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Baxter JR, Kotze A, de Bruyn M, Matlou K, Labuschagne K, Mwale M. DNA barcoding of southern African mammal species and construction of a reference library for forensic application. Genome 2024. [PMID: 38996389 DOI: 10.1139/gen-2023-0050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2024]
Abstract
Combating wildlife crimes in South Africa requires accurate identification of traded species and their products. Diagnostic morphological characteristics needed to identify species are often lost when specimens are processed and customs officials lack the expertise to identify species. As a potential solution, DNA barcoding can be used to identify morphologically indistinguishable specimens in forensic cases. However, barcoding is hindered by the reliance on comprehensive, validated DNA barcode reference databases, which are currently limited. To overcome this limitation, we constructed a barcode library of cytochrome c oxidase subunit 1 and cytochrome b sequences for threatened and protected mammals exploited in southern Africa. Additionally, we included closely related or morphologically similar species and assessed the database's ability to identify species accurately. Published southern African sequences were incorporated to estimate intraspecific and interspecific variation. Neighbor-joining trees successfully discriminated 94%-95% of the taxa. However, some widespread species exhibited high intraspecific distances (>2%), suggesting geographic sub-structuring or cryptic speciation. Lack of reliable published data prevented the unambiguous discrimination of certain species. This study highlights the efficacy of DNA barcoding in species identification, particularly for forensic applications. It also highlights the need for a taxonomic re-evaluation of certain widespread species and challenging genera.
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Affiliation(s)
- J R Baxter
- South African National Biodiversity Institute, PO BOX 754, Pretoria 0001, South Africa
| | - A Kotze
- South African National Biodiversity Institute, PO BOX 754, Pretoria 0001, South Africa
- Department of Genetics, Faculty of Natural and Agricultural Sciences, University of the Free State, PO Box 339, Bloemfontein 9300, South Africa
| | - M de Bruyn
- South African National Biodiversity Institute, PO BOX 754, Pretoria 0001, South Africa
| | - K Matlou
- South African National Biodiversity Institute, PO BOX 754, Pretoria 0001, South Africa
| | - K Labuschagne
- South African National Biodiversity Institute, PO BOX 754, Pretoria 0001, South Africa
| | - M Mwale
- South African National Biodiversity Institute, PO BOX 754, Pretoria 0001, South Africa
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2
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Cicero C, Koo MS, Braker E, Abbott J, Bloom D, Campbell M, Cook JA, Demboski JR, Doll AC, Frederick LM, Linn AJ, Mayfield-Meyer TJ, McDonald DL, Nachman MW, Olson LE, Roberts D, Sikes DS, Witt CC, Wommack EA. Arctos: Community-driven innovations for managing natural and cultural history collections. PLoS One 2024; 19:e0296478. [PMID: 38820381 PMCID: PMC11142579 DOI: 10.1371/journal.pone.0296478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 04/22/2024] [Indexed: 06/02/2024] Open
Abstract
More than tools for managing physical and digital objects, museum collection management systems (CMS) serve as platforms for structuring, integrating, and making accessible the rich data embodied by natural history collections. Here we describe Arctos, a scalable community solution for managing and publishing global biological, geological, and cultural collections data for research and education. Specific goals are to: (1) Describe the core features and implementation of Arctos for a broad audience with respect to the biodiversity informatics principles that enable high quality research; (2) Highlight the unique aspects of Arctos; (3) Illustrate Arctos as a model for supporting and enhancing the Digital Extended Specimen concept; and (4) Emphasize the role of the Arctos community for improving data discovery and enabling cross-disciplinary, integrative studies within a sustainable governance model. In addition to detailing Arctos as both a community of museum professionals and a collection database platform, we discuss how Arctos achieves its richly annotated data by creating a web of knowledge with deep connections between catalog records and derived or associated data. We also highlight the value of Arctos as an educational resource. Finally, we present the financial model of fiscal sponsorship by a nonprofit organization, implemented in 2022, to ensure the long-term success and sustainability of Arctos.
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Affiliation(s)
- Carla Cicero
- Museum of Vertebrate Zoology, University of California, Berkeley, California, United States of America
| | - Michelle S. Koo
- Museum of Vertebrate Zoology, University of California, Berkeley, California, United States of America
| | - Emily Braker
- University of Colorado Museum of Natural History, University of Colorado, Boulder, Colorado, United States of America
| | - John Abbott
- Department of Museums Research and Collections and Alabama Museum of Natural History, The University of Alabama, Tuscaloosa, Alabama, United States of America
| | - David Bloom
- VertNet, Sebastopol, California, United States of America
| | - Mariel Campbell
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Joseph A. Cook
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
- Department of Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - John R. Demboski
- Denver Museum of Nature & Science, Denver, Colorado, United States of America
| | - Andrew C. Doll
- Denver Museum of Nature & Science, Denver, Colorado, United States of America
| | - Lindsey M. Frederick
- New Mexico Museum of Natural History & Science, Albuquerque, New Mexico, United States of America
| | - Angela J. Linn
- University of Alaska Museum, University of Alaska Fairbanks, Fairbanks, Alaska, United States of America
| | | | | | - Michael W. Nachman
- Museum of Vertebrate Zoology, University of California, Berkeley, California, United States of America
| | - Link E. Olson
- University of Alaska Museum, University of Alaska Fairbanks, Fairbanks, Alaska, United States of America
| | - Dawn Roberts
- Chicago Academy of Sciences, Chicago, Illinois, United States of America
| | - Derek S. Sikes
- University of Alaska Museum, University of Alaska Fairbanks, Fairbanks, Alaska, United States of America
- Department of Biology & Wildlife, University of Alaska Fairbanks, Fairbanks, Alaska, United States of America
| | - Christopher C. Witt
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
- Department of Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Elizabeth A. Wommack
- University of Wyoming Museum of Vertebrates, University of Wyoming, Laramie, Wyoming, United States of America
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3
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Díaz-Ferguson E, Chial M, Gonzalez M, Muñoz E, Chen O, Durán O, Vega AJ, Delgado CR. Building a Teleost Fish Traceability Program Based on Genetic Data from Pacific Panama Fish Markets. Animals (Basel) 2023; 13:2272. [PMID: 37508050 PMCID: PMC10376180 DOI: 10.3390/ani13142272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/30/2023] [Accepted: 07/03/2023] [Indexed: 07/30/2023] Open
Abstract
Fish tissue samples from 203 adult individuals were collected in the main ports and markets of the Pacific coast of Panama. Molecular identification based on a cytochrome oxidase I gene segment of all species was verified by GENBANK reference sequences. A total of 34 species from 14 families (Ariidae, Caranjidae, Centropomidae, Gerreidae, Haemulidae, Lobotidae, Lutjanidae, Malacanthidae, Mugilidae, Scianidae, Scombridae, Serranidae, Sphyraenidae, Stromateidae) were identified at the species level from 164 sequences. Additionally, three Caribbean species were molecularly identified among the analyzed samples (Mycteroperca xenarcha, Paralonchurus brasilensis and Lobotes surinamensis). Species diversity was slightly higher in the Gulf of Panama than in the Gulf of Chiriquí. For species with five or more individual sequences, genetic diversity and genetic connectivity parameters such as total number of haplotypes (H), haplotype diversity (Hd), and nucleotide diversity (π) were calculated. Overall, pelagic-migratory species showed higher values of genetic diversity than coastal and estuarine species with some exceptions. Connectivity between Gulf areas was compared using values of genetic distances and genetic differentiation (Fst). The high level of connectivity observed between the Gulf of Chiriqui and the Gulf of Montijo indicates the existence of a single stock in that area for the following species: Scomberomorus sierra, Caranx caninus and Lutjanus guttatus. The demographic history of the most common species was examined using Tajima's D values, suggesting population expansion for two snapper species, L. peru and L. argentiventris, having significant and higher values. Another important contribution from this research was the production of primers and dual-labeled probes for environmental DNA detection using qPCR for the five most abundant species (spotted rose snapper, yellow snapper, green jack, Pacific crevalle jack and the Pacific sierra fish). These markers represent a new set of tools for environmental DNA (eDNA) detection and molecular traceability of three commercially important fish species along the supply chain including landing sites and markets of the main fishery areas.
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Affiliation(s)
- Edgardo Díaz-Ferguson
- Coiba Scientific Station (COIBA AIP), Gustavo Lara Street, Bld. 145B, City of Knowledge, Clayton, Panama City 0843-01853, Panama
| | - Magaly Chial
- Coiba Scientific Station (COIBA AIP), Gustavo Lara Street, Bld. 145B, City of Knowledge, Clayton, Panama City 0843-01853, Panama
- Faculty of Natural and Exact Sciences, Department of Genetics and Molecular Biology, University of Panama, Panama City 0824-3366, Panama
| | - Maribel Gonzalez
- Faculty of Natural and Exact Sciences, Department of Genetics and Molecular Biology, University of Panama, Panama City 0824-3366, Panama
| | - Edgardo Muñoz
- Center of Marine Science and Limnology, Department of Marine Biology, University of Panama, Panama City 0824-01853, Panama
| | - Olga Chen
- Faculty of Natural and Exact Sciences, Department of Genetics and Molecular Biology, University of Panama, Panama City 0824-3366, Panama
| | - Ovidio Durán
- Faculty of Natural and Exact Sciences, Department of Genetics and Molecular Biology, University of Panama, Panama City 0824-3366, Panama
| | - Angel Javier Vega
- Coiba Scientific Station (COIBA AIP), Gustavo Lara Street, Bld. 145B, City of Knowledge, Clayton, Panama City 0843-01853, Panama
- School of Biology, Regional Center, University of Panama, Santiago de Veraguas 0923-00125, Panama
| | - Carlos Ramos Delgado
- Coiba Scientific Station (COIBA AIP), Gustavo Lara Street, Bld. 145B, City of Knowledge, Clayton, Panama City 0843-01853, Panama
- Faculty of Natural and Exact Sciences, Department of Genetics and Molecular Biology, University of Panama, Panama City 0824-3366, Panama
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Santos BF, Miller ME, Miklasevskaja M, McKeown JTA, Redmond NE, Coddington JA, Bird J, Miller SE, Smith A, Brady SG, Buffington ML, Chamorro ML, Dikow T, Gates MW, Goldstein P, Konstantinov A, Kula R, Silverson ND, Solis MA, deWaard SL, Naik S, Nikolova N, Pentinsaari M, Prosser SWJ, Sones JE, Zakharov EV, deWaard JR. Enhancing DNA barcode reference libraries by harvesting terrestrial arthropods at the Smithsonian's National Museum of Natural History. Biodivers Data J 2023; 11:e100904. [PMID: 38327288 PMCID: PMC10848724 DOI: 10.3897/bdj.11.e100904] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 03/30/2023] [Indexed: 02/09/2024] Open
Abstract
The use of DNA barcoding has revolutionised biodiversity science, but its application depends on the existence of comprehensive and reliable reference libraries. For many poorly known taxa, such reference sequences are missing even at higher-level taxonomic scales. We harvested the collections of the Smithsonian's National Museum of Natural History (USNM) to generate DNA barcoding sequences for genera of terrestrial arthropods previously not recorded in one or more major public sequence databases. Our workflow used a mix of Sanger and Next-Generation Sequencing (NGS) approaches to maximise sequence recovery while ensuring affordable cost. In total, COI sequences were obtained for 5,686 specimens belonging to 3,737 determined species in 3,886 genera and 205 families distributed in 137 countries. Success rates varied widely according to collection data and focal taxon. NGS helped recover sequences of specimens that failed a previous run of Sanger sequencing. Success rates and the optimal balance between Sanger and NGS are the most important drivers to maximise output and minimise cost in future projects. The corresponding sequence and taxonomic data can be accessed through the Barcode of Life Data System, GenBank, the Global Biodiversity Information Facility, the Global Genome Biodiversity Network Data Portal and the NMNH data portal.
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Affiliation(s)
- Bernardo F. Santos
- National Museum of Natural History, Smithsonian Institution, Washington, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashingtonUnited States of America
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire naturelle, CNRS, SU, EPHE, UA, Paris, FranceInstitut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire naturelle, CNRS, SU, EPHE, UAParisFrance
| | - Meredith E. Miller
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
| | - Margarita Miklasevskaja
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
| | - Jaclyn T. A. McKeown
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
| | - Niamh E. Redmond
- National Museum of Natural History, Smithsonian Institution, Washington, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashingtonUnited States of America
| | - Jonathan A. Coddington
- National Museum of Natural History, Smithsonian Institution, Washington, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashingtonUnited States of America
| | - Jessica Bird
- National Museum of Natural History, Smithsonian Institution, Washington, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashingtonUnited States of America
| | - Scott E. Miller
- National Museum of Natural History, Smithsonian Institution, Washington, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashingtonUnited States of America
| | - Ashton Smith
- National Museum of Natural History, Smithsonian Institution, Washington, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashingtonUnited States of America
| | - Seán G. Brady
- National Museum of Natural History, Smithsonian Institution, Washington, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashingtonUnited States of America
| | - Matthew L. Buffington
- Systematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Washington, United States of AmericaSystematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of AgricultureWashingtonUnited States of America
| | - M. Lourdes Chamorro
- Systematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Washington, United States of AmericaSystematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of AgricultureWashingtonUnited States of America
| | - Torsten Dikow
- National Museum of Natural History, Smithsonian Institution, Washington, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashingtonUnited States of America
| | - Michael W. Gates
- Systematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Washington, United States of AmericaSystematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of AgricultureWashingtonUnited States of America
| | - Paul Goldstein
- Systematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Washington, United States of AmericaSystematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of AgricultureWashingtonUnited States of America
| | - Alexander Konstantinov
- Systematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Washington, United States of AmericaSystematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of AgricultureWashingtonUnited States of America
| | - Robert Kula
- Systematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Washington, United States of AmericaSystematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of AgricultureWashingtonUnited States of America
| | - Nicholas D. Silverson
- National Museum of Natural History, Smithsonian Institution, Washington, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashingtonUnited States of America
| | - M. Alma Solis
- Systematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Washington, United States of AmericaSystematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of AgricultureWashingtonUnited States of America
| | - Stephanie L. deWaard
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
| | - Suresh Naik
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
- Department of Integrative Biology, University of Guelph, Guelph, CanadaDepartment of Integrative Biology, University of GuelphGuelphCanada
| | - Nadya Nikolova
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
| | - Mikko Pentinsaari
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
| | - Sean W. J. Prosser
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
| | - Jayme E. Sones
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
| | - Evgeny V. Zakharov
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
- Department of Integrative Biology, University of Guelph, Guelph, CanadaDepartment of Integrative Biology, University of GuelphGuelphCanada
| | - Jeremy R. deWaard
- National Museum of Natural History, Smithsonian Institution, Washington, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashingtonUnited States of America
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
- School of Environmental Sciences, University of Guelph, Guelph, CanadaSchool of Environmental Sciences, University of GuelphGuelphCanada
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5
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Wu YH, Hou SB, Yuan ZY, Jiang K, Huang RY, Wang K, Liu Q, Yu ZB, Zhao HP, Zhang BL, Chen JM, Wang LJ, Stuart BL, Chambers EA, Wang YF, Gao W, Zou DH, Yan F, Zhao GG, Fu ZX, Wang SN, Jiang M, Zhang L, Ren JL, Wu YY, Zhang LY, Yang DC, Jin JQ, Yin TT, Li JT, Zhao WG, Murphy RW, Huang S, Guo P, Zhang YP, Che J. DNA barcoding of Chinese snakes reveals hidden diversity and conservation needs. Mol Ecol Resour 2023. [PMID: 36924341 DOI: 10.1111/1755-0998.13784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 02/25/2023] [Accepted: 03/10/2023] [Indexed: 03/17/2023]
Abstract
DNA barcoding has greatly facilitated studies of taxonomy, biodiversity, biological conservation, and ecology. Here, we establish a reliable DNA barcoding library for Chinese snakes, unveiling hidden diversity with implications for taxonomy, and provide a standardized tool for conservation management. Our comprehensive study includes 1638 cytochrome c oxidase subunit I (COI) sequences from Chinese snakes that correspond to 17 families, 65 genera, 228 named species (80.6% of named species) and 36 candidate species. A barcode gap analysis reveals gaps, where all nearest neighbour distances exceed maximum intraspecific distances, in 217 named species and all candidate species. Three species-delimitation methods (ABGD, sGMYC, and sPTP) recover 320 operational taxonomic units (OTUs), of which 192 OTUs correspond to named and candidate species. Twenty-eight other named species share OTUs, such as Azemiops feae and A. kharini, Gloydius halys, G. shedaoensis, and G. intermedius, and Bungarus multicinctus and B. candidus, representing inconsistencies most probably caused by imperfect taxonomy, recent and rapid speciation, weak taxonomic signal, introgressive hybridization, and/or inadequate phylogenetic signal. In contrast, 43 species and candidate species assign to two or more OTUs due to having large intraspecific distances. If most OTUs detected in this study reflect valid species, including the 36 candidate species, then 30% more species would exist than are currently recognized. Several OTU divergences associate with known biogeographic barriers, such as the Taiwan Strait. In addition to facilitating future studies, this reliable and relatively comprehensive reference database will play an important role in the future monitoring, conservation, and management of Chinese snakes.
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Affiliation(s)
- Yun-He Wu
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Shao-Bing Hou
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, Yunnan, 650204, China
| | - Zhi-Yong Yuan
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Ke Jiang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Ru-Yi Huang
- Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Kai Wang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Qin Liu
- Faculty of Agriculture, Forest and Food Engineering, Yibin University, Yibin, Sichuan, 644007, China
| | - Zhong-Bin Yu
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Hai-Peng Zhao
- School of Life Science, Henan University, Kaifeng, Henan, 475001, China
| | - Bao-Lin Zhang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Jin-Min Chen
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Li-Jun Wang
- School of Life Sciences, Hainan Normal University, Haikou, Hainan, 571158, China
| | - Bryan L Stuart
- Section of Research & Collections, North Carolina Museum of Natural Sciences, Raleigh, North Carolina, 27601, USA
| | - E Anne Chambers
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, California, 94720, USA
| | - Yu-Fan Wang
- Zhejiang Forest Resource Monitoring Center, Hangzhou, Zhejiang, 310020, China
| | - Wei Gao
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Da-Hu Zou
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- College of Science, Tibet University, Lhasa, Tibet, 850000, China
| | - Fang Yan
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Gui-Gang Zhao
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Zhong-Xiong Fu
- Yunnan Senye Biotechnology Co., Ltd, Xishuangbanna, Yunnan, 666100, China
| | - Shao-Neng Wang
- Bureau of Guangxi Mao'er Mountain Nature Reserve, Guilin, Guangxi, 541316, China
| | - Ming Jiang
- Gongshan Bureau of Gaoligongshan National Nature Reserve, Gongshan, Yunnan, 650224, China
| | - Liang Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, Guangdong, 510260, China
| | - Jin-Long Ren
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, 610041, China
| | - Ya-Yong Wu
- Faculty of Agriculture, Forest and Food Engineering, Yibin University, Yibin, Sichuan, 644007, China
| | - Lu-Yang Zhang
- Beijing Mountains & Seas Eco Technology Co. Ltd, Beijing, 101100, China
| | - Dian-Cheng Yang
- Anhui Province Key Laboratory of the Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, 241000, China
| | - Jie-Qiong Jin
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Ting-Ting Yin
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Jia-Tang Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, 610041, China
| | - Wen-Ge Zhao
- College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang, 150025, China
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- Reptilia Zoo and Education Centre, Vaughn, Ontario, L4K 2N6, Canada
| | - Song Huang
- Anhui Province Key Laboratory of the Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, 241000, China
| | - Peng Guo
- Faculty of Agriculture, Forest and Food Engineering, Yibin University, Yibin, Sichuan, 644007, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
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6
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Mulcahy DG, Ibáñez R, Jaramillo CA, Crawford AJ, Ray JM, Gotte SW, Jacobs JF, Wynn AH, Gonzalez-Porter GP, McDiarmid RW, Crombie RI, Zug GR, de Queiroz K. DNA barcoding of the National Museum of Natural History reptile tissue holdings raises concerns about the use of natural history collections and the responsibilities of scientists in the molecular age. PLoS One 2022; 17:e0264930. [PMID: 35245325 PMCID: PMC8896674 DOI: 10.1371/journal.pone.0264930] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 02/22/2022] [Indexed: 01/09/2023] Open
Abstract
Natural history collections are essential to a wide variety of studies in biology because they maintain large collections of specimens and associated data, including genetic material (e.g., tissues) for DNA sequence data, yet they are currently under-funded and collection staff have high workloads. With the advent of aggregate databases and advances in sequencing technologies, there is an increased demand on collection staff for access to tissue samples and associated data. Scientists are rapidly developing large DNA barcode libraries, DNA sequences of specific genes for species across the tree of life, in order to document and conserve biodiversity. In doing so, mistakes are made. For instance, inconsistent taxonomic information is commonly taken from different lending institutions and deposited in data repositories, such as the Barcode of Life Database (BOLD) and GenBank, despite explicit disclaimers regarding the need for taxonomic verification by the lending institutions. Such errors can have profound effects on subsequent research based on these mis-labelled sequences in data repositories. Here, we present the production of a large DNA barcode library of reptiles from the National Museum of Natural History tissue holdings. The library contains 2,758 sequences (2,205 COI and 553 16S) from 2260 specimens (four crocodilians, 37 turtles, and 2,219 lizards, including snakes), representing 583 named species, from 52 countries. In generating this library, we noticed several common mistakes made by scientists depositing DNA barcode data in public repositories (e.g., BOLD and GenBank). Our goal is to raise awareness of these concerns and offer advice to avoid such mistakes in the future to maintain accurate DNA barcode libraries to properly document Earth’s biodiversity.
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Affiliation(s)
- Daniel G. Mulcahy
- Division of Amphibians and Reptiles, Department of Vertebrate Zoology, National Museum of Natural History, Washington, DC, United States of America
- * E-mail:
| | - Roberto Ibáñez
- Smithsonian Tropical Research Institute, Panama City, Republic of Panama
- Sistema Nacional de Investigación, SENACYT, Panamá City, República de Panamá
- Departamento de Zoología, Universidad de Panamá, Panamá City, República de Panamá
| | - Cesar A. Jaramillo
- Smithsonian Tropical Research Institute, Panama City, Republic of Panama
- Departamento de Histología y Neuroanatomía, Facultad de Medicina, Universidad de Panamá, Panamá City, República de Panamá
| | - Andrew J. Crawford
- Smithsonian Tropical Research Institute, Panama City, Republic of Panama
- Department of Biological Sciences, Museo de Historia Natural C.J. Marinkelle, Universidad de los Andes, Bogotá, Colombia
| | - Julie M. Ray
- Department of Biology, University of Nevada, Reno, Nevada, United States of America
| | - Steve W. Gotte
- Division of Amphibians and Reptiles, Department of Vertebrate Zoology, National Museum of Natural History, Washington, DC, United States of America
| | - Jeremy F. Jacobs
- Division of Amphibians and Reptiles, Department of Vertebrate Zoology, National Museum of Natural History, Washington, DC, United States of America
| | - Addison H. Wynn
- Division of Amphibians and Reptiles, Department of Vertebrate Zoology, National Museum of Natural History, Washington, DC, United States of America
| | | | - Roy W. McDiarmid
- Division of Amphibians and Reptiles, Department of Vertebrate Zoology, National Museum of Natural History, Washington, DC, United States of America
| | - Ronald I. Crombie
- Department of Herpetology, California Academy of Sciences, San Francisco, California, United States of America
| | - George R. Zug
- Division of Amphibians and Reptiles, Department of Vertebrate Zoology, National Museum of Natural History, Washington, DC, United States of America
| | - Kevin de Queiroz
- Division of Amphibians and Reptiles, Department of Vertebrate Zoology, National Museum of Natural History, Washington, DC, United States of America
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Pragmatic Applications and Universality of DNA Barcoding for Substantial Organisms at Species Level: A Review to Explore a Way Forward. BIOMED RESEARCH INTERNATIONAL 2022; 2022:1846485. [PMID: 35059459 PMCID: PMC8766189 DOI: 10.1155/2022/1846485] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 12/06/2021] [Indexed: 01/04/2023]
Abstract
DNA barcodes are regarded as hereditary succession codes that serve as a recognition marker to address several queries relating to the identification, classification, community ecology, and evolution of certain functional traits in organisms. The mitochondrial cytochrome c oxidase 1 (CO1) gene as a DNA barcode is highly efficient for discriminating vertebrate and invertebrate animal species. Similarly, different specific markers are used for other organisms, including ribulose bisphosphate carboxylase (rbcL), maturase kinase (matK), transfer RNA-H and photosystem II D1-ApbsArabidopsis thaliana (trnH-psbA), and internal transcribed spacer (ITS) for plant species; 16S ribosomal RNA (16S rRNA), elongation factor Tu gene (Tuf gene), and chaperonin for bacterial strains; and nuclear ITS for fungal strains. Nevertheless, the taxon coverage of reference sequences is far from complete for genus or species-level identification. Applying the next-generation sequencing approach to the parallel acquisition of DNA barcode sequences could greatly expand the potential for library preparation or accurate identification in biodiversity research. Overall, this review articulates on the DNA barcoding technology as applied to different organisms, its universality, applicability, and innovative approach to handling DNA-based species identification.
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Stöck M, Dedukh D, Reifová R, Lamatsch DK, Starostová Z, Janko K. Sex chromosomes in meiotic, hemiclonal, clonal and polyploid hybrid vertebrates: along the 'extended speciation continuum'. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200103. [PMID: 34304588 PMCID: PMC8310718 DOI: 10.1098/rstb.2020.0103] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/12/2021] [Indexed: 12/15/2022] Open
Abstract
We review knowledge about the roles of sex chromosomes in vertebrate hybridization and speciation, exploring a gradient of divergences with increasing reproductive isolation (speciation continuum). Under early divergence, well-differentiated sex chromosomes in meiotic hybrids may cause Haldane-effects and introgress less easily than autosomes. Undifferentiated sex chromosomes are more susceptible to introgression and form multiple (or new) sex chromosome systems with hardly predictable dominance hierarchies. Under increased divergence, most vertebrates reach complete intrinsic reproductive isolation. Slightly earlier, some hybrids (linked in 'the extended speciation continuum') exhibit aberrant gametogenesis, leading towards female clonality. This facilitates the evolution of various allodiploid and allopolyploid clonal ('asexual') hybrid vertebrates, where 'asexuality' might be a form of intrinsic reproductive isolation. A comprehensive list of 'asexual' hybrid vertebrates shows that they all evolved from parents with divergences that were greater than at the intraspecific level (K2P-distances of greater than 5-22% based on mtDNA). These 'asexual' taxa inherited genetic sex determination by mostly undifferentiated sex chromosomes. Among the few known sex-determining systems in hybrid 'asexuals', female heterogamety (ZW) occurred about twice as often as male heterogamety (XY). We hypothesize that pre-/meiotic aberrations in all-female ZW-hybrids present Haldane-effects promoting their evolution. Understanding the preconditions to produce various clonal or meiotic allopolyploids appears crucial for insights into the evolution of sex, 'asexuality' and polyploidy. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)'.
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Affiliation(s)
- Matthias Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries - IGB (Forschungsverbund Berlin), Müggelseedamm 301, 12587 Berlin, Germany
- Amphibian Research Center, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Dmitrij Dedukh
- Institute of Animal Physiology and Genetics, Laboratory of Fish Genetics, The Czech Academy of Sciences, 277 21 Libechov, Czech Republic
| | - Radka Reifová
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, Prague 2, 128 00, Czech Republic
| | - Dunja K. Lamatsch
- Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Zuzana Starostová
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, Prague 2, 128 00, Czech Republic
| | - Karel Janko
- Institute of Animal Physiology and Genetics, Laboratory of Fish Genetics, The Czech Academy of Sciences, 277 21 Libechov, Czech Republic
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, 701 03 Ostrava, Czech Republic
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10
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Appleyard SA, Maher S, Pogonoski JJ, Bent SJ, Chua XY, McGrath A. Assessing DNA for fish identifications from reference collections: the good, bad and ugly shed light on formalin fixation and sequencing approaches. JOURNAL OF FISH BIOLOGY 2021; 98:1421-1432. [PMID: 33484178 DOI: 10.1111/jfb.14687] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 01/12/2021] [Accepted: 01/19/2021] [Indexed: 06/12/2023]
Abstract
Natural history collections are repositories of biodiversity and are potentially used by molecular ecologists for comparative taxonomic, phylogenetic, biogeographic and forensic purposes. Specimens in fish collections are preserved using a combination of methods with many fixed in formalin and then preserved in ethanol for long-term storage. Formalin fixation damages DNA, thereby limiting genetic analyses. In this study, the authors compared the DNA barcoding and identification success for frozen and formalin-fixed tissues obtained from specimens in the CSIRO Australian National Fish Collection. They studied 230 samples from fishes (consisting of >160 fish species). An optimized formalin-fixed, paraffin-embedded DNA extraction method resulted in usable DNA from degraded tissues. Four mini barcoding assays of the mitochondrial DNA (mtDNA) were characterized with Sanger and Illumina amplicon sequencing. In the good quality DNA (without exposure to formalin), up to 88% of the specimens were correctly matched at the species level using the cytochrome oxidase subunit 1 (COI) mini barcodes, whereas up to 58% of the specimens exposed to formalin for less than 8 weeks were correctly identified to species. In contrast, 16S primers provided higher amplification success with formalin-exposed tissues, although the COI gene was more successful for identification. Importantly, the authors found that DNA of a certain size and quality can be amplified and sequenced despite exposure to formalin, and Illumina sequencing provided them with greater power of resolution for taxa identification even when there was little DNA present. Overall, within parameter constraints, this study highlights the possibilities of recovering DNA barcodes for identification from formalin-fixed fish specimens, and the authors provide guidelines for when successful identification could be expected.
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Affiliation(s)
- Sharon A Appleyard
- CSIRO Australian National Fish Collection, National Research Collections Australia, Hobart, Tasmania, Australia
- CSIRO Environomics Future Science Platform, Canberra, Australian Capital Territory, Australia
| | - Safia Maher
- CSIRO Australian National Fish Collection, National Research Collections Australia, Hobart, Tasmania, Australia
- CSIRO Environomics Future Science Platform, Canberra, Australian Capital Territory, Australia
| | - John J Pogonoski
- CSIRO Australian National Fish Collection, National Research Collections Australia, Hobart, Tasmania, Australia
- CSIRO Environomics Future Science Platform, Canberra, Australian Capital Territory, Australia
| | - Stephen J Bent
- CSIRO Environomics Future Science Platform, Canberra, Australian Capital Territory, Australia
- Data 61, CSIRO, Brisbane, Queensland, Australia
| | - Xin-Yi Chua
- CSIRO Environomics Future Science Platform, Canberra, Australian Capital Territory, Australia
- Data 61, CSIRO, Brisbane, Queensland, Australia
- School of Electrical Engineering and Computer Science, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Annette McGrath
- CSIRO Environomics Future Science Platform, Canberra, Australian Capital Territory, Australia
- Data 61, CSIRO, Brisbane, Queensland, Australia
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11
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Kundu S, Lalremsanga HT, Biakzuala L, Decemson H, Muansanga L, Tyagi K, Chandra K, Kumar V. Genetic diversity of the Pegu Rice Frog, Microhyla berdmorei (Anura: Microhylidae) based on mitochondrial DNA. Mitochondrial DNA B Resour 2021; 6:1586-1591. [PMID: 34212080 PMCID: PMC8218842 DOI: 10.1080/23802359.2021.1920504] [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: 02/10/2021] [Accepted: 04/18/2021] [Indexed: 11/18/2022] Open
Abstract
The Pegu Rice Frog, Microhyla berdmorei is distributed across ten Asian countries. However, the DNA barcoding information (COI gene) is restricted to only Southeast Asian countries. Here, we sampled a specimen of M. berdmorei in Mizoram state, northeast India to allow the genetic diversity of the species across its range. We generated both COI and 16S ribosomal RNA sequences of the studied species to check the population genetic diversity. The Bayesian analyses clearly discriminate M. berdmorei from its sister species Microhyla pulchra. The present datasets of M. berdmorei also revealed 11 and 19 haplotypes with high uncorrected pairwise genetic distances in COI (3.8-11.8%) and 16S rRNA (0-4.6%) gene, respectively. Owing to the high intra-species genetic distances and different haplotypes with sufficient mutational steps in both mitochondrial genes, this study affirms the existence of M. berdmorei species complex or cryptic diversity within its range distribution in South and Southeast Asia.
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Affiliation(s)
- Shantanu Kundu
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Hmar Tlawmte Lalremsanga
- Developmental Biology and Herpetology Laboratory, Department of Zoology, Mizoram University, Aizawl, Mizoram, India
| | - Lal Biakzuala
- Developmental Biology and Herpetology Laboratory, Department of Zoology, Mizoram University, Aizawl, Mizoram, India
| | - Ht. Decemson
- Developmental Biology and Herpetology Laboratory, Department of Zoology, Mizoram University, Aizawl, Mizoram, India
| | - Lal Muansanga
- Developmental Biology and Herpetology Laboratory, Department of Zoology, Mizoram University, Aizawl, Mizoram, India
| | - Kaomud Tyagi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Kailash Chandra
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Vikas Kumar
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
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12
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Abstract
A new species of the genus Atelopus, Atelopus fronterizo sp. nov., from eastern Panama is described herein based on molecular, morphological, and bioacoustic evidence. The new species can be distinguished from its congeners occurring in the region by a combination of the following characters: (1) phalangeal reduction in thumb; (2) SVL (females only) (35.1-50.1; n=13), HW/SVL (0.23-0.34; n=59), EYND/HW (0.27-0.39; n=60), TIBL/SVL (0.41-0.56; n=58), and HAL/SVL (0.22-0.28; n=49); (3) dorsal color pattern with green or yellow background and extensive dark olive blotches forming transversal bands or mottling; (4) advertisement call duration 176-235 ms with 19-34 pulses, average pulse rate 131.69 pulses/s, and dominant frequency 2 422.50-2 606.50 Hz. The new species is nested within the Central American clade of Atelopus. The minimum Kimura-2-parameter (K2P) genetic divergence between Atelopus fronterizo sp. nov. and its most phylogenetically similar congeners ( A. certus and A. glyphus) is >2.6% for 16S and >4.9% for COI (Table 1). The phylogenetic relationship is strongly supported by ultrafast bootstrap values for the maximum-likelihood trees of both genetic markers (16S, 96; COI, 100, Figure 1A). Bayesian analysis of the concatenated sequences resulted in a tree with similar topology and high posterior probability support (0.99; Supplementary Figure S1). In addition, haplotype networks inferred from COI and 16S (Supplementary Figure S2) showed a well-separated clade containing the new species (two for COI, four for 16S). The number of mutational steps between haplotypes for the new species samples is very low (1-4 in 16S; one in COI), and the minimum number of mutational steps from the nearest species is nine for 16S (distance to A. certus) and 28 for COI (distance to A. glyphus).
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Affiliation(s)
- Milan Veselý
- Department of Zoology, Faculty of Natural Sciences, Palacky University, Olomouc 77146, Czech Republic
| | - Abel Batista
- Universidad Autónoma de Chiriquí, Ciudad Universitaria El Cabrero David, Chiriquí 427, Panamá.,Asociación ADOPTA el Bosque Panamá, Gamboa 119x, Panamá.,Fundación Los Naturalistas, David, Chiriquí 426-01459, Panamá. E-mail:
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13
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Beyond the comfort zone: amphibian diversity and distribution in the West Sahara-Sahel using mtDNA and nuDNA barcoding and spatial modelling. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01331-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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14
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Li Y, Wang Y, Bai Y, Lv Y, Xiong J. Mitochondrial genome of Diploderma micangshanense and its implications for phylogeny of the genus Diploderma. Mitochondrial DNA B Resour 2021; 6:798-802. [PMID: 33763583 PMCID: PMC7954499 DOI: 10.1080/23802359.2021.1882908] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The lizard Diploderma micangshanense, which belongs to the family Agamidae is endemic to China. Here, we determined the complete mitogenome of D. micangshanense using an Illumina Hiseq X Ten sequencer. This mitogenome’s structure is a typical circular molecule of 16,467 bp in length, consisting of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and a control region. The overall base composition of D. micangshanensis is 34.1% A, 23.64% T, 13.62% C, and 28.64% G with a slight AT bias of 57.74%. Most mitochondrial genes except ND6 and seven tRNAs were encoded on the heavy strand. Notably, the trnP gene was encoded on the heavy strand instead of its typical light strand position, providing an example of gene inversion in vertebrate mitogenomes. Phylogenetic analysis indicated that D. micangshanensis had a close relationship with D. zhaoermii.
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Affiliation(s)
- Yanping Li
- Key Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, College of Life Sciences, Neijiang Normal University, Neijiang, China
| | - Yongming Wang
- Key Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, College of Life Sciences, Neijiang Normal University, Neijiang, China
| | - Yinlong Bai
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Yunyun Lv
- Key Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, College of Life Sciences, Neijiang Normal University, Neijiang, China
| | - Jianli Xiong
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
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15
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D'Ercole J, Prosser SWJ, Hebert PDN. A SMRT approach for targeted amplicon sequencing of museum specimens (Lepidoptera)-patterns of nucleotide misincorporation. PeerJ 2021; 9:e10420. [PMID: 33520432 PMCID: PMC7811786 DOI: 10.7717/peerj.10420] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 11/02/2020] [Indexed: 12/28/2022] Open
Abstract
Natural history collections are a valuable resource for molecular taxonomic studies and for examining patterns of evolutionary diversification, particularly in the case of rare or extinct species. However, the recovery of sequence information is often complicated by DNA degradation. This article describes use of the Sequel platform (Pacific Biosciences) to recover the 658 bp barcode region of the mitochondrial cytochrome c oxidase I (COI) gene from 380 butterflies with an average age of 50 years. Nested multiplex PCR was employed for library preparation to facilitate sequence recovery from extracts with low concentrations of highly degraded DNA. By employing circular consensus sequencing (CCS) of short amplicons (circa 150 bp), full-length barcodes could be assembled without a reference sequence, an important advance from earlier protocols which required reference sequences to guide contig assembly. The Sequel protocol recovered COI sequences (499 bp on average) from 318 of 380 specimens (84%), much higher than for Sanger sequencing (26%). Because each read derives from a single molecule, it was also possible to quantify the incidence of substitutions arising from DNA damage. In agreement with past work on sequence changes induced by DNA degradation, the transition C/G → T/A was the most prevalent category of change, but its rate of occurrence (4.58E−4) was so low that it did not impede the recovery of reliable sequences. Because the current protocol recovers COI sequence from most museum specimens, and because sequence fidelity is unaffected by nucleotide misincorporations, large-scale sequence characterization of museum specimens is feasible.
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Affiliation(s)
- Jacopo D'Ercole
- Centre for Biodiversity Genomics, Guelph, ON, Canada.,Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | | | - Paul D N Hebert
- Centre for Biodiversity Genomics, Guelph, ON, Canada.,Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
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16
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Genetic variation of blue-tongue skinks of the genus Tiliqua (Squamata: Scincidae) from New Guinea and Wallacea. Biologia (Bratisl) 2021. [DOI: 10.2478/s11756-020-00646-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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17
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Identification and Species Delimitation of the Enigmatic Marsh Frog Pulchrana rawa (Matsui, Mumpuni, and Hamidy, 2012): Second Confirmed Specimen and First Country Record for Malaysia. J HERPETOL 2020. [DOI: 10.1670/19-132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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18
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Molecular and morphometric divergence of four species of butterflies (Nymphalidae and Pieridae) from the Western Himalaya, India. Mol Biol Rep 2020; 47:8687-8699. [PMID: 33070284 DOI: 10.1007/s11033-020-05913-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 10/10/2020] [Indexed: 10/23/2022]
Abstract
Morphometric and molecular divergence among four butterfly species of the families Nymphalidae and Pieridae from the western Himalaya region were investigated using molecular tools, traditional morphometric measures and a truss network system. The considered species were Danaus chrysippus, Vanessa cardui, Pieris brassicae and Pieris canidia. Traditional taxonomy is sometimes unable to discriminate cryptic species or species that have close morphological features. Although taxonomists carefully examine external body features to differentiate the species; however, there is a risk for misidentification during a visual assessment of cryptic species. Therefore, we aimed to use the truss network system of 14 morphological landmarks interconnected to yield 90 variables about molecular taxonomy. Principal component analysis (PCA), discriminant function analysis (DFA) and cluster analysis (CA) were employed to determine morphometric variations. In the traditional analysis, 79, 68, 16 and 5 characters out of 90 were found significant (p < 0.05) for D. chrysippus, V. cardui, P. brassicae and P. canidia, respectively. One to seven principal components were extracted through PCA; they explained 87.5-100% of the total variance in samples. Notably, DFA correctly classified 100% of the original grouped cases and 100% of the cross-validated grouped cases. However, the variations were not the same for the two different methods (truss and traditional) employed for the analysis. We correctly identified all the species; the interspecies sequence divergence was between 0.1034 and 0.1398, and the intra-species sequence divergence range was 0.0001 to 0.0128 using the Cytochrome c oxidase subunit-I (COI) gene. The present study provides useful information about the application and complementary role of traditional with truss morphometric analysis for the precise identification and classification of the selected species.
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Kundu S, Lalremsanga HT, Biakzuala L, Chandra K, Kumar V. DNA barcoding reveals distinct population of Dopasia gracilis (Squamata: Anguidae) in Mizoram, Northeast India. Mitochondrial DNA B Resour 2020; 5:3229-3233. [PMID: 33458121 PMCID: PMC7782129 DOI: 10.1080/23802359.2020.1810147] [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: 05/15/2020] [Accepted: 08/11/2020] [Indexed: 10/29/2022] Open
Abstract
The DNA barcode data of Asian Glass Lizard, Dopasia gracilis, is limited in the global database, especially from India. The present study aimed to generate a barcode sequence of morphologically identified D. gracilis from the Mizoram state in northeast India and compared with other Anguidae species. The studied species showed monophyletic clustering in the Bayesian analysis (BA) phylogeny with strong posterior probability support and also discriminated sufficient Kimura 2 parameter genetic distances. The barcode data of D. gracilis revealed high intra-species genetic variability and formed two clusters in BA phylogeny. The Templeton, Crandall, and Sing network also depicted four different haplotypes within the barcode sequences of D. gracilis. The DNA sequences generated from northeast India showed 6.5-6.6% and 7.3% genetic distances with the sequences generated from Yunnan Province and Tibetan Plateau, respectively. Considering the high genetic distances, multiple clustering, and distinct haplotypes, the present study assumed the presence of possible cryptic diversity of D. gracilis in the Indochina sub-region and a distinct population in northeast India. We recommended the generation of more DNA information from different localities to elucidate the actual diversity of D. gracilis within the known range distribution.
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Affiliation(s)
- Shantanu Kundu
- Molecular Systematics Division, Zoological Survey of India, Centre for DNA Taxonomy, Kolkata, India
| | - Hmar Tlawmte Lalremsanga
- Developmental Biology and Herpetology Laboratory, Department of Zoology, Mizoram University, Aizawl, India
| | - Lal Biakzuala
- Developmental Biology and Herpetology Laboratory, Department of Zoology, Mizoram University, Aizawl, India
| | - Kailash Chandra
- Molecular Systematics Division, Zoological Survey of India, Centre for DNA Taxonomy, Kolkata, India
| | - Vikas Kumar
- Molecular Systematics Division, Zoological Survey of India, Centre for DNA Taxonomy, Kolkata, India
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20
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Kundu S, Lalremsanga HT, Purkayastha J, Biakzuala L, Chandra K, Kumar V. DNA barcoding elucidates the new altitude record and range-extension of lesser-known bullfrog ( Hoplobatrachus litoralis) in northeast India. Mitochondrial DNA B Resour 2020. [DOI: 10.1080/23802359.2020.1787259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
- Shantanu Kundu
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Hmar Tlawmte Lalremsanga
- Developmental Biology and Herpetology Laboratory, Department of Zoology, Mizoram University, Mizoram, India
| | | | - Lal Biakzuala
- Developmental Biology and Herpetology Laboratory, Department of Zoology, Mizoram University, Mizoram, India
| | - Kailash Chandra
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Vikas Kumar
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
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21
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Kundu S, Lalremsanga HT, Rahman MM, Ahsan MF, Biakzuala L, Kumar V, Chandra K, Siddiki AMAMZ. DNA barcoding elucidates the population genetic diversity of venomous cobra species (Reptilia: Elapidae) in Indo-Bangladesh region. Mitochondrial DNA B Resour 2020. [DOI: 10.1080/23802359.2020.1778552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Affiliation(s)
- Shantanu Kundu
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Hmar Tlawmte Lalremsanga
- Developmental Biology and Herpetology Laboratory, Department of Zoology, Mizoram University, Aizawl, India
| | - Md. Mizanur Rahman
- Venom Research Centre Bangladesh, Department of Medicine, Chittagong Medical College, Chattogram, Bangladesh
| | - Md. Farid Ahsan
- Department of Zoology, University of Chittagong, Chattogram, Bangladesh
| | - Lal Biakzuala
- Developmental Biology and Herpetology Laboratory, Department of Zoology, Mizoram University, Aizawl, India
| | - Vikas Kumar
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Kailash Chandra
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - A. M. A. M. Zonaed Siddiki
- Department of Pathology and Parasitology, Chittagong Veterinary and Animal Sciences University, Chattogram, Bangladesh
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22
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Bohmann K, Mirarab S, Bafna V, Gilbert MTP. Beyond DNA barcoding: The unrealized potential of genome skim data in sample identification. Mol Ecol 2020; 29:2521-2534. [PMID: 32542933 PMCID: PMC7496323 DOI: 10.1111/mec.15507] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 06/03/2020] [Accepted: 06/05/2020] [Indexed: 02/06/2023]
Abstract
Genetic tools are increasingly used to identify and discriminate between species. One key transition in this process was the recognition of the potential of the ca 658bp fragment of the organelle cytochrome c oxidase I (COI) as a barcode region, which revolutionized animal bioidentification and lead, among others, to the instigation of the Barcode of Life Database (BOLD), containing currently barcodes from >7.9 million specimens. Following this discovery, suggestions for other organellar regions and markers, and the primers with which to amplify them, have been continuously proposed. Most recently, the field has taken the leap from PCR-based generation of DNA references into shotgun sequencing-based "genome skimming" alternatives, with the ultimate goal of assembling organellar reference genomes. Unfortunately, in genome skimming approaches, much of the nuclear genome (as much as 99% of the sequence data) is discarded, which is not only wasteful, but can also limit the power of discrimination at, or below, the species level. Here, we advocate that the full shotgun sequence data can be used to assign an identity (that we term for convenience its "DNA-mark") for both voucher and query samples, without requiring any computationally intensive pretreatment (e.g. assembly) of reads. We argue that if reference databases are populated with such "DNA-marks," it will enable future DNA-based taxonomic identification to complement, or even replace PCR of barcodes with genome skimming, and we discuss how such methodology ultimately could enable identification to population, or even individual, level.
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Affiliation(s)
- Kristine Bohmann
- Section for Evolutionary GenomicsThe GLOBE InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Siavash Mirarab
- Department of Electrical and Computer EngineeringUniversity of CaliforniaSan DiegoCAUSA
| | - Vineet Bafna
- Department of Computer Science and EngineeringUniversity of CaliforniaSan DiegoCAUSA
| | - M. Thomas P. Gilbert
- Section for Evolutionary GenomicsThe GLOBE InstituteUniversity of CopenhagenCopenhagenDenmark
- Center for Evolutionary HologenomicsThe GLOBE InstituteUniversity of CopenhagenCopenhagenDenmark
- NTNU University MuseumTrondheimNorway
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23
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Bell RC, Mulcahy DG, Gotte SW, Maley AJ, Mendoza C, Steffensen G, Barron II JC, Hyman O, Flint W, Wynn A, Mcdiarmid RW, Mcleod DS. The Type Locality Project: collecting genomic-quality, topotypic vouchers and training the next generation of specimen-based researchers. SYST BIODIVERS 2020. [DOI: 10.1080/14772000.2020.1769224] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Rayna C. Bell
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Daniel G. Mulcahy
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Steve W. Gotte
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
- U. S. Geological Survey, Patuxent Wildlife Research Center, National Museum of Natural History, Museum Support Center, Suitland, MD 20746, USA
| | - Abigail J. Maley
- Biology Department, Eastern Mennonite University, Harrisonburg, VA 22802, USA
- Division of Integrated Sciences, Wilson College, Chambersburg, PA 17201, USA
| | - Cerrie Mendoza
- Biology Department, Eastern Mennonite University, Harrisonburg, VA 22802, USA
| | - Gregory Steffensen
- Department of Biology, James Madison University, Harrisonburg, VA 22807, USA
| | - Joseph C. Barron II
- Department of Fish and Wildlife Conservation, Virginia Tech, Blacksburg, VA 24060, USA
| | - Oliver Hyman
- Department of Biology, James Madison University, Harrisonburg, VA 22807, USA
| | - William Flint
- Department of Biology, James Madison University, Harrisonburg, VA 22807, USA
| | - Addison Wynn
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Roy W. Mcdiarmid
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
- U. S. Geological Survey, Patuxent Wildlife Research Center, National Museum of Natural History, Museum Support Center, Suitland, MD 20746, USA
| | - David S. Mcleod
- Department of Biology, James Madison University, Harrisonburg, VA 22807, USA
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24
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Kundu S, Lalremsanga HT, Tyagi K, Biakzuala L, Kumar V, Chandra K. Mitochondrial DNA discriminates distinct population of two deadly snakes (Reptilia: Elapidae) in Northeast India. Mitochondrial DNA B Resour 2020. [DOI: 10.1080/23802359.2020.1742210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Affiliation(s)
- Shantanu Kundu
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | | | - Kaomud Tyagi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Lal Biakzuala
- Department of Zoology, Mizoram University, Aizawl, India
| | - Vikas Kumar
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Kailash Chandra
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
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25
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Zangl L, Daill D, Schweiger S, Gassner G, Koblmüller S. A reference DNA barcode library for Austrian amphibians and reptiles. PLoS One 2020; 15:e0229353. [PMID: 32163447 PMCID: PMC7067431 DOI: 10.1371/journal.pone.0229353] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 02/04/2020] [Indexed: 11/19/2022] Open
Abstract
In the last few years, DNA barcoding became an established method for species identification in biodiversity inventories and monitoring studies. Such studies depend on the access to a comprehensive reference data base, covering all relevant taxa. Here we present a comprehensive DNA barcode inventory of all amphibian and reptile species native to Austria, except for the putatively extinct Vipera ursinii rakosiensis and Lissotriton helveticus, which has been only recently reported for the very western edge of Austria. A total of 194 DNA barcodes were generated in the framework of the Austrian Barcode of Life (ABOL) initiative. Species identification via DNA barcodes was successful for most species, except for the hybridogenetic species complex of water frogs (Pelophylax spp.) and the crested newts (Triturus spp.), in areas of sympatry. However, DNA barcoding also proved powerful in detecting deep conspecific lineages, e.g. within Natrix natrix or the wall lizard (Podarcis muralis), resulting in more than one Barcode Index Number (BIN) per species. Moreover, DNA barcodes revealed the presence of Natrix helvetica, which has been elevated to species level only recently, and genetic signatures of the Italian water frog Pelophylax bergeri in Western Austria for the first time. Comparison to previously published DNA barcoding data of European amphibians and reptiles corroborated the results of the Austrian data but also revealed certain peculiarities, underlining the particular strengths and in the case of the genus Pelophylax also the limitations of DNA barcoding. Consequently, DNA barcoding is not only powerful for species identification of all life stages of most Austrian amphibian and reptile species, but also for the detection of new species, the monitoring of gene flow or the presence of alien populations and/or species. Thus, DNA barcoding and the data generated in this study may serve both scientific and national or even transnational conservation purposes.
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Affiliation(s)
- Lukas Zangl
- Institute of Biology, University of Graz, Graz, Austria
- Studienzentrum Naturkunde, Universalmuseum Joanneum, Graz, Austria
- * E-mail: (LZ); (SK)
| | - Daniel Daill
- Institute of Biology, University of Graz, Graz, Austria
- Consultants in Aquatic Ecology and Engineering—blattfisch e.U., Wels, Austria
| | - Silke Schweiger
- First Zoological Department, Herpetological Collection, Museum of Natural History Vienna, Vienna, Austria
| | - Georg Gassner
- First Zoological Department, Herpetological Collection, Museum of Natural History Vienna, Vienna, Austria
| | - Stephan Koblmüller
- Institute of Biology, University of Graz, Graz, Austria
- * E-mail: (LZ); (SK)
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26
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Tuschhoff EJ, Hutter CR, Glor RE. Improving sustainable use of genetic resources in biodiversity archives. PeerJ 2020; 8:e8369. [PMID: 32095317 PMCID: PMC7024571 DOI: 10.7717/peerj.8369] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 12/09/2019] [Indexed: 11/20/2022] Open
Abstract
Tissue sample databases housed in biodiversity archives represent a vast trove of genetic resources, and these tissues are often destructively subsampled and provided to researchers for DNA extractions and subsequent sequencing. While obtaining a sufficient quantity of DNA for downstream applications is vital for these researchers, it is also important to preserve tissue resources for future use given that the original material is destructively and consumptively sampled with each use. It is therefore necessary to develop standardized tissue subsampling and loaning procedures to ensure that tissues are being used efficiently. In this study, we specifically focus on the efficiency of DNA extraction methods by using anuran liver and muscle tissues maintained at a biodiversity archive. We conducted a series of experiments to test whether current practices involving coarse visual assessments of tissue size are effective, how tissue mass correlates with DNA yield and concentration, and whether the amount of DNA recovered is correlated with sample age. We found that tissue samples between 2 and 8 mg resulted in the most efficient extractions, with tissues at the lower end of this range providing more DNA per unit mass and tissues at the higher end of this range providing more total DNA. Additionally, we found no correlation between tissue age and DNA yield. Because we find that even very small tissue subsamples tend to yield far more DNA than is required by researchers for modern sequencing applications (including whole genome shotgun sequencing), we recommend that biodiversity archives consider dramatically improving sustainable use of their archived material by providing researchers with set quantities of extracted DNA rather than with the subsampled tissues themselves.
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Affiliation(s)
- E. J. Tuschhoff
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
- University of Kansas Biodiversity Institute, Lawrence, KS, USA
| | - Carl R. Hutter
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
- University of Kansas Biodiversity Institute, Lawrence, KS, USA
| | - Richard E. Glor
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
- University of Kansas Biodiversity Institute, Lawrence, KS, USA
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27
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Everman S, Wang SY. Distinguishing Anuran species by high-resolution melting analysis of the COI barcode (COI-HRM). Ecol Evol 2019; 9:13515-13520. [PMID: 31871662 PMCID: PMC6912877 DOI: 10.1002/ece3.5808] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 10/08/2019] [Accepted: 10/09/2019] [Indexed: 11/06/2022] Open
Abstract
Taxonomic identification can be difficult when two or more species appear morphologically similar. DNA barcoding based on the sequence of the mitochondrial cytochrome c oxidase 1 gene (COI) is now widely used in identifying animal species. High-resolution melting analysis (HRM) provides an alternative method for detecting sequence variations among amplicons without having to perform DNA sequencing. The purpose of this study was to determine whether HRM of the COI barcode can be used to distinguish animal species. Using anurans as a model, we found distinct COI melting profiles among three congeners of both Lithobates spp. and Hyla spp. Sequence variations within species shifted the melting temperature of one or more melting domains slightly but do not affect the distinctness of the melting profiles for each species. An NMDS ordination plot comparing melting peak profiles among eight Anuran species showed overlapping profiles for Lithobates sphenocephala and Gastrophryne carolinensis. The COI amplicon for both species contained two melting domains with melting temperatures that were similar between the two species. The two species belong to two different families, highlighting the fact that COI melting profiles do not reveal phylogenetic relationships but simply reflect DNA sequence differences among stretches of DNA within amplicons. This study suggests that high-resolution melting analysis of COI barcodes (COI-HRM) may be useful as a simple and rapid method to distinguish animal species that appear morphologically similar.
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Affiliation(s)
- Steven Everman
- Department of Biological SciencesThe University of Southern MississippiLong BeachMSUSA
| | - Shiao Y. Wang
- Department of Biological SciencesThe University of Southern MississippiLong BeachMSUSA
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28
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Statham MJ, (Smith) Woollett DA, Fresquez S, Pfeiffer J, Richmond J, Whitelaw A, Richards NL, Westphal MF, Sacks BN. Noninvasive Identification of Herpetofauna: Pairing Conservation Dogs and Genetic Analysis. J Wildl Manage 2019. [DOI: 10.1002/jwmg.21772] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Mark J. Statham
- Department of Population Health and Reproduction, School of Veterinary Medicine, Mammalian Ecology and Conservation Unit, Veterinary Genetics LaboratoryUniversity of California One Shields Avenue Davis CA 95616‐8744 USA
| | | | - Susan Fresquez
- Mammalian Ecology and Conservation Unit, Veterinary Genetics LaboratoryUniversity of California One Shields Avenue Davis CA 95616‐8744 USA
| | - Jerene Pfeiffer
- Mammalian Ecology and Conservation Unit, Veterinary Genetics LaboratoryUniversity of California One Shields Avenue/Old Davis Road Davis CA 95616‐8744 USA
| | - Jonathan Richmond
- U.S. Geological Survey 4165 Spruance Rd. Suite 200 San Diego CA 92101 USA
| | - Alice Whitelaw
- Working Dogs for Conservation P.O. Box 280 Bozeman MT 59771 USA
| | | | - Michael F. Westphal
- U.S. Bureau of Land Management Central Coast Field Office Marina CA 93933 USA
| | - Benjamin N. Sacks
- Department of Population Health and Reproduction, School of Veterinary Medicine, Mammalian Ecology and Conservation Unit, Veterinary Genetics LaboratoryUniversity of California One Shields Avenue Davis CA 95616‐8744 USA
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29
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Nguete Nguiffo D, Mpoame M, Wondji CS. Genetic diversity and population structure of goliath frogs ( Conraua goliath) from Cameroon. Mitochondrial DNA A DNA Mapp Seq Anal 2019; 30:657-663. [PMID: 31092076 DOI: 10.1080/24701394.2019.1615060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The goliath frog (Conraua goliath) is an Endangered species exclusively found in Cameroon and Equatorial Guinea. Climate change, deforestation and overhunting are principal causes driving this species to extinction. Therefore, a better understanding of the genetic diversity and population structure of this species is necessary to improve conservation efforts. Here we used two mitochondrial genes (Cytochrome Oxidase subunit 1 (COI) and 16S) extracted from 54 C. goliath individuals from six localities in Cameroon to examine their genetic diversity. The result shows a low DNA substitution between the sequences. There were four 16S and two COI haplotypes in total. Overall, genetic diversity was very low for all the genes with nucleotide diversity of 0.00106 and 0.00007 for 16S and COI respectively. The Tajima D and Fu Fs statistics were negative. The TCS haplotype network revealed a predominant and ancestral haplotype (H1) for these genes which is distributed in the 6 populations. Pairwise genetic differentiation (FST) generated between these populations using 16S revealed very high differentiation between populations from Nkam and Mungo Administrative Divisions in Cameroon. In contrast, we observed low differentiation among the geographically clustered Mungo and Nkam populations. Overall, human activities and perhaps climate change can appear to have depleted genetic diversity in the scattered populations that remain of this amphibian. To sustain the Goliath frog, we suggest to the Cameroonian government to implement more effective strategies to conserve and manage remnant populations of this iconic species through more effort against poaching which contribute to reduce the genetic diversity.
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Affiliation(s)
- Daniel Nguete Nguiffo
- a Research Unit of Biology and Applied Ecology, Department of Animal Biology, Faculty of Science , University of Dschang , Dschang , Cameroon.,b Centre for Research in Infectious Diseases (CRID) , Dschang , Cameroon
| | - Mbida Mpoame
- a Research Unit of Biology and Applied Ecology, Department of Animal Biology, Faculty of Science , University of Dschang , Dschang , Cameroon
| | - Charles S Wondji
- b Centre for Research in Infectious Diseases (CRID) , Dschang , Cameroon.,c Vector Biology Department , Liverpool School of Tropical Medicine , Liverpool , UK
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30
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Puschendorf R, Wallace M, Chavarría MM, Crawford AJ, Wynne F, Knight M, Janzen DH, Hallwachs W, Palmer C, Price SJ. Cryptic diversity and ranavirus infection of a critically endangered Neotropical frog before and after population collapse. Anim Conserv 2019. [DOI: 10.1111/acv.12498] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- R. Puschendorf
- School of Biological and Marine Sciences University of Plymouth Devon UK
| | - M. Wallace
- Department of Zoology University of Oxford Oxford UK
| | - M. M. Chavarría
- Programa de Investigación Área de Conservación Guanacaste Liberia Costa Rica
| | - A. J. Crawford
- Departamento de Ciencias Biológicas Universidad de los Andes Bogotá Colombia
| | - F. Wynne
- School of Biological and Marine Sciences University of Plymouth Devon UK
| | - M. Knight
- School of Biological and Marine Sciences University of Plymouth Devon UK
| | - D. H. Janzen
- Department of Biology University of Pennsylvania Philadelphia PA USA
| | - W. Hallwachs
- Department of Biology University of Pennsylvania Philadelphia PA USA
| | - C.V. Palmer
- School of Biological and Marine Sciences University of Plymouth Devon UK
| | - S. J. Price
- UCL Genetics Institute London UK
- Institute of Zoology, ZSL London UK
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31
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Cryer J, Wynne F, Price SJ, Puschendorf R. Cryptic diversity in Lithobateswarszewitschii (Amphibia, Anura, Ranidae). Zookeys 2019; 838:49-69. [PMID: 31048968 PMCID: PMC6477815 DOI: 10.3897/zookeys.838.29635] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 02/25/2019] [Indexed: 11/12/2022] Open
Abstract
Lithobateswarszewitschii is a species of ranid frog distributed from southern Honduras to Panama. This species suffered severe population declines at higher elevations (above 500 m a.s.l.) from the 1980s to early 1990s, but there is more recent evidence of recovery in parts of its range. Here we advocate for the status of Lithobateswarszewitschii as a candidate cryptic species complex based on sequence data from mitochondrial genes CO1 and 16S. Using concatenated phylogenies, nucleotide diversity (K2P-π), net between group mean distance (NBGMD) (πnet) and species delimitation methods, we further elucidate cryptic diversity within this species. All phylogenies display polyphyletic lineages within Costa Rica and Panama. At both loci, observed genetic polymorphism (K2P-π) is also high within and between geographic populations, surpassing proposed species threshold values for amphibians. Additionally, patterns of phylogeographic structure are complicated for this species, and do not appear to be explained by geographic barriers or isolation by distance. These preliminary findings suggest L.warszewitschii is a wide-ranging species complex. Therefore, we propose further research within its wider range, and recommend integrative taxonomic assessment is merited to assess species status.
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Affiliation(s)
- James Cryer
- School of Biological and Marine Sciences, University of Plymouth, Devon, PL4 8AA, UKUniversity of PlymouthPlymouthUnited Kingdom
| | - Felicity Wynne
- School of Biological and Marine Sciences, University of Plymouth, Devon, PL4 8AA, UKUniversity of PlymouthPlymouthUnited Kingdom
| | - Stephen J. Price
- UCL Genetics Institute, Gower Street, London, WC1E 6BT, UKUCL Genetics InstituteLondonUnited Kingdom
- Institute of Zoology, ZSL, Regents Park, London NW1 4RY, UKInstitute of Zoology, ZSLLondonUnited Kingdom
| | - Robert Puschendorf
- School of Biological and Marine Sciences, University of Plymouth, Devon, PL4 8AA, UKUniversity of PlymouthPlymouthUnited Kingdom
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32
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Chiovitti A, Thorpe F, Gorman C, Cuxson JL, Robevska G, Szwed C, Duncan JC, Vanyai HK, Cross J, Siemering KR, Sumner J. A citizen science model for implementing statewide educational DNA barcoding. PLoS One 2019; 14:e0208604. [PMID: 30629584 PMCID: PMC6328199 DOI: 10.1371/journal.pone.0208604] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 11/20/2018] [Indexed: 01/05/2023] Open
Abstract
Our aim was to develop a widely available educational program in which students conducted authentic research that met the expectations of both the scientific and educational communities. This paper describes the development and implementation of a citizen science project based on DNA barcoding of reptile specimens obtained from the Museums Victoria frozen tissue collection. The student program was run by the Gene Technology Access Centre (GTAC) and was delivered as a "one day plus one lesson" format incorporating a one-day wet laboratory workshop followed by a single lesson at school utilising online bioinformatics tools. The project leveraged the complementary resources and expertise of the research and educational partners to generate robust scientific data that could be analysed with confidence, meet the requirements of the Victorian state education curriculum, and provide participating students with an enhanced learning experience. During two 1-week stints in 2013 and 2014, 406 students mentored by 44 postgraduate university students participated in the project. Students worked mainly in pairs to process ~200 tissue samples cut from 53 curated reptile specimens representing 17 species. A total of 27 novel Cytochrome Oxidase subunit 1 (CO1) sequences were ultimately generated for 8 south-east Australian reptile species of the families Scincidae and Agamidae.
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Affiliation(s)
- Anthony Chiovitti
- Gene Technology Access Centre (GTAC), The University High School, Parkville, Victoria, Australia
- School of Biosciences, University of Melbourne, Victoria, Australia
- * E-mail: ,
| | - Frazer Thorpe
- Gene Technology Access Centre (GTAC), The University High School, Parkville, Victoria, Australia
| | - Christopher Gorman
- Gene Technology Access Centre (GTAC), The University High School, Parkville, Victoria, Australia
| | - Jennifer L. Cuxson
- Gene Technology Access Centre (GTAC), The University High School, Parkville, Victoria, Australia
| | - Gorjana Robevska
- Gene Technology Access Centre (GTAC), The University High School, Parkville, Victoria, Australia
| | - Christopher Szwed
- Gene Technology Access Centre (GTAC), The University High School, Parkville, Victoria, Australia
| | - Jacinta C. Duncan
- Gene Technology Access Centre (GTAC), The University High School, Parkville, Victoria, Australia
| | - Hannah K. Vanyai
- Gene Technology Access Centre (GTAC), The University High School, Parkville, Victoria, Australia
| | - Joseph Cross
- Texas A&M University, College Station, Texas, United States of America
| | - Kirby R. Siemering
- Australian Genome Research Facility (AGRF), Victorian Comprehensive Cancer Centre, Melbourne, Victoria, Australia
| | - Joanna Sumner
- Museums Victoria, Carlton Gardens, Victoria, Australia
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33
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DNA barcodes from snake venom: a broadly applicable method for extraction of DNA from snake venoms. Biotechniques 2018; 65:339-345. [PMID: 30477329 DOI: 10.2144/btn-2018-0096] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
DNA barcoding is a simple technique used to develop a large-scale system of classification that is broadly applicable across a wide variety of taxa. DNA-based analysis of snake venoms can provide a system of classification independent of currently accepted taxonomic relationships by generating DNA barcodes specific to each venom sample. DNA purification from dried snake venoms has previously required large amounts of starting material, has resulted in low yields and inconsistent amplification, and was possible with front-fanged snakes only. Here, we present a modified DNA extraction protocol applied to venoms of both front- and rear-fanged snakes that requires significantly less starting material (1 mg) and yields sufficient amounts of DNA for successful PCR amplification of regions commonly used for DNA barcoding. [Formula: see text].
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34
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Amador L, Parada A, D'Elía G, Guayasamin JM. Uncovering hidden specific diversity of Andean glassfrogs of the Centrolene buckleyi species complex (Anura: Centrolenidae). PeerJ 2018; 6:e5856. [PMID: 30402351 PMCID: PMC6215445 DOI: 10.7717/peerj.5856] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 10/02/2018] [Indexed: 11/20/2022] Open
Abstract
The glassfrog Centrolene buckleyi has been recognized as a species complex. Herein, using coalescence-based species delimitation methods, we evaluate the specific diversity within this taxon. Four coalescence approaches (generalized mixed Yule coalescents, Bayesian general mixed Yule-coalescent, Poisson tree processes, and Bayesian Poisson tree processes) were consistent with the delimitation results, identifying four lineages within what is currently recognized as C. buckleyi. We propose three new candidate species that should be tested with nuclear markers, morphological, and behavioral data. In the meantime, for conservation purposes, candidate species should be considered evolutionary significant units, in light of observed population crashes in the C. buckleyi species complex. Finally, our results support the validity of C. venezuelense, formerly considered as a subspecies of C. buckleyi.
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Affiliation(s)
- Luis Amador
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile.,Departamento de Investigación Científica, Universidad Laica Vicente Rocafuerte de Guayaquil, Guayaquil, Ecuador
| | - Andrés Parada
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Guillermo D'Elía
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Juan M Guayasamin
- Instituto BIÓSFERA-USFQ, Laboratorio de Biología Evolutiva, Colegio de Ciencias Biológicas y Ambientales COCIBA, Universidad San Francisco de Quito, Quito, Ecuador.,Centro de Investigación de la Biodiversidad y Cambio Climático, Ingeniería en Biodiversidad y Recursos Genéticos, Facultad de Ciencias del Medio Ambiente, Universidad Tecnológica Indoamérica, Quito, Ecuador
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35
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Yang JH, Zheng X. A New Species of the GenusCalamaria(Squamata: Colubridae) from Yunnan Province, China. COPEIA 2018. [DOI: 10.1643/ch-17-663] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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36
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Garg S, Das A, Kamei RG, Biju SD. Delineating Microhyla ornata (Anura, Microhylidae): mitochondrial DNA barcodes resolve century-old taxonomic misidentification. Mitochondrial DNA B Resour 2018; 3:856-861. [PMID: 33474344 PMCID: PMC7800528 DOI: 10.1080/23802359.2018.1501286] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Microhyla ornata, a species originally described from the southwest coast of India in 1841, was long reported to be wide-ranging throughout South, Southeast, and East Asia. Although the name M. ornata is restricted to populations from South Asia, the species is still considered to occur widely in India and its neighboring regions. To clarify the identity and geographical distribution of M. ‘ornata’, we performed DNA barcoding using a fragment of the mitochondrial 16S rRNA gene from 62 newly obtained samples. Our results show that this taxon is restricted to Peninsular India and Sri Lanka, whereas, populations from the other parts represent three different species – M. mukhlesuri, M. mymensinghensis, and M. nilphamariensis, creating new country records for India. Our work reemphasizes the benefits of DNA barcoding for rapidly identifying populations of widespread species and provides insights into the patterns of genetic differentiation in the M. ‘ornata’ species complex of South Asia.
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Affiliation(s)
- Sonali Garg
- Systematics Lab, Department of Environmental Studies, University of Delhi, Delhi, India
| | - Abhijit Das
- Wildlife Institute of India, Dehradun, India
| | - Rachunliu G Kamei
- Systematics Lab, Department of Environmental Studies, University of Delhi, Delhi, India.,Department of Life Sciences, The Natural History Museum, London, UK
| | - S D Biju
- Systematics Lab, Department of Environmental Studies, University of Delhi, Delhi, India
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37
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Chang CH, Dai WY, Chen TY, Lee AH, Hou HY, Liu SH, Jang-Liaw NH. DNA barcoding reveals CITES-listed species among Taiwanese government-seized chelonian specimens. Genome 2018; 61:615-624. [PMID: 29916730 DOI: 10.1139/gen-2017-0264] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Compared to traditional morphological identification, DNA barcoding-molecular identification based on sequencing of a segment of mitochondrial cytochrome c oxidase subunit I (COI)-provides a shortcut to authenticating chelonian identifications. Here, we selected 63 government-seized chelonian specimens deposited at Taipei Zoo for DNA barcoding analysis. DNA barcoding and subsequent phylogenetic analysis successfully authenticated 36 chelonian species, including five that are listed in CITES Appendix I. Approximately 90% (57/63) of the specimens were successfully authenticated by our molecular approach, but lack or error of BOLD reference sequences, biological processes such as hybridization, and uncertain species delimitation all reduced the accuracy of DNA barcoding. To increase the accuracy of DNA barcoding, Taipei Zoo will continue to enrich the BOLD database and also establish a genetic database, to include additional genetic markers, by using government-seized chelonian specimens. A fast and accurate method to authenticate seized samples could assist law enforcement agencies to prosecute criminals and restrict illegal exploitation of wild chelonian resources.
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Affiliation(s)
- Chia-Hao Chang
- a Department of Animal Biology, University of Illinois, 202 Shelford Vivarium, 606 East Healey St., Champaign, IL 61820, USA
| | - Wei-Yu Dai
- b Taipei Zoo, No. 30, Section 2, Xinguang Rd., Wenshan District, Taipei City 11656, Taiwan
| | - Ting-Yu Chen
- b Taipei Zoo, No. 30, Section 2, Xinguang Rd., Wenshan District, Taipei City 11656, Taiwan
| | - An-Hsin Lee
- b Taipei Zoo, No. 30, Section 2, Xinguang Rd., Wenshan District, Taipei City 11656, Taiwan
| | - Hsuan-Yi Hou
- b Taipei Zoo, No. 30, Section 2, Xinguang Rd., Wenshan District, Taipei City 11656, Taiwan
| | - Shih-Hui Liu
- c Biodiversity Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei City 11529, Taiwan
| | - Nian-Hong Jang-Liaw
- b Taipei Zoo, No. 30, Section 2, Xinguang Rd., Wenshan District, Taipei City 11656, Taiwan
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38
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Kornilios P, Kumlutaş Y, Lymberakis P, Ilgaz Ç. Cryptic diversity and molecular systematics of the Aegean Ophiomorus
skinks (Reptilia: Squamata), with the description of a new species. J ZOOL SYST EVOL RES 2018. [DOI: 10.1111/jzs.12205] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
| | - Yusuf Kumlutaş
- Department of Biology; Faculty of Science; Dokuz Eylül University; Buca-Izmir Turkey
| | - Petros Lymberakis
- Natural History Museum of Crete; University of Crete; Irakleio, Crete Greece
| | - Çetin Ilgaz
- Department of Biology; Faculty of Science; Dokuz Eylül University; Buca-Izmir Turkey
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Marcus JM. Our love-hate relationship with DNA barcodes, the Y2K problem, and the search for next generation barcodes. AIMS GENETICS 2018; 5:1-23. [PMID: 31435510 PMCID: PMC6690253 DOI: 10.3934/genet.2018.1.1] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 01/11/2018] [Indexed: 01/27/2023]
Abstract
DNA barcodes are very useful for species identification especially when identification by traditional morphological characters is difficult. However, the short mitochondrial and chloroplast barcodes currently in use often fail to distinguish between closely related species, are prone to lateral transfer, and provide inadequate phylogenetic resolution, particularly at deeper nodes. The deficiencies of short barcode identifiers are similar to the deficiencies of the short year identifiers that caused the Y2K problem in computer science. The resolution of the Y2K problem was to increase the size of the year identifiers. The performance of conventional mitochondrial COI barcodes for phylogenetics was compared with the performance of complete mitochondrial genomes and nuclear ribosomal RNA repeats obtained by genome skimming for a set of caddisfly taxa (Insect Order Trichoptera). The analysis focused on Trichoptera Family Hydropsychidae, the net-spinning caddisflies, which demonstrates many of the frustrating limitations of current barcodes. To conduct phylogenetic comparisons, complete mitochondrial genomes (15 kb each) and nuclear ribosomal repeats (9 kb each) from six caddisfly species were sequenced, assembled, and are reported for the first time. These sequences were analyzed in comparison with eight previously published trichopteran mitochondrial genomes and two triochopteran rRNA repeats, plus outgroup sequences from sister clade Lepidoptera (butterflies and moths). COI trees were not well-resolved, had low bootstrap support, and differed in topology from prior phylogenetic analyses of the Trichoptera. Phylogenetic trees based on mitochondrial genomes or rRNA repeats were well-resolved with high bootstrap support and were largely congruent with each other. Because they are easily sequenced by genome skimming, provide robust phylogenetic resolution at various phylogenetic depths, can better distinguish between closely related species, and (in the case of mitochondrial genomes), are backwards compatible with existing mitochondrial barcodes, it is proposed that mitochondrial genomes and rRNA repeats be used as next generation DNA barcodes.
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Affiliation(s)
- Jeffrey M. Marcus
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, Canada, R3T 2N2
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40
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Zhao H, Yang J, Wang C, Li P, Murphy RW, Che J, Yuan Z. A new species of the genus Rana from Henan, central China (Anura, Ranidae). Zookeys 2017:95-108. [PMID: 29134001 PMCID: PMC5672780 DOI: 10.3897/zookeys.694.12513] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 06/08/2017] [Indexed: 11/12/2022] Open
Abstract
A new species of brown frog Rana luanchuanensis Zhao & Yuan, sp. n. is described from Luanchuan County, western Henan, central China. The mitochondrial genealogy suggests that the new species is the sister taxon to the clade including R. amurensis and R. coreana, and is separated by uncorrected pairwise distances more than 12.5%. Morphologically, this new species differs from its congeners by a suite of characters. Analyses of partial sequences of cytochrome oxidase subunit I (COI) resolve the new species as a single matriline.
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Affiliation(s)
- Haipeng Zhao
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, Yunnan, China.,School of Life Science, Henan University, Kaifeng 475004, Henan, China
| | - Junxiao Yang
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, Yunnan, China
| | - Chunping Wang
- Henan Forestry Survey and Planning Institute, Zhengzhou 450045, Henan, China
| | - Pipeng Li
- Center for Chinese Endemic Herp-breeding and Conservation Research, and Liaoning Key Laboratory of Evolution and Biodiversity, Shenyang Normal University, Shenyang 110034, Liaoning, China
| | - Robert W Murphy
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, Yunnan, China.,Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, 100 Queen's Park, Toronto M5S 2C6, Canada
| | - Jing Che
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, China
| | - Zhiyong Yuan
- College of Forestry, Southwest Forestry University, Kunming 650224, Yunnan, China
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41
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Deichmann JL, Mulcahy DG, Vanthomme H, Tobi E, Wynn AH, Zimkus BM, McDiarmid RW. How many species and under what names? Using DNA barcoding and GenBank data for west Central African amphibian conservation. PLoS One 2017; 12:e0187283. [PMID: 29131846 PMCID: PMC5683629 DOI: 10.1371/journal.pone.0187283] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 09/06/2017] [Indexed: 11/19/2022] Open
Abstract
Development projects in west Central Africa are proceeding at an unprecedented rate, often with little concern for their effects on biodiversity. In an attempt to better understand potential impacts of a road development project on the anuran amphibian community, we conducted a biodiversity assessment employing multiple methodologies (visual encounter transects, auditory surveys, leaf litter plots and pitfall traps) to inventory species prior to construction of a new road within the buffer zone of Moukalaba-Doudou National Park, Gabon. Because of difficulties in morphological identification and taxonomic uncertainty of amphibian species observed in the area, we integrated a DNA barcoding analysis into the project to improve the overall quality and accuracy of the species inventory. Based on morphology alone, 48 species were recognized in the field and voucher specimens of each were collected. We used tissue samples from specimens collected at our field site, material available from amphibians collected in other parts of Gabon and the Republic of Congo to initiate a DNA barcode library for west Central African amphibians. We then compared our sequences with material in GenBank for the genera recorded at the study site to assist in identifications. The resulting COI and 16S barcode library allowed us to update the number of species documented at the study site to 28, thereby providing a more accurate assessment of diversity and distributions. We caution that because sequence data maintained in GenBank are often poorly curated by the original submitters and cannot be amended by third-parties, these data have limited utility for identification purposes. Nevertheless, the use of DNA barcoding is likely to benefit biodiversity inventories and long-term monitoring, particularly for taxa that can be difficult to identify based on morphology alone; likewise, inventory and monitoring programs can contribute invaluable data to the DNA barcode library and the taxonomy of complex groups. Our methods provide an example of how non-taxonomists and parataxonomists working in understudied parts of the world with limited geographic sampling and comparative morphological material can use DNA barcoding and publicly available sequence data (GenBank) to rapidly identify the number of species and assign tentative names to aid in urgent conservation management actions and contribute to taxonomic resolution.
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Affiliation(s)
- Jessica L. Deichmann
- Center for Conservation and Sustainability, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, United States of America
| | - Daniel G. Mulcahy
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States of America
| | - Hadrien Vanthomme
- Center for Conservation and Sustainability, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, United States of America
| | - Elie Tobi
- Center for Conservation and Sustainability, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, United States of America
| | - Addison H. Wynn
- Department of Vertebrate Zoology, Division of Amphibians and Reptiles, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States of America
| | - Breda M. Zimkus
- Museum of Comparative Zoology, Harvard University, Cambridge, MA, United States of America
| | - Roy W. McDiarmid
- USGS, Patuxent Wildlife Research Center, National Museum of Natural History, Washington DC, United States of America
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42
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Malato G, Shervette VR, Navarrete Amaya R, Valdiviezo Rivera J, Nugra Salazar F, Calle Delgado P, Karpan KC, Aguirre WE. Parallel body shape divergence in the Neotropical fish genus Rhoadsia (Teleostei: Characidae) along elevational gradients of the western slopes of the Ecuadorian Andes. PLoS One 2017; 12:e0179432. [PMID: 28658255 PMCID: PMC5489170 DOI: 10.1371/journal.pone.0179432] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 05/29/2017] [Indexed: 12/26/2022] Open
Abstract
Neotropical mountain streams are important contributors of biological diversity. Two species of the characid genus Rhoadsia differing for an ecologically important morphological trait, body depth, have been described from mountain streams of the western slopes of the Andes in Ecuador. Rhoadsia altipinna is a deeper-bodied species reported from low elevations in southwestern Ecuador and northern Peru, and Rhoadsia minor is a more streamlined species that was described from high elevations (>1200 m) in the Esmeraldas drainage in northwestern Ecuador. Little is known about these species and their validity as distinct species has been questioned. In this study, we examine how their body shape varies along replicated elevational gradients in different drainages of western Ecuador using geometric morphometrics and the fineness ratio. We also use sequences of the mitochondrial cytochrome oxidase c I gene and the second intron of the S7 nuclear gene to examine whether genetic data are consistent with the existence of two species. We found that body depth varies continuously among populations within drainages as a function of elevation, and that body shape overlaps among drainages, such that low elevation populations of R. minor in the Esmeraldas drainage have similar body depths to higher elevation R. altipinna in southern drainages. Although a common general trend of declining body depth with elevation is clear, the pattern and magnitude of body shape divergence differed among drainages. Sequencing of mitochondrial and nuclear genes failed to meet strict criteria for the recognition of two species (e.g., reciprocal monophyly and deep genetic structure). However, there was a large component of genetic variation for the COI gene that segregated among drainages, indicating significant genetic divergence associated with geographic isolation. Continued research on Rhoadsia in western Ecuador may yield significant insight into adaptation and speciation in Neotropical mountain streams.
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Affiliation(s)
- Grace Malato
- Department of Biological Sciences, DePaul University, Chicago, Illinois, United States of America
| | - Virginia R. Shervette
- Department of Biology/Geology, University of South Carolina, Aiken, South Carolina, United States of America
| | | | | | - Fredy Nugra Salazar
- Laboratorio de Zoología de Vertebrados de la Universidad del Azuay, Cuenca, Ecuador
| | - Paola Calle Delgado
- Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral, Guayaquil, Ecuador
| | - Kirby C. Karpan
- Department of Biological Sciences, DePaul University, Chicago, Illinois, United States of America
| | - Windsor E. Aguirre
- Department of Biological Sciences, DePaul University, Chicago, Illinois, United States of America
- * E-mail:
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43
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Barratt CD, Bwong BA, Onstein RE, Rosauer DF, Menegon M, Doggart N, Nagel P, Kissling WD, Loader SP. Environmental correlates of phylogenetic endemism in amphibians and the conservation of refugia in the Coastal Forests of Eastern Africa. DIVERS DISTRIB 2017. [DOI: 10.1111/ddi.12582] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Affiliation(s)
- Christopher D. Barratt
- Biogeography Research Group; Department of Environmental Sciences; University of Basel; Basel Switzerland
- Institute for Biodiversity and Ecosystem Dynamics (IBED); University of Amsterdam; Amsterdam The Netherlands
| | - Beryl A. Bwong
- Biogeography Research Group; Department of Environmental Sciences; University of Basel; Basel Switzerland
- Herpetology Section; National Museums of Kenya; Nairobi Kenya
| | - Renske E. Onstein
- Institute for Biodiversity and Ecosystem Dynamics (IBED); University of Amsterdam; Amsterdam The Netherlands
| | - Dan F. Rosauer
- Research School of Biology and Centre for Biodiversity Analysis; Australian National University; Acton ACT Australia
| | - Michele Menegon
- Tropical Biodiversity Section; Museo delle Scienze; Trento Italy
| | - Nike Doggart
- Tanzania Forest Conservation Group; Dar es Salaam Tanzania
| | - Peter Nagel
- Biogeography Research Group; Department of Environmental Sciences; University of Basel; Basel Switzerland
| | - W. Daniel Kissling
- Institute for Biodiversity and Ecosystem Dynamics (IBED); University of Amsterdam; Amsterdam The Netherlands
| | - Simon P. Loader
- Biogeography Research Group; Department of Environmental Sciences; University of Basel; Basel Switzerland
- Department of Life Sciences; University of Roehampton; London UK
- Department of Life Sciences; Natural History Museum; London UK
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44
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Ashfaq M, Akhtar S, Rafi MA, Mansoor S, Hebert PDN. Mapping global biodiversity connections with DNA barcodes: Lepidoptera of Pakistan. PLoS One 2017; 12:e0174749. [PMID: 28339501 PMCID: PMC5365146 DOI: 10.1371/journal.pone.0174749] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 03/14/2017] [Indexed: 11/20/2022] Open
Abstract
Sequences from the DNA barcode region of the mitochondrial COI gene are an effective tool for specimen identification and for the discovery of new species. The Barcode of Life Data Systems (BOLD) (www.boldsystems.org) currently hosts 4.5 million records from animals which have been assigned to more than 490,000 different Barcode Index Numbers (BINs), which serve as a proxy for species. Because a fourth of these BINs derive from Lepidoptera, BOLD has a strong capability to both identify specimens in this order and to support studies of faunal overlap. DNA barcode sequences were obtained from 4503 moths from 329 sites across Pakistan, specimens that represented 981 BINs from 52 families. Among 379 species with a Linnaean name assignment, all were represented by a single BIN excepting five species that showed a BIN split. Less than half (44%) of the 981 BINs had counterparts in other countries; the remaining BINs were unique to Pakistan. Another 218 BINs of Lepidoptera from Pakistan were coupled with the 981 from this study before being compared with all 116,768 BINs for this order. As expected, faunal overlap was highest with India (21%), Sri Lanka (21%), United Arab Emirates (20%) and with other Asian nations (2.1%), but it was very low with other continents including Africa (0.6%), Europe (1.3%), Australia (0.6%), Oceania (1.0%), North America (0.1%), and South America (0.1%). This study indicates the way in which DNA barcoding facilitates measures of faunal overlap even when taxa have not been assigned to a Linnean species.
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Affiliation(s)
- Muhammad Ashfaq
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
- * E-mail:
| | - Saleem Akhtar
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | | | - Shahid Mansoor
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
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45
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Lyra ML, Haddad CFB, de Azeredo-Espin AML. Meeting the challenge of DNA barcoding Neotropical amphibians: polymerase chain reaction optimization and new COI primers. Mol Ecol Resour 2017; 17:966-980. [PMID: 28029226 DOI: 10.1111/1755-0998.12648] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 12/09/2016] [Accepted: 12/15/2016] [Indexed: 01/17/2023]
Abstract
Amphibians are one of the most threatened vertebrate classes, yet at the same time new species are being described every year, demonstrating that the number of existing species is grossly underestimated. In groups such as amphibians, with high extinction rates and poorly known species boundaries, DNA barcoding is a tool that can rapidly assess genetic diversity and estimate species richness for prioritizing conservation decisions. However, reliable recovery of the 5' region of the cytochrome c oxidase subunit 1 (COI) gene is critical for the ongoing effort to gather DNA barcodes for all amphibian species. Here, we provide new PCR conditions and tested new primers that increase the efficiency of barcode recovery in amphibians. We found that a low extension temperature for PCR cycles significantly improves the efficiency of amplification for all combinations of primers. Combining low PCR extension temperature and primers AnF1 + AnR1, we were able to recover COI sequences for 100% of the species analysed (N = 161), encompassing ~15% of the species known from Brazil (representing 77 genera and 23 families), which is an important improvement over previous studies. The preliminary assessment of species diversity suggested that number of species might be underestimated by about 25%. We conclude that DNA barcoding is an efficient, simple, and standardized protocol for identifying cryptic diversity in amphibians and advocate for its use in biodiversity inventories and across widespread populations within known species.
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Affiliation(s)
- Mariana L Lyra
- Departamento de Zoologia, Instituto de Biociências, UNESP - Univ Estadual Paulista, Campus Rio Claro, Av. 24 A, No. 1515, Bela Vista, CEP 13506-970, Rio Claro, SP, Brazil
| | - Célio F B Haddad
- Departamento de Zoologia, Instituto de Biociências, UNESP - Univ Estadual Paulista, Campus Rio Claro, Av. 24 A, No. 1515, Bela Vista, CEP 13506-970, Rio Claro, SP, Brazil
| | - Ana Maria L de Azeredo-Espin
- Centro de Biologia Molecular e Engenharia Genética and Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Rua Cândido Rondon No. 400, CEP 13083-875, Campinas, São Paulo, Brazil
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46
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Koch C, Venegas PJ. A large and unusually colored new snake species of the genus Tantilla (Squamata; Colubridae) from the Peruvian Andes. PeerJ 2016; 4:e2767. [PMID: 27994975 PMCID: PMC5157193 DOI: 10.7717/peerj.2767] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 11/07/2016] [Indexed: 11/23/2022] Open
Abstract
A new colubrid species of the genus Tantilla from the dry forest of the northern Peruvian Andes is described on the basis of two specimens, which exhibit a conspicuous sexual dimorphism. Tantilla tjiasmantoi sp. nov. represents the third species of the genus in Peru. The new species is easily distinguished from its congeners by the combination of scalation characteristics and the unusual transversely-banded color pattern on the dorsum. A detailed description of the skull morphology of the new species is given based on micro-computed tomography images. The habitat of this new species is gravely threatened due to human interventions. Conservation efforts are urgently needed in the inter-Andean valley of the Maranon River.
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Affiliation(s)
- Claudia Koch
- Department of Herpetology, Zoologisches Forschungsmuseum Alexander Koenig (ZFMK) , Bonn , Germany
| | - Pablo J Venegas
- Department of Herpetology, Centro de Ornitología y Biodiversidad (CORBIDI) , Lima , Peru
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47
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Estupiñán RA, Ferrari SF, Gonçalves EC, Barbosa MSR, Vallinoto M, Schneider MPC. Evaluating the diversity of Neotropical anurans using DNA barcodes. Zookeys 2016; 637:89-106. [PMID: 28138277 PMCID: PMC5240124 DOI: 10.3897/zookeys.637.8637] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2016] [Accepted: 10/08/2016] [Indexed: 11/17/2022] Open
Abstract
This study tested the effectiveness of COI barcodes for the discrimination of anuran species from the Amazon basin and other Neotropical regions. Barcodes were determined for a total of 59 species, with a further 58 species being included from GenBank. In most cases, distinguishing species using the barcodes was straightforward. Each species had a distinct COI barcode or codes, with intraspecific distances ranging from 0% to 9.9%. However, relatively high intraspecific divergence (11.4-19.4%) was observed in some species, such as Ranitomeya ventrimaculata, Craugastor fitzingeri, Hypsiboas leptolineatus, Scinax fuscomarginatus and Leptodactylus knudseni, which may reflect errors of identification or the presence of a species complex. Intraspecific distances recorded in species for which samples were obtained from GenBank (Engystomops pustulosus, Atelopus varius, Craugastor podiciferus, and Dendropsophus labialis) were greater than those between many pairs of species. Interspecific distances ranged between 11-39%. Overall, the clear differences observed between most intra- and inter-specific distances indicate that the COI barcode is an effective tool for the identification of Neotropical species in most of the cases analyzed in the present study.
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48
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Lukhtanov VA, Pazhenkova EA, Novikova AV. Mitochondrial chromosome as a marker of animal migratory routes: DNA barcoding revealed Asian (non-African) origin of a tropical migrant butterfly Junonia orithya in south Israel. COMPARATIVE CYTOGENETICS 2016; 10:671-677. [PMID: 28123687 PMCID: PMC5240517 DOI: 10.3897/compcytogen.v10i4.11085] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Accepted: 11/16/2016] [Indexed: 05/31/2023]
Abstract
The blue pansy Junonia orithya Linnaeus, 1758 (Lepidoptera, Nymphalidae) is widely distributed along the tropical areas of Africa, Asia and Australia. It is also known as a migrant species in the Levant. Here we record Junonia orithya in south Israel and provide a DNA-barcode-based evidence for its Asian (non-African) origin.
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Affiliation(s)
- Vladimir A. Lukhtanov
- Department of Karyosystematics, Zoological Institute of Russian Academy of Sciences, Universitetskaya nab. 1, 199034 St. Petersburg, Russia
- Department of Entomology, St. Petersburg State University, Universitetskaya nab. 7/9, 199034 St. Petersburg, Russia
| | - Elena A. Pazhenkova
- Department of Karyosystematics, Zoological Institute of Russian Academy of Sciences, Universitetskaya nab. 1, 199034 St. Petersburg, Russia
- Department of Entomology, St. Petersburg State University, Universitetskaya nab. 7/9, 199034 St. Petersburg, Russia
| | - Asya V. Novikova
- Department of Ecology, Evolution and Behavior, the Hebrew University of Jerusalem, Givat Ram, Berman bldg, 91904 Jerusalem, Israel
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