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Mitochondrial DNA barcoding of mosquito species (Diptera: Culicidae) in Thailand. PLoS One 2022; 17:e0275090. [DOI: 10.1371/journal.pone.0275090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 09/09/2022] [Indexed: 01/19/2023] Open
Abstract
The correct identification of mosquito species is important for effective mosquito vector control. However, the standard morphological identification of mosquito species based on the available keys is not easy with specimens in the field due to missing or damaged morphological features during mosquito collections, often leading to the misidentification of morphologically indistinguishable. To resolve this problem, we collected mosquito species across Thailand to gather genetic information, and evaluated the DNA barcoding efficacy for mosquito species identification in Thailand. A total of 310 mosquito samples, representing 73 mosquito species, were amplified using mitochondrial cytochrome c oxidase subunit I (COI) primers. The average maximum intraspecific genetic variation of the 73 mosquito species was 1% ranged from 0–5.7%. While, average minimum interspecific genetic variation (the distance to the nearest neighbour) of the 73 mosquito species was 7% ranged from 0.3–12.9%. The identification of success rates based on the “Best Match,” “Best Close Match,” and “All Species Barcodes” methods were 97.7%, 91.6%, and 81%, respectively. Phylogenetic analyses of Anopheles COI sequences demonstrated a clear separation between almost all species (except for those between An. baimaii and An. dirus), with high bootstrap support values (97%–99%). Furthermore, phylogenetic analyses revealed potential sibling species of An. annularis, An. tessellatus, and An. subpictus in Thailand. Our results indicated that DNA barcoding is an effective molecular approach for the accurate identification of mosquitoes in Thailand.
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Sangster G, Luksenburg JA, Päckert M, Roselaar CS, Irestedt M, Ericson PGP. Integrative taxonomy documents two additional cryptic
Erithacus
species on the Canary Islands (Aves). ZOOL SCR 2022. [DOI: 10.1111/zsc.12561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- George Sangster
- Naturalis Biodiversity Center Leiden The Netherlands
- Department of Bioinformatics and Genetics Swedish Museum of Natural History Stockholm Sweden
| | - Jolanda A. Luksenburg
- Institute of Environmental Sciences Leiden University Leiden The Netherlands
- Department of Environmental Science and Policy George Mason University Fairfax Virginia USA
| | - Martin Päckert
- Senckenberg Natural History Collections Dresden Dresden Germany
| | | | - Martin Irestedt
- Department of Bioinformatics and Genetics Swedish Museum of Natural History Stockholm Sweden
| | - Per G. P. Ericson
- Department of Bioinformatics and Genetics Swedish Museum of Natural History Stockholm Sweden
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Kittelberger KD, Buechley ER, Ford M, Ağırkaya K, Hakkı Şekercioğlu Ç. First satellite-tracked migration of an Eurasian Thick-knee (Burhinus oedicnemus) in the Middle East ends in human-caused mortality. ZOOLOGY IN THE MIDDLE EAST 2021. [DOI: 10.1080/09397140.2021.1918183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
| | - Evan R. Buechley
- Smithsonian Migratory Bird Center, Washington D.C., USA
- HawkWatch International, Salt Lake City, USA
| | | | | | - Çağan Hakkı Şekercioğlu
- School of Biological Sciences, University of Utah, Salt Lake City, USA
- Koç University, Faculty of Sciences, Rumelifeneri, Istanbul, Sarıyer, Turkey
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Gaber A, Hassan MM, Boland C, Alsuhaibany A, Babbington J, Pereira J, Budd J, Shobrak M. Molecular identification of Todiramphus chloris subspecies on the Arabian Peninsula using three mitochondrial barcoding genes and ISSR markers. Saudi J Biol Sci 2020; 27:480-488. [PMID: 31889874 PMCID: PMC6933276 DOI: 10.1016/j.sjbs.2019.11.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 10/20/2019] [Accepted: 11/17/2019] [Indexed: 11/03/2022] Open
Abstract
The Collared Kingfisher (Todiramphus chloris) is widely distributed across the Indian and western Pacific Oceans and consists of about 50 subspecies. Two different subspecies of T. chloris occur in the Arabian Peninsula: T. c. abyssinicus from the Red Sea coast and T. c. kalbaensis from the Arabian Sea coast in the United Arab Emirates and Oman. The aim of this study was to determine the molecular relationship between the two Arabian subspecies and to establish the first DNA barcodes from the Arabian Peninsula for this species. Three different mitochondrial genes were used: (i) cytochrome c oxidase subunit I (COI), (ii) 12S rRNA (12S) and (iii) NADH dehydrogenase-1 (ND1). The COI gene sequences of the two subspecies were 100% identical, while the 12S and ND1 gene sequences revealed a unique single nucleotide variation between the two subspecies. Thus, this single nucleotide variation can be used as a DNA barcode to discriminate between two subspecies. Furthermore, the genetic profile or fingerprint for both subspecies were compared using ten primers of the highly polymorphic nuclear markers (Inter Simple Sequence Repeat, ISSR). As expected, the DNA analysis of the ISSR markers was able to distinguish between the specimens of the two subspecies. These results suggest that T. c. abyssinicus and T. c. kalbaensis are not identical and thus belong to different subspecies. Besides, the sequences of the COI gene for T. c. abyssinicus and T. c. kalbaensis differs by only 1.28% from T. sanctus suggesting that the Arabian subspecies are closely related to the Sacred Kingfisher (T. sanctus).
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Affiliation(s)
- Ahmed Gaber
- Department of Biology, Faculty of Science, Taif University, Saudi Arabia.,Department of Genetics, Faculty of Agriculture, Cairo University, Egypt
| | - Mohamed M Hassan
- Department of Biology, Faculty of Science, Taif University, Saudi Arabia.,Department of Genetics, Faculty of Agriculture, Menoufia University, Egypt
| | - Christopher Boland
- Saudi Aramco, Environmental Protection Department, Dhahran, Saudi Arabia
| | - Abdullah Alsuhaibany
- Ministry of Environment, Water, and Agriculture, National Wildlife Center, Riyadh, Saudi Arabia
| | - Jem Babbington
- Saudi Aramco, EXPEC Advance Research Center, Dhahran, Saudi Arabia
| | - John Pereira
- Environment & Protected Areas Authority, Sharjah, United Arab Emirates
| | - Jane Budd
- Environment & Protected Areas Authority, Sharjah, United Arab Emirates
| | - Mohammed Shobrak
- Department of Biology, Faculty of Science, Taif University, Saudi Arabia.,Saudi Wildlife Authority, Prince Saud Al Faisal Research Center, Taif, Saudi Arabia
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Andersen JC, Oboyski P, Davies N, Charlat S, Ewing C, Meyer C, Krehenwinkel H, Lim JY, Noriyuki S, Ramage T, Gillespie RG, Roderick GK. Categorization of species as native or nonnative using DNA sequence signatures without a complete reference library. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2019; 29:e01914. [PMID: 31050090 PMCID: PMC7079013 DOI: 10.1002/eap.1914] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 03/18/2019] [Accepted: 04/01/2019] [Indexed: 05/26/2023]
Abstract
New genetic diagnostic approaches have greatly aided efforts to document global biodiversity and improve biosecurity. This is especially true for organismal groups in which species diversity has been underestimated historically due to difficulties associated with sampling, the lack of clear morphological characteristics, and/or limited availability of taxonomic expertise. Among these methods, DNA sequence barcoding (also known as "DNA barcoding") and by extension, meta-barcoding for biological communities, has emerged as one of the most frequently utilized methods for DNA-based species identifications. Unfortunately, the use of DNA barcoding is limited by the availability of complete reference libraries (i.e., a collection of DNA sequences from morphologically identified species), and by the fact that the vast majority of species do not have sequences present in reference databases. Such conditions are critical especially in tropical locations that are simultaneously biodiversity rich and suffer from a lack of exploration and DNA characterization by trained taxonomic specialists. To facilitate efforts to document biodiversity in regions lacking complete reference libraries, we developed a novel statistical approach that categorizes unidentified species as being either likely native or likely nonnative based solely on measures of nucleotide diversity. We demonstrate the utility of this approach by categorizing a large sample of specimens of terrestrial insects and spiders (collected as part of the Moorea BioCode project) using a generalized linear mixed model (GLMM). Using a training data set of known endemic (n = 45) and known introduced species (n = 102), we then estimated the likely native/nonnative status for 4,663 specimens representing an estimated 1,288 species (412 identified species), including both those specimens that were either unidentified or whose endemic/introduced status was uncertain. Using this approach, we were able to increase the number of categorized specimens by a factor of 4.4 (from 794 to 3,497), and the number of categorized species by a factor of 4.8 from (147 to 707) at a rate much greater than chance (77.6% accuracy). The study identifies phylogenetic signatures of both native and nonnative species and suggests several practical applications for this approach including monitoring biodiversity and facilitating biosecurity.
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Affiliation(s)
- Jeremy C. Andersen
- Department of Environmental Science Policy and ManagementUniversity of California Berkeley130 Mulford HallBerkeleyCalifornia94720‐3114USA
| | - Peter Oboyski
- Essig Museum of EntomologyUniversity of California BerkeleyBerkeleyCalifornia94720USA
| | - Neil Davies
- Gump South Pacific Research StationUniversity of California BerkeleyMaharepaMooreaFrench Polynesia
| | - Sylvain Charlat
- Biométrie et Biologie ÉvolutiveUMR CNRS69622VilleurbanneFrance
| | - Curtis Ewing
- Komohana Research and Extension CenterUniversity of Hawai'i at MānoaHiloHawaii96720USA
| | | | | | - Jun Ying Lim
- Department of Integrated BiologyUniversity of California Berkeley3040 Valley Life Sciences BuildingBerkeleyCalifornia94720USA
| | - Suzuki Noriyuki
- Faculty of Agriculture and Marine ScienceKochi UniversityKochiJapan
| | | | - Rosemary G. Gillespie
- Department of Environmental Science Policy and ManagementUniversity of California Berkeley130 Mulford HallBerkeleyCalifornia94720‐3114USA
| | - George K. Roderick
- Department of Environmental Science Policy and ManagementUniversity of California Berkeley130 Mulford HallBerkeleyCalifornia94720‐3114USA
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Tizard J, Patel S, Waugh J, Tavares E, Bergmann T, Gill B, Norman J, Christidis L, Scofield P, Haddrath O, Baker A, Lambert D, Millar C. DNA barcoding a unique avifauna: an important tool for evolution, systematics and conservation. BMC Evol Biol 2019; 19:52. [PMID: 30744573 PMCID: PMC6369544 DOI: 10.1186/s12862-019-1346-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 01/02/2019] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND DNA barcoding utilises a standardised region of the cytochrome c oxidase I (COI) gene to identify specimens to the species level. It has proven to be an effective tool for identification of avian samples. The unique island avifauna of New Zealand is taxonomically and evolutionarily distinct. We analysed COI sequence data in order to determine if DNA barcoding could accurately identify New Zealand birds. RESULTS We sequenced 928 specimens from 180 species. Additional Genbank sequences expanded the dataset to 1416 sequences from 211 of the estimated 236 New Zealand species. Furthermore, to improve the assessment of genetic variation in non-endemic species, and to assess the overall accuracy of our approach, sequences from 404 specimens collected outside of New Zealand were also included in our analyses. Of the 191 species represented by multiple sequences, 88.5% could be successfully identified by their DNA barcodes. This is likely a conservative estimate of the power of DNA barcoding in New Zealand, given our extensive geographic sampling. The majority of the 13 groups that could not be distinguished contain recently diverged taxa, indicating incomplete lineage sorting and in some cases hybridisation. In contrast, 16 species showed evidence of distinct intra-species lineages, some of these corresponding to recognised subspecies. For species identification purposes a character-based method was more successful than distance and phylogenetic tree-based methods. CONCLUSIONS DNA barcodes accurately identify most New Zealand bird species. However, low levels of COI sequence divergence in some recently diverged taxa limit the identification power of DNA barcoding. A small number of currently recognised species would benefit from further systematic investigations. The reference database and analysis presented will provide valuable insights into the evolution, systematics and conservation of New Zealand birds.
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Affiliation(s)
- Jacqueline Tizard
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Selina Patel
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - John Waugh
- Unitec Institute of Technology, Auckland, New Zealand
| | - Erika Tavares
- Department of Natural History, Royal Ontario Museum, 100 Queen's Park, Toronto, Ontario, M5S 2C6, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcox Street, Toronto, Ontario, M5S 3B2, Canada
- Present address: Laboratory Research Project Manager, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Tjard Bergmann
- Institute for Animal Ecology and Cell Biology, University of Veterinary Medicine Hannover Foundation, Bünteweg 17d, D-30559, Hannover, Germany
| | - Brian Gill
- Associate Emeritus, Auckland War Memorial Museum, Private Bag 92018, Auckland, 1142, New Zealand
| | - Janette Norman
- Molecular Biology Sciences Department, Museum Victoria, GPO Box 666, Melbourne, Victoria, 3001, Australia
- Present address: Graduate School, Southern Cross University, Lismore, New South Wales, Australia
| | - Les Christidis
- National Marine Science Centre, Southern Cross University, Coffs Harbour, New South Wales, Australia
| | - Paul Scofield
- Canterbury Museum, Rolleston Ave, Christchurch, 8001, New Zealand
| | - Oliver Haddrath
- Department of Natural History, Royal Ontario Museum, 100 Queen's Park, Toronto, Ontario, M5S 2C6, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcox Street, Toronto, Ontario, M5S 3B2, Canada
| | - Allan Baker
- Department of Natural History, Royal Ontario Museum, 100 Queen's Park, Toronto, Ontario, M5S 2C6, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcox Street, Toronto, Ontario, M5S 3B2, Canada
| | - David Lambert
- Environmental Futures Research Institute, Griffith University, 170 Kessels Road, Brisbane, Queensland, 4111, Australia
| | - Craig Millar
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand.
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