealed that the subtropical EBLFs existed in Southwest China during the Miocene, the historical construction of these forests remains poorly known. Here, we used the tea family (Theaceae), a characteristic component of the subtropical EBLFs, to gain new insights into the assembly of this important biome. Using a robust phylogenetic framework of Theaceae based on plastome and nuclear ribosomal DNA sequence data, the temporal history of the family was reconstructed. Data from other characteristic components of subtropical EBLFs, including Fagaceae, Lauraceae and Magnoliaceae, were also integrated. Most of the essential elements of the subtropical EBLFs appear to have originated around the Oligocene-Miocene (O-M) boundary. However, small woody lineages (e.g. Camellia, Hartia) from Theaceae were dated to the late Miocene. Accelerated net diversification rates within Theaceae were also detected near the O-M transition period and the late Miocene. Our results suggest that two independent intensifications of the East Asian summer monsoon (EASM) around the O-M boundary and the late Miocene may have facilitated the historical assembly of the subtropical EBLFs in East Asia.

Background and Aims Theaceae, with three tribes, nine genera and more than 200 species, are of great economic and ecological importance. Recent phylogenetic analyses based on plastomic data resolved the relationships among the three tribes and the intergeneric relationships within two of those tribes. However, generic-level relationships within the largest tribe, Theeae, were not fully resolved. The role of putative whole genome duplication (WGD) events in the family and possible hybridization events among genera within Theeae also remains to be tested further. Methods Transcriptomes or low-depth whole-genome sequencing of 57 species of Theaceae, as well as additional plastome sequence data were generated. Using a dataset of low-copy nuclear genes, we reconstructed phylogenetic relationships using concatenated, species tree and phylogenetic network approaches. We further conducted molecular dating analyses and inferred possible WGD events by examining the distribution of the number of synonymous substitutions per synonymous site (KS) for paralogs in each species. For plastid protein-coding sequences (CDS), phylogenies were reconstructed for comparison with the results obtained from analysis of the nuclear dataset. Results Based on the 610 low-copy nuclear genes (858,606 bp in length) investigated, Stewartieae was resolved as sister to the other two tribes. Within Theeae, the Apterosperma-Laplacea clade grouped with Pyrenaria, leaving Camellia and Polyspora as sister. The estimated ages within Theaceae were largely consistent with previous studies based mainly on plastome data. Two reticulation events within Camellia and one between the common ancestor of Gordonia and Schima were found. All members of the tea family shared two WGD events, an older At-γ and a recent Ad-β; both events were also shared with the outgroups (Diapensiaceae, Pentaphylacaceae, Styracaceae and Symplocaceae). Conclusions Our analyses using low-copy nuclear genes improved understanding of phylogenetic relationships at the tribal and generic levels previously proposed based on plastome data, but the phylogenetic position of the Apterosperma-Laplacea clade needs more attention. There is no evidence for extensive intergeneric hybridization within Theeae or for a Theaceae-specific WGD event. Land bridges (e.g. the Bering land bridge) during the Late Oligocene may have permitted the intercontinental plant movements that facilitated the putative ancient introgression between the common ancestor of Gordonia and Schima.

The rapid expansion of next-generation sequencing (NGS) has generated a powerful array of approaches to address fundamental questions in biology. Several genome-partitioning strategies to sequence selected subsets of the genome have emerged in the fields of phylogenomics and evolutionary genomics. In this review, we summarize the applications, advantages and limitations of four NGS-based genome-partitioning approaches in plant phylogenomics: genome skimming, transcriptome sequencing (RNA-seq), restriction site associated DNA sequencing (RAD-Seq), and targeted capture (Hyb-seq). Of these four genome-partitioning approaches, targeted capture (especially Hyb-seq) shows the greatest promise for plant phylogenetics over the next few years. This review will aid researchers in their selection of appropriate genome-partitioning approaches to address questions of evolutionary scale, where we anticipate continued development and expansion of whole-genome sequencing strategies in the fields of plant phylogenomics and evolutionary biology research.

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The development of new taxonomical theories and approaches, particularly molecular phylogenetics, has led to the expansion of traditional morphology-based taxonomy into the concept of “integrative taxonomy.” Taxonomic knowledge has assumed greater significance in recent years, particularly because of growing concerns over the looming biodiversity crisis. Since its establishment in 1938, the Kunming Institute of Botany (KIB), which is located in Yunnan province in Southwest China, has focused attention on the taxonomy and conservation of the flora of China. For the forthcoming 80th anniversary of KIB, we review the achievements of researchers at KIB and their associates with respect to the taxonomy of land plants, fungi, and lichen. Major taxonomic advances are summarized for families of Calymperaceae, Cryphaeaceae, Lembophyllaceae, Neckeraceae, Polytrichaceae and Pottiaceae of mosses, Pteridaceae and Polypodiaceae of ferns, Taxaceae and Cycadaceae of gymnosperms, Asteraceae, Begoniaceae, Ericaceae, Euphorbiaceae, Gesneriaceae, Lamiaceae, Orchidaceae, Orobanchaceae, Poaceae, Theaceae and Urticaceae of angiosperms, Agaricaceae, Amanitaceae, Boletaceae, Cantharellaceae, Physalacriaceae Russulaceae, Suillaceae and Tuberaceae of fungi, and Ophioparmaceae and Parmeliaceae of lichens. Regarding the future development of taxonomy at KIB, we recommend that taxonomists continue to explore the biodiversity of China, integrate new theories and technologies with traditional taxonomic approaches, and engage in creative monographic work, with support from institutions, funding agencies, and the public.

Plastid genome and nuclear ribosomal DNA (nrDNA) arrays, proposed recently as “super‐barcodes,” might provide additional discriminatory power and overcome the limitations of traditional barcoding loci, yet super‐barcodes need to be tested for their effectiveness in more plant groups. Morphological homoplasy among Schima species makes the genus a model for testing the efficacy of super‐barcodes. In this study, we generated multiple data sets comprising standard DNA barcodes (matK, rbcL, trnH‐psbA, nrITS) and super‐barcodes (plastid genome, nrDNA arrays) across 58 individuals from 12 out of 13 species of Schima from China. No samples were correctly assigned to species using standard DNA barcodes and nrDNA arrays, while only 27.27% of species with multiple accessions were distinguished using the plastid genome and its partitioned data sets—the lowest estimated rate of super‐barcode success in the literature so far. For Schima and other taxa with similarly recently divergence and low levels of genetic variation, incomplete lineage sorting, hybridization or taxonomic oversplitting are all possible causes of the failure. Taken together, our study suggests that by no means are super‐barcodes immune to the challenges imposed by evolutionary complexity. We therefore call for developing multilocus nuclear markers for species discrimination in plant groups.

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