A Taxonomically-verified and Vouchered Checklist of the Vascular Plants of the Republic of Guinea.

The Checklist of the Vascular Plants of the Republic of Guinea (CVPRG) is a specimen-based, expert-validated knowledge product, which provides a concise synthesis and overview of current knowledge on 3901 vascular plant species documented from Guinea (Conakry), West Africa, including their accepted names and synonyms, as well as their distribution and status within Guinea (indigenous or introduced, endemic or not). The CVPRG is generated automatically from the Guinea Collections Database and the Guinea Names Backbone Database, both developed and maintained at the Royal Botanic Gardens, Kew, in collaboration with the staff of the National Herbarium of Guinea. A total of 3505 indigenous vascular plant species are reported of which 3328 are flowering plants (angiosperms); this represents a 26% increase in known indigenous angiosperms since the last floristic overview. Intended as a reference for scientists documenting the diversity and distribution of the Guinea flora, the CVPRG will also inform those seeking to safeguard the rich plant diversity of Guinea and the societal, ecological and economic benefits accruing from these biological resources.

Four new species and a new record of Orchidinae (Orchidaceae: Orchideae) from China.

Four new species of Orchidaceae from China, Heminium lijiangense, Peristylus fasciculatus, Platanthera milinensis, and Ponerorchis gongshanensis, together with a new country record, Peristylus tenuicallus, are described and illustrated based on morphological and/or phylogenetic analyses. Heminium lijiangense is closely related to H. elisabethae but differs from it by having the dorsal sepal ovate-orbicular and lip mid-lobe distinctly shorter than lateral lobes. P. fasciculatus is close to Peristylus tradescantifolius but is distinguished from it by having several fascicled and straight, root-like tubers (vs. one or two oblongoid tubers), old stems usually persistent, middle lobe of lip narrowly ligulate-lanceolate and half as long as the lateral lobes (vs. middle lobe deltoid, about a third as long as the lateral lobes or less), a raised callus at the base of each lateral lobe (vs. callus absent), spur gradually attenuate toward the apex (vs. spur clavate). Platanthera milinensis is similar to P. stenochila by sharing small green flowers and lip without a spur, but differs in having a creeping rhizome, a corymbose inflorescence, and a broadly ovate and slightly 3-lobed lip. Ponerochis gongshanensis is similar to P. faberi in its small flowers, but differs in having a linear leaf c. 3 mm wide (vs. leaf 5-13 mm wide), in the lip having collar-like raised margins on the sides of the spur entrance, and a mid-lobe which is notched at the apex but not divided into two divergent lobules that are nearly as large as the lateral lobes, as in P. faberi. All the proposed species obtained high support in phylogenetic analysis as new species. The recently described genus Apetalanthe is reduced to synonymy of Ponerorchis and a new combination is made.

Diversification in Qinghai-Tibet Plateau: Orchidinae (Orchidaceae) clades exhibiting pre-adaptations play critical role.

We explore the origins of the extraordinary plant diversity in the Qinghai-Tibetan Plateau (QTP) using Orchidinae (Orchidaceae) as a model. Our results indicate that six major clades in Orchidinae exhibited substantial variation in the temporal and spatial sequence of diversification. Our time-calibrated phylogenetic model suggests that the species-richness of Orchidinae arose through a combination of in situ diversification, colonisation, and local recruitment. There are multiple origins of species-richness of Orchidinae in the QTP, and pre-adaptations in clades from North Temperate and alpine regions were crucial for in situ diversification. The geographic analysis identified 29 dispersals from Asia, Africa and Europe into the QTP and 15 dispersals out. Most endemic species of Orchidinae evolved within the past six million years.

Molecular phylogenetic study of the tribe Tropidieae (Orchidaceae, Epidendroideae) with taxonomic and evolutionary implications.

The orchid tribe Tropidieae comprises three genera, Tropidia, Corymborkis and Kalimantanorchis. There are three fully mycoheterotrophic species within Tropidieae: Tropidia saprophytica, T. connata and Kalimantanorchis nagamasui. A previous phylogenetic study of K. nagamasui, based only on plastid matK data, placed K. nagamasui outside the clade of Tropidia and Corymborkis without support. In this study, we performed phylogenetic analyses using a nuclear ribosomal DNA spacer (ITS1-5.8S-ITS2), a low-copy nuclear coding gene (Xdh) and a mitochondrial intron (nad1b-c intron) to study the phylogenetic relationships within Tropidieae. We included six photosynthetic and all three fully mycoheterotrophic Tropidieae species. The resulting phylogenetic trees placed these fully mycoheterotrophic species inside the Tropidia clade with high support. In our trees, these three species do not form a monophyletic group together, because the photosynthetic T. graminea is nested amongst them. Our results also suggest that the loss of photosynthetic ability occurred at least twice in Tropidia.

Phylogenomics of Orchidaceae based on plastid and mitochondrial genomes.

To advance our knowledge of orchid relationships and timing of their relative divergence, we used 76 protein-coding genes from plastomes (ptCDS) and 38 protein-coding genes from mitochondrial genomes (mtCDS) of 74 orchids representing the five subfamilies and 18 tribes of Orchidaceae, to reconstruct the phylogeny and temporal evolution of the Orchidaceae. In our results, the backbone of orchid tree well supported with both datasets, but there are conflicts between these trees. The phylogenetic positions of two subfamilies (Vanilloideae and Cypripedioideae) are reversed in these two analyses. The phylogenetic positions of several tribes and subtribes, such as Epipogiinae, Gastrodieae, Nerviliinae, and Tropidieae, are well resolved in mtCDS tree. Thaieae have a different position among higher Epidendroideae, instead of sister to the higher Epidendroideae. Interrelationships of several recently radiated tribes within Epidendroideae, including Vandeae, Collabieae, Cymbidieae, Epidendreae, Podochileae, and Vandeae, have good support in the ptCDS tree, but most are not resolved in the mtCDS tree. Conflicts between the two datasets may be attributed to the different substitution rates in these two genomes and heterogeneity of substitution rate of plastome. Molecular dating indicated that the first three subfamilies, Apostasioideae, Cypripedioideae and Vanilloideae, diverged relatively quickly, and then there was a longer period before the last two subfamilies, Orchidoideae and Epidendroideae, began to radiate. Most mycoheterotrophic clades of Orchidaceae evolved in the last 30 million years with the exception of Gastrodieae.

The use and misuse of herbarium specimens in evaluating plant extinction risks.

Herbarium specimens provide verifiable and citable evidence of the occurrence of particular plants at particular points in space and time, and are vital resources for assessing extinction risk in the tropics, where plant diversity and threats to plants are greatest. We reviewed approaches to assessing extinction risk in response to the Convention on Biological Diversity's Global Strategy for Plant Conservation Target 2: an assessment of the conservation status of all known plant species by 2020. We tested five alternative approaches, using herbarium-derived data for trees, shrubs and herbs in five different plant groups from temperate and tropical regions. All species were previously fully assessed for the IUCN Red List. We found significant variation in the accuracy with which different approaches classified species as threatened or not threatened. Accuracy was highest for the machine learning model (90%) but the least data-intensive approach also performed well (82%). Despite concerns about spatial, temporal and taxonomic biases and uncertainties in herbarium data, when specimens represent the best available evidence for particular species, their use as a basis for extinction risk assessment is appropriate, necessary and urgent. Resourcing herbaria to maintain, increase and disseminate their specimen data is essential to guide and focus conservation action.This article is part of the theme issue 'Biological collections for understanding biodiversity in the Anthropocene'.

Phylogenetics of subtribe Orchidinae s.l. (Orchidaceae; Orchidoideae) based on seven markers (plastid matK, psaB, rbcL, trnL-F, trnH-psba, and nuclear nrITS, Xdh): implications for generic delimitation.

BACKGROUND: Subtribe Orchidinae (Orchidaceae, Orchidoideae) are a nearly cosmopolitan taxon of terrestrial orchids, comprising about 1800 species in 47 to 60 genera. Although much progress has been made in recent years of phylogenetics of Orchidinae, considerable problems remain to be addressed. Based on molecular phylogenetics, we attempt to illustrate the phylogenetic relationships and discuss generic delimitation within Orchidinae. Seven DNA markers (five plastid and two nuclear), a broad sampling of Orchidinae (400 species in 52 genera) and three methods of phylogenetic analysis (maximum likelihood, maximum parsimony and Bayesian inference) were used. RESULTS: Orchidinae s.l. are monophyletic. Satyrium is sister to the rest of Orchidinae s.l. Brachycorythis and Schizochilus are successive sister to Asian-European Orchidinae s.s. Sirindhornia and Shizhenia are successive sister to clade formed by Tsaiorchis-Hemipilia-Ponerorchis alliance. Stenoglottis is sister to the Habenaria-Herminium-Peristylus alliance. Habenaria, currently the largest genus in Orchidinae, is polyphyletic and split into two distant clades: one Asian-Australian and the other African-American-Asian. Diplomeris is sister to Herminium s.l. plus Asian-Australian Habenaria. CONCLUSIONS: We propose to recognize five genera in the Ponerorchis alliance: Hemipilia, Ponerorchis s.l., Sirindhornia, Shizhenia and Tsaiorchis. Splitting Habenaria into two genera based on morphological characters and geographical distribution may be the least disruptive approach, and it is reasonable to keep Satyrium in Orchidinae.

A taxonomic revision of Herminium L. (Orchidoideae, Orchidaceae).

Herminium (Orchidaceae, Orchidoideae) is a medium-sized genus widespread in the northern hemisphere, with a clear centre of diversity in the Himalayas. We present a comprehensive taxonomic revision of Herminium based on field observations and morphological studies, for which we examined about 2500 specimens. We recognize 49 species grouped into six formal sections, including one new species, Herminium tibeticum, from Tibet. We provide an identification key to the species, descriptions of the species, notes on ecology and distribution, and complete nomenclature for each species, including typifications. We here designate lectotypes for five species and reduce four taxa to synonymy.

Coelogyne putaoensis (Orchidaceae), a new species from Myanmar.

Coelogyne putaoensis, a new species of section Ocellatae from Putao, Kachin State, Myanmar, is described and illustrated. It is morphologically similar to C. taronensis and C. weixiensis, presumably its nearest relatives. An identification key and colour photographs are provided. A preliminary risk-of-extinction assessment according to the IUCN Red List categories and criteria is given for the new species.

Four new orchid species from the Lengguru fold belt, West Papua, Indonesia.

Bulbophyllum leucoglossum, Dendrobium centrosepalum, Dendrobium taeniocaule, and Taeniophyllum pyriforme are here described as new species, based on herbarium specimens collected from the Lengguru fold-and-thrust belt in the West Papua Bird's neck, Indonesian New Guinea. All four novelties were found growing in submontane forest (elevation > 1000 m a.s.l.) on limestone karst. Information concerning the distribution and habitat for these taxa is provided along with diagnostic features, line drawings, high resolution photographs, and a map of collecting localities. More field studies are required to find additional populations of these new species, in order to better characterize their habitat, ecology and conservation status.

(French) Bulbophyllum leucoglossum, Dendrobium centrosepalum, Dendrobium taeniocaule et Taeniophyllum pyriforme sont décrits et illustrés, sur base de spécimens d'herbier collectés dans la zone de plissement et de chevauchement de Lengguru, dans la moitié occidentale indonésienne de l'île de Nouvelle-Guinée. Ces quatre nouveautés taxonomiques ont toutes été découvertes dans des forêts karstiques submontagnardes (altitude > 1000 m). Les informations concernant la distribution et l'habitat de ces espèces sont fournies avec leurs diagnoses, des dessins, des photographies à haute résolution, ainsi qu'une carte des localités inventoriées. Des études de terrain complémentaires sont nécessaires pour trouver des nouvelles populations pour ces espèces, afin de mieux caractériser leur habitat, leur écologie et leur statut de conservation.

A phylogenetic analysis of molecular and morphological characters of Herminium (Orchidaceae, Orchideae): evolutionary relationships, taxonomy, and patterns of character evolution.

The first comprehensive phylogenetic study of the orchid genus Herminium and its allies is presented, based on seven molecular markers (nuclear internal transcribed spacer, Xdh, chloroplast matK, psaB, psbA-trnH, rbcL and trnL-F) and 37 morphological characters. Phylogenetic analyses indicate that Herminium as currently delimited is paraphyletic and that several genera are deeply nested within it. Based on parsimony analysis of total evidence, the generic circumscription of Herminium is expanded to include Androcorys, Bhutanthera, Frigidorchis and Porolabium. Apomorphic and plesiomorphic character states are identified for various clades recovered in this study. A few species currently wrongly assigned to Peristylus and Platanthera are here included in Herminium. All necessary new combinations are made.

Molecular systematics of subtribe Orchidinae and Asian taxa of Habenariinae (Orchideae, Orchidaceae) based on plastid matK, rbcL and nuclear ITS.

The subtribe Orchidinae, distributed predominantly in Eastern Asia and the Mediterranean, presents some of the most intricate taxonomic problems in the family Orchidaceae with respect to generic delimitation. Based on three DNA markers (plastid matK, rbcL, and nuclear ITS), morphological characters, and a broad sampling of Orchidinae and selected Habenariinae mainly from Asia (a total of 153 accessions of 145 species in 31 genera), generic delimitation and phylogenetic relationships within the subtribe Orchidinae and Habenariinae from Asia were assessed. Orchidinae and Asian Habenariinae are monophyletic, and Orchidinae is divided into distinct superclades. Many genera, such as Amitostigma, Habenaria, Hemipilia, Herminium, Platanthera, Peristylus and Ponerorchis, are not monophyletic. Habenaria is subdivided into two distantly related groups, while Platanthera is subdivided into three even more disparate groups. Many previously undetected phylogenetic relationships, such as clades formed by the Amitostigma-Neottianthe-Ponerorchis complex, Platanthera latilabris group, Ponerorchis chrysea, Sirindhornia, and Tsaiorchis, are well supported by both molecular and morphological evidence. We propose to combine Hemipiliopsis with Hemipilia, Amitostigma and Neottianthe with Ponerorchis, Smithorchis with Platanthera, and Aceratorchis and Neolindleya with Galearis, and to establish a new genus to accommodate Ponerorchis chrysea. Tsaiorchis and Sirindhornia are two distinctive genera supported by both molecular data and morphological characters. A new genus, Hsenhsua, and 41 new combinations are proposed based on these findings.

Phylogenetics of tribe Collabieae (Orchidaceae, Epidendroideae) based on four chloroplast genes with morphological appraisal.

Collabieae (Orchidaceae) is a long neglected tribe with confusing tribal and generic delimitation and little-understood phylogenetic relationships. Using plastid matK, psaB, rbcL, and trnH-psbA DNA sequences and morphological evidence, the phylogenetic relationships within the tribe Collabieae were assessed as a basis for revising their tribal and generic delimitation. Collabieae (including the previously misplaced mycoheterotrophic Risleya) is supported as monophyletic and nested within a superclade that also includes Epidendreae, Podochileae, Cymbidieae and Vandeae. Risleya is nested in Collabiinae and sister to Chrysoglossum, a relationship which, despite their great vegetative differences, is supported by floral characters. Ania is a distinct genus supported by both morphological and molecular evidence, while redefined Tainia includes Nephelaphyllum and Mischobulbum. Calanthe is paraphyletic and consists four clades; the genera Gastrorchis, Phaius and Cephalantheropsis should be subsumed within Calanthe. Calanthe sect. Ghiesbreghtia is nested within sect. Calanthe, to which the disputed Calanthe delavayi belongs as well. Our results indicate that, in Collabieae, habit evolved from being epiphytic to terrestrial.

Molecular systematics of Dendrobium (Orchidaceae, Dendrobieae) from mainland Asia based on plastid and nuclear sequences.

Dendrobium is one of the three largest genera and presents some of the most intricate taxonomic problems in the family Orchidaceae. Based on five DNA markers and a broad sampling of Dendrobium and its relatives from mainland Asia (109 species), our results indicate that mainland Asia Dendrobium is divided into eight clades (with two unplaced species) that form polytomies along the spine of the cladogram. Both Dendrobium and Epigeneium are well supported as monophyletic, whereas sect. Dendrobium, sect. Densiflora, sect. Breviflores, sect. Holochrysa, are paraphyletic/polyphyletic. Many ignored phylogenetic relationships, such as the one of major clades formed by D. jenkinsii and D. lindleyi (two members of sect. Densiflora), the Aphyllum group, the Devonianum group, the Catenatum group, the Crepidatum group, and the Dendrobium moniliforme complex are well supported by both molecular and morphological evidence. Based on our data, we propose to broaden sect. Dendrobium to include sect. Stuposa, sect. Breviflores, and sect. Holochrysa and to establish a new section to accommodate D. jenkinsii and D. lindleyi. Our results indicated that it is preferable to use a broad generic concept of Dendrobium and to pursue an improved infrageneric classification at sectional level, taking into account both morphology and current molecular findings.

Remarkable growth pattern in Chrysoglossum ornatum Blume and observations in related species.

The aim of this study was to characterise the remarkable architectural development of the orchid species Chrysoglossum ornatum Blume. Living specimens were collected in two sites in Laos, a country where this species had not been recorded before. Examination of herbarium material of the three other species of Chrysoglossum has confirmed the regularity of this growth pattern at the genus level. Such a vegetative architecture, unique within the plant kingdom, was first described by Barthélémy (1987) for a South American orchid species, Gongora quinquenervis Ruiz and Pav. The nature of this growth pattern within the genus Chrysoglossum and within this particular species, as well as the occurrence of similar patterns in the Orchidaceae is discussed.

Epiphytism and pollinator specialization: drivers for orchid diversity?

Epiphytes are a characteristic component of tropical rainforests. Out of the 25,000 orchid species currently known to science, more than 70% live in tree canopies. Understanding when and how these orchids diversified is vital to understanding the history of epiphytic biomes. We investigated whether orchids managed to radiate so explosively owing to their predominantly epiphytic habit and/or their specialized pollinator systems by testing these hypotheses from a statistical and phylogenetic standpoint. For the first approach, species numbers of 100 randomly chosen epiphytic and terrestrial genera were compared. Furthermore, the mean number of pollinators per orchid species within the five subfamilies was calculated and correlated with their time of diversification and species richness. In the second approach, molecular epiphytic orchid phylogenies were screened for clades with specific suites of epiphytic adaptations. Epiphytic genera were found to be significantly richer in species than terrestrial genera both for orchids and non-orchids. No evidence was found for a positive association between pollinator specialization and orchid species richness. Repeated associations between a small body size, short life cycle and specialized clinging roots of twig epiphytes in Bulbophyllinae and Oncidiinae were discovered. The development of twig epiphytism in the first group seems repeatedly correlated with speciation bursts.