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Journal article
Towards a Monophyletic Infrageneric Circumscription of Adesmia DC. (Dalbergieae, Leguminosae): a Taxonomic Revision in Adesmia series Adesmia.
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Journal article
Taxonomic characterisation of the Regianum clade (genus Tuber) and the trait evolution of spore size among true truffles.
The genus comprises ectomycorrhizal fungal species producing belowground ascomata, including the gastronomically most prominent hypogeous fungi. Since the discovery and description of new species are ongoing, the proportion of undescribed species can be considerable and the taxonomy of the genus goes often through changes. The taxonomy of the genus would... -
Journal article
Three new species in Russula subsection Xerampelinae supported by genealogical and phenotypic coherence.
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Journal article
The genus Fomitopsis (Polyporales, Basidiomycota) reconsidered.
Based on seven- and three-gene datasets, we discuss four alternative approaches for a reclassification of ( , ). After taking into account morphological diversity in the family, we argue in favour of distinguishing three genera only, , and . becomes a large genus with 128 accepted species, containing almost all...Spirin, V. ; Runnel, K. ; Vlasák, J. ; Viner, I. ; Barrett, M. D. …
Taxonomy, New Species, Brown-rot fungi, Polypores, and Phylogeny
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Journal article
Online tree expansion could help solve the problem of scalability in Bayesian phylogenetics.
Bayesian phylogenetics is now facing a critical point. Over the last 20 years, Bayesian methods have reshaped phylogenetic inference and gained widespread popularity due to their high accuracy, the ability to quantify the uncertainty of inferences and the possibility of accommodating multiple aspects of evolutionary processes in the models that...Truszkowski, Jakub ; Perrigo, Allison ; Broman, David ; Ronquist, Fredrik ; Antonelli, Alexandre
Phylogeny, MCMC, Bayesian inference, and Sequential Monte Carlo
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Journal article
Akanthomyces zaquensis (Cordycipitaceae, Hypocreales), a new species isolated from both the stroma and the sclerotium of Ophiocordyceps sinensis in Qinghai, China.
An undescribed taxon of entomopathogenic fungi, Akanthomyces zaquensis, was introduced based on the collections from Duoxiao Village beside the Za Qu River in Qinghai Province, China. The taxon is characterized by its host and habitat of isolations from both the stroma and the sclerotium of Ophiocordyceps sinensis and by producing...Wang, Yong-Hui ; Wang, Wen-Jing ; Wang, Ke ; Dong, Cai-Hong ; Hao, Ji-Rong …
Akanthomyces zaquensis, Taxonomy, Tibetan Plateau, Morphology, Qinghai (China), Fungi, and Phylogeny
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Journal article
Morphological Continua Make Poor Species: Genus-Wide Morphometric Survey of the European Bee Orchids (Ophrys L.).
Despite (or perhaps because of) intensive multidisciplinary research, opinions on the optimal number of species recognised within the Eurasian orchid genus Ophrys range from nine to at least 400. The lower figure of nine macrospecies is based primarily on seeking small but reliable discontinuities in DNA ‘barcode’ regions, an approach... -
Journal article
Three new species of Millettia (Leguminosae-Papilionoideae: Millettieae) from the Indo-Chinese region.
Mattapha, Sawai ; Forest, Felix ; Schrire, Brian D. ; Lewis, Gwilym P. ; Hawkins, Julie …
Khao Yai National Park, Thailand, Indo-China, Taxonomy, Phylogeny, New species, Millettia, and Vietnam
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Journal article
Phylogenetic relationships and biogeography of Asia Callicarpa (Lamiaceae), with consideration of a long-distance dispersal across the Pacific Ocean —insights into divergence modes of pantropical flora.
There are about 140 species of L. 1753 (Lamiaceae), with more species richness in tropical to subtropical Asia and the New World. The genus might provide an insight into the amphi-Pacific disjunction pattern of tropical and subtropical vegetation. This study has greatly improved the phylogenetic underpinning for , derived from...Cai, Huimin ; Liu, Xing ; Wang, Wenqiao ; Ma, Zhonghui ; Li, Bo …
Callicarpa, Amphi-Pacific tropical disjunction, Long-distance dispersal, Historical biogeography, Pacific Ocean, and Phylogeny
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Journal article
The evolutionary history of the Central Asian steppe-desert taxon Nitraria (Nitrariaceae) as revealed by integration of fossil pollen morphology and molecular data.
The transition from a greenhouse to an icehouse world at the Eocene-Oligocene Transition (EOT) coincided with a large decrease of pollen from the steppe-adapted genus Nitraria. This genus, now common along the Mediterranean coast, Asia and Australia, has a proposed coastal origin and a geographically widespread fossil record. Here we... -
Journal article
Phylogenetic placement and reappraisal of Diorygma karnatakense including the new synonym, Diorygma dandeliense, from Maharashtra, India.
This study re-examined the status of species of Eshw. known from the Western Ghats using an integrative taxonomy approach that includes morphological and chemical data, as well as multigene phylogenetic analyses. Prior to this work, the two species and were distinguished primarily on lirellae morphology (branching pattern) and the number... -
Journal article
Phylogenomic inference of the African tribe Monodoreae (Annonaceae) and taxonomic revision of Dennettia, Uvariodendron and Uvariopsis.
Monodoreae (Annonaceae) is a tribe composed of 11 genera and 90 species restricted to the tropical African rain forests. All the genera are taxonomically well circumscribed except the species rich genera and which lack a recent taxonomic revision. Here, we used a robust phylogenomic approach, including all the 90 currently... -
Journal article
A phylogenetic framework to study desirable traits in the wild relatives of Theobroma cacao L. (Malvaceae).
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Journal article
An integrative approach to species delimitation sinks three Chinese limestone karst Elatostema (Urticaceae) species.
is recognized as a taxonomically difficult group due to the reduced nature of the tiny flowers and inflorescences, also the large number of species (ca 650 to 700). Different opinions on morphological species delimitation have resulted in instability, which is problematic in such a speciose group. In this paper, the... -
Journal article
Phylogeny and infrageneric classification of Clerodendrum (Lamiaceae).
The infrageneric classification of the genus Clerodendrum (Lamiaceae) has been highly problematic due to different concepts and subdivisions being applied to the treatment of Asian, Australian, and African species. Earlier molecular phylogenetic studies based on Sanger sequencing and limited sampling have indicated that previous morphology-based infrageneric classifications are not congruent... -
Journal article
A Remarkable New Species of Euphorbia section Helioscopia (Euphorbia subgenus Esula, Euphorbiaceae) from Jiufeng Mountains in Fujian Province, Eastern China.
, a new species of Euphorbiaceae from Eastern China, supported by morphological and molecular evidence, is illustrated and described here. It can be distinguished from its closest relatives by the combination of several characters, including taller stature (up to 1.6 m), leaves of 5‐18 × 0.6‐3 cm in size, color...China, Flora of China, Fujian Province (China), Leafy spurges, Euphorbia xiangxiui, Phylogeny, Taxonomy, and Jiufeng Mountains (China)
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Journal article
Molecular and Morphological Analysis Supports the Separation of Robrichia as a Genus Distinct from Enterolobium (Leguminosae: Caesalpinioideae: Mimosoid Clade).
As currently circumscribed, the legume genus comprises 11 species in two sections: sect. and sect. , with an overall distribution from Mexico to Argentina and a centre of diversity in Amazonia. In the absence of the characteristic indehiscent fruits, is difficult to distinguish from other genera in the ingoid clade,...Rodrigues de Souza, Élvia ; Ranielly Monteiro Luz, Anne ; Rocha, Lamarck ; Lewis, Gwilym P.
Molecular biology, Plant morphology, Robrichia, Phylogeny, and Enterolobium
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Journal article
Molecular approaches reveal speciation between red- and blue-flowered plants in the Mediterranean Lysimachia arvensis and L. monelli (Primulaceae).
Flower colour has played a decisive role as an evolutionary force in many groups of plants by driving speciation. A well-known example of colour polymorphism is found across the Mediterranean populations of Lysimachia arvensis and L. monelli, in which blue- and red-flowered plants can be found. Previous studies recognized two... -
Journal article
The rise of grasslands is linked to atmospheric CO2 decline in the late Palaeogene.
Grasslands are predicted to experience a major biodiversity change by the year 2100. A better understanding of how grasslands have responded to past environmental changes will help predict the outcome of current and future environmental changes. Here, we explore the relationship between past atmospheric CO and temperature fluctuations and the...Palazzesi, Luis ; Hidalgo, Oriane ; Barreda, Viviana D. ; Forest, Félix ; Höhna, Sebastian
Palaeogene, Grasslands, Evolution, Environmental sciences, and Phylogeny
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Journal article
Insights into the evolution of the chloroplast genome and the phylogeny of Begonia.
Begonia (Begoniaceae) is one of the largest angiosperm genera, comprising more than 2000 species; this makes it ideal as a model to investigate the genomic basis of species radiations. Here we present the results of the first genus-wide comparative study of plastid genome structure, sequence diversity, and phylogenetics of Begoniaceae,... -
Journal article
Genetic patterns of Magnolia in the Lesser Antilles: Stepwise colonisation leading to highly inbred island ‘populations’.
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Journal article
Chlorophytum delicatulum (Asparagaceae), a newly described species from Zambia.
Osborne, Vollesen & Bjorå from Zambia is described, illustrated and placed within the context of recent taxonomic and phylogenetic work on in Africa. This delicate herb has leaf bases furnished with conspicuous dark red setae resembling eyelashes. Its phylogenetic position, ecology, phytogeography and conservation status are discussed. is assessed as...Osborne, J. ; Vollesen, K. ; Bjorå, C. S. ; Grall, A. ; Merrett, L. …
Conservation status, Taxonomy, Phylogeny, Chlorophytum delicatulum, New species, Zambia, Africa, and Ecology
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Journal article
Phylogenetic conservatism explains why plants are more likely to produce fleshy fruits in the tropics.
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Journal article
Phylogeny and systematics of the tribe Sonerileae (Melastomataceae) in Africa: A revised taxonomic classification.
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Journal article
A Bird’s Eye View of the Systematics of Convolvulaceae: Novel Insights From Nuclear Genomic Data.
Convolvulaceae is a family of c. 2,000 species, distributed across 60 currently recognized genera. It includes species of high economic importance, such as the crop sweet potato ( L.), the ornamental morning glories ( L.), bindweeds ( L.), and dodders, the parasitic vines ( L.). Earlier phylogenetic studies, based predominantly...Simões, Ana Rita G. ; Eserman, Lauren A. ; Zuntini, Alexandre R. ; Chatrou, Lars W. ; Utteridge, Timothy M. A. …
Angiosperms353, Cuscuta, Classification, Phylogeny, Convolvulus, and Ipomoea
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Book chapter
Marah CUCURBITACEAE.
Newton, L. E.
Succulent plants, Marah, Taxonomy, Etymology, Geographical distribution, Phylogeny, Descriptors, and Classification
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Journal article
Reinstatement of Ticanto (Leguminosae-Caesalpinioideae) – the final piece in the Caesalpinia group puzzle.
A recent molecular phylogenetic analysis of the Caesalpinia group demonstrated that it comprises 26 genera, but the recognition of a putative 27 genus, , remained in doubt. This study presents a phylogenetic analysis of ITS and five plastid loci revealing a robustly supported monophyletic group representing the Ticanto clade, sister... -
Journal article
Phylogenomics and generic limits of Dypsidinae (Arecaceae), the largest palm radiation in Madagascar.
Eiserhardt, Wolf L. ; Bellot, Sidonie ; Cowan, Robyn S. ; Dransfield, John ; Hansen, Lars Emil S.F. …
Target sequence capture, Madagascar, Hyb-Seq, Dypsis, Phylogeny, Chrysalidocarpus, and Palmae
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Journal article
Spatio‐temporal evolution of the catuaba clade in the Neotropics: Morphological shifts correlate with habitat transitions.
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Journal article
Genetic patterns of Magnolia in the Lesser Antilles: Stepwise colonisation leading to highly inbred island ‘populations’.
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Journal article
Hygrophorus sect. Olivaceoumbrini: new boundaries, extended biogeography and unexpected diversity unravelled by transatlantic studies.
As currently delineated, sect. is a polyphyletic assembly within subg. , encompassing glutinous and pigmented taxa. According to available literature, between a dozen and twenty species may belong in the section, mostly represented in continental and boreal forests of Europe and North America. However, the limited phylogenetic and biogeographic coverage...Bellanger, J.-M. ; Lebeuf, R. ; Sesli, E. ; Loizides, M. ; Schwarz, C. …
Waxcap, Hygrophorus latitabundus, Hygrophorus persoonii, Phylogeny, Taxonomy, and Hygrophorus olivaceoalbus
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Journal article
Notes on the systematics of Cuscuta sect. Subulatae (subg. Grammica) with the description of Cuscuta mantiqueirana, a new species from Brazil.
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Journal article
Discovery and Extrolite Production of Three New Species of Talaromyces Belonging to Sections Helici and Purpurei from Freshwater in Korea.
Three novel fungal species, Talaromyces gwangjuensis, T. koreana, and T. teleomorpha were found in Korea during an investigation of fungi in freshwater. The new species are described here using morphological characters, a multi-gene phylogenetic analysis of the ITS, BenA, CaM, RPB2 regions, and extrolite data. Talaromyces gwangjuensis is characterized by restricted growth...Nguyen, Thuong T. T. ; Frisvad, Jens Christian ; Kirk, Paul M. ; Lim, Hyo Jin ; Lee, Hyang Burm
New taxa, Trichocomaceae, Morphology, Phylogeny, and Taxonomy
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Journal article
Discovery of Novel Backusella (Backusellaceae, Mucorales) Isolated from Invertebrates and Toads in Cheongyang, Korea.
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Journal article
A New and Expanded Phylogenetic Analysis of Hyptidinae (Ocimeae-Lamiaceae).
Hyptidinae, ca. 400 species, is an important component of Neotropical vegetation formations. Members of the subtribe possess flowers arranged in variously modified bracteolate cymes and nutlets with an expanded areole and all share a unique explosive mechanism of pollen release, except for . In a recent phylogenetic study, the group... -
Journal article
Plants used traditionally as antimalarials in Latin America: Mining the tree of life for potential new medicines
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Journal article
Phylogenetic study of tropical Asian Ardisia and relatives shows non-monophyly of generic and subgeneric classifications.
Julius , Avelinah ; Gutiérrez-Ortega, José Said ; Sabran, Suzana ; Tagane, Shuichiro ; Naiki, Akiyo …
Ardisia, nrITS, Ericales, Phylogeny, Myrsinoideae, Malesia, and Primulaceae
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Journal article
The best of both worlds: Combining lineage-specific and universal bait sets in target-enrichment hybridization reactions.
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Journal article
Challenges of applying monophyly in the phylogenetic shallows: taxonomic reappraisal of the Dactylorhiza maculata group.
The first study of the taxonomically critical European orchid genus to use next-generation DNA sequencing generated the statistically best-supported reconstruction of its phylogeny to date. However, the two competing topologies obtained within the monophyletic Section differed radically in the placement of the s.s.– clade. Both topologies showed to be nested... -
Journal article
Fungal diversity notes 1387–1511: taxonomic and phylogenetic contributions on genera and species of fungal taxa.
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Journal article
The Implications of Interrelated Assumptions on Estimates of Divergence Times and Rates of Diversification.
Phylogenies are increasingly being used as a basis to provide insight into macroevolutionary history. Here, we use simulation experiments and empirical analyses to evaluate methods that use phylogenies as a basis to make estimates of divergence times and rates of diversification. This is the first study to present a comprehensive...Carruthers, Tom ; Scotland, Robert W
Divergence time estimation, Phylogeny, Macroevolution, Diversification rates, and Macroevolutionary history
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Journal article
Pollen sterols are associated with phylogeny and environment but not with pollinator guilds.
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Journal article
Two new species and a new species record of Aglaia (Meliaceae) from Indonesia.
Two new species of from Indonesia are described, restricted to West Papua, and occurring on Borneo (Kalimantan, Brunei, Sabah and Sarawak). A phylogenetic analysis using nuclear ITS and ETS, and plastid sequence data indicates that the two new species of are also genetically distinct. belongs to sectionAmoora, while is included...Pannell, Caroline M. ; Schnitzler, Jan ; Muellner-Riehl, Alexandra N.
Conservation status, Aglaia, Indonesia, Phylogeny, Taxonomy, and Meliaceae
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Journal article
Molecular phylogenetic study of the tribe Tropidieae (Orchidaceae, Epidendroideae) with taxonomic and evolutionary implications.
The orchid tribe Tropidieae comprises three genera, Tropidia, Corymborkis and Kalimantanorchis. There are three fully mycoheterotrophic species within Tropidieae: Tropidia saprophytica, T. connata and Kalimantanorchis nagamasui. A previous phylogenetic study of K. nagamasui, based only on plastid matK data, placed K. nagamasui outside the clade of Tropidia and Corymborkis without...Sabino Kikuchi, Izai A. B. ; Keβler, Paul J. A. ; Schuiteman, André ; Murata, Jin ; Ohi-Toma, Tetsuo …
Corymborkis, Tropidia, Mycoheterotrophy, Phylogeny, and Kalimantanorchis
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Journal article
Mission impossible completed: unlocking the nomenclature of the largest and most complicated subgenus of Cortinarius, Telamonia.
So far approximately 144,000 species of fungi have been named but sequences of the majority of them do not exist in the public databases. Therefore, the quality and coverage of public barcode databases is a bottleneck that hinders the study of fungi. is the largest genus of Agaricales with thousands...Liimatainen, Kare ; Niskanen, Tuula ; Dima, Bálint ; Ammirati, Joseph F. ; Kirk, Paul M. …
Telamonia, Barcode, Cortinarius, Section, Neotype, Phylogeny, ITS, and Type study
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Journal article
Phylogenomic Study of Monechma Reveals Two Divergent Plant Lineages of Ecological Importance in the African Savanna and Succulent Biomes.
Monechma Hochst. s.l. (Acanthaceae) is a diverse and ecologically important plant group in sub-Saharan Africa, well represented in the fire-prone savanna biome and with a striking radiation into the non-fire-prone succulent biome in the Namib Desert. We used RADseq to reconstruct evolutionary relationships within Monechma s.l. and found it to...Darbyshire, Iain ; Kiel, Carrie A. ; Astroth, Corine M. ; Dexter, Kyle G. ; Chase, Frances M. …
Phylogeny, Savannas, Africa, Succulents, Biome, Justicia, Plant diversity, RADseq, and Monechma
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Journal article
A large-scale species level dated angiosperm phylogeny for evolutionary and ecological analyses.
Phylogenies are a central and indispensable tool for evolutionary and ecological research. Even though most angiosperm families are well investigated from a phylogenetic point of view, there are far less possibilities to carry out large-scale meta-analyses at order level or higher. Here, we reconstructed a large-scale dated phylogeny including nearly...Janssens, Steven ; Couvreur, Thomas L.P. ; Mertens, Arne ; Dauby, Gilles ; Dagallier, Leo-Paul …
Ecology, Phylogeny, Evolution, Large-scale dating analyses, and Angiosperms
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Journal article
Fungal diversity notes 1151–1276: taxonomic and phylogenetic contributions on genera and species of fungal taxa.
Fungal diversity notes is one of the important journal series of fungal taxonomy that provide detailed descriptions and illustrations of new fungal taxa, as well as providing new information of fungal taxa worldwide. This article is the 11th contribution to the fungal diversity notes series, in which 126 taxa distributed...