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  • 1
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    Phylogenetic lineages in Entomophthoromycota (2013)
    In:  Persoonia - Molecular Phylogeny and Evolution of Fungi (0031-05850) vol.30 (2013) nr.1 p.94
    Details
    Publication Date: 2015-04-20
    Description: Entomophthoromycota is one of six major phylogenetic lineages among the former phylum Zygomycota. These early terrestrial fungi share evolutionarily ancestral characters such as coenocytic mycelium and gametangiogamy as a sexual process resulting in zygospore formation. Previous molecular studies have shown the monophyly of Entomophthoromycota, thus justifying raising the taxonomic status of these fungi to a phylum. Multi-gene phylogenies have identified five major lineages of Entomophthoromycota. In this review we provide a detailed discussion about the biology and taxonomy of these lineages: I) Basidiobolus (Basidiobolomycetes: Basidiobolaceae; primarily saprobic); II) Conidiobolus (Entomophthoromycetes, Ancylistaceae; several clades of saprobes and invertebrate pathogens), as well as three rapidly evolving entomopathogenic lineages in the family Entomophthoraceae centering around; III) Batkoa; IV) Entomophthora and allied genera; and V) the subfamily Erynioideae which includes Zoophthora and allied genera. Molecular phylogenic analysis has recently determined the relationships of several taxa that were previously unresolved based on morphology alone: Eryniopsis, Macrobiotophthora, Massospora, Strongwellsea and two as yet undescribed genera of Basidiobolaceae.
    Keywords: Basidiobolus ; Batkoa ; Bayesian inference (BI) ; Conidiobolus ; Entomophthora ; Entomophthorales ; Entomophthoromycotina ; maximum likelihood (ML) ; phylogeny ; Zoophthora
    Repository Name: National Museum of Natural History, Netherlands
    Type: Article / Letter to the editor
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  • 2
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    The family structure of the Mucorales: a synoptic revision based on comprehensive multigene-genealogies (2013)
    In:  Persoonia - Molecular Phylogeny and Evolution of Fungi vol. 30 no. 1, pp. 57-76
    Details
    Publication Date: 2024-01-12
    Description: The Mucorales (Mucoromycotina) are one of the most ancient groups of fungi comprising ubiquitous, mostly saprotrophic organisms. The first comprehensive molecular studies 11 yr ago revealed the traditional classification scheme, mainly based on morphology, as highly artificial. Since then only single clades have been investigated in detail but a robust classification of the higher levels based on DNA data has not been published yet. Therefore we provide a classification based on a phylogenetic analysis of four molecular markers including the large and the small subunit of the ribosomal DNA, the partial actin gene and the partial gene for the translation elongation factor 1-alpha. The dataset comprises 201 isolates in 103 species and represents about one half of the currently accepted species in this order. Previous family concepts are reviewed and the family structure inferred from the multilocus phylogeny is introduced and discussed. Main differences between the current classification and preceding concepts affects the existing families Lichtheimiaceae and Cunninghamellaceae, as well as the genera Backusella and Lentamyces which recently obtained the status of families along with the Rhizopodaceae comprising Rhizopus, Sporodiniella and Syzygites. Compensatory base change analyses in the Lichtheimiaceae confirmed the lower level classification of Lichtheimia and Rhizomucor while genera such as Circinella or Syncephalastrum completely lacked compensatory base changes.
    Keywords: Mucorales ; families ; phylogeny
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 3
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    Phylogenetic lineages in Entomophthoromycota (2013)
    In:  Persoonia - Molecular Phylogeny and Evolution of Fungi vol. 30 no. 1, pp. 94-105
    Details
    Publication Date: 2024-01-12
    Description: Entomophthoromycota is one of six major phylogenetic lineages among the former phylum Zygomycota.\nThese early terrestrial fungi share evolutionarily ancestral characters such as coenocytic mycelium and gametangiogamy as a sexual process resulting in zygospore formation. Previous molecular studies have shown the monophyly of Entomophthoromycota, thus justifying raising the taxonomic status of these fungi to a phylum. Multi-gene phylogenies have identified five major lineages of Entomophthoromycota. In this review we provide a detailed discussion about the biology and taxonomy of these lineages: I) Basidiobolus (Basidiobolomycetes: Basidiobolaceae; primarily saprobic); II) Conidiobolus (Entomophthoromycetes, Ancylistaceae; several clades of saprobes and invertebrate pathogens), as well as three rapidly evolving entomopathogenic lineages in the family Entomophthoraceae centering around; III) Batkoa; IV) Entomophthora and allied genera; and V) the subfamily Erynioideae which includes Zoophthora and allied genera. Molecular phylogenic analysis has recently determined the relationships of several taxa that were previously unresolved based on morphology alone: Eryniopsis, Macrobiotophthora, Massospora, Strongwellsea and two as yet undescribed genera of Basidiobolaceae.
    Keywords: Basidiobolus ; Batkoa ; Bayesian inference (BI) ; Conidiobolus ; Entomophthora ; Entomophthorales ; Entomophthoromycotina ; maximum likelihood (ML) ; phylogeny ; Zoophthora
    Repository Name: National Museum of Natural History, Netherlands
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  • 4
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    Redefining the damselfly families: a comprehensive molecular phylogeny of Zygoptera (Odonata) (2014)
    In:  Various articles (1365-3113) vol.39 (2014) p.68
    Details
    Publication Date: 2016-08-18
    Description: An extensive molecular phylogenetic reconstruction of the suborder Zygoptera of the Odonata is presented, based on mitochondrial (16S, COI) and nuclear (28S) data of 59% of the 310 genera recognized and all (suspected) families except the monotypic Hemiphlebiidae. A partial reclassification is proposed, incorporating morphological characters. Many traditional families are recovered as monophyletic, but reorganization of the superfamily Coenagrionoidea into three families is proposed: Isostictidae, Platycnemididae and Coenagrionidae. Archboldargia Lieftinck, Hylaeargia Lieftinck, Palaiargia Forster, ¨ Papuargia Lieftinck and Onychargia Selys are transferred from Coenagrionidae to Platycnemididae, and Leptocnemis Selys, Oreocnemis Pinhey and Thaumatagrion Lieftinck from Platycnemididae to Coenagrionidae. Each geographically well-defined clade of Platycnemididae is recognized as a subfamily, and thus Disparoneurinae (i.e. Old World ‘Protoneuridae’) is incorporated, Calicnemiinae is restricted, and Allocnemidinae (type genus: Allocnemis Selys) subfam.n., Idiocnemidinae (type genus: Idiocnemis Selys) subfam.n. and Onychargiinae (type genus: Onychargia Selys) subfam.n. and Coperini trib.n. (type genus: Copera Kirby) are described. Half of Coenagrionidae belongs to a well-supported clade incorporating Coenagrion Kirby and the potential subfamilies Agriocnemidinae, Ischnurinae and Pseudagrioninae. The remainder is less well defined, but includes the Pseudostigmatidae and New World Protoneuridae that, with Argiinae and Teinobasinae, may prove valid subfamilies with further evidence. Ninety-two per cent of the genera formerly included in the polyphyletic Amphipterygidae and Megapodagrionidae were studied. Pentaphlebiidae, Rimanellidae and Devadattidae fam.n. (type genus: Devadatta Kirby) are separated from Amphipterygidae, and Argiolestidae, Heteragrionidae, Hypolestidae, Philogeniidae, Philosinidae and Thaumatoneuridae from Megapodagrionidae. Eight further groups formerly placed in the latter are identified, but are retained as incertae sedis; the validity of Lestoideidae, Philogangidae and Pseudolestidae is confirmed. For some families (e.g. Calopterygidae, Chlorocyphidae) a further subdivision is possible; Protostictinae subfam.n. (type genus: Protosticta Selys) is introduced in Platystictidae. Numerous new combinations are proposed in the Supporting Information. Many long-established families lack strong morphological apomorphies. In particular, venation is incongruent with molecular results, stressing the need to review fossil Odonata taxonomy: once defined by the reduction of the anal vein, Protoneuridae dissolves completely into six clades from five families.
    Keywords: damselflies ; phylogeny ; Zygoptera ; Odonata
    Repository Name: National Museum of Natural History, Netherlands
    Type: Article / Letter to the editor
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  • 5
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    Diversity and systematics of the sequestrate genus Octaviania in Japan: two new subgenera and eleven new species (2012)
    In:  Persoonia - Molecular Phylogeny and Evolution of Fungi vol. 28 no. 1, pp. 85-112
    Details
    Publication Date: 2024-01-12
    Description: The sequestrate fungi of Japan, including truffle and truffle-like fungi, have not been well characterized but are potentially diverse. We investigated the diversity and phylogeny of Japanese Octaviania specimens using a multifaceted approach including scanning and transmission electron microscopy as well as analysis of nuclear ribosomal DNA (ITS and LSU) and EF-1\xce\xb1 (tef1) sequences. Phylogenetic analyses indicate that the genus Octaviania is divided into three major clades, and that there are at least 12 species-level lineages in Japan. Accordingly, we describe two new subgenera, Parcaea and Fulvoglobus, and eleven new species. Subgenus Parcaea accommodates four highly divergent, but macromorphologically almost indiscernible cryptic species. We discuss not only the diversity and species delimitation within the genus Octaviania but also the phylogeography of the Japanese taxa and their relatives.
    Keywords: Biogeography ; Boletaceae ; cryptic species ; hypogeous fungi ; phylogeny ; taxonomy
    Repository Name: National Museum of Natural History, Netherlands
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  • 6
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    Resolving the Diaporthe species occurring on soybean in Croatia (2012)
    In:  Persoonia - Molecular Phylogeny and Evolution of Fungi vol. 27 no. 1, pp. 9-19
    Details
    Publication Date: 2024-01-12
    Description: Diaporthe (anamorph = Phomopsis) species are plant pathogens and endophytes on a wide range of hosts including economically important crops. At least four Diaporthe taxa occur on soybean and they are responsible for serious diseases and significant yield losses. Although several studies have extensively described the culture and morphological characters of these pathogens, their taxonomy has not been fully resolved. Diaporthe and Phomopsis isolates were obtained from soybean and other plant hosts throughout Croatia. Phylogenetic relationships were determined through analyses of partial translation elongation factor 1-alpha (EF1-\xce\xb1) gene and\nITS\nnrDNA sequence data. By combining morphological and molecular data, four species could be distinguished on soybeans in Croatia. Diaporthe phaseolorum is described in this study and its synonyms are discussed. Diaporthe phaseolorum var. caulivora is raised to species status and the name Diaporthe caulivora is introduced to accommodate it. A species previously known as Phomopsis sp. 9 from earlier studies on sunflower, grapevine, rooibos and hydrangea is reported for the first time on soybean, and is formally described as Diaporthe novem. The well-known soybean pathogen Phomopsis longicolla was also collected in the present study and was transferred to Diaporthe longicolla comb. nov. The presence of these species on herbaceous hosts raises once more the relevance of weeds as reservoirs for pathogens of economically important plants.
    Keywords: Anamorph ; EF1-\xce\xb1 ; ITS ; mating-types ; phylogeny ; systematics ; taxonomy ; teleomorph
    Repository Name: National Museum of Natural History, Netherlands
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  • 7
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    Mitochondrial and morphological differentiation in a previously unrecognized radiation of the land snail genus Parachloritis Ehrmann, 1912 on Timor (Pulmonata: Camaenidae) (2014)
    In:  Contributions to Zoology vol. 83 no. 1, pp. 1-40
    Details
    Publication Date: 2024-01-12
    Description: The present work revises the taxonomy of one group of camaenid gastropods from Timor-Leste based on the study of a large number of recently collected ethanol preserved samples as well as historic museum material, including types. By employing comparative analyses of the variation in morphological features (shell, penial anatomy) and the differentiation in mitochondrial DNA sequences of the cytochrome c oxidase subunit 1 gene (COI) and the 16S rDNA (16S), altogether nineteen species are recognized from Timor-Leste and adjacent areas in the Lesser Sunda and Moluccas, such as West-Timor, Adonara, Leti and Sermata Islands (Indonesia). Four of these species were described previously and have mostly been placed within the genus Chloritis Beck, 1837 in the few historic treatments available. Fifteen species found to be new are formally described. In contrast to the previous taxonomic treatment, placement in the genus parachloritis Ehrmann, 1912 is proposed on grounds of comparative shell morphology. Molecular phylogenetic analyses revealed that all examined species form a monophyletic group, which encompasses diverse shell forms. While most species have shells of the general chloritid type, which are of little taxonomic utility, highly distinct shell morphs (trochoid shells, dwarf forms) have originated within this radiation in independent lineages. Morphological change has occurred in some taxonomic lineages while the bulk of Parachloritis species has maintained an ancestral shell phenotype. This phenotypic stasis is attributed to stabilizing selection in species, which have maintained associations with ancestral habitats, while distinct shell forms have evolved as result of habitat shifts. Consequently, purely shellbased taxonomies are prone to errors due to misjudging the significance of shell characters. While some Parachloritis species uncovered here were found to be narrowly endemic, others had wide distributions that include more than one island. Narrow range endemism was predominantly found in dwarf species and in species that live in high altitudes.
    Keywords: Gastropoda ; Helicoidea ; new species ; phylogeny ; systematics ; taxonomy
    Repository Name: National Museum of Natural History, Netherlands
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  • 8
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    Redefining the damselfly families: a comprehensive molecular phylogeny of Zygoptera (Odonata) (2014)
    In:  Systematic Entomology vol. 39, pp. 68-96
    Details
    Publication Date: 2024-01-12
    Description: An extensive molecular phylogenetic reconstruction of the suborder Zygoptera of the Odonata is presented, based on mitochondrial (16S, COI) and nuclear (28S) data of 59% of the 310 genera recognized and all (suspected) families except the monotypic Hemiphlebiidae. A partial reclassification is proposed, incorporating morphological characters. Many traditional families are recovered as monophyletic, but reorganization of the superfamily Coenagrionoidea into three families is proposed: Isostictidae, Platycnemididae and Coenagrionidae. Archboldargia Lieftinck, Hylaeargia Lieftinck, Palaiargia Forster, \xc2\xa8 Papuargia Lieftinck and Onychargia Selys are transferred from Coenagrionidae to Platycnemididae, and Leptocnemis Selys, Oreocnemis Pinhey and Thaumatagrion Lieftinck from Platycnemididae to Coenagrionidae. Each geographically well-defined clade of Platycnemididae is recognized as a subfamily, and thus Disparoneurinae (i.e. Old World \xe2\x80\x98Protoneuridae\xe2\x80\x99) is incorporated, Calicnemiinae is restricted, and Allocnemidinae (type genus: Allocnemis Selys) subfam.n., Idiocnemidinae (type genus: Idiocnemis Selys) subfam.n. and Onychargiinae (type genus: Onychargia Selys) subfam.n. and Coperini trib.n. (type genus: Copera Kirby) are described. Half of Coenagrionidae belongs to a well-supported clade incorporating Coenagrion Kirby and the potential subfamilies Agriocnemidinae, Ischnurinae and Pseudagrioninae. The remainder is less well defined, but includes the Pseudostigmatidae and New World Protoneuridae that, with Argiinae and Teinobasinae, may prove valid subfamilies with further evidence. Ninety-two per cent of the genera formerly included in the polyphyletic Amphipterygidae and Megapodagrionidae were studied. Pentaphlebiidae, Rimanellidae and Devadattidae fam.n. (type genus: Devadatta Kirby) are separated from Amphipterygidae, and Argiolestidae, Heteragrionidae, Hypolestidae, Philogeniidae, Philosinidae and Thaumatoneuridae from Megapodagrionidae. Eight further groups formerly placed in the latter are identified, but are retained as incertae sedis; the validity of Lestoideidae, Philogangidae and Pseudolestidae is confirmed. For some families (e.g. Calopterygidae, Chlorocyphidae) a further subdivision is possible; Protostictinae subfam.n. (type genus: Protosticta Selys) is introduced in Platystictidae. Numerous new combinations are proposed in the Supporting Information. Many long-established families lack strong morphological apomorphies. In particular, venation is incongruent with molecular results, stressing the need to review fossil Odonata taxonomy: once defined by the reduction of the anal vein, Protoneuridae dissolves completely into six clades from five families.
    Keywords: damselflies ; phylogeny ; Zygoptera ; Odonata
    Repository Name: National Museum of Natural History, Netherlands
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  • 9
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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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  • 10
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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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