DNA barcode library for European Gelechiidae (Lepidoptera) suggests greatly underestimated species diversity.
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ABSTRACT:
SUBMITTER: Huemer P
PROVIDER: S-EPMC7109146 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:The checklist of European Gelechiidae covers 865 species, belonging to 109 genera, with three species records which require confirmation. Further, it is the first checklist to include a complete coverage of proved synonyms of species and at generic level. The following taxonomic changes are introduced: Pseudosophronia constanti (Nel, 1998) syn. nov. of Pseudosophronia exustellus (Zeller, 1847), Metzneria expositoi Vives, 2001 syn. nov. of Metzneria aestivella (Zeller, 1839); Sophronia ascalis Gozmány, 1951 syn. nov. of Sophronia grandii Hering, 1933, Aproaerema incognitana (Gozmány, 1957) comb. nov., Aproaerema cinctelloides (Nel & Varenne, 2012) comb. nov., Aproaerema azosterella (Herrich-Schäffer, 1854) comb. nov., Aproaerema montanata (Gozmány, 1957) comb. nov., Aproaerema cincticulella (Bruand, 1851) comb. nov., Aproaerema buvati (Nel, 1995) comb. nov., Aproaerema linella (Chrétien, 1904) comb. nov., Aproaerema captivella (Herrich-Schäffer, 1854) comb. nov., Aproaerema semicostella (Staudinger, 1871) comb. nov., Aproaerema steppicola (Junnilainen, 2010) comb. nov., Aproaerema cottienella (Nel, 2012) comb. nov., Ptocheuusa cinerella (Chrétien, 1908) comb. nov., Pragmatodes melagonella (Constant, 1895) comb. nov., Pragmatodes albagonella (Varenne & Nel, 2010) comb. nov., Pragmatodes parvulata (Gozmány, 1953) comb. nov., Oxypteryx nigromaculella (Millière, 1872) comb. nov., Oxypteryx wilkella (Linnaeus, 1758) comb. nov., Oxypteryx ochricapilla (Rebel, 1903) comb. nov., Oxypteryx superbella (Zeller, 1839) comb. nov., Oxypteryx mirusella (Huemer & Karsholt, 2013) comb. nov., Oxypteryx baldizzonei (Karsholt & Huemer, 2013) comb. nov., Oxypteryx occidentella (Huemer & Karsholt, 2011) comb. nov., Oxypteryx libertinella (Zeller, 1872) comb. nov., Oxypteryx gemerensis (Elsner, 2013) comb. nov., Oxypteryx deserta (Piskunov, 1990) comb. nov., Oxypteryx unicolorella (Duponchel, 1843) comb. nov., Oxypteryx nigritella (Zeller, 1847) comb. nov., Oxypteryx plumbella (Heinemann, 1870) comb. nov., Oxypteryx isostacta (Meyrick, 1926) comb. nov., Oxypteryx helotella (Staudinger, 1859) comb. nov., Oxypteryx parahelotella (Nel, 1995) comb. nov., Oxypteryx graecatella (Šumpich & Skyva, 2012) comb. nov.; Aproaerema genistae (Walsingham, 1908) comb. rev., Aproaerema thaumalea (Walsingham, 1905) comb. rev.; Dichomeris neatodes Meyrick, 1923 sp. rev.; Caryocolum horoscopa (Meyrick, 1926) stat. rev.; Ivanauskiella occitanica (Nel & Varenne, 2013) sp. rev.; Apodia martinii Petry, 1911 sp. rev.; Caulastrocecis cryptoxena (Gozmány, 1952) sp. rev. Following Article 23.9.2 ICZN we propose Caryocolum blandella (Douglas, 1852) (Gelechia) nom. protectum and Caryocolum signatella (Eversmann, 1844) (Lita) nom. oblitum.
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Project description:The study of global biodiversity will greatly benefit from access to comprehensive DNA barcode libraries at continental scale, but such datasets are still very rare. Here, we assemble the first high-resolution reference library for European butterflies that provides 97% taxon coverage (459 species) and 22,306 COI sequences. We estimate that we captured 62% of the total haplotype diversity and show that most species possess a few very common haplotypes and many rare ones. Specimens in the dataset have an average 95.3% probability of being correctly identified. Mitochondrial diversity displayed elevated haplotype richness in southern European refugia, establishing the generality of this key biogeographic pattern for an entire taxonomic group. Fifteen percent of the species are involved in barcode sharing, but two thirds of these cases may reflect the need for further taxonomic research. This dataset provides a unique resource for conservation and for studying evolutionary processes, cryptic species, phylogeography, and ecology.
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Project description:Although members of the crambid subfamily Pyraustinae are frequently important crop pests, their identification is often difficult because many species lack conspicuous diagnostic morphological characters. DNA barcoding employs sequence diversity in a short standardized gene region to facilitate specimen identifications and species discovery. This study provides a DNA barcode reference library for North American pyraustines based upon the analysis of 1589 sequences recovered from 137 nominal species, 87% of the fauna. Data from 125 species were barcode compliant (>500bp, <1% n), and 99 of these taxa formed a distinct cluster that was assigned to a single BIN. The other 26 species were assigned to 56 BINs, reflecting frequent cases of deep intraspecific sequence divergence and a few instances of barcode sharing, creating a total of 155 BINs. Two systems for OTU designation, ABGD and BIN, were examined to check the correspondence between current taxonomy and sequence clusters. The BIN system performed better than ABGD in delimiting closely related species, while OTU counts with ABGD were influenced by the value employed for relative gap width. Different species with low or no interspecific divergence may represent cases of unrecognized synonymy, whereas those with high intraspecific divergence require further taxonomic scrutiny as they may involve cryptic diversity. The barcode library developed in this study will also help to advance understanding of relationships among species of Pyraustinae.
| S-EPMC5063472 | biostudies-literature
Project description:The proliferation of DNA data is revolutionizing all fields of systematic research. DNA barcode sequences, now available for millions of specimens and several hundred thousand species, are increasingly used in algorithmic species delimitations. This is complicated by occasional incongruences between species and gene genealogies, as indicated by situations where conspecific individuals do not form a monophyletic cluster in a gene tree. In two previous reviews, non-monophyly has been reported as being common in mitochondrial DNA gene trees. We developed a novel web service "Monophylizer" to detect non-monophyly in phylogenetic trees and used it to ascertain the incidence of species non-monophyly in COI (a.k.a. cox1) barcode sequence data from 4977 species and 41,583 specimens of European Lepidoptera, the largest data set of DNA barcodes analyzed from this regard. Particular attention was paid to accurate species identification to ensure data integrity. We investigated the effects of tree-building method, sampling effort, and other methodological issues, all of which can influence estimates of non-monophyly. We found a 12% incidence of non-monophyly, a value significantly lower than that observed in previous studies. Neighbor joining (NJ) and maximum likelihood (ML) methods yielded almost equal numbers of non-monophyletic species, but 24.1% of these cases of non-monophyly were only found by one of these methods. Non-monophyletic species tend to show either low genetic distances to their nearest neighbors or exceptionally high levels of intraspecific variability. Cases of polyphyly in COI trees arising as a result of deep intraspecific divergence are negligible, as the detected cases reflected misidentifications or methodological errors. Taking into consideration variation in sampling effort, we estimate that the true incidence of non-monophyly is ∼23%, but with operational factors still being included. Within the operational factors, we separately assessed the frequency of taxonomic limitations (presence of overlooked cryptic and oversplit species) and identification uncertainties. We observed that operational factors are potentially present in more than half (58.6%) of the detected cases of non-monophyly. Furthermore, we observed that in about 20% of non-monophyletic species and entangled species, the lineages involved are either allopatric or parapatric-conditions where species delimitation is inherently subjective and particularly dependent on the species concept that has been adopted. These observations suggest that species-level non-monophyly in COI gene trees is less common than previously supposed, with many cases reflecting misidentifications, the subjectivity of species delimitation or other operational factors.
| S-EPMC5066064 | biostudies-literature
Project description:This study examines the performance of DNA barcodes (mt cytochrome c oxidase 1 gene) in the identification of 1004 species of Lepidoptera shared by two localities (Finland, Austria) that are 1600 km apart. Maximum intraspecific distances for the pooled data were less than 2% for 880 species (87.6%), while deeper divergence was detected in 124 species. Despite such variation, the overall DNA barcode library possessed diagnostic COI sequences for 98.8% of the taxa. Because a reference library based on Finnish specimens was highly effective in identifying specimens from Austria, we conclude that barcode libraries based on regional sampling can often be effective for a much larger area. Moreover, dispersal ability (poor, good) and distribution patterns (disjunct, fragmented, continuous, migratory) had little impact on levels of intraspecific geographic divergence. Furthermore, the present study revealed that, despite the intensity of past taxonomic work on European Lepidoptera, nearly 20% of the species shared by Austria and Finland require further work to clarify their status. Particularly discordant BIN (Barcode Index Number) cases should be checked to ascertain possible explanatory factors such as incorrect taxonomy, hybridization, introgression, and Wolbachia infections.
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Project description:We explore the potential value of DNA barcode divergence for species delimitation in the genus Caryocolum Gregor & Povolný, 1954 (Lepidoptera, Gelechiidae), based on data from 44 European species (including 4 subspecies). Low intraspecific divergence of the DNA barcodes of the mtCOI (cytochrome c oxidase 1) gene and/or distinct barcode gaps to the nearest neighbor support species status for all examined nominal taxa. However, in 8 taxa we observed deep splits with a maximum intraspecific barcode divergence beyond a threshold of 3%, thus indicating possible cryptic diversity. The taxonomy of these taxa has to be re-assessed in the future. We investigated one such deep split in Caryocolum amaurella (Hering, 1924) and found it in congruence with yet unrecognized diagnostic morphological characters and specific host-plants. The integrative species delineation leads to the description of Caryocolum crypticum sp. n. from northern Italy, Switzerland and Greece. The new species and the hitherto intermixed closest relative C. amaurella are described in detail and adults and genitalia of both species are illustrated and a lectotype of C. amaurella is designated; a diagnostic comparison of the closely related C. iranicum Huemer, 1989, is added.
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Project description:BACKGROUND: Detecting and controlling the movements of invasive species, such as insect pests, relies upon rapid and accurate species identification in order to initiate containment procedures by the appropriate authorities. Many species in the tussock moth genus Lymantria are significant forestry pests, including the gypsy moth Lymantria dispar L., and consequently have been a focus for the development of molecular diagnostic tools to assist in identifying species and source populations. In this study we expand the taxonomic and geographic coverage of the DNA barcode reference library, and further test the utility of this diagnostic method, both for species/subspecies assignment and for determination of geographic provenance of populations. METHODOLOGY/PRINCIPAL FINDINGS: Cytochrome oxidase I (COI) barcodes were obtained from 518 individuals and 36 species of Lymantria, including sequences assembled and generated from previous studies, vouchered material in public collections, and intercepted specimens obtained from surveillance programs in Canada. A maximum likelihood tree was constructed, revealing high bootstrap support for 90% of species clusters. Bayesian species assignment was also tested, and resulted in correct assignment to species and subspecies in all instances. The performance of barcoding was also compared against the commonly employed NB restriction digest system (also based on COI); while the latter is informative for discriminating gypsy moth subspecies, COI barcode sequences provide greater resolution and generality by encompassing a greater number of haplotypes across all Lymantria species, none shared between species. CONCLUSIONS/SIGNIFICANCE: This study demonstrates the efficacy of DNA barcodes for diagnosing species of Lymantria and reinforces the view that the approach is an under-utilized resource with substantial potential for biosecurity and surveillance. Biomonitoring agencies currently employing the NB restriction digest system would gather more information by transitioning to the use of DNA barcoding, a change which could be made relatively seamlessly as the same gene region underlies both protocols.
| S-EPMC3000334 | biostudies-literature
Project description:BackgroundThe construction of comprehensive reference libraries is essential to foster the development of DNA barcoding as a tool for monitoring biodiversity and detecting invasive species. The looper moths of British Columbia (BC), Canada present a challenging case for species discrimination via DNA barcoding due to their considerable diversity and limited taxonomic maturity.Methodology/principal findingsBy analyzing specimens held in national and regional natural history collections, we assemble barcode records from representatives of 400 species from BC and surrounding provinces, territories and states. Sequence variation in the barcode region unambiguously discriminates over 93% of these 400 geometrid species. However, a final estimate of resolution success awaits detailed taxonomic analysis of 48 species where patterns of barcode variation suggest cases of cryptic species, unrecognized synonymy as well as young species.Conclusions/significanceA catalog of these taxa meriting further taxonomic investigation is presented as well as the supplemental information needed to facilitate these investigations.
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Project description:The aim of the study was to establish a nationwide barcode library for the most diverse group of Austrian Lepidoptera, the Noctuoidea, with 5 families (Erebidae, Euteliidae, Noctuidae, Nolidae, Notodontidae) and around 690 species. Altogether, 3431 DNA barcode sequences from COI gene (cytochrome c oxidase 1) belonging to 671 species were gathered, with 3223 sequences >500 bp. The intraspecific divergence with a mean of only 0.17% is low in most species whereas interspecific distances to the Nearest Neighbour are significantly higher with an average of 4.95%. Diagnostic DNA barcodes were obtained for 658 species. Only 13 species (1.9% of the Austrian Noctuoidea) cannot be reliably identified from their DNA barcode (Setina aurita/Setina irrorella, Conisania leineri/Conisania poelli, Photedes captiuncula/Photedes minima, Euxoa obelisca/Euxoa vitta/Euxoa tritici, Mesapamaea secalella/Mesapamea secalis, Amphipoea fucosa/Amphipoea lucens). A similarly high identification performance was achieved by the Barcode Index (BIN) system. 671 species of Austrian Noctuoidea, representing 3202 records with BINs, are assigned to a total of 678 BINs. The vast majority of 649 species is placed into a single BIN, with only 13 species recognised as BIN-sharing (including the barcode sharing species above). Twenty-one species were assigned to more than one BIN and have to be checked for cryptic diversity in the future.
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Project description:An annotated list of 71 species of the genus Scrobipalpa in China is given. Nine species of the genus Scrobipalpa Janse, 1951 are described as new: S.triangulella sp. n. (Gansu, Ningxia, Shaanxi), S.punctulata sp. n. (Henan, Shanxi), S.septentrionalis sp. n. (Heilongjiang, Ningxia), S.zhongweina sp. n. (Ningxia), S.tripunctella sp. n. (Hebei, Ningxia, Shanxi), S.ningxica sp. n. (Ningxia), S.psammophila sp. n. (Ningxia), S.zhengi sp. n. (Inner Mongolia, Ningxia), and S.liui sp. n. (Shanxi). Scrobipalpagorodkovi Bidzilya, 2012 is synonymised with S.subnitens Povolný, 1967. The female of S.flavinerva Bidzilya & Li, 2010 is described for the first time. Two new combinations are proposed: Scrobipalpaperfecta (Povolný, 1996), comb. n., Scrobipalpasuaveolens (Povolný, 1996), comb. n. Twelve species of Scrobipalpa are recorded from China for the first time. Scrobipalpacryptica Povolný, 1996, S.proclivella (Fuchs, 1886) and S.smithi Povolný & Bradley, 1964 are removed from the list of Scrobipalpa of China due to misidentification.
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