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  • Articles  (9)
  • phylogeny  (9)
  • Naturalis Biodiversity Center  (9)
  • American Chemical Society
  • 2020-2024  (9)
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  • Articles  (9)
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  • Naturalis Biodiversity Center  (9)
  • American Chemical Society
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  • 1
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    A just overtime discovery: another new species of Echinosepala (Orchidaceae) from Costa Rica (2022)
    Naturalis Biodiversity Center
    In:  Blumea: Biodiversity, Evolution and Biogeography of Plants vol. 67 no. 2, pp. 109-112
    Details
    Publication Date: 2024-03-25
    Description: Echinosepala truncata is described as new to science and illustrated from the holotype. It is compared with E. tomentosa, from which it differs by the sparsely lanate ovary, the narrowly obovate, apically rounded synsepal, the spathulate, apically and basally rounded petals, and the rectangular, apically truncate lip. The phylogenetic relationships of the new species could be hypothesized based on a shared set of morphological characters and geographic distribution.
    Keywords: Plant Science ; Ecology ; Evolution ; Behavior and Systematics ; flora of Costa Rica ; new species ; Península de Osa ; phylogeny ; Pleurothallidinae
    Repository Name: National Museum of Natural History, Netherlands
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  • 2
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    Fungi of quarantine concern for China I: Dothideomycetes (2021)
    Naturalis Biodiversity Center
    In:  Persoonia - Molecular Phylogeny and Evolution of Fungi vol. 47, pp. 45-105
    Details
    Publication Date: 2024-04-09
    Description: The current list of Chinese quarantine pests includes 130 fungal species. However, recent changes in the taxonomy of fungi following the one fungus = one name initiative and the implementation of DNA phylogeny in taxonomic revisions, resulted in many changes of these species names, necessitating an update of the current list. In addition, many quarantine fungi lack modern morphological descriptions and authentic DNA sequences, posing significant challenges for the development of diagnostic protocols. The aim of the present study was to review the taxonomy and names of the 33 Chinese quarantine fungi in Dothideomycetes, and provide reliable DNA barcodes to facilitate rapid identification. Of these, 23 names were updated according to the single name nomenclature system, including one new combination, namely Cophinforma tumefaciens comb. nov. (syn. Sphaeropsis tumefaciens). On the basis of phylogenetic analyses and morphological comparisons, a new genus Xenosphaeropsis is introduced to accommodate the monotypic species Xenosphaeropsis pyriputrescens comb. nov. (syn. Sphaeropsis pyriputrescens), the causal agent of a post-harvest disease of pears. Furthermore, four lectotypes (Ascochyta petroselini, Mycosphaerella ligulicola, Physalospora laricina, Sphaeria lingam), three epitypes (Ascochyta petroselini, Phoma lycopersici, Sphaeria lingam), and two neotypes (Ascochyta pinodella, Deuterophoma tracheiphila) are designated to stabilise the use of these names. A further four reference strains are introduced for Cophinforma tumefaciens, Helminthosporium solani, Mycocentro spora acerina, and Septoria linicola. In addition, to assist future studies on these important pathogens, we sequenced and assembled whole genomes for 17 species, including Alternaria triticina, Boeremia foveata, B. lycopersici, Cladosporium cucumerinum, Didymella glomerata, Didymella pinodella, Diplodia mutila, Helminthosporium solani, Mycocentrospora acerina, Neofusicoccum laricinum, Parastagonospora pseudonodorum, Plenodomus libanotidis, Plenodomus lingam, Plenodomus tracheiphilus, Septoria petroselini, Stagonosporopsis chrysanthemi, and Xenosphaeropsis pyriputrescens.
    Keywords: Ecology ; Evolution ; Behavior and Systematics ; Chinese quarantine fungi ; DNA barcodes ; genomes ; morphology ; new taxa ; phylogeny ; plant pathogens ; typification
    Repository Name: National Museum of Natural History, Netherlands
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  • 3
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    Extensive morphological and behavioural diversity among fourteen new and seven described species in Phytophthora Clade 10 and its evolutionary implications (2022)
    Naturalis Biodiversity Center
    In:  Persoonia - Molecular Phylogeny and Evolution of Fungi vol. 49, pp. 1-57
    Details
    Publication Date: 2024-04-09
    Description: During extensive surveys of global Phytophthora diversity 14 new species detected in natural ecosystems in Chile, Indonesia, USA(Louisiana), Sweden, Ukraine and Vietnam were assigned to Phytophthora major Clade 10 based on a multigene phylogeny of nine nuclear and three mitochondrial gene regions. Clade 10 now comprises three subclades. Subclades 10a and 10b contain species with nonpapillate sporangia, a range of breeding systems and a mainly soil- and waterborne lifestyle. These include the previously described P. afrocarpa, P. gallica and P. intercalaris and eight of the new species: P. ludoviciana, P. procera, P. pseudogallica, P. scandinavica, P. subarctica, P. tenuimura, P. tonkinensis and P. ukrainensis. In contrast, all species in Subclade 10c have papillate sporangia and are self-fertile (or homothallic) with an aerial lifestyle including the known P. boehmeriae, P. gondwanensis, P. kernoviae and P. morindae and the new species P. celebensis, P. chilensis, P. javanensis, P. multiglobulosa, P. pseudochilensis and P. pseudokernoviae. All new Phytophthora species differed from each other and from related species by their unique combinations of morphological characters, breeding systems, cardinal temperatures and growth rates. The biogeography and evolutionary history of Clade 10 are discussed. We propose that the three subclades originated via the early divergence of pre-Gondwanan ancestors 〉 175 Mya into water- and soilborne and aerially dispersed lineages and subsequently underwent multiple allopatric and sympatric radiations during their global spread.
    Keywords: Ecology ; Evolution ; Behavior and Systematics ; allopatric ; biogeography ; evolution ; Gondwana ; Laurasia ; oomycete ; phylogeny ; radiation ; sympatric
    Repository Name: National Museum of Natural History, Netherlands
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  • 4
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    Hygrophorus sect. Olivaceoumbrini: new boundaries, extended biogeography and unexpected diversity unravelled by transatlantic studies (2021)
    Naturalis Biodiversity Center
    In:  Persoonia - Molecular Phylogeny and Evolution of Fungi vol. 46, pp. 272-312
    Details
    Publication Date: 2024-04-15
    Description: As currently delineated, Hygrophorus sect. Olivaceoumbrini is a polyphyletic assembly within subg. Colorati, 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 of the genus does not presently allow for a reliable assessment of its taxonomic boundaries, nor does it provide a complete picture of species diversity within sect. Olivaceoumbrini. In an ongoing effort to confer an evolutionary backbone to Hygrophorus systematics, we assembled and analysed a dataset comprising 268 intercontinental sequences, including holotypes of 7 taxa previously not positioned phylogenetically, and enriched with collections from largely unexplored Mediterranean and Anatolian ecosystems. Overall, 30 clades are identified within 5 distinct lineages, including 11 species putatively new to science. Seven of these are formally described here as H. agathosmoides, H. albofloccosus, H. canadensis, H. limosus, H. marcocontui, H. pinophilus and H. pustulatoides spp. nov. This enriched coverage of section Olivaceoumbrini s.lat. calls for a re-evaluation of its natural boundaries into a core monophyletic clade, including H. olivaceoalbus and five closely related lookalikes, as well as the assignment of the section rank to the four remaining lineages: sect. Fuscocinerei sect. nov., sect. Limacini sect. nov., sect. Nudolidi sect. nov. and sect. Tephroleuci, respectively. We also stabilize the usage of six historical names, H. glutinifer, H. hyacinthinus, H. mesotephrus, H. olivaceoalbus, H. pustulatus and H. tephroleucus, through designation of two neotypes, three lectotypes and four epitypes.
    Keywords: Ecology ; Evolution ; Behavior and Systematics ; Hygrophorus latitabundus ; Hygrophorus olivaceoalbus ; Hygrophorus persoonii ; phylogeny ; taxonomy ; waxcap
    Repository Name: National Museum of Natural History, Netherlands
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  • 5
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    Cortinarius subgenus Leprocybe in Europe: expanded Sanger and Next Generation Sequencing unveil unexpected diversity in the Mediterranean (2021)
    Naturalis Biodiversity Center
    In:  Persoonia - Molecular Phylogeny and Evolution of Fungi vol. 46, pp. 188-215
    Details
    Publication Date: 2024-04-23
    Description: Molecular phylogenies in the past decade have demonstrated that the described diversity of Cortinarius is still underestimated, especially outside continental and boreal ecoregions where the genus has been historically investigated. We tackled this issue by revisiting the so far unresolved subgenus Leprocybe, and focused on the largely unexplored Mediterranean hotspot of biodiversity. The sequencing and phylogenetic analysis of 161 vouchered collections from Austria, Cyprus, France, Germany, Italy and Spain, including 16 types, allowed for the delineation of 11 species in this lineage, three of them recognised as new to science and formally introduced as C. jimenezianus, C. selinolens and C. viridans spp. nov., respectively. Interestingly, the newly described species exhibit a strict Mediterranean distribution, and one of them is putatively endemic to the island of Cyprus, highlighting the remarkable potential of this neglected ecoregion to uncover further undescribed diversity of Cortinarius in the future. The present work also unveils 23 synonymies in this subgenus, as well as previously undetected crypticism within C. venetus. Next Generation Sequencing carried out on three old and contaminated holotypes, successfully decrypts their phylogenetic identity, including that of C. leproleptopus, finally settling the long-standing controversy over the taxonomic status of this species. A brief overview of each species in the subgenus is lastly provided and a key is proposed to facilitate the identification of presently known European taxa of Leprocybe in the field.
    Keywords: Ecology ; Evolution ; Behavior and Systematics ; Cedrus brevifolia ; endemism ; phylogeny ; taxonomy ; Veneti
    Repository Name: National Museum of Natural History, Netherlands
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  • 6
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    Diversity and novel lineages of black yeasts in Chaetothyriales from freshwater sediments in Spain (2023)
    Naturalis Biodiversity Center
    In:  Persoonia - Molecular Phylogeny and Evolution of Fungi vol. 51 no. 1, pp. 194-228
    Details
    Publication Date: 2024-03-06
    Description: Black yeasts comprise a group of Ascomycota of the order Chaetothyriales with highly variable morphology, \na great diversity of ecological niches and life cycles. Despite the ubiquity of these fungi, their diversity in freshwater \nsediments is still poorly understood. During a survey of culturable Ascomycota from river and stream sediments \nin various sampling sites in Spain, we obtained 47 isolates of black yeasts by using potato dextrose agar supplemented with cycloheximide. A preliminary morphological study and sequence analyses of the internal transcribed \nspacer region (ITS) and the large subunit (LSU) of the nuclear rDNA revealed that most of the isolates belonged \nto the family Herpotrichiellaceae. We have confidently identified 30 isolates representing the following species: \nCapronia pulcherrima, Cladophialophora emmonsii, Exophiala equina, Exophiala pisciphila, Exophiala radicis, and \nPhialophora americana. However, we encountered difficulty in assigning 17 cultures to any known species within \nChaetothyriales. Combining phenotypic and multi-locus phylogenetic analyses based on the ITS, LSU, \xce\xb2-tubulin \n(tub2) and translation elongation factor 1-\xce\xb1 (tef1-\xce\xb1) gene markers, we propose the new genus Aciculomyces in the \nHerpotrichiellaceae to accommodate the novel species Aciculomyces restrictus. Other novel species in this family \ninclude Cladophialophora denticulata, Cladophialophora heterospora, Cladophialophora irregularis, Exophiala \ncandelabrata, Exophiala dehoogii, Exophiala ramosa, Exophiala verticillata and Phialophora submersa. The new \nspecies Cyphellophora spiralis, closely related to Cyphellophora suttonii, is described, and the phylogeny of the \ngenus Anthopsis in the family Cyphellophoraceae is discussed. By utilizing these four markers, we were able to \nstrengthen the phylogenetic resolution and provide more robust taxonomic assessments within the studied group. \nOur findings indicate that freshwater sediments may serve as a reservoir for intriguing black yeasts, which warrant \nfurther investigation to address gaps in phylogenetic relationships, particularly within Herpotrichiellaceae.
    Keywords: Ascomycota ; biodiversity ; Cyphellophoraceae ; fluvial sediments ; Herpotrichiellaceae ; new taxa ; phylogeny ; taxonomy
    Repository Name: National Museum of Natural History, Netherlands
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  • 7
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    Stop black and white thinking: Russula subgenus Compactae (Russulaceae, Russulales) in Europe revised (2023)
    Naturalis Biodiversity Center
    In:  Persoonia - Molecular Phylogeny and Evolution of Fungi vol. 51 no. 1, pp. 152-193
    Details
    Publication Date: 2024-03-06
    Description: Russula subgenus Compactae is a group of ectomycorrhizal basidiomycetes, usually with large pileate \nfruitbodies. European members of the group are characterised by the absence of bright colours on the surfaces of \ntheir pilei, the context turning grey to black after cutting, the abundance of short lamellulae in the hymenophore, and \nspores with an inamyloid suprahilar spot and with low reticulate ornamentation. Our multi-locus phylogenetic study \nconfirmed that this morphological delimitation corresponds to a well-supported clade. Within this clade, 16 species \nare recognised in Europe, of which five belong to the R. albonigra lineage and were described in a previous study, \nwhile eleven are fully described in this study. The application of the names R. acrifolia, R. adusta, R. anthracina, \nR. atramentosa, R. densissima, R. nigricans and R. roseonigra is based on the position of sequences retrieved from \ntypes or authentic material. Based on type sequences, R. fuliginosa is synonymised with R. anthracina and two \nvarieties of R. anthracina are considered synonyms of R. atramentosa. The application of the name R. densifolia \nis based on a morphological match with the traditional species interpretation and the neotype specimen. Three \nspecies are described as new, R. marxmuelleriana sp. nov., R. picrophylla sp. nov. and R. thuringiaca sp. nov. This \nstudy recognises three major lineages and two species with isolated positions within the European Compactae \nand a morphological barcode was assigned to the species using an analysis of 23 selected characters. A search of \npublicly available sequences from the UNITE database revealed that the majority of species are host tree generalists and widely distributed in temperate and Mediterranean areas of Europe. Russula adusta is the only species so \nfar proven to form ectomycorrhiza exclusively with conifers.
    Keywords: barcode ; Basidiomycota ; coalescent species delimitation ; diversity ; ectomycorrhiza ; Fungi ; integrative taxonomy ; new taxa ; phylogeny
    Repository Name: National Museum of Natural History, Netherlands
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  • 8
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    Revision of the African species of Monanthotaxis (Annonaceae) (2021)
    Naturalis Biodiversity Center
    In:  Blumea: Biodiversity, Evolution and Biogeography of Plants vol. 66 no. 2, pp. 107-221
    Details
    Publication Date: 2024-05-04
    Description: This taxonomic revision of the continental African species of Monanthotaxis (Annonaceae) includes 79 species and one variety. Thirteen new species (M. aestuaria, M. bidaultii, M. confusa, M. glabra, M. hexamera, M. mcphersonii, M. quasilanceolata, M. sterilis, M. submontana, M. suffruticosa, M. ursus, M. vulcanica and M. wieringae) are described and 5 new combinations (M. biglandulosa, M. kenyensis, M. ochroleuca, M. pynaertii and M. seretii) are made. The genus Monanthotaxis consists of lianas or lianescent shrubs. It occurs throughout forests in tropical Africa and the highest species diversity is found in the Western Central African rain forests. A key for flowering material is provided, just like a synoptic key including 45 characters. Topics included in the revision are the history of the taxonomy of Monanthotaxis, morphology, leaf anatomy, floral biology, distribution and habitat, phylogeny and finally ethnobotany and phytochemistry. Each species is fully described including synonymy, notes on distribution, habitat & ecology, vernacular names, uses and a preliminary IUCN conservation status. Distribution maps are provided for all species, illustrations for 48 species and photographs of 22 species. An index of exsiccatae and an index of the scientific names are included at the end.
    Keywords: Plant Science ; Ecology ; Evolution ; Behavior and Systematics ; distributions ; ethnobotany ; floral biology ; habitat ; leaf anatomy ; morphology ; phylogeny ; phytochemistry ; pollination ; seed dispersion
    Repository Name: National Museum of Natural History, Netherlands
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  • 9
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    Mating genes in Calonectria and evidence for a heterothallic ancestral state (2020)
    Naturalis Biodiversity Center
    In:  Persoonia - Molecular Phylogeny and Evolution of Fungi vol. 45, pp. 163-176
    Details
    Publication Date: 2024-05-07
    Description: The genus Calonectria includes many important plant pathogens with a wide global distribution. In order to better understand the reproductive biology of these fungi, we characterised the structure of the mating type locus and flanking genes using the genome sequences for seven Calonectria species. Primers to amplify the mating type genes in other species were also developed. PCR amplification of the mating type genes and multi-gene phylogenetic analyses were used to investigate the mating strategies and evolution of mating type in a collection of 70 Calonectria species residing in 10 Calonectria species complexes. Results showed that the organisation of the MAT locus and flanking genes is conserved. In heterothallic species, a novel MAT gene, MAT1-2-12 was identified in the MAT1-2 idiomorph; the MAT1-1 idiomorph, in most cases, contained the MAT1-1-3 gene. Neither MAT1-1-3 nor MAT1-2-12 was found in homothallic Calonectria (Ca.) hongkongensis, Ca. lateralis, Ca. pseudoturangicola and Ca. turangicola. Four different homothallic MAT locus gene arrangements were observed. Ancestral state reconstruction analysis provided evidence that the homothallic state was basal in Calonectria and this evolved from a heterothallic ancestor.
    Keywords: Ecology ; Evolution ; Behavior and Systematics ; Cylindrocladium ; fungal biology ; fungal pathogens ; MAT locus ; mating type ; phylogeny ; sexual reproduction
    Repository Name: National Museum of Natural History, Netherlands
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