1,635 results on '"DNA BARCODES"'
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2. Population identification and genetic diversity analysis of Fritillaria ussuriensis (Fritillaria) based on chloroplast genes atpF and petB.
- Author
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Wang, Xin, Zhang, Zhifei, Shi, Yue, Man, Jinhui, Huang, Yuying, Zhang, Xiaoqin, Liu, Shanhu, He, Gaojie, An, Kelu, Amu, Laha, Chen, Wenqin, Liu, Ziqi, Wang, Xiaohui, and Wei, Shengli
- Abstract
The chloroplast genomes of five Fritillaria ussuriensis materials from different production areas were comparatively analyzed, atpF and petB were screened as specific DNA barcodes, and the population identification and genetic diversity of F. ussuriensis were analyzed based on them. The F. ussuriensis chloroplast genome showed a total length of 151 515–151 548 bp with a typical tetrad structure and encoded 130 genes. atpF and petB were used to amplify 183 samples from 13 populations, and they could identify 6 and 9 haplotypes, respectively. Joint analysis of the two sequences revealed 18 haplotypes, named H1–H18, with the most widely distributed and most abundant being H4. Ten haplotypes were unique for 7 populations that they could be used to distinguish from others. Haplotype diversity and nucleotide diversity were 0.99 and 2.09 × 10
−3 , respectively, indicating the genetic diversity was relatively rich. The results of the intermediary adjacency network showed that H5 was the oldest haplotype, and stellate radiation was centered around it, indicating that population expansion occurred in genuine production areas. This study lays a theoretical foundation for the population identification, genetic evolution, and breed selection of F. ussuriensis. [ABSTRACT FROM AUTHOR]- Published
- 2024
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3. Revision of the Genus Laelius (Hymenoptera, Chrysidoidea, Bethylidae) from China.
- Author
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Wang, Chunhong, He, Junhua, and Chen, Xuexin
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BIOLOGICAL pest control , *BIOLOGICAL pest control agents , *GENETIC barcoding , *FOREST products , *HYMENOPTERA - Abstract
Simple Summary: The cosmopolitan genus Laelius Ashmead belongs to the subfamily Epyrinae and includes 68 valid species. Members of Laelius mainly attack larvae of larder beetles (Coleoptera, Dermestidae), which are commonly known as pests of stored products. The taxonomic study of Laelius in China is far from enough, with only two species recorded. Taking account of the promising biocontrol agents for the pests of forest and stored products, the Chinese species of Laelius are revised in this study. Morphological characters and DNA barcoding with COI sequences are used for species delimitation. A new species, Laelius longus sp. nov., is described and illustrated. Three new records from China are updated. The genus Laelius from China is revised for the first time and six species are recognized, including one new species as well as three new records. The new species, Laelius longus sp. nov., which is supported by both morphological and molecular analyses, is described and illustrated. Three new records, L. naniwaensis, L. nigrofemoratus, and L. yamatonis, are illustrated. A key to the Chinese species of Laelius is provided. [ABSTRACT FROM AUTHOR]
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- 2024
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4. Genotypic Identification of Trees Using DNA Barcodes and Microbiome Analysis of Rhizosphere Microbial Communities.
- Author
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Hopkins, Liliana, Yim, Kayla, Rumora, Ana, Baykus, Melissa F., Martinez, Luisa, and Jimenez, Luis
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EUROPEAN beech , *DNA primers , *BACTERIAL communities , *PLANT identification , *GENETIC barcoding , *RIBOSOMAL DNA - Abstract
DNA barcodes can provide accurate identification of plants. We used previously reported DNA primers targeting the internal transcribed spacer (ITS1) region of the nuclear ribosomal cistron, internal transcribed spacer (ITS2), and chloroplast trnL (UAA) intron to identify four trees at Bergen Community College. Two of the four trees were identified as Acer rubrum and Fagus sylvatica. However, Quercus was only identified at the genus level, and the fourth tree did not show similar identification between barcodes. Next-generation sequencing of 16S rRNA genes showed that the predominant bacterial communities in the rhizosphere mainly consisted of the Pseudomonadota, Actinomycetota, Bacteroidota, and Acidobacteriota. A. rubrum showed the most diverse bacterial community while F. sylvatica was less diverse. The genus Rhodoplanes showed the highest relative bacterial abundance in all trees. Fungal ITS sequence analysis demonstrated that the communities predominantly consisted of the Ascomycota and Basidiomycota. Quercus showed the highest fungi diversity while F. sylvatica showed the lowest. Russula showed the highest abundance of fungi genera. Average similarity values in the rhizosphere for fungi communities at the phylum level were higher than for bacteria. However, at the genus level, bacterial communities showed higher similarities than fungi. Similarity values decreased at lower taxonomical levels for both bacteria and fungi, indicating each tree has selected for specific bacterial and fungal communities. This study confirmed the distinctiveness of the microbial communities in the rhizosphere of each tree and their importance in sustaining and supporting viability and growth but also demonstrating the limitations of DNA barcoding with the primers used in this study to identify genus and species for some of the trees. The optimization of DNA barcoding will require additional DNA sequences to enhance the resolution and identification of trees at the study site. [ABSTRACT FROM AUTHOR]
- Published
- 2024
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5. Molecular quantification of herbs (Herb-Q): a pyrosequencing-based approach and its application in Pinellia ternata.
- Author
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PEI, Yifei, LIU, Ziyi, YU, Dade, ZHANG, Xiangyu, SUN, Wei, CHEN, Xiaofang, FENG, Xue, and LI, Xiwen
- Abstract
Variations in herb dosage due to species adulteration and dosing inaccuracies can substantially affect clinical safety and efficacy. Accurate species quantification remains challenging, as current methods often yield inconsistent results. This study introduces a novel pyrosequencing-based technique, termed herb molecular quantification (Herb-Q), designed to precisely quantify herbal products. We evaluated its effectiveness using Pinellia ternata and five of its adulterants. Initially, we assessed commonly used DNA barcodes with sequences from a public database, identifying two candidate regions, Maturase K (mat K) and internal transcribed spacer 2 (ITS2), for screening specific single nucleotide polymorphism (SNP) loci, allowing for species-specific identification. These loci were validated by amplifying and sequencing genomic material from collected samples. Our validation studies showed that Herb-Q demonstrated excellent linearity, accuracy, repeatability, and detection limits. We established quantitative standard curves with high R
2 values (> 0.99) to enable precise species quantification, which were combined with external standards to provide clear and accurate visual quantification results. The average bias in quantifying the tuber of P. ternata was 2.38%, confirming that Herb-Q can accurately identify and quantify herbal product constituents. Moreover, the entire quantification process took less than 4 h. This study presents a novel, rapid method for accurately quantifying species in herbal products and advances the application of DNA barcoding from species identification to quantitative detection. [ABSTRACT FROM AUTHOR]- Published
- 2024
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6. Parasitoid wasps with enlarged mandibles associated with aculeate Hymenoptera: An integrative taxonomy of Chaenotetrastichus Graham and Styotrichia LaSalle (Hymenoptera: Eulophidae).
- Author
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Cao, Huan-Xi, Dale-Skey, Natalie, Guo, Peng-Fei, and Zhu, Chao-Dong
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BIOLOGICAL classification , *CYTOCHROME oxidase , *CHALCID wasps , *GENETIC variation , *MOLECULAR phylogeny - Abstract
The two genera, Chaenotetrastichus Graham and Styotrichia LaSalle (Chalcidoidea: Eulophidae: Tetrastichinae), are newly recorded from the Oriental region, based on material reared from the pupae of Auplopus carbonarius (Scopoli) (Hymenoptera: Pompilidae) and a Pisoxylon species (Hymenoptera: Crabronidae), respectively, collected using trap-nests. Styotrichia pisoxylona Cao & Zhu sp. nov. is described and illustrated as a gregarious endo-parasitoid of Pisoxylon sp. The generic diagnosis, biology, and distribution of Chaenotetrastichus and Styotrichia are updated. All described species of the two genera are reviewed and a key to them is provided. Based on morphology and available sequences of the D2 expansion region of 28S ribosomal DNA (28S D2), the relationships between the two genera and other members of the subfamily Tetrastichinae are tentatively discussed. The phylogenetic analysis of 28S D2 confirms that the two genera with enlarged mandibles, which are associated with aculeate Hymenoptera, are not closely related. DNA barcodes (mitochondrial cytochrome c oxidase I, COI) of the newly described species and C. semiflavus (Girault) are provided and analyzed alongside publicly available COI sequences of related taxa. The result suggests that the genetic or species diversity of Chaenotetrastichus is underestimated. [ABSTRACT FROM AUTHOR]
- Published
- 2024
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7. A Revision of the Phylogeny of Helicotylenchus Steiner, 1945 (Tylenchida: Hoplolaimidae) as Inferred from Ribosomal and Mitochondrial DNA
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Abraham Okki Mwamula, Oh-Gyeong Kwon, Chanki Kwon, Yi Seul Kim, Young Ho Kim, and Dong Woon Lee
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bayesian inference ,dna barcodes ,phylogenetic relationships ,species identification ,Plant culture ,SB1-1110 - Abstract
Identification of Helicotylenchus species is very challenging due to phenotypic plasticity and existence of cryptic species complexes. Recently, the use of rDNA barcodes has proven to be useful for identification of Helicotylenchus. Molecular markers are a quick diagnostic tool and are crucial for discriminating related species and resolving cryptic species complexes within this speciose genus. However, DNA barcoding is not an error-free approach. The public databases appear to be marred by incorrect sequences, arising from sequencing errors, mislabeling, and misidentifications. Herein, we provide a comprehensive analysis of the newly obtained, and published DNA sequences of Helicotylenchus, revealing the potential faults in the available DNA barcodes. A total of 97 sequences (25 nearly full-length 18S-rRNA, 12 partial 28S-rRNA, 16 partial internal transcribed spacer [ITS]-rRNA, and 44 partial cytochrome c oxidase subunit I [COI] gene sequences) were newly obtained in the present study. Phylogenetic relationships between species are given as inferred from the analyses of 103 sequences of 18S-rRNA, 469 sequences of 28S-rRNA, 183 sequences of ITS-rRNA, and 63 sequences of COI. Remarks on suggested corrections of published accessions in GenBank database are given. Additionally, COI gene sequences of H. dihystera, H. asiaticus and the contentious H. microlobus are provided herein for the first time. Similar to rDNA gene analyses, the COI sequences support the genetic distinctness and validity of H. microlobus. DNA barcodes from type material are needed for resolving the taxonomic status of the unresolved taxonomic groups within the genus.
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- 2024
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8. The bee genus Borgatomelissa Patiny, 2000 (Anthophila: Andrenidae: Panurginae) with the description of a new species from northern Oman, and a key to species.
- Author
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Monks, Joseph, Polaszek, Andrew, and Al-Jahdhami, Ali A.
- Subjects
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BEES , *NUMBERS of species , *NATURAL history museums , *SPECIES , *SOUND recordings , *LOCKS & keys - Abstract
The bee genus Borgatomelissa Patiny, 2000 (Anthophila: Andrenidae: Panurginae) is found across North Africa, the Sahel, and throughout the Arabian Peninsula. Using both morphology and DNA barcodes, a new species, B. samailensissp. n., is described from Oman, increasing the known number of species to four. Due to the holotype of B. brevipennis Walker, 1871 being lost, we designate a neotype from a specimen collected from Oman. Additionally, new country records are documented herein for B. flavimaura Ortiz-Sánchez and Patiny, 2019 and B. brevipennis, based on specimens housed in the collections of the Natural History Museum, London and Biologiezentrum Linz, Austria. A key to the species in the genus is given. [ABSTRACT FROM AUTHOR]
- Published
- 2024
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9. Unlocking the Genetic Identity of Endangered Paphiopedilum Orchids: A DNA Barcoding Approach.
- Author
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Karbarz, Małgorzata, Szlachcikowska, Dominika, Zapał, Angelika, and Leśko, Agnieszka
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GENETIC barcoding ,CONVENTION on International Trade in Endangered Species of Wild Fauna & Flora (1973) - Abstract
Orchids of the genus Paphiopedilum, also called slippers, are among the most valued representatives of the Orchidaceae family due to their aesthetic qualities. Due to overexploitation, deforestation, and illegal trade in these plants, especially in the vegetative phase, Paphiopedilum requires special protection. This genus is listed in Appendix I of the Convention on International Trade in Endangered Species of Wild Fauna and Flora. Their precise identification is of great importance for the preservation of genetic resources and biodiversity of the orchid family (Orchidaceae). Therefore, the main objective of the study was to investigate the usefulness of the DNA barcoding technique for the identification of endangered orchids of the genus Paphiopedilum and to determine the effectiveness of five loci: matK, rbcL, ITS2, atpF-atpH and trnH-psbA as potential molecular markers for species of this genus. Among single locus barcodes, matK was the most effective at identifying species (64%). Furthermore, matK, ITS2, matK + rbcL, and matK + trnH-psbA barcodes can be successfully used as a complementary tool to identify Paphiopedilum orchids while supporting morphological data provided by taxonomists. [ABSTRACT FROM AUTHOR]
- Published
- 2024
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10. Further knowledge of the genus Nyctobrya Boursin, 1957 from the Canary Islands (Spain), with description of a new species from El Hierro (Lepidoptera: Noctuidae).
- Author
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Falck, P.
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NOCTUIDAE ,LEPIDOPTERA ,CANARIES ,DNA analysis ,SPECIES - Abstract
Copyright of SHILAP Revista de Lepidopterologia is the property of Sociedad Hispano-Luso-Americana de Lepidopterologia and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
- Published
- 2024
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11. When standard DNA barcodes do not work for species identification: intermixed mitochondrial haplotypes in the Jaera albifrons complex (Crustacea: Isopoda)
- Author
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Nymoen, August Rustad, Kongsrud, Jon Anders, Willassen, Endre, and Bakken, Torkild
- Abstract
Here, we characterise the standard “Folmer region” of the mitochondrial cytochrome c oxidase subunit 1 (CO1) marker and a fragment of nuclear 28S marker in four species of the Jaera albifrons complex. Jaera albifrons (Leach, 1814), Jaera ischiosetosa Forsman, 1949, Jaera praehirsuta Forsman, 1949, and Jaera forsmani Bocquet, 1950 were collected from localities on the Norwegian coast and identified with morphological characters. We compared DNA sequences with sequences available in GenBank and BOLDsystems and calculated haplotype networks and interspecific versus intraspecific genetic distances. These analyses revealed low interspecific genetic distance (CO1 0.00–1.57%, 28S 0.00–0.39%) and extensive haplotype sharing between J. albifrons group species and specimens from both sides of the North Atlantic for both CO1 and 28S. Genetic distances between J. albifrons group species and other Jaera species, however, exceeded 29% for both CO1 and 28S, with no haplotype sharing. These assessments, together with taxonomically unconstrained analyses with software ABGD and ASAP, show that these markers are unable to distinguish between the J. albifrons group of morphospecies. The sequences do, however, clearly identify J. albifrons species complex from other Jaera species. Thus, a likely hypothesis is that taxa in this complex represent a single species. Our results corroborate previous finds where discordance between mitochondrial gene clusters, AFLP, and other data highlights the potential conflict between different “species criteria” and the well-established distinction between gene trees and species trees. In operational terms, common protocols for metabarcoding will potentially underestimate sympatric species diversity with cases like the J. albifrons complex, if the members of this complex indeed represent different species. [ABSTRACT FROM AUTHOR]
- Published
- 2024
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12. Revision of the Genus Rhagastis Rothschild & Jordan, 1903 (Lepidoptera: Sphingidae) from China, Based on Morphological and Phylogenetic Analyses.
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Jiang, Zhuo-Heng, Wang, Jia-Xin, Xu, Zhen-Bang, Kitching, Ian J., Huang, Chia-Lung, Hu, Shao-Ji, and Xiao, Yun-Li
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SPHINGIDAE , *BIOLOGICAL classification , *LEPIDOPTERA , *FEMALE reproductive organs , *GENETIC barcoding , *CHLOROPLAST DNA , *MALE reproductive organs - Abstract
Simple Summary: Simple Summary: The genus Rhagastis Rothschild & Jordan, 1903 (Lepidoptera, Sphingidae, Macroglossinae, Macroglossini) currently comprises sixteen species, ten of which are found in China; however, complex and confusing taxonomic issues have existed for a long time. We performed an analysis based on a 658-bp region of the COI mitochondrial gene (DNA barcode) and morphological characteristics such as the wing pattern and genital structure of the albomarginatus group, the castor group, the olivacea group and other species, demonstrating that subspecies of Rhagastis albomarginatus and R. castor should be treated as good species, i.e., Rhagastis dichroae stat. nov., R. everetti stat. nov., R. aurifera stat. rev., R. chinensis stat. nov., R. formosana stat. nov., and R. jordani stat. rev. Here, the taxonomy of the genus Rhagastis Rothschild & Jordan, 1903 (Lepidoptera, Sphingidae, Macroglossinae, Macroglossini) from China is revised based on differences in wing morphology, male and female genitalia, and the phylogenetic relationship of the DNA barcodes. Subspecies of Rhagastis albomarginatus (Rothschild, 1894) and R. castor (Walker, 1856) are treated as "good" species, namely Rhagastis dichroae Mell, 1922 stat. nov.; R. everetti Rothschild & Jordan, 1903 stat. nov.; R. aurifera (Butler, 1875) stat. rev.; R. chinensis Mell, 1922 stat. nov.; R. formosana Clark, 1925 stat. nov.; and R. jordani Oberthür, 1904 stat. rev. The distribution maps, biological notes, and ecological records of the genus Rhagastis Rothschild & Jordan, 1903 from China are given, and a species inventory of genus Rhagastis in the world is also included. [ABSTRACT FROM AUTHOR]
- Published
- 2024
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13. Molecular characterization and phylogenetic position of Rotylenchus pini Mamiya, 1968 (Nematoda: Hoplolaimidae) from Korea, with remarks on its morphology and morphometrics.
- Author
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Mwamula, Abraham Okki, Lee, Ho-wook, Kim, Yi Seul, Kim, Young Ho, and Lee, Dong Woon
- Abstract
Rotylenchus pini Mamiya, 1968 was reported from rhizospheric soils of Zoysia japonica in Korea. Females and males are morphologically characterized and their linked DNA barcodes (18S-rRNA, 28S-rRNA and COI) supplied. Females and males of the characterized population conform to the original species description from Japan and also to other subsequent species descriptions with variations in a few details in morphometrics including the existence of pharyngeal gland overlap in some specimen. Bayesian phylogenetic analysis of all the three DNA markers consistently grouped R. pini together with Rotylenchus species including R. zhongshanensis, a morphologically close species. Additionally, the newly obtained sequences of R. pini were found to be almost identical to the sequences assigned to Rotylenchus aff. devonensis in GenBank. These Rotylenchus aff. devonensis isolates might be representatives of R. pini populations. Polyphasic taxonomy has a potential to adequately infer clarity on morphological and molecular relationships within this genus. The current and previous phylogenetic studies supported by the recorded morphological plasticity within populations of the genus validate the proposed synonymy of Pararotylenchus with Rotylenchus. This is the first molecular characterization of R. pini. Additional molecular studies of the member species of the genus especially those with bulb-shaped pharyngeal glands are needed to aid reconstruction of phylogenetic patterns within the group. This will supplement the current generic compendia. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
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14. DNA Barcoding for Species Identification of Moss-Dwelling Invertebrates: Performance of Nanopore Sequencing and Coverage in Reference Database.
- Author
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Koblmüller, Stephan, Resl, Philipp, Klar, Nadine, Bauer, Hanna, Zangl, Lukas, and Hahn, Christoph
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GENETIC barcoding , *DATABASES , *SPECIES , *DNA data banks , *BIODIVERSITY monitoring , *IDENTIFICATION , *DNA fingerprinting - Abstract
In view of the current biodiversity crisis and our need to preserve and improve ecosystem functioning, efficient means for characterizing and monitoring biodiversity are required. DNA barcoding, especially when coupled with new sequencing technologies, is a promising method that can, in principle, also be employed by taxonomic lay people. In this study we compare the performance of DNA barcoding by means of a third-generation sequencing technology, nanopore sequencing with classical Sanger sequencing, based on a sample of invertebrates collected from moss pads in a bog in Austria. We find that our nanopore sequencing pipeline generates DNA barcodes that are at least as good as barcodes generated with Sanger sequencing, with the MinION producing better results than the Flongle flowcell. We further find that while many arthropod taxa are well covered in the international reference DNA barcode database BOLD, this clearly is not the case for important taxa like mites and springtails, which hampers large-scale biodiversity assessments. Based on examples from our study we further highlight which factors might be responsible for ambiguous species identification based on BOLD and how this can, at least partly, be solved. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
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15. Application of DNA barcodes in the genetic diversity of hard ticks (Acari: Ixodidae) in Kazakhstan.
- Author
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Zheng, Ziwei, Zeng, Weixin, Wang, Suwen, Tan, Wenbo, Lu, Xiaobo, Kairullayev, Kenesbay, Mi, Ligu, Hazihan, Wurelihazi, Liu, Gang, Yang, Meihua, and Wang, Yuanzhi
- Subjects
IXODIDAE ,GENETIC variation ,CYTOCHROME oxidase ,MITES ,DERMACENTOR ,GENETIC barcoding - Abstract
Forty-five tick species have been recorded in Kazakhstan. However, their genetic diversity and evolutionary relationships, particularly when compared to ticks in neighbouring countries, remain unclear. In the present study, 148 mitochondrial cytochrome c oxidase subunit I (COI) sequence data from our laboratory and NCBI (National Center for Biotechnology Information; https://www.ncbi.nlm.nih.gov/) data were used to address this knowledge gap. Phylogenetic analyses showed that i) Hyalomma anatolicum anatolicum (Koch, 1844) ticks from Jambyl Oblast (southeastern Kazakhstan) and Gansu Province (northwestern China) constituted a newly deviated clade; and ii) Dermacentor reticulatus (Fabricius, 1974) ticks from South Kazakhstan Oblast were closer to those in Romania and Turkey. The network diagram of haplotypes showed that i) the H-1 and H-2 haplotypes of Dermacentor marginatus (Sulzer, 1776) ticks from Zhetisu and Almaty were all newly evolved; and ii) the H-3 haplotypes of Haemaphysalis erinacei (Pavesi, 1884) from Almaty Oblast and Xinjiang Uygur Autonomous Region (northwestern China) were evolved from the H-1 haplotype from Italy. In the future, more COI data from different tick species, especially from Kazakhstan and neighbouring countries, should be employed in the field of tick DNA barcoding. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
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16. New taxa and new records of Winnertziinae and Porricondylinae (Diptera: Cecidomyiidae) from Germany
- Author
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Mathias Jaschhof
- Subjects
gall midges ,mycophages ,new genus ,new species ,DNA barcodes ,Zoology ,QL1-991 ,Botany ,QK1-989 - Abstract
Winnertziinae and Porricondylinae are two subfamilies of mycophagous Cecidomyiidae (gall midges). An earlier census in 2021 found the German fauna of both groups to comprise 53 species and 28 genera – only a small proportion of the nearly 400 species and 75 genera known from all of Europe. A 24-month inventory in 2021‒2023, whose most significant taxonomic and faunistic outcomes are presented here, yielded evidence of an additional 142 species and 24 genera present in Germany, more precisely 41 species and three genera of Winnertziinae, and 101 species and 21 genera of Porricondylinae. Included in these numbers are 30 new species (six Winnertziinae, 24 Porricondylinae) and one new genus (of Porricondylinae) described and named here. The number of potentially new species discovered during the project is considerably larger (85+), but the too poor condition of the specimens and various other circumstances do not permit their taxonomic description at this stage. New taxa named in the present paper are Johnsonomyia szadziewskii sp. nov., Rhipidoxylomyia bilobata sp. nov., Winnertzia haushoferorum sp. nov., Winnertzia incrassata sp. nov., Winnertzia macrodens sp. nov., Winnertzia subdentata sp. nov., all Winnertziinae, Asynapta doczkali sp. nov., Asynapta falcata sp. nov., Bryocrypta longissima sp. nov., Camptomyia serrata sp. nov., Cassidoides rainensis sp. nov., Cassidoides riparius sp. nov., Claspettomyia gracilostylus sp. nov., Claspettomyia parvidentata sp. nov., Divellepidosis bavarica sp. nov., Lamellepidosis luderbuschensis sp. nov., Neurepidosis hartschimmelhofensis sp. nov., Neurepidosis simplex sp. nov., Parepidosis lobata sp. nov., Porricondyla acutistylata sp. nov., Porricondyla insolita sp. nov., Porricondyla oblonga sp. nov., Porricondyla ornata sp. nov., Porricondyla pilosoides sp. nov., Porricondyla plana sp. nov., Porricondyla pumila sp. nov., Schistoneurus paraimpressus sp. nov., Schistoneurus subimpressus sp. nov., Spungisomyia germanica sp. nov., Wohllebenia gen. nov., and Wohllebenia hybrida gen. et sp. nov., all Porricondylinae. Taxonomic descriptions are based on both the morphology of males and, if available, CO1 (DNA barcode) sequences, using specimens collected by Malaise traps in Bavaria and Baden-Württemberg, the two southernmost federal states of Germany. Released here are 150 BINs new to BOLD as well as 145 species names for previously unidentified BINs in BOLD. Redescriptions of male morphology are provided for Camptomyia heterobia Mamaev, 1961, Claspettomyia carpatica Mamaev, 1998, Dicerura scirpicola Kieffer, 1898, and Winnertzia betulicola Mamaev, 1963. The state of knowledge of Germany’s fauna of mycophagous gall midges is discussed.
- Published
- 2024
- Full Text
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17. High-throughput identification of novel heat tolerance genes via genome-wide pooled mutant screens in the model green alga Chlamydomonas reinhardtii.
- Author
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Mattoon, Erin, McHargue, William, Bailey, Catherine, Zhang, Ningning, Cheng, Jianlin, Zhang, Ru, Eckhardt, James, Daum, Chris, Zane, Matt, Pennacchio, Christa, Schmutz, Jeremy, Chen, Cindy, and OMalley, Ronan
- Subjects
CLiP mutant library ,Chlamydomonas reinhardtii ,DNA barcodes ,acute high temperature ,heat responses ,heat tolerance genes (HTGs) ,moderate high temperature ,photobioreactors (PBRs) ,quantitative pooled screens ,Chlamydomonas reinhardtii ,Thermotolerance ,Chlamydomonas ,Photosynthesis ,Carbon - Abstract
Different high temperatures adversely affect crop and algal yields with various responses in photosynthetic cells. The list of genes required for thermotolerance remains elusive. Additionally, it is unclear how carbon source availability affects heat responses in plants and algae. We utilized the insertional, indexed, genome-saturating mutant library of the unicellular, eukaryotic green alga Chlamydomonas reinhardtii to perform genome-wide, quantitative, pooled screens under moderate (35°C) or acute (40°C) high temperatures with or without organic carbon sources. We identified heat-sensitive mutants based on quantitative growth rates and identified putative heat tolerance genes (HTGs). By triangulating HTGs with heat-induced transcripts or proteins in wildtype cultures and MapMan functional annotations, we presented a high/medium-confidence list of 933 Chlamydomonas genes with putative roles in heat tolerance. Triangulated HTGs include those with known thermotolerance roles and novel genes with little or no functional annotation. About 50% of these high-confidence HTGs in Chlamydomonas have orthologs in green lineage organisms, including crop species. Arabidopsis thaliana mutants deficient in the ortholog of a high-confidence Chlamydomonas HTG were also heat sensitive. This work expands our knowledge of heat responses in photosynthetic cells and provides engineering targets to improve thermotolerance in algae and crops.
- Published
- 2023
18. Phylogeny and diversification of genus Sanicula L. (Apiaceae): novel insights from plastid phylogenomic analyses
- Author
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Bo-Ni Song, Chang-Kun Liu, An-Qi Zhao, Rong-Ming Tian, Deng-Feng Xie, Yu-Lin Xiao, Huai Chen, Song-Dong Zhou, and Xing-Jin He
- Subjects
Apiaceae ,Sanicula ,Plastome ,DNA barcodes ,Phylogeny ,Divergence time ,Botany ,QK1-989 - Abstract
Abstract Background The genus Sanicula L. is a unique perennial herb that holds important medicinal values. Although the previous studies on Sanicula provided us with a good research basis, its taxonomic system and interspecific relationships have not been satisfactorily resolved, especially for those endemic to China. Moreover, the evolutionary history of this genus also remains inadequately understood. The plastid genomes possessing highly conserved structure and limited evolutionary rate have proved to be an effective tool for studying plant phylogeny and evolution. Results In the current study, we newly sequenced and assembled fifteen Sanicula complete plastomes. Combined with two previously reported plastomes, we performed comprehensively plastid phylogenomics analyses to gain novel insights into the evolutionary history of this genus. The comparative results indicated that the seventeen plastomes exhibited a high degree of conservation and similarity in terms of their structure, size, GC content, gene order, IR borders, codon bias patterns and SSRs profiles. Such as all of them displayed a typical quadripartite structure, including a large single copy region (LSC: 85,074–86,197 bp), a small single copy region (SSC: 17,047–17,132 bp) separated by a pair of inverted repeat regions (IRs: 26,176–26,334 bp). And the seventeen plastomes had similar IR boundaries and the adjacent genes were identical. The rps19 gene was located at the junction of the LSC/IRa, the IRa/SSC junction region was located between the trnN gene and ndhF gene, the ycf1 gene appeared in the SSC/IRb junction and the IRb/LSC boundary was located between rpl12 gene and trnH gene. Twelve specific mutation hotspots (atpF, cemA, accD, rpl22, rbcL, matK, ycf1, trnH-psbA, ycf4-cemA, rbcL-accD, trnE-trnT and trnG-trnR) were identified that can serve as potential DNA barcodes for species identification within the genus Sanicula. Furthermore, the plastomes data and Internal Transcribed Spacer (ITS) sequences were performed to reconstruct the phylogeny of Sanicula. Although the tree topologies of them were incongruent, both provided strong evidence supporting the monophyly of Saniculoideae and Apioideae. In addition, the sister groups between Saniculoideae and Apioideae were strongly suggested. The Sanicula species involved in this study were clustered into a clade, and the Eryngium species were also clustered together. However, it was clearly observed that the sections of Sanicula involved in the current study were not respectively recovered as monophyletic group. Molecular dating analysis explored that the origin of this genus was occurred during the late Eocene period, approximately 37.84 Ma (95% HPD: 20.33–52.21 Ma) years ago and the diversification of the genus was occurred in early Miocene 18.38 Ma (95% HPD: 10.68–25.28 Ma). Conclusion The plastome-based tree and ITS-based tree generated incongruences, which may be attributed to the event of hybridization/introgression, incomplete lineage sorting (ILS) and chloroplast capture. Our study highlighted the power of plastome data to significantly improve the phylogenetic supports and resolutions, and to efficiently explore the evolutionary history of this genus. Molecular dating analysis explored that the diversification of the genus occurred in the early Miocene, which was largely influenced by the prevalence of the East Asian monsoon and the uplift of the Hengduan Mountains (HDM). In summary, our study provides novel insights into the plastome evolution, phylogenetic relationships, taxonomic framework and evolution of genus Sanicula.
- Published
- 2024
- Full Text
- View/download PDF
19. COI-high resolution melting analysis for discrimination of four fish species in the family Notopteridae in Thailand.
- Author
-
Seetapan, Kriengkrai, Panprommin, Nontree, Wangkahart, Eakapol, Ruenkoed, Supranee, and Panprommin, Dutrudi
- Subjects
FISHERY management ,CYTOCHROME oxidase ,FISH larvae ,SUSTAINABLE fisheries ,SCIAENIDAE ,MELTING - Abstract
Species identification is an essential and vital basis for biological research. Since several fish species have similar appearances and shapes at different developmental stages and researchers lack experience identifying these fish species, molecular techniques are needed. In Thailand, fish species of the family Notopteridae consist of two genera and four species, including Notopterus notopterus , Chitala ornata , Chitala blanci , and Chitala lopis. The combination of the cytochrome c oxidase I (COI) gene sequences with a nonsequencing approach, high-resolution melting (HRM), was developed to discriminate four target species in a rapid, reliable and cost-effective manner. One of three designed primer pair sets, Notop-HRMF1/Notop-HRMR1, was the most appropriate and provided four distinct melting curves. In addition, ten fish species of other families were used for the specificity test, and only the four target species of Notopteridae were specific for this primer pair set. The results of this study indicated that COI-HRM analysis is an efficient approach for identifying species of Notopteridae in Thailand. Applications of this technique may be used to investigate species of this family in processed fish products or larval fish species in several spawning grounds for sustainable fishery resource management. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
20. In vitro propagation and DNA barcoding of the rare near endemic Plantago sinaica (Barnéoud) plant in Saint Katherine, Sinai.
- Author
-
Ghareb, Heba El-Sayed and Abouseadaa, Heba Hamdy
- Abstract
Plantago sinaica is a rare perennial shrub near-endemic to Egypt and found in Saint Katherine Protectorate in Sinai. The first successful in vitro propagation protocol was conducted to protect the plant outside its natural reserves. Shoot tip, stem node section, cotyledonary node, and root explants separated from in vitro germinated seedlings were cultured in vitro on Murashige and Skoog (MS) medium enriched with different concentrations and types of cytokinins. It was found that 6-benzyl adenine (BA) is the most efficient cytokinin. MS medium containing 3.33 µM BA and 0.54 µM α-naphthalene acetic acids (NAA) produced 10.25 and 11.30 shoots/explant using shoot tip and stem node section, respectively. Conversely, MS medium + 2.22 µM BA + 0.54 µM NAA produced 13.25 shoots from root explants. Surprisingly, the cotyledonary node explants favored MS medium free from plant growth regulators (PGRs), which produced only 4.25 shoots/explant. The multiplied shoots were rooted successfully with a 100% rooting percentage on half MS medium containing 1.23 or 2.46 µM indole-3-butyric acid (IBA). In vitro, rooted plantlets were efficiently transferred to the greenhouse with a 90% survivability. Finally, the plant was identified using three DNA barcodes; 1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL), plastid photosystem II protein D1 intergenic spacer region (psbA–trnH), and Internal Transcribed Spacer (ITS) barcodes. Additionally, psbA–trnH and ITS were novel and submitted to the GenBank databases for the first time for Plantago sinaica. Our study supports the United Nations Sustainable Development Goal number 15, which is to preserve, restore and reinstate sustainable usage of terrestrial ecosystems and to stop biodiversity loss.Key message: This is the first report in in vitro propagation of the rare Plantago sinaica (Barnéoud) and molecular identification of the plant by three DNA barcodes with two newly published barcodes. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
21. A review of recently introduced Aspergillus, Penicillium, Talaromyces and other Eurotiales species.
- Author
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Visagie, C. M., Yilmaz, N., Kocsubé, S., Frisvad, J. C., Hubka, V., Samson, R. A., and Houbraken, J.
- Subjects
TALAROMYCES ,ASPERGILLUS ,PENICILLIUM ,SPECIES ,NUMBERS of species ,INTRODUCED species ,CHLOROPLAST DNA - Abstract
The order Eurotiales is diverse and includes species that impact our daily lives in many ways. In the past, its taxonomy was difficult due to morphological similarities, which made accurate identification of species difficult. This situation improved and stabilised with recent taxonomic and nomenclatural revisions that modernised Aspergillus, Penicillium and Talaromyces. This was mainly due to the availability of curated accepted species lists and the publication of comprehensive DNA sequence reference datasets. This has also led to a sharp increase in the number of new species described each year with the accepted species lists in turn also needing regular updates. The focus of this study was to review the 160 species described between the last list of accepted species published in 2020 until 31 December 2022. To review these species, single-gene phylogenies were constructed and GCPSR (Genealogical Concordance Phylogenetic Species Recognition) was applied. Multi-gene phylogenetic analyses were performed to further determine the relationships of the newly introduced species. As a result, we accepted 133 species (37 Aspergillus, two Paecilomyces, 59 Penicillium, two Rasamsonia, 32 Talaromyces and one Xerochrysium), synonymised 22, classified four as doubtful and created a new combination for Paraxerochrysium coryli, which is classified in Xerochrysium. This brings the number of accepted species to 453 for Aspergillus, 12 for Paecilomyces, 535 for Penicillium, 14 for Rasamsonia, 203 for Talaromyces and four for Xerochrysium. We accept the newly introduced section Tenues (in Talaromyces), and series Hainanici (in Aspergillus sect. Cavernicolarum) and Vascosobrinhoana (in Penicillium sect. Citrina). In addition, we validate the invalidly described species Aspergillus annui and A. saccharicola, and series Annuorum (in Aspergillus sect. Flavi), introduce a new combination for Dichlaena lentisci (type of the genus) and place it in a new section in Aspergillus subgenus Circumdati, provide an updated description for Rasamsonia oblata, and list excluded and recently synonymised species that were previously accepted. This study represents an important update of the accepted species lists in Eurotiales. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
22. Four new species of Anyphaena Sundevall, 1833 from Xizang, China (Araneae, Anyphaenidae).
- Author
-
Shikai Li, Shilin Wang, Xiaoqi Mi, and Cheng Wang
- Subjects
- *
SPIDERS , *SPECIES , *JUMPING spiders - Abstract
Four new species of the genus Anyphaena Sundevall, 1833 collected from Xizang, China, are described: A. cibagou Wang & Mi, sp. nov. (♂♀), A. linzhi Wang & Mi, sp. nov. (♂♀), A. shufui Wang & Mi, sp. nov. (♀) and A. yejiei Wang & Mi, sp. nov. (♀). Diagnostic photos of the habitus and copulatory organs and a distributional map are provided. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
23. Discovery of five new species of Allacta from Yunnan and Hainan, China (Blattodea, Pseudophyllodromiidae).
- Author
-
Bian-Lun Li, Peng-Hui Hu, Lin Guo, Yan-Li Che, and Zong-Qing Wang
- Subjects
- *
SPECIES , *FEMALE reproductive organs - Abstract
We examined new Allacta materials from Yunnan and Hainan Province, China, and discovered new species using both morphological and molecular species delimitation (ABGD) methods. Five new species are described: A. bifolium Li & Wang, sp. nov., A. hemiptera Li & Wang, sp. nov., A. lunulara Li & Wang, sp. nov., A. redacta Li & Wang, sp. nov., and A. unicaudata Li & Wang, sp. nov. All five species are placed under the hamifera species group. An updated key and checklist of Allacta species from China are provided. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
24. 鱼胶品种的 DNA 条形码鉴定方法研究.
- Author
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姚丽锋, 张 娟, 黎财慧, 张晴阳, 周臣清, 林 靖, 丁 琦, 游淑珠, and 王小玉
- Abstract
Copyright of Journal of Food Safety & Quality is the property of Journal of Food Safety & Quality Editorial Department and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
- Published
- 2024
25. Phylogeny and diversification of genus Sanicula L. (Apiaceae): novel insights from plastid phylogenomic analyses.
- Author
-
Song, Bo-Ni, Liu, Chang-Kun, Zhao, An-Qi, Tian, Rong-Ming, Xie, Deng-Feng, Xiao, Yu-Lin, Chen, Huai, Zhou, Song-Dong, and He, Xing-Jin
- Subjects
- *
PHYLOGENY , *UMBELLIFERAE , *CHLOROPLAST DNA , *PLANT evolution , *PLANT hybridization , *MICROSATELLITE repeats , *CARROTS - Abstract
Background: The genus Sanicula L. is a unique perennial herb that holds important medicinal values. Although the previous studies on Sanicula provided us with a good research basis, its taxonomic system and interspecific relationships have not been satisfactorily resolved, especially for those endemic to China. Moreover, the evolutionary history of this genus also remains inadequately understood. The plastid genomes possessing highly conserved structure and limited evolutionary rate have proved to be an effective tool for studying plant phylogeny and evolution. Results: In the current study, we newly sequenced and assembled fifteen Sanicula complete plastomes. Combined with two previously reported plastomes, we performed comprehensively plastid phylogenomics analyses to gain novel insights into the evolutionary history of this genus. The comparative results indicated that the seventeen plastomes exhibited a high degree of conservation and similarity in terms of their structure, size, GC content, gene order, IR borders, codon bias patterns and SSRs profiles. Such as all of them displayed a typical quadripartite structure, including a large single copy region (LSC: 85,074–86,197 bp), a small single copy region (SSC: 17,047–17,132 bp) separated by a pair of inverted repeat regions (IRs: 26,176–26,334 bp). And the seventeen plastomes had similar IR boundaries and the adjacent genes were identical. The rps19 gene was located at the junction of the LSC/IRa, the IRa/SSC junction region was located between the trnN gene and ndhF gene, the ycf1 gene appeared in the SSC/IRb junction and the IRb/LSC boundary was located between rpl12 gene and trnH gene. Twelve specific mutation hotspots (atpF, cemA, accD, rpl22, rbcL, matK, ycf1, trnH-psbA, ycf4-cemA, rbcL-accD, trnE-trnT and trnG-trnR) were identified that can serve as potential DNA barcodes for species identification within the genus Sanicula. Furthermore, the plastomes data and Internal Transcribed Spacer (ITS) sequences were performed to reconstruct the phylogeny of Sanicula. Although the tree topologies of them were incongruent, both provided strong evidence supporting the monophyly of Saniculoideae and Apioideae. In addition, the sister groups between Saniculoideae and Apioideae were strongly suggested. The Sanicula species involved in this study were clustered into a clade, and the Eryngium species were also clustered together. However, it was clearly observed that the sections of Sanicula involved in the current study were not respectively recovered as monophyletic group. Molecular dating analysis explored that the origin of this genus was occurred during the late Eocene period, approximately 37.84 Ma (95% HPD: 20.33–52.21 Ma) years ago and the diversification of the genus was occurred in early Miocene 18.38 Ma (95% HPD: 10.68–25.28 Ma). Conclusion: The plastome-based tree and ITS-based tree generated incongruences, which may be attributed to the event of hybridization/introgression, incomplete lineage sorting (ILS) and chloroplast capture. Our study highlighted the power of plastome data to significantly improve the phylogenetic supports and resolutions, and to efficiently explore the evolutionary history of this genus. Molecular dating analysis explored that the diversification of the genus occurred in the early Miocene, which was largely influenced by the prevalence of the East Asian monsoon and the uplift of the Hengduan Mountains (HDM). In summary, our study provides novel insights into the plastome evolution, phylogenetic relationships, taxonomic framework and evolution of genus Sanicula. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
26. A practical workflow for forensic species identification using direct sequencing of real-time PCR products.
- Author
-
Doi, Masanori, Nakagawa, Toshifumi, and Asano, Migiwa
- Abstract
Background: Forensic scientists are often required to identify species of unknown biological samples. Although methods based on sequencing of DNA barcode regions are the gold standard for species identification in single-source forensic samples, they are cumbersome to implement as routine work in forensic laboratories that perform many tests, including human DNA typing. We have developed a species identification workflow that incorporates direct sequencing with real-time PCR products (real-time PCR–direct sequencing) as the technical trick for easy testing in forensic practice. Method and results: Following our workflow, DNA samples from vertebrates, such as mammals, amphibians, reptiles, birds, and fish, were subjected to species identification using vertebrate universal primers targeting each of the four DNA barcode regions. In real-time PCR melting curve analysis, humans and animals (nonhuman) could be differentiated by comparing melting temperatures, and subsequent real-time PCR–direct sequencing contributed to simplified sequencing. Searches against public DNA databases using the obtained sequences were compatible with the origin of the samples, indicating that this method might be used to identify animal species at the genus level. Furthermore, this workflow was effective in actual casework, which provided rapid test results according to the needs of the investigating agencies. Conclusions: The species identification workflow will simply sequence as much as possible and can be integrated into routine forensic practice. The real-time PCR–direct sequencing used in this workflow might be beneficial not only for species identification but also for DNA sequencing by using the Sanger method for a variety of life sciences. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
27. A new distribution record, first host plant record and DNA barcoding of the Neotropical micromoth Astrotischeria karsholti Puplesis & Diškus (Lepidoptera, Tischeriidae)
- Author
-
Héctor Vargas
- Subjects
Asteraceae ,Atacama Desert ,DNA barcodes ,host pla ,Biology (General) ,QH301-705.5 - Abstract
Astrotischeria Puplesis & Diškus, 2003 (Lepidoptera, Tischeriidae) is a New World genus of micromoths whose larvae are leaf miners associated mainly with plants of the family Asteraceae. The original description of the type species Astrotischeria karsholti Puplesis & Diškus, 2003 was based on adults from central Peru. No additional distribution records, host plants or DNA barcodes have been documented for this species.Astrotischeria karsholti is reported for the first time from Chile, based on adults obtained from leaf mines of Ambrosia cumanensis Kunth (Asteraceae) collected in the transverse valleys of the Atacama Desert. This discovery expands the distribution range of this micromoth nearly 900 km to the southeast and represents its first host plant record. Divergence between DNA barcodes of A. karsholti and the nearest congeneric was 6% (K2P). A Maximum Likelihood analysis, based on DNA barcodes, raises questions about the monophyly of Astrotischeria.
- Published
- 2023
- Full Text
- View/download PDF
28. Ten thousand kilometres away and still the same species? The mystery of identity of Scopelocheirus sp. (Amphipoda: Scopelocheiridae) from the South Atlantic
- Author
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Michael L. Zettler, Ralf Bastrop, and James K. Lowry
- Subjects
denmark ,namibia ,scopelocheirus hopei ,scopelocheirus sossi sp. nov. ,taxonomy ,dna barcodes ,18s rrna ,Museums. Collectors and collecting ,AM1-501 ,Evolution ,QH359-425 - Abstract
During two campaigns, one in the Kattegat (Denmark) in 2018, and the other off Namibia in 2019, the same fish baited trap was applied to catch scavenging amphipods at two stations each. The water depths in both areas were between 50 and 130 m. In addition to very few individuals of other species (Isopoda and Amphipoda), the samples consisted mainly of Scopelocheirus sp. The species from the Kattegat was identified as S. hopei. The question arises as to whether it is possible that the same species could dominate scavenging communities in sea areas more than 10,000 km apart. At first glance, the scopelocheirid amphipods of the northern and southern hemispheres appear identical, but subtle morphological and large genetic differences led to the conclusion that we are dealing with a previously undescribed species off Namibia. We have named it Scopelocheirus sossi sp. nov.
- Published
- 2023
- Full Text
- View/download PDF
29. Revision of the Genus Laelius (Hymenoptera, Chrysidoidea, Bethylidae) from China
- Author
-
Chunhong Wang, Junhua He, and Xuexin Chen
- Subjects
Epyrinae ,new species ,new records ,DNA barcodes ,key ,Science - Abstract
The genus Laelius from China is revised for the first time and six species are recognized, including one new species as well as three new records. The new species, Laelius longus sp. nov., which is supported by both morphological and molecular analyses, is described and illustrated. Three new records, L. naniwaensis, L. nigrofemoratus, and L. yamatonis, are illustrated. A key to the Chinese species of Laelius is provided.
- Published
- 2024
- Full Text
- View/download PDF
30. Genotypic Identification of Trees Using DNA Barcodes and Microbiome Analysis of Rhizosphere Microbial Communities
- Author
-
Liliana Hopkins, Kayla Yim, Ana Rumora, Melissa F. Baykus, Luisa Martinez, and Luis Jimenez
- Subjects
Acidobacteriota ,Ascomycota ,Actinomycetota ,Bacteroidota ,Basidiomycetes ,DNA barcodes ,Genetics ,QH426-470 - Abstract
DNA barcodes can provide accurate identification of plants. We used previously reported DNA primers targeting the internal transcribed spacer (ITS1) region of the nuclear ribosomal cistron, internal transcribed spacer (ITS2), and chloroplast trnL (UAA) intron to identify four trees at Bergen Community College. Two of the four trees were identified as Acer rubrum and Fagus sylvatica. However, Quercus was only identified at the genus level, and the fourth tree did not show similar identification between barcodes. Next-generation sequencing of 16S rRNA genes showed that the predominant bacterial communities in the rhizosphere mainly consisted of the Pseudomonadota, Actinomycetota, Bacteroidota, and Acidobacteriota. A. rubrum showed the most diverse bacterial community while F. sylvatica was less diverse. The genus Rhodoplanes showed the highest relative bacterial abundance in all trees. Fungal ITS sequence analysis demonstrated that the communities predominantly consisted of the Ascomycota and Basidiomycota. Quercus showed the highest fungi diversity while F. sylvatica showed the lowest. Russula showed the highest abundance of fungi genera. Average similarity values in the rhizosphere for fungi communities at the phylum level were higher than for bacteria. However, at the genus level, bacterial communities showed higher similarities than fungi. Similarity values decreased at lower taxonomical levels for both bacteria and fungi, indicating each tree has selected for specific bacterial and fungal communities. This study confirmed the distinctiveness of the microbial communities in the rhizosphere of each tree and their importance in sustaining and supporting viability and growth but also demonstrating the limitations of DNA barcoding with the primers used in this study to identify genus and species for some of the trees. The optimization of DNA barcoding will require additional DNA sequences to enhance the resolution and identification of trees at the study site.
- Published
- 2024
- Full Text
- View/download PDF
31. A practical workflow for forensic species identification using direct sequencing of real-time PCR products.
- Author
-
Doi, Masanori, Nakagawa, Toshifumi, and Asano, Migiwa
- Abstract
Background: Forensic scientists are often required to identify species of unknown biological samples. Although methods based on sequencing of DNA barcode regions are the gold standard for species identification in single-source forensic samples, they are cumbersome to implement as routine work in forensic laboratories that perform many tests, including human DNA typing. We have developed a species identification workflow that incorporates direct sequencing with real-time PCR products (real-time PCR–direct sequencing) as the technical trick for easy testing in forensic practice. Method and results: Following our workflow, DNA samples from vertebrates, such as mammals, amphibians, reptiles, birds, and fish, were subjected to species identification using vertebrate universal primers targeting each of the four DNA barcode regions. In real-time PCR melting curve analysis, humans and animals (nonhuman) could be differentiated by comparing melting temperatures, and subsequent real-time PCR–direct sequencing contributed to simplified sequencing. Searches against public DNA databases using the obtained sequences were compatible with the origin of the samples, indicating that this method might be used to identify animal species at the genus level. Furthermore, this workflow was effective in actual casework, which provided rapid test results according to the needs of the investigating agencies. Conclusions: The species identification workflow will simply sequence as much as possible and can be integrated into routine forensic practice. The real-time PCR–direct sequencing used in this workflow might be beneficial not only for species identification but also for DNA sequencing by using the Sanger method for a variety of life sciences. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
32. A new species of Concinocordis Razowski and Brown, 2012 from Kenya (Lepidoptera: Tortricidae).
- Author
-
Brown, John W. and Timm, Alicia E.
- Subjects
- *
TORTRICIDAE , *LEPIDOPTERA , *SPECIES , *NUCLEOTIDE sequence , *DNA sequencing , *CODLING moth - Abstract
Concinocordis wilsonarum Razowski and Brown, 2012 was described from seven specimens reared from native fruit (all Sapotaceae) in Kenya. The accumulation of additional specimens and re-analyses of DNA sequence data (COI barcodes) reveals that the species is actually a complex of three distinct entities, each separated from its nearest relative by COI divergences of at least 8%. Differences in forewing maculation provide additional evidence that the three are distinct. Concinocordis bartocki Brown, new species, is described, but the second new species is not because it is represented by a single male in exceedingly poor condition. A damaged pupal exuvium of C. wilsonarum shows marked dissimilarities with the pupae of other tortricids. The enigmatic tribal assignment of Concinocordis is discussed briefly. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
33. New data on the genus Scythris Hübner, [1825] from the Canary Islands (Spain), with description of six new species (Lepidoptera: Scythrididae).
- Author
-
Falck, Per
- Subjects
DNA analysis ,BEETLE anatomy ,LEPIDOPTERA ,MORPHOLOGY ,SPECIES ,INSECT anatomy ,ISLANDS ,GENITALIA - Abstract
Copyright of SHILAP Revista de Lepidopterologia is the property of Sociedad Hispano-Luso-Americana de Lepidopterologia and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
- Published
- 2023
- Full Text
- View/download PDF
34. Quelites Pasados of the Sierra Tarahumara, Chihuahua, Mexico: An Interdisciplinary Ethnobotanical Study of Leafy Green Vegetables.
- Author
-
Severiano-Pérez, Patricia, Cristians, Sol, Bye, Robert, Lucas-Florentino, Bernardo, Ramírez-Orejel, Juan Carlos, Linares, Edelmira, Mera-Ovando, Luz María, Castro-Lara, Delia, Enríquez-Maldonado, Daniel, Rodríguez-Servín, Joel, González-Pedroza, María de Guadalupe, Escalante-Martínez, Viridiana, Palma Pérez del Valle, José Emiliano, Mendoza-Cruz, Myrna, Nevarez-Durán, Alejandro, and Silvestre-Lara, Perla
- Subjects
EDIBLE greens ,AMARANTHUS palmeri ,WILD foods ,INTRODUCED species ,AGROBIODIVERSITY ,INTERDISCIPLINARY education - Abstract
Copyright of Economic Botany is the property of Springer Nature and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
- Published
- 2023
- Full Text
- View/download PDF
35. A new distribution record, first host plant record and DNA barcoding of the Neotropical micromoth Astrotischeria karsholti Puplesis & Diškus (Lepidoptera, Tischeriidae).
- Author
-
Vargas, Héctor A.
- Subjects
HOST plants ,GENETIC barcoding ,TISCHERIIDAE ,ASTERACEAE - Abstract
Background: Astrotischeria Puplesis & Diškus, 2003 (Lepidoptera, Tischeriidae) is a New World genus of micromoths whose larvae are leaf miners associated mainly with plants of the family Asteraceae. The original description of the type species Astrotischeria karsholti Puplesis & Diškus, 2003 was based on adults from central Peru. No additional distribution records, host plants or DNA barcodes have been documented for this species. New information: Astrotischeria karsholti is reported for the first time from Chile, based on adults obtained from leaf mines of Ambrosia cumanensis Kunth (Asteraceae) collected in the transverse valleys of the Atacama Desert. This discovery expands the distribution range of this micromoth nearly 900 km to the southeast and represents its first host plant record.Divergence between DNA barcodes of A. karsholti and the nearest congeneric was 6% (K2P). A Maximum Likelihood analysis, based on DNA barcodes, raises questions about the monophyly of Astrotischeria. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
36. The first record of Tricholathys Chamberlin & Ivie, 1935 (Araneae, Dictynidae) from China, with a new combination and descriptions of seven new species.
- Author
-
Lu-Yu Wang, Xian-Jin Peng, and Zhi-Sheng Zhang
- Subjects
- *
SPIDERS , *GENETIC barcoding , *JUMPING spiders , *SPECIES , *DIGITAL images , *SPIDER webs - Abstract
The genus Tricholathys, found for the first time in China, is surveyed and seven new species, T. burangensis sp. nov. (♂♀, Thibet), T. chenzhenningi sp. nov. (♂♀, Qinghai), T. hebeiensis sp. nov. (♀, Hebei), T. lhunzeensis sp. nov. (♂♀, Tibet), Tricholathys relictoides sp. nov. (♂♀, Xinjiang), T. serrata sp. nov. (♂♀, Tibet), and T. xizangensis sp. nov. (♂♀, Tibet), are described. A new combination is proposed for Tricholathys alxa (Tang, 2011) comb. nov., ex. Argenna Thorell, 1870. Descriptions of all new species are provided, together with digital images, illustrations, and a distribution map. The DNA barcode information of four recently collected species is also provided. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
37. TACHYSTOLA MULLIGANAE SP. NOV. (LEP.: OECOPHORIDAE), A WESTERN AUSTRALIAN SPECIES ADVENTIVE IN WEST LONDON.
- Author
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STERLING, MARK J., PLANT, COLIN W., PRICE, BEN W., CUBER, PIOTR, HALL, ANDIE, BEASLEY, JORDAN, and LEES, DAVID C.
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GENETIC barcoding ,SPECIES ,MITOCHONDRIAL proteins ,DATABASES ,GENETIC code - Abstract
We describe here a new species of oecophorid moth from specimens found in West London and Western Australia. This taxon is part of the Tachystola hemisema (Meyrick, 1885) DNA barcode complex, which consists of at least five different clusters, each with a distinct Barcode Index Number (BIN) on the Barcode Database of Life (BoLD). Illumina sequencing and bioinformatic processing techniques were applied to the lectotype of T. hemisema (collected in 1884) and the designated holotype of the new taxon (collected in 1886) and all 13 mitochondrial protein coding genes were recovered. Recent specimens from West London were DNA barcoded and compared to the BoLD clusters. The morphology of these specimens was compared to the extent possible (both historical specimens lack abdomens). The pairwise distance between typical T. hemisema and the new taxon measures 3.65% for CoI-5P, while there are some amino acid differences in CoI-3P and eight other genes. We also identify morphological differences for the new taxon. The generic placement of the new taxon and T. hemisema with respect to Tachystola acroxantha (Meyrick, 1885) is also considered. [ABSTRACT FROM AUTHOR]
- Published
- 2023
38. Review of the Narrow-Banded Hawkmoth, Neogurelca montana (Rothschild & Jordan, 1915) (Lepidoptera: Sphingidae) in China, with Morphological and Phylogenetic Analysis.
- Author
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Xu, Zhen-Bang, He, Ji-Bai, Yang, Nan, Kitching, Ian J., and Hu, Shao-Ji
- Subjects
- *
SPHINGIDAE , *FEMALE reproductive organs , *LEPIDOPTERA , *SUBSPECIES , *MOLECULAR phylogeny , *MALE reproductive organs ,BEETLE anatomy - Abstract
Simple Summary: The hawkmoth genus Neogurelca Hogenes & Treadaway, 1993 (Sphingidae: Macroglossinae: Macroglossini), comprises seven species, four of which are found in Asia and the other three in Central America. The members of this group in China are still poorly known, especially their distributions and taxonomy. We performed an analysis based on a 658 bp region of the COI mitochondrial gene, covering three species and including two populations of N. montana from Yunnan and Beijing, to resolve their phylogenetic positions. A morphological analysis of both sexes of the four Asian species was also undertaken. The phylogenetic analysis revealed the Beijing population of N. montana as a well-supported clade that is distinct from but close to the Yunnan population, which is consistent with the morphological differences between them. We describe the Beijing population of N. montana as a new subspecies, Neogurelca montana taihangensis ssp. nov., based on our analysis. Additionally, we collected larvae of N. montana in Beijing and describe its life history and larval hosts and compare them with those of N. himachala. Neogurelca montana (Rothschild & Jordan, 1915) is a species of the genus Neogurelca Hogenes & Treadaway, 1993, that was previously known from Sichuan, Yunnan, and Tibet, China. Recently, however, this species was also found in Beijing and Hebei. These populations differ from those in southwest China in body colour and the shape of the yellow patches of the hindwing—a paler body colour and triangular patches in the former and darker body colour and fan-like patches in the latter. Wing morphology, male and female genitalia, and molecular evidence (DNA barcodes) were analysed for the different localities of this species and three other Neogurelca species—N. hyas, N. himachala, and N. masuriensis. Our molecular data support the Beijing population of montana as a valid subspecies, which we describe as N. montana taihangensis ssp. nov. Wing and genital morphology confirm the molecular conclusions. We also collected larvae of the new subspecies in the Beijing suburbs and describe its life history and larval hosts and compare them with those of N. himachala. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
39. Phylogeny‐based assignment of functional traits to DNA barcodes outperforms distance‐based, in a comparison of approaches.
- Author
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Xie, Tingting, Orr, Michael C., Zhang, Dan, Ferrari, Rafael R., Li, Yi, Liu, Xiuwei, Niu, Zeqing, Wang, Mingqiang, Zhou, Qingsong, Hao, Jiasheng, Zhu, Chaodong, and Chesters, Douglas
- Subjects
- *
BAR codes , *LIFE history theory , *INSECT communities , *GENETIC barcoding , *BROOD parasitism , *DNA - Abstract
The full potential for using DNA barcodes for profiling functional trait diversity has yet to be determined in plants and animals; thus, we outline a general framework for quantifying functional trait diversity of insect community DNA and propose and assess the accuracy of three methods for achieving this. We built a novel dataset of traits and DNA barcodes for wild bees in China. An informatics framework was developed for phylogeny‐based integration of these data and prediction of traits for any subject barcodes, which was compared with two distance‐based methods. For Phylogenetic Assignment, we additionally conducted a species‐level analysis of publically available bee trait data. Under the specimen‐level dataset, the rate of trait assignment was negatively correlated with distance between the query and the nearest trait‐known reference, for all methods. Phylogenetic Assignment was found to perform best under several criteria; particularly, it had the lowest false‐positive rate (rarely returning a state prediction where success was unlikely; where the distance from query to the nearest reference was high). For a wider range of compiled traits, conservative life‐history traits showed the highest rates of assignment; for example, sociality was predicted with confidence at 53%, parasitism at 44% and nest location at 33%. As outlined herein, automated trait assignment might be applied at scale to either barcodes or metabarcodes. With further compilation and databasing of DNA barcode and trait data, the rate and accuracy of trait assignment is expected to increase to the point of being a widely viable and informative approach. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
40. Revealing Diversity in Gammarus (Amphipoda: Gammaridae) in the Freshwater Ecosystems of Armenia Using DNA Barcoding.
- Author
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Dallakyan, Marine, Lipinskaya, Tatsiana, Asatryan, Vardan, Golovenchik, Viktoriya, Thormann, Jana, Mark, Laura von der, and Astrin, Jonas J.
- Subjects
GENETIC barcoding ,GAMMARUS ,BIOLOGICAL classification ,AMPHIPODA ,FRESH water - Abstract
Gammarus plays a central role in the detritus cycle and constitutes an important component in food webs. At the same time, taxonomy and morphological identification to species level is highly challenging in this genus. Thus, the freshwater gammarid diversity in the Caucasus biodiversity hotspot remains largely unstudied to date. We use DNA barcoding for the first time in assessing the biodiversity and taxonomy of gammarids within the amphipod genus Gammarus in the limnic ecosystems of Armenia. The results expand the knowledge on possible diversity and evolutionary lineages of Gammarus in the region. DNA barcodes obtained from our Armenian specimens consistently indicate four to six well-defined molecular operational taxonomic units (MOTUs) within three distinct morphospecies clusters. One to three MOTUs correspond to the Gammarus balcanicus species complex, two MOTUs to the G. komareki complex, and one MOTU to the G. lacustris complex. Five BINs out of six were unique and new to BOLD. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
41. Genetic and morphological evidence of a single species of bronze featherback (Notopterus notopterus) in Sundaland
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Arif Wibowo, Haryono Haryono, Kurniawan Kurniawan, Vitas Atmadi Prakoso, Hadi Dahruddin, Indah Lestari Surbani, Boby Muslimin, Yohanes Yudha P. Jaya, Sudarsono Sudarsono, Ivor G. Stuart, Harald Ahnelt, Simon Funge-Smith, Anti Vasemägi, and Nicolas Hubert
- Subjects
DNA barcodes ,DNA-based species delimitation ,Phylogeography ,Genetic diversity ,Morphometry ,Multivariate analyses ,Ecology ,QH540-549.5 - Abstract
The bronze featherback (Notopterus notopterus) is an iconic species of freshwater fish commonly found in South-East Asia and of great commercial and patrimonial importance. At present, the genus Notopterus comprises of two distinct species, Notopterus notopterus (Pallas, 1769) and Notopterus synurus (Bloch & Schneider 1801). On the Indonesian archipelago, genetic diversity and morphology of the bronze featherback were investigated for conservation purposes. The use of DNA-based species delimitation methods, applied to 165 Cytochrome oxidase I sequences of Notopteridae (121 belonging to N. notopterus), evidence a concordance between species and Molecular Operational Taxonomic Unit (MOTU) and the two species of Notopterus are recognized. In N. notopterus, 9 haplotypes are detected among the 121 sequences analyzed, and three are restricted to Sundaland. These three haplotypes had distinct geographic distribution with a haplotype observed in Java, Sumatra and Borneo, another haplotype restricted to South Sumatra and a third haplotype only found in Northern Sumatra. The analyze of 21 morphometric and 9 meristic variables revealed two groups within N. notopterus, which were only supported by subtle differences in measurements with overlapping distributions between groups. The present study supports the validity of Notopterus notopterus in Sundaland and the remarkable genetic continuity among populations across its range distribution.
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- 2024
- Full Text
- View/download PDF
42. Unlocking the Genetic Identity of Endangered Paphiopedilum Orchids: A DNA Barcoding Approach
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Małgorzata Karbarz, Dominika Szlachcikowska, Angelika Zapał, and Agnieszka Leśko
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DNA barcodes ,Paphiopedilum ,identification ,orchid ,Genetics ,QH426-470 - Abstract
Orchids of the genus Paphiopedilum, also called slippers, are among the most valued representatives of the Orchidaceae family due to their aesthetic qualities. Due to overexploitation, deforestation, and illegal trade in these plants, especially in the vegetative phase, Paphiopedilum requires special protection. This genus is listed in Appendix I of the Convention on International Trade in Endangered Species of Wild Fauna and Flora. Their precise identification is of great importance for the preservation of genetic resources and biodiversity of the orchid family (Orchidaceae). Therefore, the main objective of the study was to investigate the usefulness of the DNA barcoding technique for the identification of endangered orchids of the genus Paphiopedilum and to determine the effectiveness of five loci: matK, rbcL, ITS2, atpF-atpH and trnH-psbA as potential molecular markers for species of this genus. Among single locus barcodes, matK was the most effective at identifying species (64%). Furthermore, matK, ITS2, matK + rbcL, and matK + trnH-psbA barcodes can be successfully used as a complementary tool to identify Paphiopedilum orchids while supporting morphological data provided by taxonomists.
- Published
- 2024
- Full Text
- View/download PDF
43. Revision of the Genus Rhagastis Rothschild & Jordan, 1903 (Lepidoptera: Sphingidae) from China, Based on Morphological and Phylogenetic Analyses
- Author
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Zhuo-Heng Jiang, Jia-Xin Wang, Zhen-Bang Xu, Ian J. Kitching, Chia-Lung Huang, Shao-Ji Hu, and Yun-Li Xiao
- Subjects
hawkmoth ,Rhagastis ,DNA barcodes ,molecular phylogeny ,genitalic structure ,Science - Abstract
Here, the taxonomy of the genus Rhagastis Rothschild & Jordan, 1903 (Lepidoptera, Sphingidae, Macroglossinae, Macroglossini) from China is revised based on differences in wing morphology, male and female genitalia, and the phylogenetic relationship of the DNA barcodes. Subspecies of Rhagastis albomarginatus (Rothschild, 1894) and R. castor (Walker, 1856) are treated as “good” species, namely Rhagastis dichroae Mell, 1922 stat. nov.; R. everetti Rothschild & Jordan, 1903 stat. nov.; R. aurifera (Butler, 1875) stat. rev.; R. chinensis Mell, 1922 stat. nov.; R. formosana Clark, 1925 stat. nov.; and R. jordani Oberthür, 1904 stat. rev. The distribution maps, biological notes, and ecological records of the genus Rhagastis Rothschild & Jordan, 1903 from China are given, and a species inventory of genus Rhagastis in the world is also included.
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- 2024
- Full Text
- View/download PDF
44. Revision of Nannocharax luapulae Boulenger, 1915 (Characiformes: Distichodontidae) from the Upper Congo basin: Evidence for a species pair.
- Author
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Katemo Manda, Bauchet, Snoeks, Jos, Decru, Eva, Brecko, Jonathan, and Vreven, Emmanuel J. W. M. N.
- Subjects
- *
CYTOCHROME oxidase , *CHARACIFORMES , *FISH conservation , *PERCIFORMES , *PECTORAL fins , *SPECIES - Abstract
For many decades, Nannocharax luapulae has been considered to be widespread in the southern part of the Upper Congo basin. However, meristic, morphometric and cytochrome c oxidase subunit I (COI) barcoding evidence revealed that its geographical distribution is restricted to the Luapula‐Moero basin. The populations of the Upper Lualaba are assigned to a new species, N. chochamandai. This new species, though highly similar to N. luapulae, can readily be distinguished from it by its lower number of lateral line scales, 41–46 (vs. 49–55), its pectoral fin reaching the pelvic‐fin insertion (vs. not reaching the pelvic‐fin insertion) and its pelvic fin reaching the base of the anal fin (vs. not reaching the base of the anal fin). Specimens of N. chochamandai display thickened pads on the first three pelvic‐fin rays that exhibit intraspecific variation in development, which appears to be related to the flow‐strength of the river in which these Nannocharax specimens occur. Nannocharax luapulae is redescribed and an updated identification key to the Nannocharax species of the Congo basin sensu lato is provided as well. Some fish conservation issues related to N. luapulae and N. chochamandai are also highlighted. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
45. Phylogenetic and biogeographic history of brook lampreys (Lampetra: Petromyzontidae) in the river basins of the Adriatic Sea based on DNA barcode data.
- Author
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Rüber, Lukas, Gandolfi, Andrea, Foresti, Danilo, Paltrinieri, Luca, Splendiani, Andrea, and Seehausen, Ole
- Subjects
- *
GENETIC barcoding , *LAMPREYS , *CYTOCHROME oxidase , *NUCLEOTIDE sequence , *GENETIC distance - Abstract
The Adriatic brook lamprey, Lampetra zanandreai Vladykov 1955, was described from northeastern Italy. Its distribution is thought to include left tributaries of the River Po and the river basins of the Adriatic Sea from the River Po to the River Isonzo/Soča in Italy, Switzerland and Slovenia. It also shows a geographically isolated distribution in the Potenza River on the Adriatic slope in Central Italy. Lampetra from the Neretva River system in Croatia and Bosnia and Herzegovina and the Morača River system in Montenegro that were previously identified as L. zanandreai were recently described as a new species Lampetra soljani Tutman, Freyhof, Dulčić, Glamuzina & Geiger 2017 based on morphological data and a genetic distance between the two species of roughly 2.5% in the DNA barcoding gene cytochrome oxidase I (COI). Since DNA barcodes for L. zanandreai are only available for one population from the upper Po River in northwestern Italy, we generated additional COI nucleotide sequence data of this species from Switzerland, northeastern and central Italy comprising near topotypic material and obtained GenBank sequences of the species from Slovenia to better assess the evolutionary history of the two brook lamprey species in the river basins of the Adriatic Sea. Our data show a low sequence divergence of <1% between L. zanandreai from Switzerland, northeastern and central Italy and Slovenia and the Balkan species L. soljani. However, members of the population previously identified as 'L. zanandreai' from northwest Italy are genetically highly divergent from those of L. zanandreai and likely belong to an undescribed species, L. sp. 'upper Po'. The presence of a unique and highly divergent brook lamprey lineage in the upper Po River suggests that L. zanandreai and Lampetra sp. 'upper Po' may have evolved in separate paleo drainages during the formation of the modern Po Valley subsequent to marine inundations in the Pliocene. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
46. The genus Errastunus in the Nearctic region (Hemiptera, Cicadellidae, Deltocephalinae).
- Author
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Kits, Joel H.
- Subjects
- *
NEARCTIC ecozone , *BIOLOGICAL classification , *HEMIPTERA , *LEAFHOPPERS , *SPECIES distribution , *CICADAS , *INSECT diversity - Abstract
The leafhopper genus Errastunus contains grass-feeding leafhoppers in the delto-cephaline tribe Paralimnini. The taxonomy of the genus in the Nearctic region has long been confused, with one to three distinct species recognized by different authors. Some populations have also been suggested to be adventive from Europe. Morphological and molecular data show that there are two distinct species in North America. These taxa are readily distinguishable morphologically although there is evidence of mitochondrial introgression between the species. The distribution of the two species based on historical material in collections suggests that Errastunus sobrinus (DeLong & Sleesman, 1929) is native to North America, while E. ocellaris (Fallén, 1806) includes both native and adventive populations. A lectotype is designated for E. sobrinus and Cicada ocellata Scopoli, 1763 is established as a nomen oblitum with Cicada ocellaris as a nomen protectum. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
47. Ten thousand kilometres away and still the same species? The mystery of identity of Scopelocheirus sp. (Amphipoda: Scopelocheiridae) from the South Atlantic.
- Author
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ZETTLER, MICHAEL L., BASTROP, RALF, and LOWRY, JAMES K.
- Subjects
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AMPHIPODA , *FISH traps , *SPECIES , *WATER depth , *FISHING baits , *BAITFISH - Abstract
During two campaigns, one in the Kattegat (Denmark) in 2018, and the other off Namibia in 2019, the same fish baited trap was applied to catch scavenging amphipods at two stations each. The water depths in both areas were between 50 and 130 m. In addition to very few individuals of other species (Isopoda and Amphipoda), the samples consisted mainly of Scopelocheirus sp. The species from the Kattegat was identified as S. hopei. The question arises as to whether it is possible that the same species could dominate scavenging communities in sea areas more than 10,000 km apart. At first glance, the scopelocheirid amphipods of the northern and southern hemispheres appear identical, but subtle morphological and large genetic differences led to the conclusion that we are dealing with a previously undescribed species off Namibia. We have named it Scopelocheirus sossi sp. nov. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
48. Plant DNA barcode library for native flowering plants in the arid region of northwestern China.
- Author
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Song, Feng, Li, Ting, Yan, Hai‐Fei, Feng, Ying, Jin, Lu, Burgess, Kevin S., and Ge, Xue‐Jun
- Subjects
- *
DNA data banks , *ARID regions , *FLOWERING of plants , *ANGIOSPERMS , *NATIVE plants , *PLANT DNA - Abstract
DNA barcoding is a well‐established tool for rapid species identification and biodiversity monitoring. A reliable and traceable DNA barcode reference library with extensive coverage is necessary but unavailable for many geographical regions. The arid region in northwestern China, a vast area of about 2.5 million km2, is ecologically fragile and often overlooked in biodiversity studies. In particular, DNA barcode data from the arid region in China are lacking. We develop and evaluate the efficacy of an extensive DNA barcode library for native flowering plants in the arid region of northwestern China. Plant specimens were collected, identified and vouchered for this purpose. The database utilized four DNA barcode markers, namely rbcL, matK, ITS and ITS2, for 1816 accessions (representing 890 species from 385 genera and 72 families), and consisted of 5196 barcode sequences. Individual barcodes varied in resolution rates: species‐ and genus‐level rates for rbcL, matK, ITS and ITS2 were 79.9%–51.1%/76.1%, 79.9%–67.2%/88.9%, 85.0%–72.0%/88.2% and 81.0%–67.4%/84.9%, respectively. The three‐barcode combination of rbcL + matK + ITS (RMI) revealed a higher species‐ and genus‐level resolution (75.5%/92.1%, respectively). A total of 110 plastomes were newly generated as super‐barcodes to increase species resolution for seven species‐rich genera, namely Astragalus, Caragana, Lactuca, Lappula, Lepidium, Silene and Zygophyllum. Plastomes revealed higher species resolution compared to standard DNA barcodes and their combination. We suggest future databases include super‐barcodes, especially for species‐rich and complex genera. The plant DNA barcode library in the current study provides a valuable resource for future biological investigations in the arid regions of China. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
49. Documenting the biodiversity of edible grasshoppers in South Africa with traditional knowledge, classic taxonomy and genetic information.
- Author
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O'Hare, Michaela, Hugel, Sylvain, Hendrickse, Megan, Greyling, Christi, Egan, Bronwyn, and van Asch, Barbara
- Subjects
TRADITIONAL knowledge ,SCIENTIFIC knowledge ,GRASSHOPPERS ,EDIBLE insects ,SCIENTIFIC method ,GENETIC barcoding ,TRADITIONAL ecological knowledge - Abstract
The diversity of edible grasshoppers worldwide remains largely undocumented due to inconsistent reporting of ethno- and scientific species, and paucity of reference DNA sequences. This study uses traditional knowledge and scientific methods for identification of ethnospecies, taxonomic species, and phylogenetic groups that likely represent genetic species. Community members in the Limpopo province of South Africa assisted with specimen collection (n = 176) and identification of 34 ethnospecies (i.e. vernacular names given by the local communities). Scientific taxa were identified by alpha taxonomy and DNA barcode sequence queries on BOLD Systems and GenBank. Genetic groups likely representing distinct species were determined by phylogenetic analysis and intragroup p-distances. Acrididae dominated the dataset with nine subfamilies and 17 genera represented. Database queries yielded high sequence similarity/identity matches (> 95%) for only 58.6% of the sequences on BOLD and 37.1% on GenBank, thus highlighting the low representation of African Orthoptera in public repositories. Phylogenetic analysis and pairwise distances revealed 36 genetic groups likely representing distinct species. Comparison of the results obtained from the different sources of information showed incomplete overlap, and numerous inconsistencies. Despite the difficulties, the overall diversity of edible grasshoppers traditionally utilized in South Africa is higher than previously reported. This work may inform future studies for documenting edible insects in Africa and other world regions. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
50. Five new species of the long-legged sac spider genus Cheiracanthium C.L. Koch, 1839 (Araneae: Cheiracanthiidae) from China
- Author
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Zhaoyi Li and Feng Zhang
- Subjects
description ,DNA barcodes ,morphology ,taxonomy ,Zoology ,QL1-991 ,Botany ,QK1-989 - Abstract
Five species of the cheiracanthiid spider genus Cheiracanthium C.L. Koch, 1839 collected from China are diagnosed and described as new to science based on morphological characters: Cheiracanthium arcilongum sp. nov. (♂♀) from Yunnan, C. circulum sp. nov. (♂♀) from Yunnan, C. digitatum sp. nov. (♂♀) from Anhui, C. jiuquan sp. nov. (♂♀) from Guangxi and C. xinjiangense sp. nov. (♂♀) from Xinjiang. In addition, the photos of the habitus, copulatory organs and distribution map are provided for all species. However, DNA barcodes information is only provided for four species.
- Published
- 2023
- Full Text
- View/download PDF
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