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  • Journals
  • Articles  (14)
  • taxonomy  (9)
  • evolution  (5)
  • 1
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    Navigating taxonomic complexity: a use-case report on FAIR scientific name-matching service usage in ENVRI Research infrastructures (2024)
    Pensoft Publishers
    In:  Research Ideas and Outcomes vol. 10 no. e121871
    Details
    Publication Date: 2024-04-12
    Description: This paper presents a use-case conducted within the ENVRI FAIR project, examining challenges and opportunities in deploying FAIR-aligned (ensuring Findability, Accessibility, Interoperability and Reusability) scientific name-matching services across Environmental Research Infrastructures (RIs). Six services were tested using various name variations, revealing inconsistencies in match types, status reporting and handling of canonical forms and typos. These diversities pose challenges for RI data pipelines and interoperability. The paper underscores the importance of standardised tools, enhanced communication, training, collaboration and shared resources. Addressing these needs can facilitate more effective FAIR implementation within the ENVRI community and biodiversity research. This, in turn, will empower RIs to seamlessly integrate and leverage scientific names, unlocking the full potential of their data for research and policy implementation.
    Keywords: scientific names ; taxonomy ; biodiversity ; FAIR ; ENVRI
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 2
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    Multiple gene genealogies and phenotypic characters differentiate several novel species of Mycosphaerella and related anamorphs\non banana (2008)
    In:  Persoonia - Molecular Phylogeny and Evolution of Fungi vol. 20 no. 1, pp. 19-37
    Details
    Publication Date: 2024-01-12
    Description: Three species of Mycosphaerella, namely M. eumusae, M. fijiensis, and M. musicola are involved in the Sigatoka disease complex of bananas. Besides these three primary pathogens, several additional species of Mycosphaerella or their anamorphs have been described from Musa. However, very little is known about these taxa, and for the majority of these species no culture or DNA is available for study. In the present study, we collected a global set of Mycosphaerella strains from banana, and compared them by means of morphology and a multi-gene nucleotide sequence data set. The phylogeny inferred from the ITS region and the combined data set containing partial gene sequences of the actin gene, the small subunit mitochondrial ribosomal DNA and the histone H3 gene revealed a rich diversity of Mycosphaerella species on Musa. Integration of morphological and molecular data sets confirmed more than 20 species of Mycosphaerella (incl. anamorphs) to occur on banana. This study reconfirmed the previously described presence of Cercospora apii, M. citri and M. thailandica, and also identified Mycosphaerella communis, M. lateralis and Passalora loranthi on this host. Moreover, eight new species identified from Musa are described, namely Dissoconium musae, Mycosphaerella mozambica, Pseudocercospora assamensis, P. indonesiana, P. longispora, Stenella musae, S. musicola, and S. queenslandica.
    Keywords: Mycosphaerella ; phylogeny ; Sigatoka disease complex ; taxonomy
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 3
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    Numerous new records of tropical non-indigenous species in the Eastern Mediterranean highlight the challenges of their recognition and identification (2021)
    Pensoft Publishers
    In:  ZooKeys vol. 1010, pp. 1-95
    Details
    Publication Date: 2024-01-12
    Description: New data on 52 non-indigenous mollusks in the Eastern Mediterranean Sea is reported. Fossarus sp. (aff. aptus sensu Blatterer 2019), Coriophora lessepsiana Albano, Bakker & Sabelli, sp. nov., Cerithiopsis sp. aff. pulvis, Joculator problematicus Albano & Steger, sp. nov., Cerithiopsis sp., Elachisina sp., Iravadia aff. elongata, Vitrinella aff. Vitrinella sp. 1 (sensu Blatterer 2019), Melanella orientalis, Parvioris aff. dilecta, Odostomia cf. dalli, Oscilla virginiae, Parthenina cossmanni, Parthenina typica, Pyrgulina craticulata, Turbonilla funiculata, Cylichna collyra, Musculus coenobitus, Musculus aff. viridulus, Chavania erythraea, Scintilla cf. violescens, Iacra seychellarum and Corbula erythraeensis are new records for the Mediterranean. An unidentified gastropod, Skeneidae indet., Triphora sp., Hypermastus sp., Sticteulima sp., Vitreolina cf. philippi, Odostomia (s.l.) sp. 1, Henrya (?) sp., and Semelidae sp. are further potential new non-indigenous species although their status should be confirmed upon final taxonomic assessment. Additionally, the status of Dikoleps micalii, Hemiliostraca clandestina comb. nov. and H. athenamariae comb. nov. is changed to non-indigenous, range extensions for nine species and the occurrence of living individuals for species previously recorded from empty shells only are reported. Opimaphora blattereri Albano, Bakker & Sabelli, sp. nov. is described from the Red Sea for comparison with the morphologically similar C. lessepsiana Albano, Bakker & Sabelli, sp. nov. The taxonomic part is followed by a discussion on how intensive fieldwork and cooperation among institutions and individuals enabled such a massive report, and how the poor taxonomic knowledge of the Indo-Pacific fauna hampers non-indigenous species detection and identification. Finally, the hypothesis that the simultaneous analysis of quantitative benthic death assemblages can support the assignment of non-indigenous status to taxonomically undetermined species is discussed.
    Keywords: Animal Science and Zoology ; Ecology ; Evolution ; Behavior and Systematics ; Cerithiopsidae ; invasion biology ; Lessepsian invasion ; Mollusca ; new species ; Red Sea ; taxonomy ; Triphoridae
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 4
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    Taxonomy, ecology, and conservation status of Philippine Rafflesia\n(Rafflesiaceae) (2009)
    In:  Blumea: Biodiversity, Evolution and Biogeography of Plants vol. 54 no. 1/3, pp. 77-93
    Details
    Publication Date: 2024-01-12
    Description: The number of Rafflesia species (Rafflesiaceae) reported for the Philippines has grown explosively from two before 2002 to ten or eleven presently. We present an overview of the current knowledge of Philippine Rafflesia by providing a comprehensive account of all the recognized species with their taxonomy, distribution and ecology, plus a key and photographs to aid in identification. Their conservation status and that of the rain forest habitats they require is discussed.
    Keywords: Conservation ; ecology ; Philippines ; Rafflesia ; Rafflesiaceae ; taxonomy
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 5
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    Eight new Halophytophthora species from marine and brackish-water ecosystems in Portugal and an updated phylogeny for the genus (2022)
    In:  Persoonia - Molecular Phylogeny and Evolution of Fungi vol. 48, pp. 54-90
    Details
    Publication Date: 2024-03-24
    Description: During an oomycete survey in December 2015, 10 previously unknown Halophytophthora taxa were isolated from marine and brackish water of tidal ponds and channels in saltmarshes, lagoon ecosystems and river estuaries at seven sites along the Algarve coast in the South of Portugal. Phylogenetic analyses of LSU and ITS datasets, comprising all described Halophytophthora species, the 10 new Halophytophthora taxa and all relevant and distinctive sequences available from GenBank, provided an updated phylogeny of the genus Halophytophthora s.str. showing for the first time a structure of 10 clades designated as Clades 1–10. Nine of the 10 new Halophytophthora taxa resided in Clade 6 together with H. polymorphica and H. vesicula. Based on differences in morphology and temperature-growth relations and a multigene (LSU, ITS, Btub, hsp90, rpl10, tigA, cox1, nadh1, rps10) phylogeny, eight new Halophytophthora taxa from Portugal are described here as H. brevisporangia, H. celeris, H. frigida, H. lateralis, H. lusitanica, H. macrosporangia, H. sinuata and H. thermoambigua. Three species, H. frigida, H. macrosporangia and H. sinuata, have a homothallic breeding system while the remaining five species are sterile. Pathogenicity and litter decomposition tests are underway to clarify their pathological and ecological role in the marine and brackish-water ecosystems. More oomycete surveys in yet undersurveyed regions of the world and population genetic or phylogenomic analyses of global populations are needed to clarify the origin of the new Halophytophthora species.
    Keywords: Ecology ; Evolution ; Behavior and Systematics ; breeding system ; ecological role ; evolution ; lifestyle ; oomycetes ; Peronosporaceae ; Phytophthora
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 6
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    Multiple new Phytophthora species from ITS Clade 6 associated with natural ecosystems in Australia: evolutionary and ecological implications (2011)
    In:  Persoonia - Molecular Phylogeny and Evolution of Fungi vol. 26 no. 1, pp. 13-39
    Details
    Publication Date: 2024-01-12
    Description: During surveys of dying vegetation in natural ecosystems and associated waterways in Australia many new taxa have been identified from Phytophthora ITS Clade 6. For representative isolates, the region spanning the internal transcribed spacer region of the ribosomal DNA, the nuclear gene encoding heat shock protein 90 and the mitochondrial cox1 gene were PCR amplified and sequenced. Based on phylogenetic analysis and morphological and physiological comparison, four species and one informally designated taxon have been described; Phytophthora gibbosa, P. gregata, P. litoralis, P. thermophila and P. taxon paludosa. Phytophthora gibbosa, P. gregata and P. taxon paludosa form a new cluster and share a common ancestor; they are homothallic and generally associated with dying vegetation in swampy or water-logged areas. Phytophthora thermophila and P. litoralis are sister species to each other and more distantly to P. gonapodyides. Both new species are common in waterways and cause scattered mortality within native vegetation. They are self-sterile and appear well adapted for survival in an aquatic environment and inundated soils, filling the niche occupied by P. gonapodyides and P. taxon salixsoil in the northern hemisphere. Currently the origin of these new taxa, their pathogenicity and their role in natural ecosystems are unknown. Following the precautionary principle, they should be regarded as a potential threat to native ecosystems and managed to minimise their further spread.
    Keywords: Aquatic habitat ; breeding systems ; evolution ; phylogeny ; radiation ; sterility ; survival
    Repository Name: National Museum of Natural History, Netherlands
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  • 7
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    Phylogeography of the Sponge Suberites diversicolor in Indonesia: insights into the evolution of marine lake populations (2013)
    In:  PLoS ONE vol. 10 no. 8
    Details
    Publication Date: 2024-01-12
    Description: The existence of multiple independently derived populations in landlocked marine lakes provides an opportunity for fundamental research into the role of isolation in population divergence and speciation in marine taxa. Marine lakes are landlocked water bodies that maintain a marine character through narrow submarine connections to the sea and could be regarded as the marine equivalents of terrestrial islands. The sponge Suberites diversicolor (Porifera: Demospongiae: Suberitidae) is typical of marine lake habitats in the Indo-Australian Archipelago. Four molecular markers (two mitochondrial and two nuclear) were employed to study genetic structure of populations within and between marine lakes in Indonesia and three coastal locations in Indonesia, Singapore and Australia. Within populations of S. diversicolor two strongly divergent lineages (A & B) (COI: p = 0.4% and ITS: p = 7.3%) were found, that may constitute cryptic species. Lineage A only occurred in Kakaban lake (East Kalimantan), while lineage B was present in all sampled populations. Within lineage B, we found low levels of genetic diversity in lakes, though there was spatial genetic population structuring. The Australian population is genetically differentiated from the Indonesian populations. Within Indonesia we did not record an East-West barrier, which has frequently been reported for other marine invertebrates. Kakaban lake is the largest and most isolated marine lake in Indonesia and contains the highest genetic diversity with genetic variants not observed elsewhere. Kakaban lake may be an area where multiple putative refugia populations have come into secondary contact, resulting in high levels of genetic diversity and a high number of endemic species.
    Keywords: Suberites diversicolor ; Indo-Australian Archipelago ; marine lakes ; evolution
    Repository Name: National Museum of Natural History, Netherlands
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  • 8
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    Malassezia vespertilionis sp. nov.: a new cold-tolerant species of yeast isolated from bats (2018)
    In:  Persoonia - Molecular Phylogeny and Evolution of Fungi vol. 41, pp. 56-70
    Details
    Publication Date: 2024-01-12
    Description: Malassezia is a genus of medically-important, lipid-dependent yeasts that live on the skin of warmblooded animals. The 17 described species have been documented primarily on humans and domestic animals, but few studies have examined Malassezia species associated with more diverse host groups such as wildlife. While investigating the skin mycobiota of healthy bats, we isolated a Malassezia sp. that exhibited only up to 92 % identity with other known species in the genus for the portion of the DNA sequence of the internal transcribed spacer region that could be confidently aligned. The Malassezia sp. was cultured from the skin of nine species of bats in the subfamily Myotinae; isolates originated from bats sampled in both the eastern and western United States. Physiological features and molecular characterisation at seven additional loci (D1/D2 region of 26S rDNA, 18S rDNA, chitin synthase, second largest subunit of RNA polymerase II, \xce\xb2-tubulin, translation elongation factor EF-1\xce\xb1, and minichromosome maintenance complex component 7) indicated that all of the bat Malassezia isolates likely represented a single species distinct from other named taxa. Of particular note was the ability of the Malassezia sp. to grow over a broad range of temperatures (7\xe2\x80\x9340 \xc2\xb0C), with optimal growth occurring at 24 \xc2\xb0C. These thermal growth ranges, unique among the described Malassezia, may be an adaptation by the fungus to survive on bats during both the host\xe2\x80\x99s hibernation and active seasons. The combination of genetic and physiological differences provided compelling evidence that this lipid-dependent yeast represents a novel species described herein as Malassezia vespertilionis sp. nov. Whole genome sequencing placed the new species as a basal member of the clade containing the species M. furfur, M. japonica, M. obtusa, and M. yamatoensis. The genetic and physiological uniqueness of Malassezia vespertilionis among its closest relatives may make it important in future research to better understand the evolution, life history, and pathogenicity of the Malassezia yeasts.
    Keywords: Chiroptera ; evolution ; hibernation ; Malassezia ; Myotis ; new species ; phylogeny
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 9
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    Back to the roots: a reappraisal of Neocosmospora (2019)
    Naturalis Biodiversity Center
    In:  Persoonia - Molecular Phylogeny and Evolution of Fungi vol. 43 no. 1, pp. 90-185
    Details
    Publication Date: 2024-01-12
    Description: The genus Neocosmospora (Fusarium solani species complex) contains saprobes, plant endophytes \nand pathogens of major economic significance as well as opportunistic animal pathogens. Advances in biological \nand phylogenetic species recognition revealed a rich species diversity which has largely remained understudied. \nMost of the currently recognised species lack formal descriptions and Latin names, while the taxonomic utility of old \nnames is hampered by the lack of nomenclatural type specimens. Therefore, to stabilise the taxonomy and nomenclature of these important taxa, we examined type specimens and representative cultures of several old names by \nmeans of morphology and phylogenetic analyses based on rDNA (ITS and LSU), rpb2 and tef1 sequences. Sixtyeight species are accepted in Neocosmospora, 29 of them described herein as new; while 13 new combinations \nare made. Eleven additional phylogenetic species are recognized, but remain as yet undescribed. Lectotypes are \nproposed for eight species, seven species are epitypified and two species are neotypified. Notes on an additional \n17 doubtful or excluded taxa are provided.
    Keywords: Ecology ; Evolution ; Behavior and Systematics ; Fusarium ; new taxa ; systematics ; taxonomy
    Repository Name: National Museum of Natural History, Netherlands
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  • 10
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    Diversity of Sporocadaceae (pestalotioid fungi) from Rosa in China (2022)
    In:  Persoonia - Molecular Phylogeny and Evolution of Fungi vol. 49 no. 1, pp. 201-260
    Details
    Publication Date: 2024-03-20
    Description: Rosa (Rosaceae) is an important ornamental and medicinal plant genus worldwide, with several species being cultivated in China. Members of Sporocadaceae (pestalotioid fungi) are globally distributed and include endophytes, saprobes but also plant pathogens, infecting a broad range of host plants on which they can cause important plant diseases. Although several Sporocadaceae species were recorded to inhabit Rosa spp., the taxa occurring on Rosa remain largely unresolved. In this study, a total of 295 diseased samples were collected from branches, fruits, leaves and spines of eight Rosa species (R. chinensis, R. helenae, R. laevigata, R. multiflora, R. omeiensis, R. rugosa, R. spinosissima and R. xanthina) in Gansu, Henan, Hunan, Qinghai, Shaanxi Provinces and the Ningxia Autonomous Region of China. Subsequently 126 strains were obtained and identified based on comparisons of DNA sequence data. Based on these results 15 species residing in six genera of Sporocadaceae were delineated, including four known species (Pestalotiopsis chamaeropis, Pes. rhodomyrtus, Sporocadus sorbi and Spo. trimorphus) and 11 new species described here as Monochaetia rosarum, Neopestalotiopsis concentrica, N. subepidermalis, Pestalotiopsis tumida, Seimatosporium centrale, Seim. gracile, Seim. nonappendiculatum, Seim. parvum, Seiridium rosae, Sporocadus brevis, and Spo. spiniger. This study also represents the first report of Pes. chamaeropis, Pes. rhodomyrtus and Spo. sorbi on Rosa. The overall data revealed that Pestalotiopsis was the most prevalent genus, followed by Seimatosporium, while Pes. chamaeropis and Pes. rhodomyrtus were the two most prevalent species. Analysis of Sporocadaceae abundance on Rosa species and plant organs revealed that spines of R. chinensis had the highest species diversity.
    Keywords: Ecology ; Evolution ; Behavior and Systematics ; Amphisphaeriales ; Ascomycota ; new taxa ; phylogeny ; taxonomy
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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