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The genus Pytinicarpa G.L.Nesom is taxonomically revised in New Caledonia with four species recognised. The circumscription of one previously published species, P. sarasinii (Däniker) G.L.Nesom, is discussed and updated, and P. neocaledonica (Guillaumin) G.L.Nesom is placed in its synonymy. The name P. comptonii Gâteblé, Lannuzel & M.Pignal, nom. nov. is proposed to accommodate the former Lagenophora neocaledonica S.Moore in Pytinicarpa, and its lectotype is designated. Two new narrowly endemic species are also described. The first is from the top of Mount Kaala massif with the name P. kaalaensis Lannuzel, Gâteblé & M.Pignal, sp. nov. The second, P. tonitrui Lannuzel, Gateblé & M.Pignal, sp. nov. is from the Babouillat peninsula, and is supposedly extinct, as extensive field research did not allow to find it. The four species are fully described, illustrated, and keyed. The distribution, ecological affinities, and threats for the four species are discussed to support the assessments of conservation status for two of them as Endangered (EN), one as Critically Endangered (CR) and one as Extinct (EX), following the IUCN Red List guidelines and criteria.

Pignal, Marc, Laudereau, Christian, Laudereau, Pierre-Louis (2023): Révision du genre Porpax (Orchidaceae, Podochileae) en Nouvelle-Calédonie. Candollea 78 (1): 17-26, DOI: 10.15553/c2023v781a3, URL: http://dx.doi.org/10.15553/c2023v781a3

Lírio, Elton John De, Zavatin, Danilo Alvarenga, Pignal, Marc (2023): Mollinedia arianeae Lírio & M.Pignal, sp. nov. (Mollinedieae, Mollinedioideae, Monimiaceae): une nouvelle espèce microendémique de la forêt atlantique dans l'état de Rio de Janeiro, Brésil. Adansonia (3) 45 (6): 83-91, DOI: 10.5252/adansonia2023v45a6

Species descriptions are stored in textual form in corpora such as in floras and faunas, but this large amount of information cannot be used directly by algorithms, nor can it be linked to other data sources. The production of knowledge bases expressing structured data can benefit from collaborative and easy-to-use platforms like Xper3 (Vignes-Lebbe et al. 2017, Kerner and Vignes 2019, Saucède et al. 2021) but is very time-consuming at the human level. It is therefore mandatory for this task to make the information contained in species descriptions measurable and compatible with computer techniques. One of the most used data structures on the web and by the deep learning community is the triplet structure. Each piece of information is represented by a set of 3 elements (subject, predicate, object). One of the first steps towards species information accessibility is developing a text-to-triplet model, also known as text-to-graph, for monograph descriptions. In this work, we developed NEARSIDE, a text-to-graph model adapted to biology corpora to create normalized morphological characteristic knowledge bases for species descriptions. In Natural Language Processing, deep learning models have proven to be effective in extracting knowledge from open domain corpora (Lample et al. 2016, Sutskever et al. 2014), especially since the emergence of attention-based models (Devlin et al. 2019b, Devlin et al. 2019a). Several works have been made also on biomedical corpora (Fries et al. 2017,Cho and Lee 2019). In our case, we propose a model adapted to floras. Fully supervised deep learning models require a large amount of annotated data for training, nevertheless, the annotation process for the text-to-triplet task implies an expensive human intervention. Distant supervision is a technique that can be used to reduce this cost. This paradigm uses a small annotated glossary to project classes at the word level on a new complex and longer text (see Fig. 1). Named Entity Recognition (NER) is an Natural Language Processing (NLP) task that consists of extracting and classifying words of interest from a text (Sutskever et al. 2014, Devlin et al. 2019b, Lample et al. 2016), while triplet extraction can be compared to the Relation Extraction task (RE) which consists of extracting the words and the semantic relations between pairs of words. Distantly supervised NER is an often studied subject in the literature in comparison to distantly supervised RE (Liang et al. 2020, Meng et al. 2021) simply because NER is a subtask to RE and distant annotations generation is less expensive for the NER task (see Fig. 2). Our first contribution is creating a distantly annotated species description dataset for Named Entity Recognition with a well-balanced test set that allows us to bypass several biases that can be induced by the distant annotation and that are often observed in NER datasets (Taillé et al. 2021). In this dataset, each word of interest will be classified into one of 15 classes, each class being a specific kind of organ or descriptor. Our second contribution is proposing a distantly supervised model trained on our dataset, since fauna and flora corpora are particularly long and use a very specific technical vocabulary. We develop a context-oriented model adapted to this data by pretraining the language model. Thus the encoder of our model provides contextualized vectors for each extracted word that can be used to measure description similarities between different species. Our model reaches 96% accuracy in named entity classification on the test set. Our third contribution is the triplet construction module that can directly be applied to our model's outputs. This module is based on class dependency rules that are inspired by Xper3’s data representation format (see Fig. 3). Finally, NEARSIDE is an end-to-end structured knowledge extraction framework from unstructured species description corpora, that can be applied to several data sources. Thus making species descriptions from different corpora easily linked, compared and measured.

Pignal, Marc, Laudereau, Christian, Laudereau, Pierre-Louis, Bruy, David (2022): Une révision de Dendrobium Sw. sect. Rhizobium Lindl. en Nouvelle-Calédonie. Adansonia (3) 44 (15): 153-164, DOI: 10.5252/adansonia2022v44a15

Pignal, Marc, Laudereau, Christian, Gâteblé, Gildas, Laudereau, Pierre-Louis (2022): Dendrobium petrophilum (Kraenzl.) Garay ex N.Hallé, a well-named species describing its unusual chasmophytic ecology. Adansonia (3) 44 (1): 1-9, DOI: 10.5252/adansonia2022v44a1

The joint use of two tools applied to plant description, XPER3 and Recolnat Annotate, made it possible to study vegetative architectural patterns (Fig. 1) of the Dendrobium (Orchidaceae) in New Caledonia defined by N. Hallé (1977). This approach is not directly related to taxonomy, but to the definition of sets of species grouped according to a growth pattern. In the course of this work, the characters stated by N. Hallé were analysed and eventually amended to produce a data matrix and generate an identification key. Study materials: Dendrobium Sw. in New Caledonia New Caledonia is an archipelago in the Pacific Ocean, a French overseas territory located east of Australia. It is one of the 36 biodiversity hotspots in the world. The genus Dendrobium Sw. sensu lato is one of the largest in the family Orchidaceae and contains over 1220 species. In New Caledonia, it includes 46 species. In his revision of the family, N. Hallé (1977) defined 14 architectural groups, into which he divided the 31 species known at that time. These models are based on those defined by F. Hallé and Oldeman (1970). But they are clearly intended to group species together for identification purposes. Architectural pattern: A pattern is a set of vegetative or reproductive characters that define the general shape of an individual. Developed by mechanisms linked to the dominance of the terminal buds, the architectural groups are differentiated by the arrangement of the leaves, the position of the inflorescences or the shape of the stem (Fig. 1). Plants obeying a given pattern do not necessarily have phylogenetic relationships. These models have a useful application in the field for identifying groups of plants. Monocotyledonous plants, and in particular the Orchidaceae, lend themselves well to this approach, which produces stable architectural patterns. Recolnat Annotate Recolnat Annotate is a free tool for observing qualitative features and making physical measurements (angle, length, area) of images. It can be used offline and downloaded from https://www.recolnat.org/en/annotate. The software is based on the setting up observation projects that group together a batch of herbarium images to be studied, associating it with a descriptive model. A file of measurements can be exported in comma separated value (csv) format for further analysis (Fig. 2). XPER3 Usually used in the context of systematics in which the items studied are taxa, XPER3 can also be used to distinguish architectural groups that are not phylogenetically related. Developed by the Laboratoire d'Informatique et Systématique (LIS) of the Institut de Systématique, Evolution, Biodiversité in Paris, XPER3 is an online collaborative platform that allows the editing of descriptive data (https://www.xper3.fr/?language=en). This tool allows the cross-referencing of items (in this case architectural groups) and descriptors (or characters). It allows the development of free access identification keys (it means without fixed sequence of identification steps). The latter can be used directly online. But it also offers to produce single-access keys, with or without using character weighting and dependencies between characters. Links between XPER3 and Recolnat Annotate The descriptive model used by Recolnat Annotate can be developed within the framework of XPER3, which provides for characters and character states. Thus the observations made by the Recolnat Annotate measurement tool can be integrated into the XPER3 platform. Specimens can then be compared, or several descriptions can be merged to express the description of a species (Fig. 3). RESULTS The joint use of XPER3 and Recolnat Annotate to manage both herbarium specimens and architectural patterns has proven to be relevant. Moreover, the measurements on the virtual specimens are fast and reliable. N. Hallé (1977) had produced a dichotomous single-accesskey that allowed the identification and attribution of a pattern to a plant observed in the field or in a herbarium. The project to build a polytomous and interactive key with XPER3 required completing the observations to give a status for each character of each vegetative architectural model. Recolnat Annotate was used to produce observations from herbarium network in France. The use of XPER3 has allowed us to redefine these models in the light of new data from the herbaria and to publish the interactive key available at dendrobium-nc.identificationkey.org.

Une nouvelle espece de Nouvelle-Caledonie, Pterostylis longilabia M.Pignal, sp. nov. est decrite et illustree. Les caracteristiques morphologiques qui distinguent le nouveau taxon de l'espece apparentee, P. ophioglossa R.Br., sont pour l'essentiel, un labelle de la meme longueur que le sepale median, sans extension basale (au lieu d'un labelle plus court et presentant une extension fimbriee a sa base) et un sinus etroitement angule entre les synsepales (au lieu d'un sinus a angle arrondi ou d'un angle ouvert). En raison des grandes menaces pesant sur sa localite, le statut de conservation de l'UICN propose est EN (En Danger). Une cle d'identification pour les especes de Pterostylis de Nouvelle-Caledonie est donnee en anglais et en francais.

International audience; A broad range of climatic and biogeographical conditions are represented in the French Overseas Territories, from sub-polar to equatorial, resulting in a high diversity of endemic species. We mobilized data from herbaria, floras, checklists, literature, the expertise of botanists and plant ecologists to compile the most complete dataset on endemic vascular plants and bryophytes in the 15 French Overseas Territories. To date, 3748 spermatophytes (seed plants), 244 pteridophytes (ferns and lycophytes) and 448 bryophytes are strictly endemic to the overseas territories. New Caledonia, French Polynesia and Réunion harbour the highest numbers of strictly endemic species, yet French Guiana and the French Antilles harbour high numbers of regional endemic species due to their proximity with other territories. The endemic flora of these territories is highly threatened. In particular, 51% of strictly endemic spermatophytes are threatened and many species at risk belong to Rubiaceae and Orchidaceae families. Around 82% and 69% of strict and regional endemic spermatophytes and pteridophytes are found in the Paris herbaria. Only 34% of endemic bryophytes have their label information fully databased so that their total number in Paris herbaria is not known. Databasing the remaining specimens in the collection will greatly enhance future research and conservation projects. To facilitate the use of the information we compiled, we provide a publicly searchable dataset of the checklist. This study not only provides a picture of the flora of French overseas territories; it also identifies gaps in knowledge on which future research efforts in systematics, ecology and conservation could focus.

International audience; A new species, Garcinia urceolata Munzinger, Bruy & M.Pignal, sp. nov. (Clusiaceae), is described from New Caledonia. It is restricted to North Province, from the Tchamba valley in the south to Mandjélia in the north of the main island of Grande-Terre, occurring in dense humid rainforests on non-ultramafic substrate. Material of this small tree species was first collected more than fifty years ago but was confused with G. virgata Vieill. ex Guillaumin as both taxa have small leaves. Garcinia urceolata, sp. nov. differs from G. virgata in a number of features of the leaves, flowers and fruits. Garcinia urceolata, sp. nov. also grows at higher elevation and in wetter conditions than G. virgata. Both species are purported to have dehiscent fruit, along with other New Caledonian members of the genus, a distinctive character that was used to justify the description of the genus Septogarcinia Kosterm., which is no longer regarded as distinct from Garcinia L. Line drawings and colour photos are provided for both the new species and for G. virgata for comparison, along with a preliminary risk of extinction assessment for each of them, which indicates that G. urceolata, sp. nov. is Vulnerable (VU) while G. virgata is Near Threatened (NT).

Pignal, M., C. Laudereau & P.-L. Laudereau (2021). Notes on Bulbophyllum sect. Pelma (Orchidaceae) in New Caledonia. Candollea 76: 65–70. In French, English and French abstracts.A contribution to our knowledge of Bulbophyllum sect. Pelma (Finet) Schltr. (Orchidaceae) from the New Caledonian archipelago is provided. Bulbophyllum savaiense Schltr. is recorded for the first time on Grande Terre, the main island of New Caledonia. The taxon is known from a single locality in the Amoa Valley. A lectotype is designated for Bulbophyllum neocaledonicum Schltr., a synonym of Bulbophyllum absconditum J.J. Sm. An identification key for the New Caledonian species of the section is provided. IUCN risk of extinction assessments of the two taxa are discussed.

Une nouvelle espece de Nouvelle-Caledonie, Dendrobium veillonii M. Pignal, sp. nov. est decrite et illustree. Les caracteres morphologiques distinguant le nouveau taxon des especes apparentees, D. pectinatum Finet, D. crassicaule Schltr. et D. cleistogamum Schltr., sont presentes. Son statut UICN de conservation est propose. Une cle d'identification est donnee pour la section Kinetochilus Schltr. Les lectotypes sont designes pour D. cleistogamum, D. crassicaule et D. pectinatum. L'architecture de la section Kinetochilus Schltr. est analysee sur la base de D. veillonii M. Pignal, sp. nov.

Morphological characters support the description of two new species of Orchidaceae from New Caledonia: Dendrobium butinii M.Pignal & Munzinger sp. nov. and Dendrobium letocartiorum Munzinger & M.Pignal sp. nov. The lectotypes of Dendrobium camaridiorum Rchb.f. and D. crassifolium Schltr. are designated here. A leaf anatomical study was conducted and provided useful characters to distinguish the five New Caledonian graminoid Dendrobiineae species. Two identification tools are provided: an anatomical key for sterile material of grass-like Dendrobiineae and a morphological key for the New Caledonian graminoid Dendrobium. We propose preliminary conservation assessments with IUCN criteria for the new taxa.

RESUME Une revision taxonomique du genre Ivodea Capuron est presentee. Trente especes sont reconnues dont 27 endemiques de Madagascar, deux endemiques des Comores et une commune aux deux archipels. Dix-sept especes sont nouvellement decrites (I. acuminata Rabarim., Rakoton., Phillipson & Lowry, sp. nov., I. analalavensis Rabarim., Rakoton., Phillipson & Lowry, sp. nov., I. ankeranensis Rabarim., Rakoton., Phillipson & Lowry, sp. nov., I. antilahimenae Rabarim., Rakoton., Phillipson & Lowry, sp. nov., I. aymoniniana Rabarim., Rakoton., Phillipson, Lowry & M.Pignal, sp. nov., I. capuronii Rabarim., Rakoton., Phillipson & Lowry, sp. nov., I. delphinensis Rabarim., Rakoton., Phillipson & Lowry, sp. nov., I. macrocarpa Rabarim., Rakoton., Phillipson & Lowry, sp. nov., I. mahaboensis Rabarim., Rakoton., Phillipson & Lowry, sp. nov., I. mananarensis Rabarim., Rakoton., Phillipson & Lowry, sp. nov., I. mayottensis Labat & M.Pignal, sp. nov., I. moheliensis M.Pignal & Labat, sp. nov., I. occidentalis Rabarim., Rak...

Vanilla sotoarenasii M.Pignal, Azofeifa-Bolaños & Grisoni sp. nov. urn:lsid:ipni.org:names:77160155-1 Figs 2, 3, 6 Diagnosis A Vanilla planifolia similis, sed folia caulesque breviores (folium: 7.6̅10.6 × 2.7̅3.3 cm versus 14.7̅14.9 × 4.8̅5 cm), laminae breviores, ellipticae-oblongaeque, Fores albiores, tubus Foris, sepala petalaque breviores, sepalum dorsale angustius, labellum angustiius cum papillis salientioribus, ovarium brevitius (3.8̅4.6 cm versus 5̅5.3 cm), fructus brevitior (11.4 cm versus 20.1̅20.3 cm) indehiscensque, sectio fructi cylindrica (versus trigona). Moleculae aromaticae fructi absimilis. Etymology This species is dedicated to Dr. Miguel Angel Soto Arenas (1963̅2009), authority in orchid Foristics and ecology, particularly in the Vanilla genus. Type material Holotype COSTA RICA: Cahuita (ex hort. parc E. Liais, from plants collected by B. Gosselin in 1993), 8 Oct. 1996, Pignal 396 b (holo-: P: P00075132). Paratypes COSTA RICA: Limón Province: Talamanca, Refugio Nacional Mixto de Vida Silvestre Gandoca- Manzanillo, 9.594° N, 82.602° W, altitude 2 m, 14 Nov. 2013 (originally collected), cultivated in BRC Vatel, Saint Pierre, La Réunion, France CRV2180, 28 Feb. 2016, M. Grisoni & J.B. Azofeifa-Bolaños V. sp. nov. V. Compounds / 100 % 100 g % Vanillin 0.26 a 10.9 2.28 b 68.0 Vanillic acid nd a 0.0 0.19 b 5.5 Vanillyl alcohol 0.73 a 31.0 0.32 b 9.6 Total vanillyl compounds 0.99 a 41.9 2.79 b 83.1 p -hydroxybenzaldehyde 0.20 a 8.5 0.18 a 5.4 p -hydroxybenzoic acid 0.37 a 15.8 0.37 a 11.2 p -hydroxybenzyl alcohol 0.27 a 11.6 0.01 b 0.3 Total p -hydroxybenzyl compounds 0.85 a 35.9 0.56 b 16.9 Anisyl alcohol 0.24 a 10.2 nd b 0.0 Anisaldehyde 0.03 b 1.4 nd b 0.0 Anisic acid 0.25 a 10.6 nd b 0.0 Total anisyl compounds 0.52 a 22.2 nd b 0.0 Total 2.36 a 100 3.35 b 100sotoarenasii planifolia g g dw g / dw JJMM01 (REU: REU13363); Canton of Talamanca, Refugio de Vida Silvestre Gandoca-Manzanillo (originally collected), cultivated in INISEFOR, Heredia, Costa Rica, 14 Nov. 2013, M. Grisoni, B. Azofeifa and J. García 2180 (CR 281507), cultivated at the same locality, B. Azofeifa and J. García 0 0 47 (CR 281508); Canton of Siquirres, Barra de Parismina (originally collected), cultivated in INISEFOR, Heredia, Costa Rica, 8 Feb. 2013, B. Azofeifa, J. García and A. Paniagua 0 0 0 2 (CR 281509). Description Hemiepiphytic vine up to 15 m high. Stems Fexuous, terete, smooth, green, 5̅6 mm thick; internodes, sometimes slightly curved apically, ca 10 cm long. Terrestrial roots pubescent, ramiFed, ca 2 mm thick; both attaching and free aerial roots terete, pubescent, ca 2 mm thick at base, ca 3.5 mm at middle. Leaves regularly alternate. Blade elliptic to obovate, slightly Feshy (ca 27 veins visible on dry specimens); base rounded to cuneate, shortly pseudopetiolate; apex shortly acuminate (acumen sharp, 12 mm long, 5 mm at base), slightly recurved; margin thinned; pseudopetiole canaliculate, 16 × 5 mm. InForescence: raceme, ca 10̅20-Fowered, 7̅13 cm, sometimes located on short axillary branches, sometimes lying on leafy stems. 3̅4 inForescence bracts, foliaceous, basal bract pseudopetiolate (40 × 20 mm), upper bract sessile and shorter (20 × 8 mm and 12 × 3 mm). Flowers at anthesis successively, ephemeral, 1̅2 simultaneously, white green, sepals forming an angle of approximately 45° with axis of column, petals more or less parallel to this axis. Ovary terete, smooth, slightly arcuate, white at base and green on upper ¾, 30 mm long and 4 mm in diameter. Parts of perianth with whitish inclusions (visible on dry specimens), longitudinally oriented, ca 0.1̅2 mm long, more numerous on petals, dorsal sepal narrow elliptic to oblanceolate, ca 11-veined, 40 × 10 mm, apex acute, rounded, base attenuate-clawed, slightly concave, canaliculate. Lateral sepals, elliptic asymmetric, slightly falciform, ca 11-veined, 38 × 10.5 mm, apex acute, slightly cupuliform, base attenuate, canaliculate, 4 mm wide. Petals elliptic asymmetric, slightly falciform, ca 12-veined, carinate dorsally (carena 1.2 mm wide), 38 × 9 mm, apex rounded, base attenuate, 3 mm wide (Fig. 6). Labellum attached to column along margins of 5/7 (ca 20 mm), funnel-shaped, spread apically (opening about 10 mm), trilobed, ca 30-veined ramiFed in distal third, margin crenulate. With 5̅6 Fmbriated scales, ca 1.5 × 1.5 mm, at about middle of labellum. Lateral lobes, obliquely triangular, ca 11-veined, 10 mm high and 7 mm wide, margins widely undulate. Midlobe quadrate, 20 mm wide and 6 mm high, about 12-veined, converging at apex. Papillae on four central veins, on apical half. Column trigonous-semicylindrical, 28 mm long, 2.5 mm wide, apically with 2 lateral auricles, crenulate, 2.5 mm high and 4 mm wide. Rostellum quadrangular, ca 3 × 3 mm. Stigma bilobed. Anther articulated, connective keel-shape, 2 × 2 mm, bicarinate on top. Operculum helmet-shaped, 2 × 3 mm. Pollinarium, 2. Fruit arcuate, banana-shaped, green, turning yellowish and then brown, 11̅16 × 1.5 cm, with cylindrical section. Phenology The Fowering period occurs from October to March in Costa Rica. IUCN status –Vulnerable The populations of V. sotoarenasii sp. nov. observed in the province of Limón showed strong vegetative development of vines and natural seed set was frequently observed. However, a small number of populations have so far been observed and only over a very limited area of Limón Province (10 populations over a coastal strip of about 50 km²), and its habitat is periodically submerged by the ocean. This makes us inclined to tentatively classify V. sotoarenasii sp. nov. as vulnerable D2 (IUCN 2012) until further data on distribution and population dynamics have been obtained. Discussion Using complementary approaches involving morphology of the reproductive and vegetative systems, molecular barcoding and the accumulation of secondary metabolites in fruits, we highlighted speciFc traits for the vanilla populations sampled on the Caribbean coast of Costa Rica which revealed a new taxon, V. sotoarenasii sp. nov. The morphology of the Fowers and leaves clearly assigned V. sotoarenasii sp. nov. within the V. planifolia group (Soto Arenas & Dressler 2010). Based on Fower morphology, V. sotoarenasii sp. nov. was more similar to V. planifolia and V. × tahitensis than to any other vanilla species of this group. However, V. sotoarenasii sp. nov. differs from the other two species by several characteristics (Table 6). Firstly, our data and previous data by Costantin & Bois (1915) and Portères (1953) showed that V. sotoarenasii sp. nov. has a signiFcantly smaller size for all organs measured (stem, leaf, Fower and fruit) compared to V. planifolia and V. × tahitensis, and had a distinct shape of the leaves: elliptic to obovate in the case of V. sotoarenasii sp. nov., elliptic to oblong for V. planifolia and narrowly oblong to lanceolate for V. × tahitensis (Table 6). In addition, the Fowers of V. sotoarenasii sp. nov. are more whitish, with a narrower label showing marked papillae, compared to those of V. planifolia, which are more greenish, with a wider label and smooth papillae. On the basis of HPLC quantiFcation of hydrolyzed volatile compounds in mature fruits, the aromatic precursors of V. sotoarenasii sp. nov. are very distinct from those of V. planifolia. In particular, fruits of V. sotoarenasii sp. nov. were characterized by less predominant vanillin content and the presence of anisyl compounds. They should develop, after over-maturation or curing, Favors extremely different from those of V. planifolia and more similar to those of V. pompona or V. × tahitensis (Pérez-Silva et al. 2006; Brunschwig et al. 2009; Maruenda et al. 2013). On the other hand, molecular analysis of nuclear DNA sequences (ITS) unambiguously separated the V. sotoarenasii sp. nov. group of plants from the V. planifolia group including 68 accessions originating from seven countries (Comoros, Costa Rica, Guatemala, Madagascar, Mayotte, Mexico, and La Réunion). This result is corroborated by ampliFed fragment length polymorphism (AFLP) analyses by Bory et al. (2008) that clearly separated V. sotoarenasii sp. nov. CR0068 from 303 V. planifolia genotypes of diverse origins with an average distance comparable to the distance between V. planifolia and V. × tahitensis. The facts that i) at the plastid DNA level (partial mat K sequence) V. sotoarenasii sp. nov. and V. planifolia share the same clade, and ii) in the ITS phylogeny V. sotoarenasii sp. nov. is in an internal position within the V. planifolia clade (like V. helleri within the V. odorata cluster), suggest the recent radiation of V. sotoarenasii sp. nov. from V. planifolia populations. So far, V. sotoarenasii sp. nov. has only been observed in the Limón Province of Costa Rica where it is sympatric with V. planifolia, which has been reported as native to Costa Rica (Soto Arenas & Dressler 2010). However, recent introductions in the country of V. planifolia cultivars and hybrids have also been documented (Soto Arenas & Dressler 2010; Belanger & Havkin-Frenkel 2011; Varela Quirós 2011). Historical, genetic and phylogenetic data are insufFcient to decide whether V. sotoarenasii sp. nov. derived from natural or introduced populations of V. planifolia, nor how and when the radiation occurred. Orchid species are often interfertile, which allows them to create interspeciFc and even intergeneric fertile hybrids. Many interspeciFc hybrids between species of Vanilla have been produced in the last decades by botanists and agronomists (Knudson 1950; Theis & Jiménez 1957; Divakaran et al. 2006). In nature, however, interspeciFc hybrids are prevented by reproductive barriers that result primarily from the inability of pollinators to transfer pollen from one species to another.Within the limits of our sampling, we have never observed intermediary types, at the genetic or morphological level, in the Limón area, which suggests that a reproductive barrier may exist between V. planifolia and V. sotoarenasii sp. nov. Indeed, in the case of sympatric populations of the two very closely related species V. barbellata Rchb. f. and V. dilloniana Correll, having synchronous Fowering and the same pollinator in western Puerto Rico, intermediary types were observed, demonstrating natural interspeciFc hybridizations (Nielsen 2000). We hypothesize that the differences in Fower morphology observed between V. planifolia and V. sotoarenasii sp. nov. impede gene Fow from one species to another, which enhanced the radiation of the population in Limón. Vanilla pollinationis bee-dependent(Ackerman1986; Gigant et al. 2011)and Fower size difference is likely to constitute a reproductive barrier between species by selecting compatible pollinators. This has been observed for instance in Peru where, due to their small size, the Mellipona bees did not remove pollen when visiting V. grandiFora Lindl. Fowers, and therefore did not contribute to its pollination (Lubinsky et al. 2006). Given the signiFcant size reduction of the Fowers of V. sotoarenasii sp. nov. compared to those of V. planifolia, it is unlikely that a bee capable of pollinating one of the two species would be able to pollinate the other. In addition to size compatibility, the probability of pollinator visits is frequently increased by the aromatic metabolites emitted by orchid Fowers, which act as bee attractants (Ackerman 1986; Pansarin & Pansarin 2014). This is particularly important for vanilla Fowers that are open a single day, which reduces the chances of pollen-pollinator encounter. Analysis of the volatile compounds emitted by Fowers from various Vanilla species (unpublished data) has shown in particular that in V. planifolia (n = 4) the major compounds are a hydrocarbon monoterpene, (E)-β-ocimene (representing 17.10 ± 14.08% of all detected compounds), and an aromatic compound, 2,6-bis (1,1-dimethylethyl)- 4-(1-oxopropyl) phenol (11.59 ± 8, 04%), while in V. sotoarenasii sp. nov. (n = 1), only (E)-β-ocimene was predominantly found (63.26%). This difference in the nature of volatile emissions between the two species could also contribute to the speciFcity of the pollinators visiting the Fowers. Furthermore, the earlier Fowering of V. sotoarenasii sp. nov. compared to V. planifolia may also contribute to favor self or geitonogamous pollination as well as provide greater reproductive success to V. sotoarenasii sp. nov., as pointed out for non-rewarding orchids (Jersáková et al. 2006; Sun et al. 2009). All these factors hindering gene Fow between populations of V. sotoarenasii sp. nov. and V. planifolia may account for the radiation that led to the emergence of V. sotoarenasii sp. nov., a species that is genetically, morphologically, and biochemically distinct from V. planifolia. Finally, given its original aromatic content combining vanilyl and anisic notes, its high level of resistance (at least for CR0068) to the Fusarium root rot of vanilla (Koyyappurath et al. 2015), and its early and abundant Fowering in culture, V. sotoarenasii sp. nov. could be a promising genitor for breeding programs aiming to produce new vanilla varieties for the agroindustry.

We describe a new vanilla species growing in sympatry with Vanilla planifolia Jacks. ex Andrews (Orchidaceae) in the province of Limón, Caribbean coast of Costa Rica. The morphology of the reproductive and vegetative organs observed on vines cultivated under shade-house, the nuclear (Internal Transcribed Spacer) and plastid (matK) nucleotide sequences, as well as the contents of aromatic compounds measured in ripe fruits, show that this species is close to but distinct from V. planifolia. The name V. sotoarenasii M.Pignal, Azofeifa-Bolaños & Grisoni sp. nov. is proposed for this new Vanilla species endemic in Costa Rica. It is especially distinguished from V. planifolia by a reduction of about 30% of the size of the fruits and flowers, by a divergence of ITS sequences for at least two species-conserved nucleotides compared to seven other species of the V. planifolia group, and by the presence of anisic compounds and low content of phenolic compounds (including vanillin) in the fruits. These results confirmed the extension of the area of distribution of V. planifolia southward to Costa Rica, where a recent speciation process occurred. Because of its particular agronomic and aromatic properties, V. sotoarenasii sp. nov. could represent a valuable biological resource for the vanilla industry. Describimos una nueva especie de vainilla que crece en simpatía con Vanilla planifolia Jacks. ex Andrews (Orchidaceae) en la provincia de Limón, costa caribeña de Costa Rica. La morfología de los órganos reproductores y vegetativos observados en vides cultivadas bajo sombra, las secuencias nucleotídicas nucleares (Internal Transcrito Spacer) y plastidios (matK), así como el contenido de compuestos aromáticos medidos en frutos maduros, muestran que esta especie es cercano pero distinto de V. planifolia. El nombre V. sotoarenasii M. Pignal, Azofeifa-Bolaños & Grisoni sp. nov. Se propone para esta nueva especie de vainilla endémica en Costa Rica. Se distingue especialmente de V. planifolia por una reducción de aproximadamente el 30% del tamaño de los frutos y flores, por una divergencia de secuencias de ITS para al menos dos especies de nucleótidos conservados en comparación con otras siete especies del grupo de V. planifolia. , y por la presencia de compuestos anísicos y bajo contenido de compuestos fenólicos (incluida la vainillina) en los frutos. Estos resultados confirmaron la extensión del área de distribución de V. planifolia hacia el sur hasta Costa Rica, donde ocurrió un reciente proceso de especiación. Por sus particulares propiedades agronómicas y aromáticas, V. sotoarenasii sp. nov. podría representar un valioso recurso biológico para la industria de la vainilla. Descrevemos uma nova espécie de baunilha que cresce em simpatia com Vanilla planifolia Jacks. ex Andrews (Orchidaceae) na província de Limón, costa caribenha da Costa Rica. A morfologia dos órgãos reprodutivos e vegetativos observados em vinhas cultivadas à sombra, as sequências de nucleotídeos nucleares (espaçador de transcrição interno) e plastídeos (matK), bem como o conteúdo de compostos aromáticos medidos em frutos maduros, mostram que esta espécie está próxima, mas diferente de V. planifolia. O nome V. sotoarenasii M. Pignal, Azofeifa-Bolaños & Grisoni sp. Nov. É proposto para esta nova espécie endêmica de baunilha na Costa Rica. É especialmente distinta de V. planifolia por uma redução de aproximadamente 30% no tamanho de frutos e flores, por uma divergência de sequências ITS para pelo menos duas espécies de nucleotídeos conservados em comparação com outras sete espécies do grupo V. planifolia. , e pela presença de compostos anísicos e baixo teor de compostos fenólicos (incluindo vanilina) nos frutos. Esses resultados confirmaram a extensão da área de distribuição de V. planifolia ao sul até a Costa Rica, onde ocorreu um recente processo de especiação. Devido às suas propriedades agronômicas e aromáticas particulares, V. sotoarenasii sp. Novembro pode representar um valioso recurso biológico para a indústria de baunilha. Universidad Nacional, Costa Rica Université de La Réunion, Francia Instituto Tecnológico de Tuxtepec, México Instituto Tecnológico de Veracruz, México Universidad Autónoma de México, México Benemérita Universidad Autónoma de Puebla, México Universidad de San Carlos de Guatemala, Guatemala. Instituto de Investigación y Servicios Forestales Escuela de Ciencias Agrarias Escuela de Ciencias Biológicas

Natural history collection data are now accessible through databases and web portals. However, ecological or morphological traits describing specimens are rarely recorded while gathering data. This lack limits queries and analyses. Manual tagging of millions of specimens will be a huge task even with the help of citizen science projects such as "les herbonautes" (http://lesherbonautes.mnhn.fr). On the other hand, deep learning methods that use convolutional neural networks (CNN) demonstrate their efficiency in various domains, such as computer vision (Krizhevsky et al. 2012, Azizpour et al. 2016), speech recognition (Abdel-Hamid et al. 2014) or face identification (Li et al. 2015, Freytag et al. 2016). We aim to use deep learning to provide a visual representation of words used to describe plants (e.g. simple, or compound leaf), and to associate those words with specimens in the Paris herbarium. This will provide a semantic description of each of the 7 millions images of the fully digitized collection of the Paris herbarium in the Muséum National d'Histoire Naturelle (MNHN, Paris, France). In a proof of concept project, we have used a CNN - pre-trained on the image database ImageNet (http://www.image-net.org) - in order to identify 4 morphological traits of leaves, using 103,000 herbarium images from 11 different taxa: margin (entire / dentate), leaf attachment (opposite / alternate), leaf organization (simple / compound), plant (woody / non-woody) (see Fig. 1) Seventy percent of images are used to train the weights of the model (in a supervised learning process that uses a training set already tagged for the 4 characteristics), 10% are used as validation set to tune the hyper-parameters of the model and to avoid overfitting, and 20% are used as test set to evaluate the generalization performances of the final neural network. The first results are encouraging with over 80% success on the test set. In a second step, we test if the neural network is not overfitting the training examples, and can generalize to new taxa. If we restrict the training set to a small number of taxa (4 taxa containing 76% of images), the success rate on the 7 other taxa (unseen during training) decreases drastically. A good sampling of the taxonomic diversity of plants appears crucial to train the neural network. A second method visualizes the area of each image that was detected by the CNN as the most important for morphological character recognition (Durand et al. 2017). This method provides an explanatory view of the automatic recognition process. In this poster we describe methods and results on botanical images for the different taxa. We discuss perspectives on image tagging of the Paris herbarium, and how to combine the citizen science project in order to annotate images with CNN automatic image description.

International audience; The new Franco-Brazilian website “Saint-Hilaire virtual herbarium” offers dynamic online consultation of all specimens and manuscripts of the naturalist Auguste de Saint-Hilaire, providing links between specimen images and associated textual data, including notes available in his field books. This tool aims at facilitating the work of taxonomy and systematic botany and allowing a more accurate reconstruction of the routes and time frame of Saint-Hilaire's exploration. All specimens are being digitized by the Paris herbarium (P) and added online. The system will also offer Saint-Hilaire's major publications online. The nomenclature and determinations are automatically updated through dynamic links to the SONNERAT/MNHN database. In this paper, we propose moreover a standard for the correct citation of Saint-Hilaire specimens.; Le nouveau site franco-brésilien « Herbier Virtuel A. de Saint-Hilaire » permettra une consultation dynamique de l’ensemble des spécimens et desmanuscrits du naturaliste Auguste de Saint-Hilaire, en offrant un lien entre les photos des spécimens et les données associées qui figurent sur les cahiers de récoltes. Cet outil facilitera le travail de taxonomie et de systématique botanique et donnera la capacité à reconstituer avec précision les trajets et la chronologie des explorations de Saint-Hilaire. L’ensemble des spécimens sera progressivement mis en ligne à la suite de la numérisation de l’herbier de Paris (P). Le site mettra également à disposition les principales publications de Saint-Hilaire. La nomenclature et les déterminations sont maintenues à jour de façon dynamique par un lien avec la base de données SONNERAT du MNHN. Dans ce travail, nous proposons en outre un standard pour la citation correcte des spécimens de Saint-Hilaire.

A new species of Neea Ruiz & Pav. (Nyctaginaceae) from the Atlantic Forest of Bahia State (Brazil). Morphological anatomical characters support the description of a new species from Brazilian Atlantic Forest, Neea alumnorum M.Pignal, Soares Filho & Romaniuc, sp. nov. A description of the leaf venation and a brief analysis of the inflorescence are given. This description is accompanied by pictures taken in the field and illustrations of the male flower, inferior epiderm details and leaf venation. A discussion of morphological affinities with the related species is presented, along with a preliminary assessment of its conservation status (VU) based on the IUCN Red List Categories and Criteria.

We provide a quantitative description of the French national herbarium vascular plants collection dataset. Held at the Muséum national d’histoire naturelle, Paris, it currently comprises records for 5,400,000 specimens, representing 90% of the estimated total of specimens. Ninety nine percent of the specimen entries are linked to one or more images and 16% have field-collecting information available. This major botanical collection represents the results of over three centuries of exploration and study. The sources of the collection are global, with a strong representation for France, including overseas territories, and former French colonies. The compilation of this dataset was made possible through numerous national and international projects, the most important of which was linked to the renovation of the herbarium building. The vascular plant collection is actively expanding today, hence the continuous growth exhibited by the dataset, which can be fully accessed through the GBIF portal or the MNHN database portal (available at: https://science.mnhn.fr/institution/mnhn/collection/p/item/search/form). This dataset is a major source of data for systematics, global plants macroecological studies or conservation assessments.

Ethnopharmacological relevance Information regarding the use of beneficial, native Brazilian plants was compiled by European naturalists in the 19th century. The French botanist Auguste de Saint-Hilaire (1779–1853) was one of the most important such naturalists; however, his manuscripts (field books) have not yet been studied, especially in the context of useful plants. Aim of the study To present data documented by Saint-Hilaire in his field book regarding the use of native plants by the Brazilians. Materials and methods Data on useful plants were obtained from field books (six volumes) deposited in the Museum national d' Histoire naturelle in Paris, France. The vernacular names of the plants, registered as “N.V.” or “Nom Vulg.” in the field book, were carefully searched. Traditional information about these plants was translated and organised using a computer. The botanical identification of each plant was determined and updated from the original descriptions and names cited in the field books by A. de Saint-Hilaire. Correlated pharmacological studies were obtained from PubMed. Results A total of 283 useful plants were recorded from the field books and 165 (58.3%) could be identified to genus or species. Fifty-eight different traditional uses were registered for the identified plants; the most common were as purgatives and febrifuges. Other data recovered were related to edible fruits and plants with interesting sensorial characteristics. For the few species that have been subjected to laboratory studies, the efficacy of the recorded traditional uses was confirmed. Conclusion The data recorded by the French naturalist A. de Saint-Hilaire represent a rich, unexplored source of information regarding the traditional uses of Brazilian plants.

We assessed the extent of recent environmental changes on leaf morphological (stomatal density, stomatal surface, leaf mass per unit area) and physiological traits (carbon isotope composition, δ(13)C(leaf) , and discrimination, Δ(13)C(leaf) , oxygen isotope composition, δ(18)O(leaf) ) of two tropical rainforest species (Dicorynia guianensis; Humiria balsamifera) that are abundant in the Guiana shield (Northern Amazonia). Leaf samples were collected in different international herbariums to cover a 200 year time-period (1790-2004) and the whole Guiana shield. Using models describing carbon and oxygen isotope fractionations during photosynthesis, different scenarios of change in intercellular CO(2) concentrations inside the leaf (C(i)), stomatal conductance (g), and photosynthesis (A) were tested in order to understand leaf physiological response to increasing air CO(2) concentrations (C(a)). Our results confirmed that both species displayed physiological response to changing C(a) . For both species, we observed a decrease of about 1.7‰ in δ(13)C(leaf) since 1950, without significant change in Δ(13)C(leaf) and leaf morphological traits. Furthermore, there was no clear change in δ(18)O(leaf) for Humiria over this period. Our simulation approach revealed that an increase in A, rather than a decrease in g, explained the observed trends for these tropical rainforest species, allowing them to maintain a constant ratio of C(i)/C(a) .

Pagina de rostoPrimeira pagina do caderno de coleta C1 Cliche Arkhenum por MNHN/Ibt/CRIA. Paralelamente a correspondencia, dois outros tipos de documentos manuscritos nos esclarecem sobre a personalidade e o metodo de trabalho de Auguste de Saint-Hilaire: seu jornal de viagem e seus cadernos de coleta. No prefacio de seu primeiro livro, Auguste de Saint-Hilaire refere-se de fato a um documento de trabalho que lhe servira a redacao de seus relatos, seu jornal de viagem: […] eu pude ver tudo qu...

The pollen morphology of Siparuna, Bracteanthus and Glossocalyx, and the ultrastructure of S. decipiens and G. longicuspis

A new Microtatorchis species (Orchidaceae, Vandeae, Aeridinae) in New Caledonia, and identification key for the aphyllous Aeridinae of the territory. Morphological characters support the description of a new species, Microtatorchis labatii M.Pignal & Munzinger, sp. nov., and allow to signal for the first time Taeniophyllum muelleri Benth. in New Caledonia. An identification key is given for the genera Microtatorchis and Taeniophyllum in New Caledonia.

Pignal, Marc, Phillipson, Peter B. (2010): A new species of Hibiscus (Malvaceae) from Madagascar. Phytotaxa 14: 43-48, DOI: 10.11646/phytotaxa.14.1.3, URL: http://biotaxa.org/Phytotaxa/article/view/phytotaxa.14.1.3

The phylogeny and the biogeographical history of the genus Vanilla was investigated using four chloroplastic genes (psbB, psbC; psaB and rbcL), on 47 accessions of Vanilla chosen from the ex situ CIRAD collection maintained in Reunion Island and additional sequences from GenBank. Bayesian methods provided a fairly well supported reconstruction of the phylogeny of the Vanilloideae sub-family and more particularly of the genus Vanilla. Three major phylogenetic groups in the genus Vanilla were differentiated, which is in disagreement with the actual classification in two sections (Foliosae and Aphyllae) based on morphological traits. Recent Bayesian relaxed molecular clock methods allowed to test the two main hypotheses of the phylogeography of the genus Vanilla. Early radiation of the Vanilla genus and diversification by vicariance consecutive to the break-up of Gondwana, 95 million years ago (Mya), was incompatible with the admitted age of origin of Angiosperm. Based on the Vanilloideae age recently estimated to 71 million years ago (Mya), we conclude that the genus Vanilla would have appeared approximately 34 Mya in South America, when continents were already separated. Nevertheless, whatever the two extreme scenarios tested, at least three long distance migration events are needed to explain the present distribution of Vanilla species in tropical areas. These transoceanic dispersions could have occurred via transoceanic passageway such as the Rio Grande Ridge and the involvement of floating vegetation mats and migratory birds.

Morphological characters support the description of a new species of Passifloraceae from Mayotte Island: Adenia barthelatii M. Pignal, Yockteng, Hearn & Labat. Morphological and molecular data suggest that A. barthelatii belongs to the ‘warty-gland’ subclade of Clade V defined by Hearn elsewhere. Since the warty-gland clade is restricted to the Malagasy region we suggest a Malagasy origin of this Maorian species of Adenia.

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