Latest Articles from PhytoKeys Latest 15 Articles from PhytoKeys https://phytokeys.pensoft.net/ Fri, 29 Mar 2024 01:39:20 +0200 Pensoft FeedCreator https://phytokeys.pensoft.net/i/logo.jpg Latest Articles from PhytoKeys https://phytokeys.pensoft.net/ Desmopsis terriflora, an extraordinary new species of Annonaceae with flagelliflory https://phytokeys.pensoft.net/article/102279/ PhytoKeys 227: 181-198

DOI: 10.3897/phytokeys.227.102279

Authors: María Fernanda Martínez-Velarde, Carlos Rodrigues-Vaz, Vincent Soulé, Francis J. Nge, George E. Schatz, Thomas L. P. Couvreur, Andrés Ernesto Ortiz-Rodriguez

Abstract: Flagelliflory refers to the production of inflorescences exclusively on long, whip-like branches which emerge from the main trunk and extend along the ground or below it. It is the rarest type of cauliflory and only a few cases have been reported in the world. Here, a new species of Annonaceae with flagelliflory is described and illustrated. The phylogenetic relationships of the new species were inferred using a hybrid-capture phylogenomic approach and we present some notes on its reproductive ecology and pollen characteristics. The new species, namely Desmopsis terriflora sp. nov., is part of a clade composed of Mexican species of Stenanona with long, awned petals. Desmopsis terriflora is distinguished by its flageliflorous inflorescences, basely fused sepals, thick red petals, reduced number of ovules per carpel, pollen grains with a weakly rugulate to fossulate exine ornamentation, and its globose, apiculate fruits with a woody testa. The morphological characteristics of the flagella suggest that these are specialized branches rather than inflorescences, and the absence of ramiflory implies an exclusively reproductive function. The flowers are infrequently visited by insects, their potential pollinators being flies and ants.

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Research Article Fri, 23 Jun 2023 15:07:49 +0300
 Polygonatum praecox (Asparagaceae), a new species from mid-eastern China revealed by morphological and molecular evidence https://phytokeys.pensoft.net/article/90456/ PhytoKeys 211: 125-138

DOI: 10.3897/phytokeys.211.90456

Authors: Yingfeng Hu, Yujun Liu, Maroof Ali, Wei Wu, Xiaohong Li, Longsheng Chen, Jianwen Shao

Abstract: A new species, Polygonatum praecox Y.F.Hu & J.W.Shao (Asparagaceae), is described and illustrated. This species is similar to P. cyrtonema, P. odoratum and P. caulialatum, but can be distinguished from P. cyrtonema by its racemose inflorescence, cylindrical hairless filaments and apex without a retrorse spur; from P. odoratum by its stout moniliform rhizome, straight stem and longer (1.7–2.2 cm long) floral tube; and from P. caulialatum by its upper part straight stem, yellowish-green corolla, lobes excurved and earlier flowering. The complete chloroplast genome of this new species is 155,115–155,256 bp in length. Phylogenetic analysis revealed that P. praecox is not genetically related to the above three morphological similar species, but is closely related to the two European species (P. multiforum and P. latifolium). This species is relatively common in mid-eastern China and has previously been confused with P. cyrtonema. As its wild resources have decreased in recent years due to over-exploitation for medicinal or edible purposes, we classify it as Near Threatened (NT) according to the IUCN Red List Criteria.

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Research Article Fri, 21 Oct 2022 14:13:58 +0300
Terniopsis yongtaiensis (Podostemaceae), a new species from South East China based on morphological and genomic data https://phytokeys.pensoft.net/article/83080/ PhytoKeys 194: 105-122

DOI: 10.3897/phytokeys.194.83080

Authors: Miao Zhang, Xiao-Hui Zhang, Chang-Li Ge, Bing-Hua Chen

Abstract: The new species Terniopsis yongtaiensis X.X. Su, Miao Zhang & Bing-Hua Chen, from Fujian Province, China, is described and illustrated. It is similar to T. heterostaminata from Thailand, but differs in its two fertile stamens, fewer but longer vegetative ramuli, fewer but shorter flowering ramuli, shorter pedicels, capsule-stalk and stamens. The complete chroloplast genome of the new species is 129,074 bp long and has a typical quadripartite structure, including two inverted repeat regions (IRs) of 18,504 bp in length, separated by a large single-copy (LSC) and a small single-copy (SSC) regions of 79,000 bp and 13,066 bp, respectively. The ycf1 and ycf2 genes were lost compared to most higher plants, leading to a substantial reduction in the IR. The phylogenetic analysis using both matK and nrITS revealed that T. yongtaiensis is sister to T. heterostaminata with moderate support, and formed a clade with other Terniopsis species, suggesting that the new species belongs to Tristichoideae.

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Research Article Mon, 18 Apr 2022 18:29:17 +0300
Species discrimination of novel chloroplast DNA barcodes and their application for identification of Panax (Aralioideae, Araliaceae) https://phytokeys.pensoft.net/article/75937/ PhytoKeys 188: 1-18

DOI: 10.3897/phytokeys.188.75937

Authors: Nguyen Nhat Linh, Pham Le Bich Hang, Huynh Thi Thu Hue, Nguyen Hai Ha, Ha Hong Hanh, Nguyen Dang Ton, Le Thi Thu Hien

Abstract: Certain species within the genus Panax L. (Araliaceae) contain pharmacological precious ginsenosides, also known as ginseng saponins. Species containing these compounds are of high commercial value and are thus of particular urgency for conservation. However, within this genus, identifying the particular species that contain these compounds by morphological means is challenging. DNA barcoding is one method that is considered promising for species level identification. However, in an evolutionarily complex genus such as Panax, commonly used DNA barcodes such as nrITS, matK, psbA-trnH, rbcL do not provide species-level resolution. A recent in silico study proposed a set of novel chloroplast markers, trnQ-rps16, trnS-trnG, petB, and trnE-trnT for species level identification within Panax. In the current study, the discriminatory efficiency of these molecular markers is assessed and validated using 91 reference barcoding sequences and 38 complete chloroplast genomes for seven species, one unidentified species and one sub-species of Panax, and two outgroup species of Aralia L. along with empirical data of Panax taxa present in Vietnam via both distance-based and tree-based methods. The obtained results show that trnQ-rps16 can classify with species level resolution every clade tested here, including the highly valuable Panax vietnamensis Ha et Grushv. We thus propose that this molecular marker to be used for identification of the species within Panax to support both its conservation and commercial trade.

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Research Article Thu, 6 Jan 2022 11:53:30 +0200
An image dataset of cleared, x-rayed, and fossil leaves vetted to plant family for human and machine learning https://phytokeys.pensoft.net/article/72350/ PhytoKeys 187: 93-128

DOI: 10.3897/phytokeys.187.72350

Authors: Peter Wilf, Scott L. Wing, Herbert W. Meyer, Jacob A. Rose, Rohit Saha, Thomas Serre, N.Rubén Cúneo, Michael P. Donovan, Diane M. Erwin, Maria A. Gandolfo, Erika Gonzalez-Akre, Fabiany Herrera, Shusheng Hu, Ari Iglesias, Kirk R. Johnson, Talia S. Karim, Xiaoyu Zou

Abstract: Leaves are the most abundant and visible plant organ, both in the modern world and the fossil record. Identifying foliage to the correct plant family based on leaf architecture is a fundamental botanical skill that is also critical for isolated fossil leaves, which often, especially in the Cenozoic, represent extinct genera and species from extant families. Resources focused on leaf identification are remarkably scarce; however, the situation has improved due to the recent proliferation of digitized herbarium material, live-plant identification applications, and online collections of cleared and fossil leaf images. Nevertheless, the need remains for a specialized image dataset for comparative leaf architecture. We address this gap by assembling an open-access database of 30,252 images of vouchered leaf specimens vetted to family level, primarily of angiosperms, including 26,176 images of cleared and x-rayed leaves representing 354 families and 4,076 of fossil leaves from 48 families. The images maintain original resolution, have user-friendly filenames, and are vetted using APG and modern paleobotanical standards. The cleared and x-rayed leaves include the Jack A. Wolfe and Leo J. Hickey contributions to the National Cleared Leaf Collection and a collection of high-resolution scanned x-ray negatives, housed in the Division of Paleobotany, Department of Paleobiology, Smithsonian National Museum of Natural History, Washington D.C.; and the Daniel I. Axelrod Cleared Leaf Collection, housed at the University of California Museum of Paleontology, Berkeley. The fossil images include a sampling of Late Cretaceous to Eocene paleobotanical sites from the Western Hemisphere held at numerous institutions, especially from Florissant Fossil Beds National Monument (late Eocene, Colorado), as well as several other localities from the Late Cretaceous to Eocene of the Western USA and the early Paleogene of Colombia and southern Argentina. The dataset facilitates new research and education opportunities in paleobotany, comparative leaf architecture, systematics, and machine learning.

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Research Article Thu, 16 Dec 2021 11:01:13 +0200
FlorItaly – the portal to the Flora of Italy https://phytokeys.pensoft.net/article/54023/ PhytoKeys 156: 55-71

DOI: 10.3897/phytokeys.156.54023

Authors: Stefano Martellos, Fabrizio Bartolucci, Fabio Conti, Gabriele Galasso, Andrea Moro, Riccardo Pennesi, Lorenzo Peruzzi, Elena Pittao, Pier Luigi Nimis

Abstract: Digital data concerning the flora of Italy are largely fragmented among different resources hosted on different platforms, and often with different data standards, which are neither connected by a common access point, nor by web services, thus constituting a relevant obstacle to data access and usage. Taxonomic incongruences add a further complication. This paper describes “FlorItaly”, an online information system which allows to access and query updated information on the checklist of the flora of Italy, aiming at becoming an aggregator for Italian botanical resources. “FlorItaly” was developed in a collaborative effort by more than 50 taxonomists, with the support of the Italian Botanical Society, and of Project “Dryades” (University of Trieste), to provide a better and reliable organization of botanical knowledge in Italy, as well as a relevant simplification for data retrieval, and a further stimulus towards a more collaborative approach in botanical research.

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Research Article Fri, 21 Aug 2020 12:13:35 +0300
Mountains of the Mist: A first plant checklist for the Bvumba Mountains, Manica Highlands (Zimbabwe-Mozambique) https://phytokeys.pensoft.net/article/49257/ PhytoKeys 145: 93-129

DOI: 10.3897/phytokeys.145.49257

Authors: Jonathan Timberlake, Petra Ballings, João de Deus Vidal Jr., Bart Wursten, Mark Hyde, Anthony Mapaura, Susan Childes, Meg Coates Palgrave, Vincent Ralph Clark

Abstract: The first comprehensive plant checklist for the Bvumba massif, situated in the Manica Highlands along the Zimbabwe-Mozambique border, is presented. Although covering only 276 km2, the flora is rich with 1250 taxa (1127 native taxa and 123 naturalised introductions). There is a high proportion of Orchidaceae and Pteridophyta, with both groups showing a higher richness than for adjacent montane areas, which may be due to the massif’s relatively high moisture levels as a result of frequent cloud cover. However, in contrast to other mesic montane regions in southern Africa, there are relatively few near-endemic or range-restricted taxa: there is only one local endemic, Aeranthes africana, an epiphytic forest orchid. This is likely to be an effect of the massif having limited natural grassland compared to forest, the former being the most endemic-rich habitat in southern African mountains outside of the Fynbos Biome. Six other near-endemic taxa with limited distribution in this portion of the Manica Highlands are highlighted. The high number of invasive species is probably a result of diverse human activities in the area. The main species of concern are Acacia melanoxylon, a tree that is invading grassland and previously cultivated land, the forest herb Hedychium gardnerianum which in places is transforming forest understorey with an adverse effect on some forest birds, and the woody herb Vernonanthura polyanthes which invades cleared forest areas after fire. Future botanical work in the massif should focus on a more detailed exploration of the poorly known Serra Vumba on the Mozambican side and on the drier western slopes. This will allow for a more detailed analysis of patterns of endemism across the Manica Highlands.

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Research Article Fri, 10 Apr 2020 10:54:07 +0300
Plastome of Quercus xanthoclada and comparison of genomic diversity amongst selected Quercus species using genome skimming https://phytokeys.pensoft.net/article/36365/ PhytoKeys 132: 75-89

DOI: 10.3897/phytokeys.132.36365

Authors: Damien Daniel Hinsinger, Joeri Sergej Strijk

Abstract: The genus Quercus L. contains several of the most economically important species for timber production in the Northern Hemisphere. It was one of the first genera described, but genetic diversity at a global scale within and amongst oak species remains unclear, despite numerous regional or species-specific assessments. To evaluate global plastid diversity in oaks, we sequenced the complete chloroplast of Quercus xanthoclada and compared its sequence with those available from other main taxonomic groups in Quercus. We quantify genomic divergence amongst oaks and performed a sliding window analysis to detect the most variable regions amongst members of the various clades, as well as divergent regions occurring in specific pairs of species. We identified private and shared SNPs amongst oaks species and sections and stress the need for a large global assessment of genetic diversity in this economically and ecologically important genus.

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Research Article Tue, 1 Oct 2019 10:51:07 +0300
Simple but long-lasting: A specimen imaging method applicable for small- and medium-sized herbaria https://phytokeys.pensoft.net/article/29434/ PhytoKeys 118: 1-14

DOI: 10.3897/phytokeys.118.29434

Authors: Atsuko Takano, Yasuhiko Horiuchi, Yu Fujimoto, Kouta Aoki, Hiromune Mitsuhashi, Akira Takahashi

Abstract: Major international herbaria, natural history museums and universities have recently begun to digitise their collections to facilitate studies and improve access to collections. In Japan, more than 10 million herbarium specimens are housed in various universities/museums; however, only 1% of these have been digitised. In this paper, we describe a new method for imaging herbarium specimens that is applicable to local/small herbaria. It is safe, fast, simple and inexpensive, but also satisfies usage guidelines for minimum image quality and can produce digital files suitable for long-term storage and future post production. During an eight-month trial at the Museum of Nature and Human Activities, Hyogo, with three part-time workers using a custom-made copy stand and a mirrorless interchangeable lens camera with a large LED light bank system, we were able to image 73,180 herbarium specimens (571 per day on average), obtaining two RAW and two JPEG files for each specimen.

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Research Article Mon, 18 Feb 2019 12:21:18 +0200
Togo National Herbarium database https://phytokeys.pensoft.net/article/25385/ PhytoKeys 109: 1-16

DOI: 10.3897/phytokeys.109.25385

Authors: Raoufou Radji, Kossi Adjonou, Marie-Luce Akossiwoa Quashie, Komlan Edjèdu Sodjinou, Francisco Pando, Kouami Kokou

Abstract: This article describes the herbarium database of the University of Lomé. The database provides a good representation of the current knowledge of the flora of Togo. The herbarium of University of Lomé, known also as Herbarium togoense is the national herbarium and is registered in Index Herbariorum with the abbreviation TOGO. It contains 15,000 specimens of vascular plants coming mostly from all Togo's ecofloristic regions. Less than one percent of the specimens are from neighbouring countries such as Ghana, Benin and Burkina Faso. Collecting site details are specified in more that 97% of the sheet labels, but only about 50% contain geographic coordinates. Besides being a research resource, the herbarium constitutes an educational collection. The dataset described in this paper is registered with GBIF and accessible at https://www.gbif.org/dataset/b05dd467-aaf8-4c67-843c-27f049057b78. It was developed with the RIHA software (Réseau Informatique des Herbiers d'Afrique). The RIHA system (Chevillotte and Florence 2006, Radji et al. 2009) allows the capture of label data and associated information such as synonyms, vernacular names, taxonomic hierarchy and references.

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Data Paper Thu, 13 Sep 2018 11:30:00 +0300
RAINBIO: a mega-database of tropical African vascular plants distributions https://phytokeys.pensoft.net/article/9723/ PhytoKeys 74: 1-18

DOI: 10.3897/phytokeys.74.9723

Authors: Gilles Dauby, Rainer Zaiss, Anne Blach-Overgaard, Luís Catarino, Theo Damen, Vincent Deblauwe, Steven Dessein, John Dransfield, Vincent Droissart, Maria Cristina Duarte, Henry Engledow, Geoffrey Fadeur, Rui Figueira, Roy E. Gereau, Olivier J. Hardy, David J. Harris, Janneke de Heij, Steven Janssens, Yannick Klomberg, Alexandra C. Ley, Barbara A. MacKinder, Pierre Meerts, Jeike L. van de Poel, Bonaventure Sonké, Marc S. M. Sosef, Tariq Stévart, Piet Stoffelen, Jens-Christian Svenning, Pierre Sepulchre, Xander van der Burgt, Jan J. Wieringa, Thomas L. P. Couvreur

Abstract: The tropical vegetation of Africa is characterized by high levels of species diversity but is undergoing important shifts in response to ongoing climate change and increasing anthropogenic pressures. Although our knowledge of plant species distribution patterns in the African tropics has been improving over the years, it remains limited. Here we present RAINBIO, a unique comprehensive mega-database of georeferenced records for vascular plants in continental tropical Africa. The geographic focus of the database is the region south of the Sahel and north of Southern Africa, and the majority of data originate from tropical forest regions. RAINBIO is a compilation of 13 datasets either publicly available or personal ones. Numerous in depth data quality checks, automatic and manual via several African flora experts, were undertaken for georeferencing, standardization of taxonomic names and identification and merging of duplicated records. The resulting RAINBIO data allows exploration and extraction of distribution data for 25,356 native tropical African vascular plant species, which represents ca. 89% of all known plant species in the area of interest. Habit information is also provided for 91% of these species.

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Data Paper Mon, 7 Nov 2016 19:45:40 +0200
Grassroots e-floras in the Poaceae: growing GrassBase and GrassWorld https://phytokeys.pensoft.net/article/5091/ PhytoKeys 48: 73-84

DOI: 10.3897/phytokeys.48.7159

Authors: Maria S. Vorontsova, Derek Clayton, Bryan K. Simon

Abstract: GrassBase and GrassWorld are the largest structured descriptive datasets in plants, publishing descriptions of 11,290 species in the DELTA format. Twenty nine years of data compilation and maintenance have created a dataset which now underpins much of the Poaceae bioinformatics. GrassBase and GrassWorld can continue to grow productively if the proliferation of alternative classifications and datasets can be brought together into a consensus system. If the datasets are reconciled instead of diverging further apart a long term cumulative process can bring knowledge together for great future utility. This paper presents the Poaceae as the first and largest model system for e-taxonomy and the study of classification development in plants. The origin, development, and content of both datasets is described and key contributors are noted. The challenges of alternative classifications, data divergence, collaborative contribution mechanisms, and software are outlined.

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Review Article Wed, 15 Apr 2015 00:00:00 +0300
The use of Optical Character Recognition (OCR) in the digitisation of herbarium specimen labels https://phytokeys.pensoft.net/article/1533/ PhytoKeys 38: 15-30

DOI: 10.3897/phytokeys.38.7168

Authors: Robyn Drinkwater, Robert Cubey, Elspeth Haston

Abstract: At the Royal Botanic Garden Edinburgh (RBGE) the use of Optical Character Recognition (OCR) to aid the digitisation process has been investigated. This was tested using a herbarium specimen digitisation process with two stages of data entry. Records were initially batch-processed to add data extracted from the OCR text prior to being sorted based on Collector and/or Country. Using images of the specimens, a team of six digitisers then added data to the specimen records. To investigate whether the data from OCR aid the digitisation process, they completed a series of trials which compared the efficiency of data entry between sorted and unsorted batches of specimens. A survey was carried out to explore the opinion of the digitisation staff to the different sorting options. In total 7,200 specimens were processed.When compared to an unsorted, random set of specimens, those which were sorted based on data added from the OCR were quicker to digitise. Of the methods tested here, the most successful in terms of efficiency used a protocol which required entering data into a limited set of fields and where the records were filtered by Collector and Country. The survey and subsequent discussions with the digitisation staff highlighted their preference for working with sorted specimens, in which label layout, locations and handwriting are likely to be similar, and so a familiarity with the Collector or Country is rapidly established.

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Research Article Mon, 19 May 2014 00:00:00 +0300
Sinfonevada: Dataset of Floristic diversity in Sierra Nevada forests (SE Spain) https://phytokeys.pensoft.net/article/1519/ PhytoKeys 35: 1-15

DOI: 10.3897/phytokeys.35.6363

Authors: Antonio Jesús Pérez-Luque, Francisco Javier Bonet, Ramón Pérez-Pérez, Rut Aspizua, Juan Lorite, Regino Zamora

Abstract: The Sinfonevada database is a forest inventory that contains information on the forest ecosystem in the Sierra Nevada mountains (SE Spain). The Sinfonevada dataset contains more than 7,500 occurrence records belonging to 270 taxa (24 of these threatened) from floristic inventories of the Sinfonevada Forest inventory. Expert field workers collected the information. The whole dataset underwent a quality control by botanists with broad expertise in Sierra Nevada flora. This floristic inventory was created to gather useful information for the proper management of Pinus plantations in Sierra Nevada. This is the only dataset that shows a comprehensive view of the forest flora in Sierra Nevada. This is the reason why it is being used to assess the biodiversity in the very dense pine plantations on this massif. With this dataset, managers have improved their ability to decide where to apply forest treatments in order to avoid biodiversity loss. The dataset forms part of the Sierra Nevada Global Change Observatory (OBSNEV), a long-term research project designed to compile socio-ecological information on the major ecosystem types in order to identify the impacts of global change in this area.

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Data Paper Mon, 17 Feb 2014 00:00:00 +0200
Fast, linked, and open – the future of taxonomic publishing for plants: launching the journal PhytoKeys https://phytokeys.pensoft.net/article/1356/ PhytoKeys 1: 1-14

DOI: 10.3897/phytokeys.1.642

Authors: Lyubomir Penev, W. John Kress, Sandra Knapp, De-Zhu Li, Susanne Renner

Abstract: The paper describes the focus, scope and the rationale of PhytoKeys, a newly established, peer-reviewed, open-access journal in plant systematics. PhytoKeys is launched to respond to four main challenges of our time: (1) Appearance of electronic publications as amendments or even alternatives to paper publications; (2) Open Access (OA) as a new publishing model; (3) Linkage of electronic registers, indices and aggregators that summarize information on biological species through taxonomic names or their persistent identifiers (Globally Unique Identifiers or GUIDs; currently Life Science Identifiers or LSIDs); (4) Web 2.0 technologies that permit the semantic markup of, and semantic enhancements to, published biological texts. The journal will pursue cutting-edge technologies in publication and dissemination of biodiversity information while strictly following the requirements of the current International Code of Botanical Nomenclature (ICBN).

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Forum Paper Mon, 1 Nov 2010 00:00:00 +0200