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Journal article
Rapid Least Concern: towards automating Red List assessments
The IUCN Red List of Threatened SpeciesTM (hereafter the Red List) is an important global resource for conservation that supports conservation planning, safeguarding critical habitat and monitoring biodiversity change (Rodrigues et al. 2006). However, a major shortcoming of the Red List is that most of the world's described species have...Bachman, Steven ; Walker, Barnaby ; Barrios, Sara ; Copeland, Alison ; Moat, Justin
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Journal article
Three new species and some nomenclatural changes in Senecio (Compositae/Asteraceae: Senecioneae) in the Flora Zambesiaca area
Three new Senecio species are described, S. fanshawei from Zambia, S. ngandae from Malawi and S. nyangani from Zimbabwe. A new combination is made under S. brachypodus and a taxon is added to the synonymy of this species; single taxa are added for the first time to the synonymy of...Beentje, Henk
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Journal article
Characterization of sequence variability hotspots in Cranichideae plastomes (Orchidaceae, Orchidoideae)
This study reports complete plastome sequences for six species of Neotropical Cranichideae and focuses on identification of the most variable regions (hotspots) in this group of orchids. These structure of these six plastomes is relatively conserved, exhibiting lengths ranging between 142,599 to 154,562 bp with 36.7% GC on average and...Smidt, Eric de Camargo ; Páez, Michelle Zavala ; Vieira, Leila do Nascimento ; Viruel, Juan ; de Baura, Valter Antônio …
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Journal article
The Global Museum: natural history collections and the future of evolutionary science and public education
Natural history museums are unique spaces for interdisciplinary research and educational innovation. Through extensive exhibits and public programming and by hosting rich communities of amateurs, students, and researchers at all stages of their careers, they can provide a place-based window to focus on integration of science and discovery, as well... -
Journal article
A taxonomic monograph of Ipomoea integrated across phylogenetic scales
Taxonomic monographs have the potential to make a unique contribution to the understanding of global biodiversity. However, such studies, now rare, are often considered too daunting to undertake within a realistic time frame, especially as the world’s collections have doubled in size in recent times. Here, we report a global-scale...Muñoz-Rodríguez, Pablo ; Carruthers, Tom ; Wood, John R. I. ; Williams, Bethany R. M. ; Weitemier, Kevin …
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Journal article
Lepiniopsis ternatensis sap stimulates fibroblast proliferation and down regulates macrophage TNF-α secretion
The sap of the tree Lepiniopsis ternatensis is used as a topical treatment for cutaneous leg ulcers in Papua New Guinea. This study, which is the first investigation of this medicinal plant, examines the effect of the sap on wound healing biology using human-derived primary cell lines. NMR spectra from...Moses, Rachael L. ; Dally, Jordanna ; Lundy, Fionnuala T. ; Langat, Moses K. ; Kiapranis, Robert …
fibroblast, Lepiniopsis ternatensis, trifucol, TNF-α, Papua New Guinea, and wound healing
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Journal article
High-quality genome sequence of white lupin provides insight into soil exploration and seed quality
White lupin (Lupinus albus L.) is an annual crop cultivated for its protein-rich seeds. It is adapted to poor soils due to the production of cluster roots, which are made of dozens of determinate lateral roots that drastically improve soil exploration and nutrient acquisition (mostly phosphate). Using long-read sequencing technologies,...Hufnagel, Bárbara ; Marques, André ; Soriano, Alexandre ; Marquès, Laurence ; Divol, Fanchon …
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Journal article
The British species of Otidea (3): taxa present in Britain
An account of British species and taxa of Otidea is presented based on morphology and molecular data obtained from the fungarium collections, at Royal Botanic Gardens, Kew (K) and elsewhere. Based on a phylogenetic analysis using the internal transcribed spacer (ITS) sequences of the fungal nuclear rDNA, sixteen named and...Parslow, Mariko ; Suz, Laura M. ; Spooner, Brian
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Journal article
A new genus and species of foliicolous lichen in a new family of Strigulales (Ascomycota: Dothideomycetes) reveals remarkable class-level homoplasy
Phylogenetic analysis of some foliicolous lichens collected in Hainan Province, China, revealed a new lineage morphologically similar to Porina but phylogenetically related to Strigulaceae (Dothideomycetes), differing from the latter in ascus type. The monospecific genus Tenuitholiascus gen. nov. is introduced for the single species, T. porinoides sp. nov., which is...Jiang, Shu Hua ; Hawksworth, David L. ; Lücking, Robert ; Wei, Jiang Chun
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Journal article
Lack of adequate seed supply is a major bottleneck for effective ecosystem restoration in Chile: friendly amendment to Bannister et al. (2018)
We argue that the need for a quality seed supply chain is a major bottleneck for the restoration of Chile's native ecosystems, thus supplementing the list of bottlenecks proposed by Bannister et al. in 2018. Specifically, there is a need for defining seed transfer zones, developing standards and capacities for...León‐Lobos, Pedro ; Bustamante‐Sánchez, Marcela A. ; Nelson, Cara R. ; Alarcón, Diego ; Hasbún, Rodrigo …
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Journal article
ddRAD analyses reveal a credible phylogenetic relationship of the four main genera of Bambusa-Dendrocalamus-Gigantochloa complex (Poaceae: Bambusoideae)
The Bambusa-Dendrocalamus-Gigantochloa complex (BDG complex) is the most diversified and phylogenetically recalcitrant group of the paleotropical woody bamboos. Species of this complex occur in tropical and subtropical Asia and most of them are of great economic, cultural and ecological value. The lack of resolution achieved through the analyses of previous...Liu, Jing-Xia ; Zhou, Meng-Yuan ; Yang, Guo-Qian ; Zhang, Yu-Xiao ; Ma, Peng-Fei …
ancient introgression, nDNA-plastid DNA associations, morphological evidence, genome-wide SNPs, and BDG complex
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Journal article
A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project
High-throughput DNA sequencing techniques enable time- and cost-effective sequencing of large portions of the genome. Instead of sequencing and annotating whole genomes, many phylogenetic studies focus sequencing effort on large sets of pre-selected loci, which further reduces costs and bioinformatic challenges while increasing coverage. One common approach that enriches loci...Andermann, Tobias ; Torres Jiménez, Maria Fernanda ; Matos-Maraví, Pável ; Batista, Romina ; Blanco-Pastor, José L. …
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Journal article
Ninety-three new combinations in Euploca for species of Heliotropium section Orthostachys (Boraginaceae sensu APG)
Many new combinations are needed in Euploca, previously regarded as Heliotropium section Orthostachys, to correspond with results of our forthcoming, world-wide, molecular phylogenetic analysis. We also need these names for our many δ13C determinations that identify many Euploca species exhibiting C4 photosynthesis and show that other Euploca species are not...Frohlich, Michael W. ; Thulin, Mats ; Chase, Mark W.
carbon assimilation systems, Eudicots, Australia, and Heliotropiaceae
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Journal article
Drymaria veliziae (Caryophyllaceae), a new species from the Andes of Cajamarca (North Peru)
A new species from the Northern Peruvian Andes (Cajamarca department), Drymaria veliziaesp. nov., is proposed in the present paper. It grows in the high-elevation montane grasslands and it is morphologically similar to D. auriculipetala from which it differs in having elliptic-ovate leaves, blade margin bases glandular, large number of stipules...Montesinos-Tubée, Daniel B. ; Tovar, Carolina ; Iberico-Vela, Gustavo ; Montoya-Quino, Juan ; Sanchez-Vega, Isidoro
Cajamarca, Caryophyllaceae, new species, and Andes
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Journal article
Mcdadea: A New Genus of Acanthaceae Endemic to the Namib Desert of Southwestern Angola
Acanthaceae represent one of the most ecologically dominant families of plants in the Namib Desert and adjacent portions of Namibia and Angola yet have never been comprehensively treated from a taxonomic perspective in the region. Recent fieldwork in Angola yielded discovery of two populations of plants, morphologically allied to the...Tripp, Erin A. ; Darbyshire, Iain
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Journal article
A third of the tropical African flora is potentially threatened with extinction
Preserving tropical biodiversity is an urgent challenge when faced with the growing needs of countries. Despite their crucial importance for terrestrial ecosystems, most tropical plant species lack extinction risk assessments, limiting our ability to identify conservation priorities. Using a novel approach aligned with IUCN Red List criteria, we conducted a...Stévart, T. ; Dauby, G. ; Lowry, P. P. ; Blach-Overgaard, A. ; Droissart, V. …
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Journal article
Early growth phase and caffeine content response to recent and projected increases in atmospheric carbon dioxide in coffee (Coffea arabica and C. canephora)
While [CO2] effects on growth and secondary chemistry are well characterized for annual plant species, little is known about perennials. Among perennials, production of Coffea arabica and C. canephora (robusta) have enormous economic importance worldwide. Three Arabica cultivars (Bourbon, Catimor, Typica) and robusta coffee were grown from germination to ca....Vega, Fernando E. ; Ziska, Lewis H. ; Simpkins, Ann ; Infante, Francisco ; Davis, Aaron P. …
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Journal article
Hanceola suffruticosa (Lamiaceae, Nepetoideae), a new species from the Sino-Vietnamese border
Hanceola is a genus of eight herbaceous species previously thought to be endemic to southern China. However, H. suffruticosa, a new species described here from China and Vietnam, differs from all other species of Hanceola by its subshrubby habit. It is also distinct in its shallowly bicrenate laminae and densely...Chen, Ya-Ping ; Paton, Alan J. ; Xiang, Chun-Lei
Hanceola, Sino-Vietnamese border, Hanceolinae, Ocimeae, and new species
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Journal article
Historic herbarium specimens as biocultural assets: An examination of herbarium specimens and their in situ plant communities of the Agulhas National Park, South Africa
Globally there is a need for protected areas to conserve both biodiversity and heritage. Historic specimen localities, although significant to botanists, are not known or recognized under the global heritage umbrella; yet they form an important component of the protected area landscape. We aimed to articulate the conservation and heritage...Cowell, Carly R. ; Anderson, Pippin M. L. ; Annecke, Wendy A.
conservation, fynbos, botanical collectors, biocultural heritage, Cape Colony, Agulhas Plain, and Bolus
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Journal article
Implications of next-generation sequencing for the systematics and evolution of the terrestrial orchid genus Epipactis, with particular reference to the British Isles
Recent application of next-generation sequencing technology to Eurasian taxa of the primitive epidendroid orchid clade Epipactis section Epipactis has further advanced our knowledge of what has become a model system for studying the origins of numerous autogamous taxa from within arguably only one allogamous ancestral species, E. helleborine s.s. Current...Bateman, Richard M.
ancestor-descendant relationships, species circumscription, evolutionary radiation, autogamy, allogamy, speciation, geitonogamy, species concept, and fluctuating asymmetry
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Journal article
Comparative carpological study of Poikilospermum (Urticaceae) in relation to taxonomy
Fruit morphology and the anatomical structure of the pericarp, fruiting perianth, and seed coat were studied in 15 species of Poikilospermum, a genus whose position within the Urticaceae has long been controversial. Possible evolutionary trends of their transformation are suggested for both subgenera; plesiomorphies were found in P. oblongifolium and...Kravtsova, T. I. ; Moore, A. ; Wilmot-Dear, C. M. ; Zhinkina, N. A.
Urticeae, taxonomy, evolution, fruit and seed anatomy, and dispersal
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Journal article
Dichapetalum stahlii (Dichapetalaceae), a new species from Ecuador
A new species, Dichapetalum stahlii, is described from Los Rios in western Ecuador. It is the ninth species of the genus with fimbriate stipules. A key is provided for the seven known Ecuadorian species of the genus.Prance, Ghillean T.
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Journal article
New combinations in Guilandina (Leguminosae: Caesalpinioideae)
The Caesalpinia Group (Leguminosae: Caesalpinioideae) and the genus Caesalpinia sensu lato were recently reclassified resulting in a reduction in the number of species in Caesalpinia sensu stricto to nine. Of the genera now accepted as distinct from Caesalpinia, the pantropical genus Guilandina lacks any recent global taxonomic account and estimates...Lewis, G. P.
nomenclature and Fabaceae
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Journal article
Endemism patterns are scale dependent
Areas of endemism are important in biogeography because they capture facets of biodiversity not represented elsewhere. However, the scales at which they are relevant to research and conservation are poorly analysed. Here, we calculate weighted endemism (WE) and phylogenetic endemism (PE) separately for all birds and amphibians across the globe....Daru, Barnabas H. ; Farooq, Harith ; Antonelli, Alexandre ; Faurby, Søren
biogeography, evolutionary ecology, and conservation biology
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Journal article
FluentDNA: Nucleotide Visualization of Whole Genomes, Annotations, and Alignments
Researchers seldom look at naked genome assemblies: instead the attributes of DNA sequences are mediated through statistics, annotations and high level summaries. Here we present software that visualizes the bare sequences of whole genome assemblies in a zoomable interface. This can assist in detection of chromosome architecture and contamination by... -
Journal article
outsider: Install and run programs, outside of R, inside of R
In many areas of research, product development and software engineering, analytical pipelines – workflows connecting output from multiple software – are key for processing and running tests on data. They can provide results in a consistent, modular and transparent manner. Pipelines also make it easier to demonstrate the reproducibility of...Bennett, Dominic ; Hettling, Hannes ; Silvestro, Daniele ; Vos, Rutger ; Antonelli, Alexandre
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Journal article
Strategies for reducing per‐sample costs in target capture sequencing for phylogenomics and population genomics in plants
The reduced cost of high‐throughput sequencing and the development of gene sets with wide phylogenetic applicability has led to the rise of sequence capture methods as a plausible platform for both phylogenomics and population genomics in plants. An important consideration in large targeted sequencing projects is the per‐sample cost, which... -
Editorial
Flowers and inflorescences of eudicots
Angiosperms dominate our terrestrial ecosystems, and the remarkable flowers and inflorescences have evolved into a spectacular and remarkably diversity. However, despite much research on their unique reproductive structures, there is still much that we do not know about how angiosperms rose to such dominance, how the first flowers evolved and...Bachelier, Julien B. ; Fay, Michael F.
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Journal article
A new species of Myrsine (Primulaceae-Myrsinoideae) from New Guinea
Myrsine exquisitorum Utteridge & Lepschi (Primulaceae-Myrsinoideae) is described and illustrated as a new species endemic to the Western Highlands Province from Papua New Guinea. The new species is unique in the relatively large, almost orbicular leaves with entire margins, and the tetramerous flowers arranged in axillary fascicles without forming short...Utteridge, Timothy M.A. ; Lepschi, Brendan J.
Rapanea, Papuasia, Eudicots, taxonomy, Malesia, and Myrsinaceae
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Journal article
Direct and indirect effects of fragmentation on seed dispersal traits in a fragmented agricultural landscape.
Dener, Efrat ; Ovadia, Ofer ; Shemesh, Hagai ; Altman, Ariel ; Chen, Si-Chong …
Structural equation modeling, Seed dispersal, Agricultural landscape, Fragmentation, and Indirect effects
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Journal article
Seeing through the clouds - Mapping desert fog oasis ecosystems using 20 years of MODIS imagery over Peru and Chile.
Moat, Justin ; Orellana-Garcia, Alfonso ; Tovar, Carolina ; Arakaki, Mónica ; Arana, César …
Tillandsia, Oasis de Niebla, Remote sensing, Google Earth Engine, Atacama, and Lomas
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Journal article
Expansion of Calanthe to include the species of Cephalantheropsis, Gastrorchis and Phaius (Collabieae; Orchidaceae).
Chase, Mark W. ; Christenhusz, Maarten J. M. ; Schuiteman, André
Pantropical orchid genera, orchid classification, Monocots, Epidendroidae, Calanthe, Orchid classification, and Monocots
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Journal article
Seed cryopreservation of orchid Coelogyne nitida (Wall. ex Don) Lindl. using air desiccation and vitrification techniques.
Chaudhury, Rekha ; Shankar, M. ; Rampal ; Awasthi , Manuj ; Thongam , Biseshwori …
Protocorms, Orchidaceae, TTC, Coelogyne nitida, Asymbiotic germination, and Cryobanking
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Journal article
The enigma of Link’s Sphaeria ericophila : nomenclature, taxonomy, molecular phylogeny, and implications for the placement of Metacapnodium.
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Journal article
Light in the darkness: how ferns flourished in the ancestral angiosperm forest.
This article is a Commentary on Cai et al. (2021), 230: 1201–1213.Chater, Caspar C. C.
Ferns, Light levels, Fern radiation, Fern evolution, and Fossil record
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Journal article
Low dispersal and ploidy differences in a grass maintain photosynthetic diversity despite gene flow and habitat overlap.
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Journal article
The diverse assemblage of fungal endophytes from orchids in Madagascar linked to abiotic factors and seasonality.
This article belongs to the Special Issue The Ecology and Diversity of Orchids.Yokoya, Kazutomo ; Zettler, Lawrence W. ; Bell, Jake ; Kendon, Jonathan P. ; Jacob, Alison S. …
Conservation, Madacascar, Mycorrhiza, Orchidaceae, In vitro, and Biodiversity hotspots
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Journal article
Central Asian wild tulip conservation requires a regional approach, especially in the face of climate change.
Wilson, Brett ; Burgess, Benjamin J. ; Clubbe, Colin ; Shalpykov, Kaiyrkul ; Ganybaeva, Myskalai …
Species distribution modelling , Climate change , Tulipa, Wild tulips , Central Asia, and MaxEnt
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Journal article
Patterns of transmission and horizontal gene transfer in the Dioscorea sansibarensis leaf symbiosis revealed by whole-genome sequencing.
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Journal article
Palynological characterization of the Southeast Asian woody climbers Decalobanthus Ooststr. (Convolvulaceae).
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Journal article
Shade alters the growth and architecture of tropical grasses by reducing root biomass.
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Journal article
In situ morphometric survey elucidates the evolutionary systematics of the orchid genus Gymnadenia in the British Isles.
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Journal article
Rediscovering Rhipsalis hoelleri (Cactaceae), a Critically Endangered species from Brazilian Atlantic Forest.
Cardoso, Weverson Cavalcante ; Negrão, Raquel ; Dutra, Valquiria Ferreira ; Sakuragui, Cassia Mônica
Distribution, Eudicots, Rhipsalis hoelleri , Flora, Rhipsalideae, Eastern Brazil, and Conservation
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Journal article
Phylogenomics of Brosimum (Moraceae) and allied genera, including a revised subgeneric system.
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Journal article
Checklist of Kilimanjaro grasses shows that both plot and herbarium methods are necessary to record diversity.
Prunera-Olivé, Joan ; Vorontsova , Maria S. ; Williams , Emma V. ; Mollel , Neduvoto P. ; Hemp, Andreas
Diversity, Tanzania, diversity, Monocots, Checklist, Grasses, Kilimanjaro, and Poaceae
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Journal article
Physiological and environmental control of seed germination timing in Mediterranean mountain populations of Gundelia tournefortii.
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Journal article
Phylogeny and historical biogeography of the pantropical genus Parkia (Leguminosae, Caesalpinioideae, mimosoid clade).
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Journal article
Fire‑mediated germination syndromes in Leucadendron (Proteaceae) and their functional correlates.
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Journal article
Contrasting genetic signal of recolonisation after rainforest fragmentation in African trees with different dispersal abilities.
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Journal article
Towards a global list of accepted species III. Independence and stakeholder inclusion.
Conix, Stijn ; Garnett, Stephen T. ; Thiele, Kevin R. ; Christidis, Les ; Dijk, Peter Paul van …
Users of taxonomy, Independence of science, Taxonomic list , Freedom of science, and Values in science
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Journal article
The role of Quaternary glaciations in shaping biogeographic patterns in a recently evolved clade of South American epiphytic orchids.
To contribute to what is known about involvement of vegetation dynamics in Neotropical speciation, we used the Epidendrum latilabre complex, a taxonomically well-defined species group, to investigate past connections between Amazonian (AM) and Atlantic (AF) forests and address the following topics: (1) divergence times between sister species currently distributed in... -
Journal article
Floral development and vasculature in Eriocaulon (Eriocaulaceae) provide insights into the evolution of Poales.
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Journal article
Distribution changes in páramo plants from the equatorial high Andes in response to increasing temperature and humidity variation since 1880.
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Editorial
Linking Stomatal Development and Physiology: From Stomatal Models to Non-model Species and Crops.
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Journal article
Plastid phylogenomics of Pleurothallidinae (Orchidaceae): Conservative plastomes, new variable markers, and comparative analyses of plastid, nuclear, and mitochondrial data.
We present the first comparative plastome study of Pleurothallidinae with analyses of structural and molecular characteristics and identification of the ten most-variable regions to be incorporated in future phylogenetic studies. We sequenced complete plastomes of eight species in the subtribe and compared phylogenetic results of these to parallel analyses of... -
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