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Clear species boundaries are crucial for plans and actions on biodiversity conservation. However, morphological similarities among allied species can result in taxonomic difficulties, thus impeding conservation efforts. In China, Cinnamomum japonicumSiebold is a well‐known endangered plant, yet suffers from longstanding taxonomic issues. Here, we explicitly evaluate whether C. japonicum, C. chenii, and C. chekiangense are the same phylogenetic species on the basis of a multi‐individual sampling strategy. We identified three sets of low‐copy orthologous genes from 19 Lauraceae taxa for phylogenetic inferences. Both the concatenation and coalescent‐based phylogenies supported that C. chenii individuals were embedded in the C. japonicum clade, indicating these two taxa are conspecific. Meanwhile, C. chekiangense accessions formed a monophyly which was not sister to C. japonicum. This result, together with the morphological differences that the leaves of C. japonicum are glabrous with a faveolate pattern of venation while those of C. chekiangense have trichomes and inevident lateral veins, led us to consider both as two distinct species. Based on 17 728 neutral single nucleotide polymorphisms (SNPs), the ADMIXTURE analysis suggested that the Chinese C. japonicum populations in Zhoushan Archipelago (=C. chenii) were genetically differentiated from the Japanese and Korean ones. Furthermore, ecological niche modeling predicted that the present distribution area of Chinese C. japonicum is likely to be unsuitable under global warming scenarios. Together with its limited distribution and genetic uniqueness, we recommend that Chinese C. japonicum deserves conservation priorities. [ABSTRACT FROM AUTHOR]

Stewartia sichuanensis is a rare plant species of Theaceae and is endemic to China. Its distribution area is highly restricted, and genomic information is extremely limited. The present study reports the first complete chloroplast of S. sichuanensis. The chloroplast genome length was 158,903 bp, with a GC content of 37.3%. The chloroplast genome was comprised of an 87,736 bp long large single copy (LSC), an 18,435 bp long small single copy (SSC), and two copies of inverted repeat (IR) regions of 26,366 bp. It contained 129 genes, including 85 encoding, 36 transfer RNA, and eight ribosomal RNA genes. The phylogenetic analysis suggested that S. sichuanensis was closely related to S. laotica and S. pteropetiolata. [ABSTRACT FROM AUTHOR]

Accurate species delimitation is the key to precise estimation of species diversity and is fundamental to most branches of biology. Unclear species boundaries within species complexes could lead to the underestimation of species diversity. However, species delimitation of species complexes remains challenging due to the continuum of phenotypic variations. To robustly examine species boundaries within a species complex, integrative approaches in phylogeny, ecology, and morphology were applied to the Stewartia sinensis complex (Theaceae) endemic to China. Multispecies coalescent‐based species delimitation using 572 nuclear ortholog sequences (anchored enrichment) supported reciprocal phylogenetic monophyly of the northern lineage (NL) and southern lineage (SL), which were not sister clades. Niche equivalency and similarity tests demonstrated significant climatic niche differentiation between NL and SL with observed Warren et al.'s I = 0.0073 and Schoener's D = 0.0021. Species distribution modeling also separated their potential distribution. Morphometric analyses suggested significant interlineage differentiation of multiple traits including the ratio of length and width, leaf width, and pedicel length, although overall similarity did not differ. Based on the integrative species concept, two distinct species were proposed with legitimate names of Stewartia gemmata for SL and S. sinensis for NL. Our empirical study of the S. sinensis complex highlights the importance of applying multiple species criteria, in particular the underappreciated niche differentiation, to species delimitation in species complexes pervasive in plants. [ABSTRACT FROM AUTHOR]

This account presents information on all aspects of the biology of Ginkgo biloba L. (Ginkgo, Maidenhair tree) that are relevant to understanding its ecological characteristics. The main topics are presented within the standard framework of the International Biological Flora: distribution, habitat, communities, responses to biotic factors, responses to environment, structure and physiology, phenology, reproductive and seed characters, herbivores and disease, history, conservation and global heterogeneity.Globally, Ginkgo survives a wide range of mean annual temperature (−3.3 to 23.3°C) and annual precipitation (34–3925 mm) conditions, according to a meta‐analysis. It prefers a warm, humid, open‐canopy and a well‐drained environment. The species shows strong tolerance to drought, freezing, fire, air pollution, heavy metals and low‐level salt, whereas it is intolerant to long‐time shade and waterlogging. Six Ginkgo trees even survived the atom bomb in Hiroshima, Japan, during World War II.Ginkgo is susceptible to few diseases. Those occurring in nursery seedlings and juvenile trees involve stem rot and leaf blight. The former is caused by Macrophomina phaseoli, which could lead to a mortality rate of 5%–12% (up to 31.8%) for seedlings. This disease can be mitigated by a 4‐h shading treatment and applying organic fertilisers. The pathogens inducing leaf blight include Alternaria alternata, Colletotrichum gloeosporioides and Pestalotia ginkgo, which may infect 100% juvenile trees in some regions. The application of 45% carbendazim or 50% Tuzet can effectively prevent leaf blight.Ginkgo biloba is one of the world's most distinctive trees with an important position in plant evolution and human society. It is a tall deciduous dioecious tree native to China. Refugial populations were identified in three glacial refugia located in eastern, southern and south‐western China, respectively, with a patchy distribution pattern and a small population size. It typically grows along flood‐disturbed streamsides in warm‐temperate deciduous (and evergreen mixed) broadleaved forests. Ginkgo may have been introduced repeatedly out of China since the sixth century. It has been planted as a landscape tree world‐wide, except in Antarctica. Ginkgo is also of great value for edible nuts, herbal medicine, religion and art. It is a natural and cultural symbol of China. [ABSTRACT FROM AUTHOR]

• Cyto-nuclear conflicts occurred in Stewartia s. l. phylogeny. • Hartia was nested in Stewartia s.s. with the basal S. malacodendron in America. • Introgression was prevailing in shallow phylogeny with a consistent backbone. • Ancient co-distribution and dispersal contributed to introgression in Asian. Phylogenetic analyses using diverse datasets can yield conflicting inference of evolutionary history. Phylogenetic conflicts observed in both animal and plant systems have often been explained by two competing (but not mutually exclusive) hypotheses, i.e., hybridization vs. incomplete lineage sorting (ILS). The likelihood of either process contributing to phylogenetic conflict in a given group is context-dependent, involving attributes of life history, distribution, and phylogeny, among others. Here we explore phylogenetic conflict in Stewartia s.l. , a genus with ca. 20 species of trees and shrubs from the tea family (Theaceae) disjunctly distributed between eastern Asia (EAS) and eastern North America (ENA). We use both restriction-site associated DNA sequencing (RAD-seq) and complete plastome sequence data to reconstruct the phylogeny of the group using concatenation and coalescence approaches. Our results indicate strong conflicts between the topologies reconstructed using nuclear and plastid data. Four-taxon D -statistic (ABBA-BABA) tests detected prevailing signals of introgression. Bayesian Analysis of Macro-evolutionary Mixtures (BAMM) inferred that species diversification occurred in the middle to late Miocene. Ancestral range reconstructions indicated co-distribution of ancestral species (represented by internal nodes) for both the Hartia clade (in southern China) and the EAS Stewartia s.s. clade (Japan Archipelago and the Yangtze Valley of China). The latter clade experienced multiple events of dispersal and vicariance during its diversification history. Ancient introgressive hybridization following species diversification in the mid- to late-Miocene likely caused diverging histories in the nuclear and plastid genomes, leading to phylogenetic conflict in Stewartia s.l. Our study indicates that species diversification driven by both the intensification of the East Asian summer monsoon since the late Miocene and reduced risks of extinction due to frequent dispersal possibly via East China Sea Land Bridge impacted the anomalous species richness between EAS and ENA. Our study highlights the importance of using data from different genomes while reconstructing deep and shallow phylogenies of organisms. [ABSTRACT FROM AUTHOR]

As Charles Darwin anticipated, living fossils provide excellent opportunities to study evolutionary questions related to extinction, competition, and adaptation. Ginkgo (Ginkgo biloba L.) is one of the oldest living plants and a fascinating example of how people have saved a species from extinction and assisted its resurgence. By resequencing 545 genomes of ginkgo trees sampled from 51 populations across the world, we identify three refugia in China and detect multiple cycles of population expansion and reduction along with glacial admixture between relict populations in the southwestern and southern refugia. We demonstrate multiple anthropogenic introductions of ginkgo from eastern China into different continents. Further analyses reveal bioclimatic variables that have affected the geographic distribution of ginkgo and the role of natural selection in ginkgo's adaptation and resilience. These investigations provide insights into the evolutionary history of ginkgo trees and valuable genomic resources for further addressing various questions involving living fossil species.