Phylogeny of the Diploid Species of Rubus (Rosaceae).

Rubus L. (Rosaceae, Rosoideae) contains around 700 species distributed on all continents except Antarctica, with the highest species diversity in temperate to subtropical regions of the northern hemisphere. The taxonomy of Rubus is challenging due to the frequency of polyploidy, hybridization and apomixis. Previous studies mostly sampled sparsely and used limited DNA sequence data. The evolutionary relationships between infrageneric taxa, therefore, remain to be further clarified. In the present study, genotyping by sequencing (GBS) reduced-representation genome sequencing data from 186 accessions representing 65 species, 1 subspecies and 17 varieties of Rubus, with emphasis on diploid species, were used to infer a phylogeny using maximum likelihood and maximum parsimony methods. The major results were as follows: (1) we confirmed or reconfirmed the polyphyly or paraphyly of some traditionally circumscribed subgenera, sections and subsections; (2) 19 well-supported clades, which differed from one another on molecular, morphological and geographical grounds, were identified for the species sampled; (3) characteristics such as plants with dense bristles or not, leaves leathery or papyraceous, number of carpels, instead of inflorescences paniculate or not, aggregate fruits and leaves abaxially tomentose or not, may be of some use in classifying taxa whose drupelets are united into a thimble-shaped aggregate fruit that falls in its entirety from the dry receptacle; and (4) a preliminary classification scheme of diploid species of Rubus is proposed based on our results combined with those from previous phylogenetic analyses.

Phylogeny and Taxonomic Synopsis of the Genus Bougainvillea (Nyctaginaceae).

Bougainvillea Comm. ex Juss. is one of the renowned genera in the Nyctaginaceae, but despite its recognized horticultural value, the taxonomy and phylogeny of the genus is not well-studied. Phylogenetic reconstructions based on plastid genomes showed that B. pachyphylla and B. peruviana are basal taxa, while B. spinosa is sister to two distinct clades: the predominantly cultivated Bougainvillea clade (B. spectabilis, B. glabra, B. arborea, B. cultivar, B. praecox) and the clade containing wild species of Bougainvillea (B. berberidifolia, B. campanulata, B. infesta, B. modesta, B. luteoalba, B. stipitata, and B. stipitata var. grisebachiana). Early divergence of B. peruviana, B. pachyphylla and B. spinosa is highly supported, thus the previously proposed division of Bougainvillea into two subgenera (Bougainvillea and Tricycla) was not reflected in this study. Morphological analysis also revealed that leaf arrangement, size, and indumentum together with the perianth tube and anthocarp shape and indumentum are important characteristics in differentiating the species of Bougainvillea. In the present study, 11 species and one variety are recognized in Bougainvillea. Six names are newly reduced to synonymy, and lectotypes are designated for 27 names. In addition, a revised identification key and illustrations of the distinguishing parts are also provided in the paper.

Evolution of coastal forests based on a full set of mangrove genomes.

Genomic studies are now poised to explore whole communities of species. The ~70 species of woody plants that anchor the coastal ecosystems of the tropics, collectively referred to as mangroves, are particularly suited to this exploration. In this study, we de novo sequenced the whole genomes of 32 mangroves, which we combined with other sequences of 30 additional species, comprising almost all mangroves globally. These community-wide genomic data will be valuable for ecology, evolution and biodiversity research. While the data revealed 27 independent origins of mangroves, the total phylogeny shows only modest increases in species number, even in coastal areas of active speciation, suggesting that mangrove extinction is common. A possible explanation for common extinction is the frequent sea-level rises and falls (SLRs and SLFs) documented in the geological record. Indeed, near-extinctions of species with extremely small population size (N) often happened during periods of rapid SLR, as revealed by the genome-wide heterozygosity of almost all mangroves. Reduction in N has possibly been further compounded by population fragmentation and the subsequent accumulation of deleterious mutations, thus pushing mangroves even closer to extinction. Crucially, the impact of the next SLR will be exacerbated by human encroachment into these mangrove habitats, potentially altering the ecosystems of tropical coasts irreversibly.

Paraphlomisjinggangshanensis (Lamiaceae), a new species from Jiangxi, China.

Paraphlomisjinggangshanensis (Lamiaceae), a new species from Jiangxi Province, China, is described and illustrated. The new species is morphologically similar to P.intermedia, but can be easily distinguished from the latter by its cordate leaf base (vs. cuneate, decurrent), stem and calyx tube with glandular hairs (vs. short pubescent), and glabrous anthers (vs. ciliate anthers). A phylogenetic analysis, based on ITS regions, suggests that P.jinggangshanensis represents a separate branch in Paraphlomis and is closely related to Clade II. It is currently known only from Jinggangshan National Natural Reserve. Because of its limited distribution and small population size, the species was assessed as Near Threatened (NT) according to the IUCN Red List Categories and Criteria.

Nomenclature and typification of Cathayaargyrophylla (Pinaceae).

In 1958, Chun and Kuang described Cathaya Chun & Kuang as a new genus of Pinaceae. They included one fossil species, C.loehri (Engelh. & Kink.) Chun & Kuang and two extant species, C.argyrophylla Chun & Kuang and C.nanchuanensis Chun & Kuang. Under Art. 40.1 of the Shenzhen Code, they did not validly publish Cathaya because they did not designate a type species for the generic name. Four years later (Chun and Kuang 1962), they again published on Cathaya (in Chinese) where they cited the 1958 publication and included one species C.argyrophylla (with C.nanchuanensis in synonymy) under Cathaya. According to Art. 40.3, they validated both the generic name Cathaya and C.argyrophylla in 1962. Further examination of the type collection and botanical history of the discovery of C.argyrophylla revealed that the type collection Guang-Fu-Lin-Qu Exped. 00198 consists of 11 duplicates in the South China Institute of Botany (IBSC) and 9 duplicates in other herbaria (GAC, IBK, PE, SZ) and that the intended type specimen (IBSC0000004) consists of two gatherings: the bark, reproductive shoot and seed cones collected in 1955, whereas pollen-bearing cones were collected in 1956. We thus lectotypify the name C.argyrophylla with the specimen Guang-Fu-Lin-Qu Exped. 00198 (IBSC0000004 excl. pollen-bearing cones).

Grade of Membership models reveal geographical and environmental correlates of floristic structure in a temperate biodiversity hotspot.

Identifying the contours and correlates of species turnover is central to understanding the nature of biogeographical regions. The Hengduan Mountains region of south-central China (HMR) is well known for its high diversity of plants, but its boundaries and internal floristic structure are poorly understood, especially in relation to geographical and environmental factors. With data on occurrences and elevational ranges of seed plants across the HMR and adjacent areas of the greater Qinghai-Tibet Plateau, we identified motifs (distinct species assemblages) by Grade of Membership models, and characterized relative contributions of geography, elevation, and climate to their spatial patterns. Motifs segregate primarily by latitude, elevation, and correlated environmental variables, most sharply across the tropical-temperate divide. Secondarily, they segregate by longitude and geographical features, and reveal a novel divide across the Jinsha River. A core set of motifs corresponds to previous delineations of the HMR. The HMR biodiversity hotspot is more a mosaic of floristic elements than a cohesive entity. Grade of Membership models effectively reveal the geographical contours of biotic structure, and are a valuable new tool for biogeographical analysis.

Twenty years of Chinese vascular plant novelties, 2000 through 2019.

From 2000 to 2019, 11,895 new names or new additions to the Chinese vascular flora were proposed by 4226 individuals (4086 articles and 140 books), as documented in the Chinese Plant Names Index (CPNI). During those 20 years, 4407 new taxa of vascular plants were described from China, including 7 new families, 132 new genera, 3543 new species, 68 new subspecies, 497 new varieties and 160 new forms. Additionally, 3562 new combinations and names at new rank and 306 new replacement names were also proposed. Among these various new names were 150 invalid names and 108 illegitimate names, including some that have not been resolved. Six hundred and forty three vascular plants were reported as new to China, while 2349 names were reduced to synonyms of 1406 taxa. The data show that the Chinese flora increased in size at the rate of about 200 taxa annually during those years. Despite the increased attention given to biodiversity in recent years, the evidence indicates that a large number of species in China have yet to be discovered. Further basic investigation of the Chinese flora is needed. Additionally, in the past two decades only 8.5% of the newly published species have been based on molecular evidence, but in the past five years such data have increased significantly, reaching about 20%. Molecular data will undoubtedly become increasingly significant in the discovery of new species in the coming years. Yunnan, Guangxi, Sichuan, Xizang and Taiwan were important sources of new discoveries, with more than 3300 new taxa and records from these five provinces. By area, Taiwan and Hainan, two islands in southern China, have the highest density of newly discovered species. Regional plant surveys are still needed, especially in areas in the southwest and on the southern islands.

Convergent adaptation of the genomes of woody plants at the land-sea interface.

Sequencing multiple species that share the same ecological niche may be a new frontier for genomic studies. While such studies should shed light on molecular convergence, genomic-level analyses have been unsuccessful, due mainly to the absence of empirical controls. Woody plant species that colonized the global tropical coasts, collectively referred to as mangroves, are ideal for convergence studies. Here, we sequenced the genomes/transcriptomes of 16 species belonging in three major mangrove clades. To detect convergence in a large phylogeny, a CCS+ model is implemented, extending the more limited CCS method (convergence at conservative sites). Using the empirical control for reference, the CCS+ model reduces the noises drastically, thus permitting the identification of 73 convergent genes with P true (probability of true convergence) > 0.9. Products of the convergent genes tend to be on the plasma membrane associated with salinity tolerance. Importantly, convergence is more often manifested at a higher level than at amino-acid (AA) sites. Relative to >50 plant species, mangroves strongly prefer 4 AAs and avoid 5 others across the genome. AA substitutions between mangrove species strongly reflect these tendencies. In conclusion, the selection of taxa, the number of species and, in particular, the empirical control are all crucial for detecting genome-wide convergence. We believe this large study of mangroves is the first successful attempt at detecting genome-wide site convergence.

The origin, diversification and adaptation of a major mangrove clade (Rhizophoreae) revealed by whole-genome sequencing.

Mangroves invade some very marginal habitats for woody plants-at the interface between land and sea. Since mangroves anchor tropical coastal communities globally, their origin, diversification and adaptation are of scientific significance, particularly at a time of global climate change. In this study, a combination of single-molecule long reads and the more conventional short reads are generated from Rhizophora apiculata for the de novo assembly of its genome to a near chromosome level. The longest scaffold, N50 and N90 for the R. apiculata genome, are 13.3 Mb, 5.4 Mb and 1.0 Mb, respectively. Short reads for the genomes and transcriptomes of eight related species are also generated. We find that the ancestor of Rhizophoreae experienced a whole-genome duplication ~70 Myrs ago, which is followed rather quickly by colonization and species diversification. Mangroves exhibit pan-exome modifications of amino acid (AA) usage as well as unusual AA substitutions among closely related species. The usage and substitution of AAs, unique among plants surveyed, is correlated with the rapid evolution of proteins in mangroves. A small subset of these substitutions is associated with mangroves' highly specialized traits (vivipary and red bark) thought to be adaptive in the intertidal habitats. Despite the many adaptive features, mangroves are among the least genetically diverse plants, likely the result of continual habitat turnovers caused by repeated rises and falls of sea level in the geologically recent past. Mangrove genomes thus inform about their past evolutionary success as well as portend a possibly difficult future.

Molecular evidence for natural intergeneric hybridization between Liquidambar and Altingia.

Since its establishment, a hybrid origin for Semiliquidambar has been proposed based on morphological intermediacy and sympatric distribution with Altingia and Liquidambar. This hypothesis, however, has lacked convincing molecular evidence. In this study, two nuclear genes, pin2 and cab4, and a chloroplast gene, matK, from Semiliquidambar cathayensis and its putative parental species Liquidambar and Altingia in Jianfengling, Hainan, and Heishiding and Nanling, Guangdong, China, were sequenced to test this hypothesis. Our results showed that L. formosana and L. acalycina were closely related and constituted an inseparable clade in the phylogenetic trees of both pin2 and cab4 genes. Phylogenetic analyses revealed two types of sequences for S. cathayensis, which were clustered with its putative parents, L. formosana-L. acalycina and A. obovata in Jianfengling, and with L. formosana-L. acalycina and A. chinensis in Heishiding and Nanling. The partial chloroplast matK gene sequences showed four nucleotide substitutions between L. formosana and A. obovata in Jianfengling; the sequences of the two individuals of S. cathayensis were identical with those of A. obovata. No diagnostic chloroplast markers including matK and three other chloroplast genes were found to distinguish L. formosana and A. chinensis in Heishiding and Nanling. Molecular data clearly demonstrated that S. cathayensis is of intergeneric hybrid origin between L. formosana-L. acalycina and A. obovata or A. chinensis and that A. obovata functions as the maternal parent in the hybridization event in Jianfengling, Hainan.

Adaptive evolution of rbcL in Conocephalum (Hepaticae, bryophytes).

An excess of nonsynonymous substitutions over synonymous ones has been regarded as an important indicator of adaptive evolution or positive selection at the molecular level. We now report such a case for rbcL sequences among cryptic species in Conocephalum (Hepaticae, Bryophytes). This finding can be regarded as evidence of adaptive evolution in several cryptic species (especially in F and JN types) within the genus. Bryophytes are small land plants with simple morphology. We can therefore expect the existence of several biologically distinct units or cryptic species within each morphological species. In our previous study, we found three rbcL types in Asian Conocephalum japonicum (Thunb.) Grolle and also found evidence strongly suggesting that the three types are reproductively isolated cryptic species. Additionally, we examined rbcL sequence variation in six cryptic species of C. conicum (L.) Dumort. previously recognized by allozyme analyses. As a result, we were able to discriminate the six cryptic species based only on their rbcL sequences. We were able to show that rbcL sequence variation is also useful in finding cryptic species of C. conicum.

A CLADISTIC ANALYSIS OF CIRCAEA (ONAGRACEAE).

Abstract- Circaea (Onagraceae), a genus of seven species from the northern hemisphere, forms a monophylctic group defined by the following synapomorphies: two stamens (opposite the sepals), fruits indehiscent capsules, hooked hairs on the fruits, and perianth parts reduced to two. A cladistic analysis of the genus was performed using 22 characters from morphology, anatomy and palynology. The seven species and seven additional subspecies were considered the terminal taxa. Polarity of the characters is based on the outgroup comparison method. Eighteen equally parsimonious cladograms were produced, each with 32 steps and a consistency index of 0.75. A successive weighting procedure was applied, resulting in six cladograms with a consistency index of 0.95. All 24 cladograms share the following seven monophylctic groups: (1) all species except C. cordala and C. glabrescens (stipules deciduous); (2) the group of C. mollis, the three subspecies of C. lutetiana and C. erubescens (exsertcd nectary); (3) C. repens and all six subspecies of C. alpina (single-seeded fruits, stolons terminated by tubers, and viscin threads reduced or absent); (4) the six subspecies of C. alpina (unilocular ovaries with no trace of a second loculc and tardily opening perianth); (5) C. alpina subspecies alpina, micrantha, pacifica, and imaicola (flowers opening on ascending to erect pedicels); (6) C. alpina subspecies alpina, micrantha, and pacifica (translucent leaves); (7) C. alpina subspecies alpina and murantha (glabrous stems). Results of the cladistic analysis support most of the current systematic classification of the genus, except for the relationships among the three subspecies of C. lutetiana.