Browsing by Subject "Taxonomy"

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  • Murillo-Ramos, Leidys; Brehm, Gunnar; Sihvonen, Pasi; Hausmann, Axel; Holm, Sille; Reza Ghanavi, Hamid; Õunap, Erki; Truuverk, Andro; Staude, Hermann; Friedrich, Egbert; Tammaru, Toomas; Wahlberg, Niklas (2019)
    Our study aims to investigate the relationships of the major lineages within the moth family Geometridae, with a focus on the poorly studied Oenochrominae-Desmobathrinae complex, and to translate some of the results into a coherent subfamilial and tribal level classification for the family. We analyzed a molecular dataset of 1,206 Geometroidea terminal taxa from all biogeographical regions comprising up to 11 molecular markers that includes one mitochondria) (COI) and 10 protein-coding nuclear gene regions (wingless, ArgK, MDH, RpS5, GAPDH, IDH, Ca-ATPase, Nex9, EF-1 alpha, CAD). The molecular data set was analyzed using maximum likelihood as implemented in IQ-TREE and RAxML. We found high support for the subfamilies Larentiinae, Geometrinae and Ennominae in their traditional scopes. Sterrhinae becomes monophyletic only if Ergavia Walker, Ametris Hubner and Macrotes Westwood, which are currently placed in Oenochrominae, are formally transferred to Sterrhinae. Desmobathrinae and Oenochrominae are found to be polyphyletic. The concepts of Oenochrominae and Desmobathrinae required major revision and, after appropriate rearrangements, these groups also form monophyletic subfamily-level entities. Oenochrominae s.str. as originally conceived by Guenee is phylogenetically distant from Epidesmia and its close relatives. The latter is hereby described as the subfamily Epidesmiinae Murillo-Ramos, Sihvonen & Brehm, subfam. nov. Epidesmiinae are a lineage of "slender-bodied Oenochrominae" that include the genera Ecphyas Turner, Systatica Turner, Adeixis Warren, Dichromodes Guenee, Phrixocomes Turner, Abraxaphantes Warren, Epidesmia Duncan & Westwood and Phrataria Walker. Archiearinae are monophyletic when Dirce and Acalyphes are formally transferred to Ennominae. We also found that many tribes were para- or polyphyletic and therefore propose tens of taxonomic changes at the tribe and subfamily levels. Archaeobalbini stat. rev. Viidalepp (Geometrinae) is raised from synonymy with Pseudoterpnini Warren to tribal rank. Chlorodontoperini Murillo-Ramos, Sihvonen & Brehm, trib. nov. and Drepanogynini Murillo-Ramos, Sihvonen & Brehm, trib. nov. are described as new tribes in Geometrinae and Ennominae, respectively.
  • Wang, Yanhao; Li, Yuchen; Fan, Ju; Ye, Chang; Chai, Mingke (2021)
    Graphs are commonly used for representing complex structures such as social relationships, biological interactions, and knowledge bases. In many scenarios, graphs not only represent topological relationships but also store the attributes that denote the semantics associated with their vertices and edges, known as attributed graphs. Attributed graphs can meet demands for a wide range of applications, and thus a variety of queries on attributed graphs have been proposed. However, these diverse types of attributed graph queries have not been systematically investigated yet. In this paper, we provide an extensive survey of several typical types of attributed graph queries. We propose a taxonomy of attributed graph queries based on query inputs and outputs. We summarize the definitions of queries that fall into each category and present a fine-grained classification of queries within each category by analyzing the semantics and algorithmic motivations behind these queries. Moreover, we discuss the insights of how existing studies address the technical challenges of query processing and outline several promising future research directions.
  • Rikkinen, Jouko; Meinke, Kristin; Grabenhorst, Heinrich; Gröhn, Carsten; Kobbert, Max; Wunderlich, Jörg; Schmidt, Alexander (2018)
    Calicioid lichens and fungi are a polyphyletic grouping of tiny ascomycetes that accumulate a persistent spore mass (mazaedium) on top of their usually well-stalked ascomata ('mazaediate fungi'). In addition to extant forms, six fossils of the group were previously known from European Paleogene amber. Here we report nine new fossils and analyze the preserved features of all fossils to assess their applicability for dating molecular phylogenies. Many fossils are extremely well preserved, allowing detailed comparisons with modern taxa. SEM investigation reveals that even fine details of ascospore wall ultrastructure correspond to those seen in extant specimens. All fossils can confidently be assigned to modern genera: three to Calicium (Caliciaceae, Lecanoromycetes), five to Chaenotheca (Coniocybaceae, Coniocybomycetes), six to Chaenothecopsis (Mycocaliciaceae, Eurotiales), and one to Phaeocalicium (Mycocaliciaceae, Eurotiales). Several Calicium and Chaenotheca fossils are assignable to specific lineages within their genera, while the Chaenothecopsis fossils demonstrate the extent of intraspecific variation within one such lineage. Some features in the morphology of Chaenotheca succina nov. sp. seem to be ancestral as they have not been reported from modern species of the genus. (C) 2018 Elsevier Masson SAS. All rights reserved.
  • Tojibaev, Komiljon Sh; Khassanov, Furkat O.; Beshko, Natalya Yu; Tajetdinova, Dilarom M.; Turginov, Orzimat T.; Sennikov, Alexander N.; Chang, Kae Sun; Oh, Seung-Hwan; Jang, Chang-gee (2020)
    This article presents a new checklist of Scrophularia in Uzbekistan. The synopsis includes 21 species; one of them is national endemic, and seven species were newly recorded for Uzbekistan as a result of field collecting missions, studies, and examination of Tashkent (TASH), St.-Petersburg (LE), Almaty (AA), and Moscow (MW) herbarium collections. The geographical distribution of Scrophularia in Uzbekistan was mapped and analyzed. The identification key, a table of comparative diagnostic characters, nomenclatural types, and ecological data are provided. (C) 2019 National Science Museum of Korea (NSMK) and Korea National Arboretum (KNA), Publishing Services by Elsevier.
  • Pohjoismäki, Jaakko; Kahanpää, Jere Veikko; Mutanen, Marko (2016)
    This data release provides COI barcodes for 366 species of parasitic flies (Diptera: Tachinidae), enabling the DNA based identification of the majority of northern European species and a large proportion of Palearctic genera, regardless of the developmental stage. The data will provide a tool for taxonomists and ecologists studying this ecologically important but challenging parasitoid family. A comparison of minimum distances between the nearest neighbors revealed the mean divergence of 5.52% that is approximately the same as observed earlier with comparable sampling in Lepidoptera, but clearly less than in Coleoptera. Full barcode-sharing was observed between 13 species pairs or triplets, equaling to 7.36% of all species. Delimitation based on Barcode Index Number (BIN) system was compared with traditional classification of species and interesting cases of possible species oversplits and cryptic diversity are discussed. Overall, DNA barcodes are effective in separating tachinid species and provide novel insight into the taxonomy of several genera.
  • Radnaeva, Larisa D.; Popov, Dmitry V.; Grahl-Nielsen, Otto; Khanaev, Igor V.; Bazarsadueva, Selmeg V.; Kakela, Reijo (2017)
    Lake Baikal is a unique freshwater environment with maximum depths over 1600 m. The high water pressure at the lakebed strengthens the solidifying effect of low water temperature on animal tissue lipids, and thus the effective temperatures in the depths of the lake equal subzero temperatures in shallow waters. Cottoidei species has colonized the different water layers of the lake, and developed different ecology and physiology reflected in their tissue biochemistry. We studied by gas chromatography the composition of fatty acids (FAs), largely responsible for tissue lipid physical properties, in the white muscle tissue of 13 species of the Cottoidei fish; five benthic abyssal, six benthic eurybathic and two benthopelagic species. The FA profiles reflected habitat depth. The muscles of the deepest living species contained little polyunsaturated FAs (PUFAs) and were instead rich in monounsaturated FAs (MUFAs), which may be due to occasional weak food web links to the PUFA-rich primary producers of the photic water layer, high MUFA supply from their benthic diet, and conversion of saturated FAs (SFAs) to MUFAs in the tissues of the fish. Despite the MUFA percentage among the abyssal species reached even 50% (by weight) of total FAs, the PUFA percentage still remained above 20% in every species. The muscle MUFA/SFA ratio correlated negatively with the PUFA content of the fish muscle, suggesting viscosity control integrating the fluidity contributions from the dietary PUFAs and potentially endogenous MUFAs.
  • Ekmark, Risto (Helsingin yliopisto, 2020)
    Soft rot diseases of potato (Solanum tuberosum) cause significant economic losses worldwide as S. tuberosum is the fourth most important food crop in the world and extensively cultivated. S. tuberosum is susceptible to diseases during storage, where the two most important soft rot causing bacterial genera Pectobacterium and Dickeya can efficiently cause rotting in humid conditions with limited oxygen concentration. The focus of this study was in two Pectobacterium isolates that exhibit orange pigmentation during their infection of S. tuberosum tubers. The genomes of the isolates were sequenced and then assembled into contigs with SPAdes genome assembler. The draft genomes were compared to reference genomes of Pectobacterium species by average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) methods. The isolates were determined to be of Pectobacterium versatile species by ANI score of 97.6%, analyzed by pyANI, and dDDH similarity of 78.6%, analyzed by Type (Strain) Genome Server of DSMZ-German Collection of Micro-organisms and Cell Cultures GmbH. The genomes of the isolates were annotated with the Automated Annotation Server of Kyoto Encyclopedia of Genes and Genomes. The characteristic features of Pectobacteria, Quorum Sensing and Bacterial Secretion Systems, were among the most numerous genes along with essential genes for metabolism and biosynthesis. To support the taxonomic analyses, pangenomic analysis was carried out with Rapid large-scale prokaryote pangenome analysis software Roary with annotation data provided by rapid prokaryotic genome annotation software PROKKA. The genomes of the isolates and reference genomes were used as an input for PROKKA. The pangenomic analysis grouped the Pectobacterium versatile reference genomes and the isolates to the same branch as expected. Comparing reference Pectobacterium versatile genomes with the isolates also showed that the Pectobacterium core genome consists only of 56% of the total number of genes in the genomes. The role of the orange pigmentation still remains unclear and requires extensive further study. However, the isolates were shown to contain genes that were homologous to a previously published gene cluster responsible for the production of an orange pigment by Pectobacterium carotovorum isolate SCRI193. It is hypothesized that the homologous genes present in the characterized isolates are responsible for the pigmentation of infected S. tuberosum tissue.
  • Malysheva, Vera; Schoutteten, Nathan; Verbeken, Annemieke; Spirin, Viacheslav (2021)
    The identity of Achroomyces effusus is re-established with the use of morphological and DNA methods, and a neotype is selected. The species is conspecific with Colacogloea peniophorae, the generic type of Colacogloea, and has a priority over it. A new combination, C. effusa, is proposed.
  • Ritari, Jarmo; Salojärvi, Jarkko; Lahti, Leo; de Vos, Willem M. (2015)
    Background: Current sequencing technology enables taxonomic profiling of microbial ecosystems at high resolution and depth by using the 16S rRNA gene as a phylogenetic marker. Taxonomic assignation of newly acquired data is based on sequence comparisons with comprehensive reference databases to find consensus taxonomy for representative sequences. Nevertheless, even with well-characterised ecosystems like the human intestinal microbiota it is challenging to assign genus and species level taxonomy to 16S rRNA amplicon reads. A part of the explanation may lie in the sheer size of the search space where competition from a multitude of highly similar sequences may not allow reliable assignation at low taxonomic levels. However, when studying a particular environment such as the human intestine, it can be argued that a reference database comprising only sequences that are native to the environment would be sufficient, effectively reducing the search space. Results: We constructed a 16S rRNA gene database based on high-quality sequences specific for human intestinal microbiota, resulting in curated data set consisting of 2473 unique prokaryotic species-like groups and their taxonomic lineages, and compared its performance against the Greengenes and Silva databases. The results showed that regardless of used assignment algorithm, our database improved taxonomic assignation of 16S rRNA sequencing data by enabling significantly higher species and genus level assignation rate while preserving taxonomic diversity and demanding less computational resources. Conclusion: The curated human intestinal 16S rRNA gene taxonomic database of about 2500 species-like groups described here provides a practical solution for significantly improved taxonomic assignment for phylogenetic studies of the human intestinal microbiota.
  • Malysheva, Vera; Spirin, Viacheslav; Miettinen, Otto; Kout, Jiří; Savchenko, Anton; Larsson, Karl-Henrik (2019)
    In the present paper, we select a neotype for Tremella cerasi and prove that it is conspecific with Ditangium insigne (the genus type of Ditangium). We argue that Ditangium should be restored as a correct genus for T. cerasi, while the currently used generic name Craterocolla is to be treated as its younger synonym. Morphological, ecological and genetic variability of Ditangium cerasi is discussed, and two other Ditangium species are described—D. altaicum, sp. nov. and D. incarnatum, comb. nov. In addition, Exidia fulva is combined in Globulisebacina.
  • Spirin, Viacheslav; Malysheva, Vera; Miettinen, Otto; Vlasak, Josef; Mendes Alvarenga, Renato Lucio; Gibertoni, Tatiana Baptista; Ryvarden, Leif; Larsson, Karl-Henrik (2019)
    The taxonomy of Protomerulius and Heterochaetella is revised based on DNA data and morphological evidence, and their type species, P. brasiliensis and H. dubia, are proved to be congeneric. As a consequence, H. dubia and related species, of which four are described as new, are placed in Protomerulius. Heterochaete microspora is also combined in Protomerulius, and the genus concept is redefined to encompass effused species with smooth or spiny hymenophore and monomitic hyphal structure. Psilochaete multifora, gen. and spec. nov. is a distant relative of Protomerulius spp. found in Norway. Heterochaetella cystidiophora is re-collected in Brazil and placed in the synonyms of Heterochaete sanctae-catharinae. This species does not belong to the Protomerulius-Heterochaetella lineage, and it is transferred to Metulochaete, gen. nov.
  • Spirin, Viacheslav; Volobuev, Sergey; Viner, Ilya; Miettinen, Otto; Vlasák, Josef; Schoutteten, Nathan; Motato-Vásquez, Viviana; Kotiranta, Heikki; Hernawati, Nana; Larsson, Karl-Henrik (2021)
    The taxonomy of Sistotremastrum (Trechisporales, Basidiomycota) is revised based on morphology and DNA data. The genus is shown to be polyphyletic, and therefore it is split into two units-Sistotremastrum s. str. and Sertulicium, gen. nov. (typified with Corticium niveocremeum). Sistotremastrum s. str. is retained for eleven species of which eight are described as new while Sertulicium encompasses at least six species, including one new to science. Both of these genera are only distantly related to other representatives of the Trechisporales. Additionally, a new poroid neotropical species, Porpomyces abiens (Hydnodontaceae), is described as morphologically similar to some members of Sistotremastrum s. str.
  • Viranta, Suvi; Atickem, Anagaw; Werdelin, Lars; Stenseth, Nils C (BioMed Central, 2017)
    Abstract Background The African wolf, for which we herein recognise Canis lupaster Hemprich and Ehrenberg, 1832 (Symbolae Physicae quae ex Itinere Africam Borealem er Asoam Occidentalem Decas Secunda. Berlin, 1833) as the valid species name (we consider the older name Canis anthus Cuvier, 1820 [Le Chacal de Sénégal, Femelle. In: Geoffroy St.-Hilaire E, Cuvier F, editors. Histoire Naturelle des Mammifères Paris, A. Belin, 1820] a nomen dubium), is a medium-sized canid with wolf-like characters. Because of phenotypic similarity, specimens of African wolf have long been assigned to golden jackal (Canis aureus Linnaeus, 1758 [Systema Naturae per Regna Tria Naturae, Secundum Classes, Ordines, Genera, Species, cum Characteribus, Differentiis, Synonymis, Locis. Tomus I. Editio decima, reformata, 1758]). Results Here we provide, through rigorous morphological analysis, a species description for this taxonomically overlooked species. Through molecular sequencing we assess its distribution in Africa, which remains uncertain due to confusion regarding possible co-occurrence with the Eurasian golden jackal. Canis lupaster differs from all other Canis spp. including the golden jackal in its cranial morphology, while phylogenetically it shows close affinity to the Holarctic grey wolf (Canis lupus Linnaeus, 1758 [Systema Naturae per Regna Tria Naturae, Secundum Classes, Ordines, Genera, Species, cum Characteribus, Differentiis, Synonymis, Locis. Tomus I. Editio decima, reformata, 1758]). All sequences generated during this study clustered with African wolf specimens, consistent with previous data for the species. Conclusions We suggest that the estimated current geographic range of golden jackal in Africa represents the African wolf range. Further research is needed in eastern Egypt, where a hybrid zone between Eurasian golden jackal and African wolf may exist. Our results highlight the need for improved studies of geographic range and population surveys for the taxon, which is classified as ‘least concern’ by the IUCN due to its erroneous identification as golden jackal. As a species exclusively distributed in Africa, investigations of the biology and threats to African wolf are needed.
  • Malysheva, Vera; Spirin, Viacheslav; Miettinen, Otto; Motato-Vasquez, Viviana; Hernawati,; Seelan, Jaya Seelan Sathiya; Larsson, Karl-Henrik (2018)
    Three species currently addressed to Protohydnum (Auriculariales) are studied with morphological and DNA methods. The genus Protohydnum is retained for the type species only, P. cartilagineum, recently re-collected in Brazil. The European species, P. piceicola, is not congeneric with P. cartilagineum and, therefore, placed in its own genus, Hyalodon, gen. nov. Another Hyalodon species, H. antui, is described from East Asia. The third member of Protohydnum sensu lato, P. sclerodontium from South-East Asia, is transferred to Elmerina.
  • Spirin, Viacheslav; Runnel, Kadri; Vlasák, Josef; Miettinen, Otto; Põldmaa, Kadri (2015)
    Abstract Antrodia is a polyphyletic genus, comprising brown-rot polypores with annual or short-lived perennial resupinate, dimitic basidiocarps. Here we focus on species that are closely related to Antrodia crassa, and investigate their phylogeny and species delimitation using geographic, ecological, morphological and molecular data (ITS and LSU rDNA, tef1). Phylogenetic analyses distinguished four clades within the monophyletic group of eleven conifer-inhabiting species (five described herein): (1)A. crassa s. str. (boreal Eurasia), Antrodia cincta sp. nova (North America) and Antrodia cretacea sp. nova (holarctic), all three being characterized by inamyloid skeletal hyphae that dissolve quickly in KOH solution; (2) Antrodia ignobilis sp. nova, Antrodia sitchensis and Antrodia sordida from North America, and Antrodia piceata sp. nova (previously considered conspecific with A. sitchensis) from Eurasia, possessing amyloid skeletal hyphae; (3) Antrodia ladiana sp. nova from the southern part of the USA, Antrodia pinea from East Asia, and Antrodia ferox – so far known from subtropical North America, but here reported also from Eurasia. These three species have inamyloid hyphae and narrow basidiospores; (4) the North American Antrodia pini-cubensis, sharing similar morphological characters with A. pinea, forming a separate clade. The habitat data indicate that several species are threatened by intensive forestry.
  • Spirin, Viacheslav; Malysheva, Vera; Schoutteten, Nathan; Viner, Ilya; Miettinen, Otto; Nordén, Jenni; Ryvarden, Leif; Kotiranta, Heikki; Verbeken, Annemieke; Weiss, Michael; Larsson, Karl-Henrik (2021)
    Taxonomy of Basidiodendron caesiocinereum complex is revised based on morphological and molecular methods (with the use of nc LSU rDNA, ITS and TEF1 regions). The basidiospore ornamentation is justified as a key morphological character for the species recognition in the group. As redefined here, B. caesiocinereum is an angiosperm-dwelling species with smooth basidiospores. Bourdotia cinerella and B. cinerella var. trachyspora are proved to represent separate species with warted basidiospores; they are reintroduced as Basidiodendron cinerellum and B. trachysporum. Additionally, eight new species related to B. caesiocinereum are described based on material from Eurasia, North America and Africa, and identity of B. spinosum from Oceania is discussed.
  • Seung, Jinbae; Lee, Seunghwan; Muona, Jyrki (2017)
    Three eucnemid genera and species are recognized for the first time from Korea: Eutyptycluts vicinus Fleutiaux, 1923, Fornax consobrinus Hisamatsu, 1963, and Feaia nipparensis (Hisamatsu, 1957) new combination (= Heterotaxis nipparensis Hisamatsu, 1957).A key to species, diagnoses, redescriptions, and photographs of diagnostic characters are provided for known Korean species. (C) 2017 Published by Elsevier B.V. on behalf of Korean Society of Applied Entomology, Taiwan Entomological Society and Malaysian Plant Protection Society.
  • Mignotte, Antoine; Garros, Claire; Gardes, Laetitia; Balenghien, Thomas; Duhayon, Maxime; Rakotoarivony, Ignace; Tabourin, Laura; Poujol, Lea; Mathieu, Bruno; Ibanez-Justicia, Adolfo; Deniz, Ahmet; Cvetkovikj, Aleksandar; Purse, Bethan; Ramilo, David W.; Stougiou, Despoina; Werner, Doreen; Pudar, Dubravka; Petric, Dusan; Veronesi, Eva; Jacobs, Frans; Kampen, Helge; da Fonseca, Isabel Pereira; Lucientes, Javier; Navarro, Javier; de la Puente, Josue Martinez; Stefanovska, Jovana; Searle, Kate R.; Khallaayoune, Khalid; Culverwell, C. Lorna; Larska, Magdalena; Bourquia, Maria; Goffredo, Maria; Bisia, Marina; England, Marion; Robin, Matthew; Quaglia, Michela; Miranda-Chueca, Miguel Angel; Bodker, Rene; Estrada-Pena, Rosa; Carpenter, Simon; Tchakarova, Simona; Boutsini, Sofia; Sviland, Stale; Schafer, Stefanie M.; Ozolina, Zanda; Seglina, Zanda; Vatansever, Zati; Huber, Karine (2020)
    BackgroundCulicoides obsoletus is an abundant and widely distributed Holarctic biting midge species, involved in the transmission of bluetongue virus (BTV) and Schmallenberg virus (SBV) to wild and domestic ruminants. Females of this vector species are often reported jointly with two morphologically very close species, C. scoticus and C. montanus, forming the Obsoletus/Scoticus Complex. Recently, cryptic diversity within C. obsoletus was reported in geographically distant sites. Clear delineation of species and characterization of genetic variability is mandatory to revise their taxonomic status and assess the vector role of each taxonomic entity. Our objectives were to characterize and map the cryptic diversity within the Obsoletus/Scoticus Complex.MethodsPortion of the cox1 mitochondrial gene of 3763 individuals belonging to the Obsoletus/Scoticus Complex was sequenced. Populations from 20 countries along a Palaearctic Mediterranean transect covering Scandinavia to Canary islands (North to South) and Canary islands to Turkey (West to East) were included. Genetic diversity based on cox1 barcoding was supported by 16S rDNA mitochondrial gene sequences and a gene coding for ribosomal 28S rDNA. Species delimitation using a multi-marker methodology was used to revise the current taxonomic scheme of the Obsoletus/Scoticus Complex.ResultsOur analysis showed the existence of three phylogenetic clades (C. obsoletus clade O2, C. obsoletus clade dark and one not yet named and identified) within C. obsoletus. These analyses also revealed two intra-specific clades within C. scoticus and raised questions about the taxonomic status of C. montanus.ConclusionsTo our knowledge, our study provides the first genetic characterization of the Obsoletus/Scoticus Complex on a large geographical scale and allows a revision of the current taxonomic classification for an important group of vector species of livestock viruses in the Palaearctic region.
  • Mignotte, Antoine; Garros, Claire; Gardès, Laetitia; Balenghien, Thomas; Duhayon, Maxime; Rakotoarivony, Ignace; Tabourin, Laura; Poujol, Léa; Mathieu, Bruno; Ibañez-Justicia, Adolfo; Deniz, Ahmet; Cvetkovikj, Aleksandar; Purse, Bethan V; Ramilo, David W; Stougiou, Despoina; Werner, Doreen; Pudar, Dubravka; Petrić, Dušan; Veronesi, Eva; Jacobs, Frans; Kampen, Helge; Pereira da Fonseca, Isabel; Lucientes, Javier; Navarro, Javier; de la Puente, Josue M; Stefanovska, Jovana; Searle, Kate R; Khallaayoune, Khalid; Culverwell, C. L; Larska, Magdalena; Bourquia, Maria; Goffredo, Maria; Bisia, Marina; England, Marion; Robin, Matthew; Quaglia, Michela; Miranda-Chueca, Miguel Á; Bødker, René; Estrada-Peña, Rosa; Carpenter, Simon; Tchakarova, Simona; Boutsini, Sofia; Sviland, Ståle; Schäfer, Stefanie M; Ozoliņa, Zanda; Segliņa, Zanda; Vatansever, Zati; Huber, Karine (BioMed Central, 2020)
    Abstract Background Culicoides obsoletus is an abundant and widely distributed Holarctic biting midge species, involved in the transmission of bluetongue virus (BTV) and Schmallenberg virus (SBV) to wild and domestic ruminants. Females of this vector species are often reported jointly with two morphologically very close species, C. scoticus and C. montanus, forming the Obsoletus/Scoticus Complex. Recently, cryptic diversity within C. obsoletus was reported in geographically distant sites. Clear delineation of species and characterization of genetic variability is mandatory to revise their taxonomic status and assess the vector role of each taxonomic entity. Our objectives were to characterize and map the cryptic diversity within the Obsoletus/Scoticus Complex. Methods Portion of the cox1 mitochondrial gene of 3763 individuals belonging to the Obsoletus/Scoticus Complex was sequenced. Populations from 20 countries along a Palaearctic Mediterranean transect covering Scandinavia to Canary islands (North to South) and Canary islands to Turkey (West to East) were included. Genetic diversity based on cox1 barcoding was supported by 16S rDNA mitochondrial gene sequences and a gene coding for ribosomal 28S rDNA. Species delimitation using a multi-marker methodology was used to revise the current taxonomic scheme of the Obsoletus/Scoticus Complex. Results Our analysis showed the existence of three phylogenetic clades (C. obsoletus clade O2, C. obsoletus clade dark and one not yet named and identified) within C. obsoletus. These analyses also revealed two intra-specific clades within C. scoticus and raised questions about the taxonomic status of C. montanus. Conclusions To our knowledge, our study provides the first genetic characterization of the Obsoletus/Scoticus Complex on a large geographical scale and allows a revision of the current taxonomic classification for an important group of vector species of livestock viruses in the Palaearctic region.