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Major T, Renk P, Reissig J, Paijmans JLA, Morris E, Hofreiter M, Barlow A, Broadley DG, Wüster W. Museum DNA reveals a new, potentially extinct species of rinkhals (Serpentes: Elapidae: Hemachatus) from the Eastern Highlands of Zimbabwe. PLoS One 2023; 18:e0291432. [PMID: 37756254 PMCID: PMC10529548 DOI: 10.1371/journal.pone.0291432] [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: 01/12/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023] Open
Abstract
Genetic information plays a pivotal role in species recognition and delimitation, but rare or extinct animals can be difficult to obtain genetic samples from. While natural history wet collections have proven invaluable in the description of novel species, the use of these historical samples in genetic studies has been greatly impeded by DNA degradation, especially because of formalin-fixation prior to preservation. Here, we use recently developed museum genomics approaches to determine the status of an isolated population of the elapid snake genus Hemachatus from Zimbabwe. We used multiple digestion phases followed by single strand sequencing library construction and hybridisation capture to obtain 12S and 16S rDNA sequences from a poorly preserved tissue sample of this population. Phylogenetic and morphological analyses in an integrated taxonomic framework demonstrate that the Zimbabwean rinkhals population represents an old and highly distinct lineage, which we describe as a new species, Hemachatus nyangensis sp. nov. Our phylogenetic dating analysis is compatible with venom spitting having evolved in response to the threat posed by early hominins, although more data are required for a robust test of this hypothesis. This description demonstrates the power of museum genomics in revealing rare or even extinct species: Hemachatus from Zimbabwe are only known from a small area of the Eastern Highlands known for high endemism. No living specimens have been seen since the 1980s, most likely due to dramatic land-use changes in the Eastern Highlands, suggesting that the species could be extinct. In view of its recognition as a highly distinct lineage, urgent action is required to determine whether any populations survive, and to safeguard remaining habitat.
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Affiliation(s)
- Tom Major
- Molecular Ecology and Evolution at Bangor, School of Natural Sciences, Bangor University, Bangor, Wales, United Kingdom
| | - Pia Renk
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Jens Reissig
- Ultimate Creatures, Kelvin, Sandton, South Africa
| | | | - Ellie Morris
- Molecular Ecology and Evolution at Bangor, School of Natural Sciences, Bangor University, Bangor, Wales, United Kingdom
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Axel Barlow
- Molecular Ecology and Evolution at Bangor, School of Natural Sciences, Bangor University, Bangor, Wales, United Kingdom
| | | | - Wolfgang Wüster
- Molecular Ecology and Evolution at Bangor, School of Natural Sciences, Bangor University, Bangor, Wales, United Kingdom
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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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Illuminating type collections of nectriaceous fungi in Saccardo's fungarium. Persoonia - Molecular Phylogeny and Evolution of Fungi 2021; 45:221-249. [PMID: 34456378 PMCID: PMC8375352 DOI: 10.3767/persoonia.2020.45.09] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 09/21/2020] [Indexed: 11/25/2022]
Abstract
Specimens of Nectria spp. and Nectriella rufofusca were obtained from the fungarium of Pier Andrea Saccardo, and investigated via a morphological and molecular approach based on MiSeq technology. ITS1 and ITS2 sequences were successfully obtained from 24 specimens identified as 'Nectria' sensu Saccardo (including 20 types) and from the type specimen of Nectriella rufofusca. For Nectria ambigua, N. radians and N. tjibodensis only the ITS1 sequence was recovered. On the basis of morphological and molecular analyses new nomenclatural combinations for Nectria albofimbriata, N. ambigua, N. ambigua var. pallens, N. granuligera, N. peziza subsp. reyesiana, N. radians, N. squamuligera, N. tjibodensis and new synonymies for N. congesta, N. flageoletiana, N. phyllostachydis, N. sordescens and N. tjibodensis var. crebrior are proposed. Furthermore, the current classification is confirmed for Nectria coronata, N. cyanostoma, N. dolichospora, N. illudens, N. leucotricha, N. mantuana, N. raripila and Nectriella rufofusca. This is the first time that these more than 100-yr-old specimens are subjected to molecular analysis, thereby providing important new DNA sequence data authentic for these names.
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Pfarrer B, Rowson B, Tattersfield P, Neubert E. Phylogenetic position of African Vitrinidae: Old family groups unraveled. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Beat Pfarrer
- Department of Invertebrate Animals Natural History Museum Bern Bern Switzerland
- Institute of Ecology and Evolution University of Bern Bern Switzerland
| | - Ben Rowson
- Department of Natural Sciences Amgueddfa Cymru – National Museum Wales Cardiff UK
| | - Peter Tattersfield
- Department of Natural Sciences Amgueddfa Cymru – National Museum Wales Cardiff UK
| | - Eike Neubert
- Department of Invertebrate Animals Natural History Museum Bern Bern Switzerland
- Institute of Ecology and Evolution University of Bern Bern Switzerland
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Abstract
Taxonomy is the science that explores, describes, names, and classifies all organisms. In this introductory chapter, we highlight the major historical steps in the elaboration of this science, which provides baseline data for all fields of biology and plays a vital role for society but is also an independent, complex, and sound hypothesis-driven scientific discipline.In a first part, we underline that plant taxonomy is one of the earliest scientific disciplines that emerged thousands of years ago, even before the important contributions of the Greeks and Romans (e.g., Theophrastus, Pliny the Elder, and Dioscorides). In the fifteenth-sixteenth centuries, plant taxonomy benefited from the Great Navigations, the invention of the printing press, the creation of botanic gardens, and the use of the drying technique to preserve plant specimens. In parallel with the growing body of morpho-anatomical data, subsequent major steps in the history of plant taxonomy include the emergence of the concept of natural classification , the adoption of the binomial naming system (with the major role of Linnaeus) and other universal rules for the naming of plants, the formulation of the principle of subordination of characters, and the advent of the evolutionary thought. More recently, the cladistic theory (initiated by Hennig) and the rapid advances in DNA technologies allowed to infer phylogenies and to propose true natural, genealogy-based classifications.In a second part, we put the emphasis on the challenges that plant taxonomy faces nowadays. The still very incomplete taxonomic knowledge of the worldwide flora (the so-called taxonomic impediment) is seriously hampering conservation efforts that are especially crucial as biodiversity has entered its sixth extinction crisis. It appears mainly due to insufficient funding, lack of taxonomic expertise, and lack of communication and coordination. We then review recent initiatives to overcome these limitations and to anticipate how taxonomy should and could evolve. In particular, the use of molecular data has been era-splitting for taxonomy and may allow an accelerated pace of species discovery. We examine both strengths and limitations of such techniques in comparison to morphology-based investigations, we give broad recommendations on the use of molecular tools for plant taxonomy, and we highlight the need for an integrative taxonomy based on evidence from multiple sources.
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Affiliation(s)
- Germinal Rouhan
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, Sorbonne Université, Ecole Pratique des Hautes Etudes, Université des Antilles, CNRS, Paris, France.
| | - Myriam Gaudeul
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, Sorbonne Université, Ecole Pratique des Hautes Etudes, Université des Antilles, CNRS, Paris, France
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Rebelo H, Ferreira S, Amorim F, Horta P, Raposeira H, Santos H, Beja P, Mata VA. Hidden in our pockets: building of a DNA barcode library unveils the first record of Myotis alcathoe for Portugal. Biodivers Data J 2020; 8:e54479. [PMID: 32821211 PMCID: PMC7403162 DOI: 10.3897/bdj.8.e54479] [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: 05/19/2020] [Accepted: 06/29/2020] [Indexed: 11/12/2022] Open
Abstract
Background The advent and boom of DNA barcoding technologies have provided a powerful tool for the fields of ecology and systematics. Here, we present the InBIO Barcoding Initiative Database: Portuguese Bats (Chiroptera) dataset containing DNA sequences of 63 specimens representing the 25 bat species currently known for continental Portugal. For that, we sequenced tissues samples obtained in a vast array of projects spanning the last two decades. New information We added four new Barcoding Index Numbers (BINs) to existing Chiroptera barcodes on BOLD, two belonging to Myotisescalerai, one to Plecotusauritus and the other to Rhinolophushipposideros. Surprisingly, one of the samples initially identified in the field as Myotismystacinus turned out to be Myotisalcathoe, which represents the first record of this species for Portugal. The presence of Nyctalusnoctula in Portugal was also genetically confirmed for the first time. This case study shows the power and value of DNA barcoding initiatives to unravel new data that may be hidden on biological collections.
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Affiliation(s)
- Hugo Rebelo
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto Vairão Portugal.,CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Instituto Superior de Agronomia, Lisboa, Portugal CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Instituto Superior de Agronomia Lisboa Portugal
| | - Sónia Ferreira
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto Vairão Portugal
| | - Francisco Amorim
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto Vairão Portugal
| | - Pedro Horta
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal Departamento de Biologia, Faculdade de Ciências, Universidade do Porto Porto Portugal.,CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto Vairão Portugal
| | - Helena Raposeira
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal Departamento de Biologia, Faculdade de Ciências, Universidade do Porto Porto Portugal.,CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto Vairão Portugal
| | - Helena Santos
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto Vairão Portugal
| | - Pedro Beja
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto Vairão Portugal.,CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Instituto Superior de Agronomia, Lisboa, Portugal CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Instituto Superior de Agronomia Lisboa Portugal
| | - Vanessa A Mata
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto Vairão Portugal
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The Octocorals of Dongsha Atoll (South China Sea): An Iterative Approach to Species Identification Using Classical Taxonomy and Molecular Barcodes. Zool Stud 2018; 57:e50. [PMID: 31966290 DOI: 10.6620/zs.2018.57-50] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 09/16/2018] [Indexed: 01/04/2023]
Abstract
Yehuda Benayahu, Leendert Pieter van Ofwegen, Chang-feng Dai, Ming-Shiou Jeng, Keryea Soong, Alex Shlagman, Samuel W. Du, Prudence Hong, Nimrah H. Imam, Alice Chung, Tiana Wu, and Catherine S. McFadden (2018) Surveys of octocorals from Dongsha Atoll, Taiwan were conducted during 2011, 2013 and 2015 by SCUBA at a depth range of 6-25 m. The collections yielded ~540 specimens, encompassing the variety of taxa occurring in the explored sites; estimates of their abundances were also recorded. Dongsha features a highly diverse octocoral fauna, and octocorals are the dominant benthic organisms in the surveyed reef sites, often covering the majority of the hard substratum. Specimens were identified to the genus and species levels based on an iterative approach that integrates classical taxonomy with character-based molecular barcodes. A total of 51 nominal species representing 20 genera belonging to seven families were recorded, plus ~30 colonies that could only be assigned to a genus. Members of the family Alcyoniidae were the most abundant and diverse taxa, with 27 nominal species plus at least one potentially new, undescribed species of Sinularia, and 5-7 species each of Cladiella, Lobophytum and Sarcophyton. Problems with the taxonomic identification and phylogenetic relationships of species in these genera are discussed. The peculiarity of the Dongsha octocoral species composition is noted, and the composition is also compared to the other Taiwanese reef systems.
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Dormontt EE, van Dijk KJ, Bell KL, Biffin E, Breed MF, Byrne M, Caddy-Retalic S, Encinas-Viso F, Nevill PG, Shapcott A, Young JM, Waycott M, Lowe AJ. Advancing DNA Barcoding and Metabarcoding Applications for Plants Requires Systematic Analysis of Herbarium Collections—An Australian Perspective. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00134] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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Yu M, Jiao L, Guo J, Wiedenhoeft AC, He T, Jiang X, Yin Y. DNA barcoding of vouchered xylarium wood specimens of nine endangered Dalbergia species. PLANTA 2017; 246:1165-1176. [PMID: 28825134 DOI: 10.1007/s00425-017-2758-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 08/08/2017] [Indexed: 06/07/2023]
Abstract
ITS2+ trnH - psbA was the best combination of DNA barcode to resolve the Dalbergia wood species studied. We demonstrate the feasibility of building a DNA barcode reference database using xylarium wood specimens. The increase in illegal logging and timber trade of CITES-listed tropical species necessitates the development of unambiguous identification methods at the species level. For these methods to be fully functional and deployable for law enforcement, they must work using wood or wood products. DNA barcoding of wood has been promoted as a promising tool for species identification; however, the main barrier to extensive application of DNA barcoding to wood is the lack of a comprehensive and reliable DNA reference library of barcodes from wood. In this study, xylarium wood specimens of nine Dalbergia species were selected from the Wood Collection of the Chinese Academy of Forestry and DNA was then extracted from them for further PCR amplification of eight potential DNA barcode sequences (ITS2, matK, trnL, trnH-psbA, trnV-trnM1, trnV-trnM2, trnC-petN, and trnS-trnG). The barcodes were tested singly and in combination for species-level discrimination ability by tree-based [neighbor-joining (NJ)] and distance-based (TaxonDNA) methods. We found that the discrimination ability of DNA barcodes in combination was higher than any single DNA marker among the Dalbergia species studied, with the best two-marker combination of ITS2+trnH-psbA analyzed with NJ trees performing the best (100% accuracy). These barcodes are relatively short regions (<350 bp) and amplification reactions were performed with high success (≥90%) using wood as the source material, a necessary factor to apply DNA barcoding to timber trade. The present results demonstrate the feasibility of using vouchered xylarium specimens to build DNA barcoding reference databases.
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Affiliation(s)
- Min Yu
- Department of Wood Anatomy and Utilization, Chinese Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing, 100091, China
- Wood Collections (WOODPEDIA), Chinese Academy of Forestry, Beijing, 100091, China
| | - Lichao Jiao
- Department of Wood Anatomy and Utilization, Chinese Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing, 100091, China
- Wood Collections (WOODPEDIA), Chinese Academy of Forestry, Beijing, 100091, China
| | - Juan Guo
- Department of Wood Anatomy and Utilization, Chinese Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing, 100091, China
- Wood Collections (WOODPEDIA), Chinese Academy of Forestry, Beijing, 100091, China
| | - Alex C Wiedenhoeft
- Center for Wood Anatomy Research, USDA Forest Service, Forest Products Laboratory, Madison, WI, 53726, USA
- Department of Botany, University of Wisconsin, Madison, WI, 53706, USA
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN, 47907, USA
- Ciências Biológicas (Botânica), Univesidade Estadual Paulista, Botucatu, São Paulo, Brazil
| | - Tuo He
- Department of Wood Anatomy and Utilization, Chinese Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing, 100091, China
- Wood Collections (WOODPEDIA), Chinese Academy of Forestry, Beijing, 100091, China
| | - Xiaomei Jiang
- Department of Wood Anatomy and Utilization, Chinese Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing, 100091, China
- Wood Collections (WOODPEDIA), Chinese Academy of Forestry, Beijing, 100091, China
| | - Yafang Yin
- Department of Wood Anatomy and Utilization, Chinese Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing, 100091, China.
- Wood Collections (WOODPEDIA), Chinese Academy of Forestry, Beijing, 100091, China.
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Russo D, Ancillotto L, Hughes AC, Galimberti A, Mori E. Collection of voucher specimens for bat research: conservation, ethical implications, reduction, and alternatives. Mamm Rev 2017. [DOI: 10.1111/mam.12095] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Danilo Russo
- Wildlife Research Unit; Laboratorio di Ecologia Applicata; Sezione di Biologia e Protezione dei Sistemi Agrari e Forestali; Dipartimento di Agraria; Università degli Studi di Napoli Federico II; via Università 100 80055 Portici Napoli Italy
- School of Biological Sciences; University of Bristol; 24 Tyndall Avenue BS8 1TQ Bristol UK
| | - Leonardo Ancillotto
- Wildlife Research Unit; Laboratorio di Ecologia Applicata; Sezione di Biologia e Protezione dei Sistemi Agrari e Forestali; Dipartimento di Agraria; Università degli Studi di Napoli Federico II; via Università 100 80055 Portici Napoli Italy
| | - Alice C. Hughes
- Xishuangbanna Tropical Botanical Garden; Chinese Academy of Sciences; Menglun Jinghong China
| | - Andrea Galimberti
- ZooPlantLab; BTBS; Dipartimento di Biotecnologie e Bioscienze; Università degli Studi di Milano Bicocca; Piazza della Scienza 2 20126 Milano Italy
| | - Emiliano Mori
- Research Unit of Behavioural Ecology; Ethology and Wildlife Management; Department of Life Sciences; University of Siena; via P.A. Mattioli 4 53100 Siena Italy
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Lemaitre R, Felder DL, Poupin J. Discovery of a new micro-pagurid fauna (Crustacea: Decapoda: Paguridae) in the Lesser Antilles, Caribbean Sea. ZOOSYSTEMA 2017. [DOI: 10.5252/z2017n2a1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Rafael Lemaitre
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 4210 Silver Hill Road, Suitland, MD 20746 (United States)
| | - Darryl L. Felder
- Department of Biology and Laboratory for Crustacean Research, University of Louisiana at Lafayette, P.O. Box 42451, Lafayette, Louisiana 70504-2451 (United States)
| | - Joseph Poupin
- Institut de Recherche de l'École navale, IRENav, Écoles navale et groupe des écoles du Poulmic, CC 600 — Lanvéoc, F-29240 Brest cedex 09 (France)
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12
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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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13
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Jaksch K, Eschner A, Rintelen TV, Haring E. DNA analysis of molluscs from a museum wet collection: a comparison of different extraction methods. BMC Res Notes 2016; 9:348. [PMID: 27430899 PMCID: PMC4950716 DOI: 10.1186/s13104-016-2147-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 07/01/2016] [Indexed: 11/25/2022] Open
Abstract
Background DNA isolation and PCR amplification from molluscan taxa is considered as problematic because polysaccharides in tissue and mucus presumably co-precipitate with the DNA and inhibit the activity of DNA polymerase. In the present study we tested two common extraction methods on specimens from the mollusc collection of the Natural History Museum Vienna (NHMW). We analysed a broad variety of taxa covering a large temporal span (acquisition years 1877 to 1999), which distinguishes our study from previous ones where mostly fresh material was used. We also took other factors into account: effects of sample age, effects of formaldehyde treatment and taxon-specific problems. We used several primer combinations to amplify amplicons of different lengths of two mitochondrial genes: cytochrome c oxidase subunit 1 (COI) and 16S rRNA gene (16S). Results Overall PCR success was 43 % in the 576 extractions (including all primer combinations). The smallest amplicon (~240 bp) showed the best results (49 % positive reactions), followed by the 400 bp amplicon (40.5 %). Both short sections yielded significantly better results than the 700 bp long amplicon (27 %). Comparatively, the Gen-ial-First, All-tissue DNA-Kit—extraction method performed significantly better than Promega-Tissue and Hair Extraction Kit. Generally, PCR success is age-dependent. Nonetheless, we were able to obtain the longest amplicon even from 137-year-old material. Importantly, formaldehyde traces did not totally inhibit amplification success, although very high concentrations did. Conclusions Museum material has gained importance for DNA analysis in recent years, especially for DNA barcoding projects. In some cases, however, the amplification of the standard barcoding region (partial sequence of the COI) is problematic with old material. Our study clearly shows that the COI barcoding region could be amplified in up to 49 % of PCRs (varying with amplicon length), which is, for museum samples, quite a high percentage. The difference between extraction methods was minimal and we recommend using an established kit for a first attempt because experience and routine in handling might be more important than slight performance differences of the various kits. Finally, we identify fixation, storage, sample conservation and documentation of the specimens’ history rather than the DNA extraction method to be the most crucial factors for PCR success. Electronic supplementary material The online version of this article (doi:10.1186/s13104-016-2147-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Katharina Jaksch
- Central Research Laboratories, Natural History Museum Vienna, Burgring 7, 1010, Vienna, Austria. .,Department of Integrative Zoology, University of Vienna, Althanstraße 14, 1090, Vienna, Austria.
| | - Anita Eschner
- Third Zoological Department, Natural History Museum Vienna, Burgring 7, 1010, Vienna, Austria
| | - Thomas V Rintelen
- Leibniz Institute for Research on Evolution and Biodiversity, Museum für Naturkunde, Invalidenstraße 43, 10115, Berlin, Germany
| | - Elisabeth Haring
- Central Research Laboratories, Natural History Museum Vienna, Burgring 7, 1010, Vienna, Austria.,Department of Integrative Zoology, University of Vienna, Althanstraße 14, 1090, Vienna, Austria
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14
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Castelin M, Van Steenkiste N, Pante E, Harbo R, Lowe G, Gilmore SR, Therriault TW, Abbott CL. A new integrative framework for large-scale assessments of biodiversity and community dynamics, using littoral gastropods and crabs of British Columbia, Canada. Mol Ecol Resour 2016; 16:1322-1339. [DOI: 10.1111/1755-0998.12534] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 03/18/2016] [Accepted: 03/18/2016] [Indexed: 11/27/2022]
Affiliation(s)
- M. Castelin
- Pacific Biological Station; Fisheries and Oceans Canada; 3190 Hammond Bay Road Nanaimo BC Canada V9T 6N7
| | - N. Van Steenkiste
- Pacific Biological Station; Fisheries and Oceans Canada; 3190 Hammond Bay Road Nanaimo BC Canada V9T 6N7
| | - E. Pante
- LIENSs Laboratory; UMR 7266 CNRS-Université de La Rochelle; 2 rue Olympe de Gouges La Rochelle 17000 France
| | - R. Harbo
- Invertebrate Zoology; Royal BC Museum; 675 Belleville Street Victoria BC Canada V8W 9W2
| | - G. Lowe
- Pacific Biological Station; Fisheries and Oceans Canada; 3190 Hammond Bay Road Nanaimo BC Canada V9T 6N7
| | - S. R. Gilmore
- Pacific Biological Station; Fisheries and Oceans Canada; 3190 Hammond Bay Road Nanaimo BC Canada V9T 6N7
| | - T. W. Therriault
- Pacific Biological Station; Fisheries and Oceans Canada; 3190 Hammond Bay Road Nanaimo BC Canada V9T 6N7
| | - C. L. Abbott
- Pacific Biological Station; Fisheries and Oceans Canada; 3190 Hammond Bay Road Nanaimo BC Canada V9T 6N7
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15
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Chambers EA, Hebert PDN. Assessing DNA Barcodes for Species Identification in North American Reptiles and Amphibians in Natural History Collections. PLoS One 2016; 11:e0154363. [PMID: 27116180 PMCID: PMC4846166 DOI: 10.1371/journal.pone.0154363] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 04/12/2016] [Indexed: 11/19/2022] Open
Abstract
Background High rates of species discovery and loss have led to the urgent need for more rapid assessment of species diversity in the herpetofauna. DNA barcoding allows for the preliminary identification of species based on sequence divergence. Prior DNA barcoding work on reptiles and amphibians has revealed higher biodiversity counts than previously estimated due to cases of cryptic and undiscovered species. Past studies have provided DNA barcodes for just 14% of the North American herpetofauna, revealing the need for expanded coverage. Methodology/Principal Findings This study extends the DNA barcode reference library for North American herpetofauna, assesses the utility of this approach in aiding species delimitation, and examines the correspondence between current species boundaries and sequence clusters designated by the BIN system. Sequences were obtained from 730 specimens, representing 274 species (43%) from the North American herpetofauna. Mean intraspecific divergences were 1% and 3%, while average congeneric sequence divergences were 16% and 14% in amphibians and reptiles, respectively. BIN assignments corresponded with current species boundaries in 79% of amphibians, 100% of turtles, and 60% of squamates. Deep divergences (>2%) were noted in 35% of squamate and 16% of amphibian species, and low divergences (<2%) occurred in 12% of reptiles and 23% of amphibians, patterns reflected in BIN assignments. Sequence recovery declined with specimen age, and variation in recovery success was noted among collections. Within collections, barcodes effectively flagged seven mislabeled tissues, and barcode fragments were recovered from five formalin-fixed specimens. Conclusions/Significance This study demonstrates that DNA barcodes can effectively flag errors in museum collections, while BIN splits and merges reveal taxa belonging to deeply diverged or hybridizing lineages. This study is the first effort to compile a reference library of DNA barcodes for herpetofauna on a continental scale.
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Affiliation(s)
- E. Anne Chambers
- Department of Integrative Biology, University of Texas, Austin, Texas, United States of America
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
- * E-mail:
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
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16
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Morard R, Escarguel G, Weiner AKM, André A, Douady CJ, Wade CM, Darling KF, Ujiié Y, Seears HA, Quillévéré F, de Garidel-Thoron T, de Vargas C, Kucera M. Nomenclature for the Nameless: A Proposal for an Integrative Molecular Taxonomy of Cryptic Diversity Exemplified by Planktonic Foraminifera. Syst Biol 2016; 65:925-40. [PMID: 27073250 DOI: 10.1093/sysbio/syw031] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 04/04/2016] [Indexed: 11/12/2022] Open
Abstract
Investigations of biodiversity, biogeography, and ecological processes rely on the identification of "species" as biologically significant, natural units of evolution. In this context, morphotaxonomy only provides an adequate level of resolution if reproductive isolation matches morphological divergence. In many groups of organisms, morphologically defined species often disguise considerable genetic diversity, which may be indicative of the existence of cryptic species. The diversity hidden by morphological species can be disentangled through genetic surveys, which also provide access to data on the ecological distribution of genetically circumscribed units. These units can be identified by unique DNA sequence motifs and allow studies of evolutionary and ecological processes at different levels of divergence. However, the nomenclature of genetically circumscribed units within morphological species is not regulated and lacks stability. This represents a major obstacle to efforts to synthesize and communicate data on genetic diversity for multiple stakeholders. We have been confronted with such an obstacle in our work on planktonic foraminifera, where the stakeholder community is particularly diverse, involving geochemists, paleoceanographers, paleontologists, and biologists, and the lack of stable nomenclature beyond the level of formal morphospecies prevents effective transfer of knowledge. To circumvent this problem, we have designed a stable, reproducible, and flexible nomenclature system for genetically circumscribed units, analogous to the principles of a formal nomenclature system. Our system is based on the definition of unique DNA sequence motifs collocated within an individual, their typification (in analogy with holotypes), utilization of their hierarchical phylogenetic structure to define levels of divergence below that of the morphospecies, and a set of nomenclature rules assuring stability. The resulting molecular operational taxonomic units remain outside the domain of current nomenclature codes, but are linked to formal morphospecies as regulated by the codes. Subsequently, we show how this system can be applied to classify genetically defined units using the SSU rDNA marker in planktonic foraminifera and we highlight its potential use for other groups of organisms where similarly high levels of connectivity between molecular and formal taxonomies can be achieved.
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Affiliation(s)
- Raphaël Morard
- MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, 28359 Bremen, Germany,
| | - Gilles Escarguel
- Université de Lyon; UMR5023 Ecologie des Hydrosystémes Naturels et Anthropisés; Universiteì Lyon 1; ENTPE; CNRS; 6 rue Raphaël Dubois, 69622 Villeurbanne, France
| | - Agnes K M Weiner
- MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, 28359 Bremen, Germany, Japan Agency for Marine Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Kanagawa, Japan
| | - Aurore André
- Université de Reims-Champagne-Ardenne, UFR Sciences Exactes et Naturelles, Campus Moulin de la Housse, Batiment 18, 51100 REIMS, France
| | - Christophe J Douady
- Université de Lyon; UMR5023 Ecologie des Hydrosystémes Naturels et Anthropisés; Universiteì Lyon 1; ENTPE; CNRS; 6 rue Raphaël Dubois, 69622 Villeurbanne, France, Institut Universitaire de France, 103 Boulevard Saint-Michel, 75005 Paris, France
| | - Christopher M Wade
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Kate F Darling
- School of GeoSciences, University of Edinburgh, Edinburgh EH9 3JW, UK, School of Geography and GeoSciences, University of St Andrews, Fife KY16 9AL, UK
| | - Yurika Ujiié
- Department of Biology, Shinshu University, Asahi3-1-1, Matsumoto, Nagano 390-8621, Japan
| | - Heidi A Seears
- Department of Biology, Gilmer Hall, University of Virginia, 485 McCormick Road, Charlottesville, VA 22904, USA
| | - Frédéric Quillévéré
- Univ Lyon, Université Lyon 1, ENS de Lyon, CNRS, UMR 5276 LGL-TPE, F-69622 Villeurbanne, France
| | - Thibault de Garidel-Thoron
- Centre Européen de Recherche et d'Enseignement de Géosciences de l'Environnement, Centre National de la Recherche Scientifique, et Aix-Marseille Université, Aix-en-Provence, France
| | - Colomban de Vargas
- Centre National de la Recherche Scientifique, UMR 7144, EPEP, Station Biologique de Roscoff, 29680 Roscoff, France, and Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Michal Kucera
- MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, 28359 Bremen, Germany
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17
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Hartvig I, Czako M, Kjær ED, Nielsen LR, Theilade I. The Use of DNA Barcoding in Identification and Conservation of Rosewood (Dalbergia spp.). PLoS One 2015; 10:e0138231. [PMID: 26375850 PMCID: PMC4573973 DOI: 10.1371/journal.pone.0138231] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 08/26/2015] [Indexed: 11/19/2022] Open
Abstract
The genus Dalbergia contains many valuable timber species threatened by illegal logging and deforestation, but knowledge on distributions and threats is often limited and accurate species identification difficult. The aim of this study was to apply DNA barcoding methods to support conservation efforts of Dalbergia species in Indochina. We used the recommended rbcL, matK and ITS barcoding markers on 95 samples covering 31 species of Dalbergia, and tested their discrimination ability with both traditional distance-based as well as different model-based machine learning methods. We specifically tested whether the markers could be used to solve taxonomic confusion concerning the timber species Dalbergia oliveri, and to identify the CITES-listed Dalbergia cochinchinensis. We also applied the barcoding markers to 14 samples of unknown identity. In general, we found that the barcoding markers discriminated among Dalbergia species with high accuracy. We found that ITS yielded the single highest discrimination rate (100%), but due to difficulties in obtaining high-quality sequences from degraded material, the better overall choice for Dalbergia seems to be the standard rbcL+matK barcode, as this yielded discrimination rates close to 90% and amplified well. The distance-based method TaxonDNA showed the highest identification rates overall, although a more complete specimen sampling is needed to conclude on the best analytic method. We found strong support for a monophyletic Dalbergia oliveri and encourage that this name is used consistently in Indochina. The CITES-listed Dalbergia cochinchinensis was successfully identified, and a species-specific assay can be developed from the data generated in this study for the identification of illegally traded timber. We suggest that the use of DNA barcoding is integrated into the work flow during floristic studies and at national herbaria in the region, as this could significantly increase the number of identified specimens and improve knowledge about species distributions.
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Affiliation(s)
- Ida Hartvig
- Forest Genetics and Diversity, Department of Geosciences and Natural Resource Management, University of Copenhagen, Frederiksberg, Denmark
| | - Mihaly Czako
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, United States of America
| | - Erik Dahl Kjær
- Forest Genetics and Diversity, Department of Geosciences and Natural Resource Management, University of Copenhagen, Frederiksberg, Denmark
| | - Lene Rostgaard Nielsen
- Forest Genetics and Diversity, Department of Geosciences and Natural Resource Management, University of Copenhagen, Frederiksberg, Denmark
| | - Ida Theilade
- Global Development, Department of Food and Resource Economics, University of Copenhagen, Frederiksberg, Denmark
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18
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Krehenwinkel H, Pekar S. An Analysis of Factors Affecting Genotyping Success from Museum Specimens Reveals an Increase of Genetic and Morphological Variation during a Historical Range Expansion of a European Spider. PLoS One 2015; 10:e0136337. [PMID: 26309219 PMCID: PMC4550360 DOI: 10.1371/journal.pone.0136337] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 08/01/2015] [Indexed: 11/19/2022] Open
Abstract
Natural history collections house an enormous amount of plant and animal specimens, which constitute a promising source for molecular analyses. Storage conditions differ among taxa and can have a dramatic effect on the success of DNA work. Here, we analyze the feasibility of DNA extraction from ethanol preserved spiders (Araneae). We tested genotyping success using several hundred specimens of the wasp spider, Argiope bruennichi, deposited in two large German natural history collections. We tested the influence of different factors on the utility of specimens for genotyping. Our results show that not the specimen’s age, but the museum collection is a major predictor of genotyping success. These results indicate that long term storage conditions should be optimized in natural history museums to assure the utility of collections for DNA work. Using historical material, we also traced historical genetic and morphological variation in the course of a poleward range expansion of A. bruennichi by comparing contemporary and historical specimens from a native and an invasive population in Germany. We show that the invasion of A. bruennichi is tightly correlated with an historical increase of genetic and phenotypic variation in the invasive population.
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Affiliation(s)
- Henrik Krehenwinkel
- Max Planck Institute for Evolutionary Biology, Department of Evolutionary Genetics, August Thienemann Strasse 2, 24306, Plön, Germany
- University of California, Department of Environmental Science, Policy, and Management, 130 Mulford Hall, Berkeley, United States of America
- * E-mail:
| | - Stano Pekar
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
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19
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Saslis-Lagoudakis CH, Bruun-Lund S, Iwanycki NE, Seberg O, Petersen G, Jäger AK, Rønsted N. Identification of common horsetail (Equisetum arvense L.; Equisetaceae) using Thin Layer Chromatography versus DNA barcoding. Sci Rep 2015; 5:11942. [PMID: 26165523 PMCID: PMC4499799 DOI: 10.1038/srep11942] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 05/11/2015] [Indexed: 11/09/2022] Open
Abstract
The global herbal products market has grown in recent years, making regulation of these products paramount for public healthcare. For instance, the common horsetail (Equisetum arvense L.) is used in numerous herbal products, but it can be adulterated with closely related species, especially E. palustre L. that can produce toxic alkaloids. As morphology-based identification is often difficult or impossible, the identification of processed material can be aided by molecular techniques. In this study, we explore two molecular identification techniques as methods of testing the purity of these products: a Thin Layer Chromatography approach (TLC-test) included in the European Pharmacopoeia and a DNA barcoding approach, used in recent years to identify material in herbal products. We test the potential of these methods for distinguishing and identifying these species using material from herbarium collections and commercial herbal products. We find that both methods can discriminate between the two species and positively identify E. arvense. The TLC-test is more cost- and time-efficient, but DNA barcoding is more powerful in determining the identity of adulterant species. Our study shows that, although DNA barcoding presents certain advantages, other established laboratory methods can perform as well or even better in confirming species' identity in herbal products.
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Affiliation(s)
- C. Haris Saslis-Lagoudakis
- Evolutionary Genomics Section, Natural History Museum of Denmark, Sølvgade 83S, Copenhagen, DK-1307, Denmark
| | - Sam Bruun-Lund
- Evolutionary Genomics Section, Natural History Museum of Denmark, Sølvgade 83S, Copenhagen, DK-1307, Denmark
| | - Natalie E. Iwanycki
- Evolutionary Genomics Section, Natural History Museum of Denmark, Sølvgade 83S, Copenhagen, DK-1307, Denmark
| | - Ole Seberg
- Evolutionary Genomics Section, Natural History Museum of Denmark, Sølvgade 83S, Copenhagen, DK-1307, Denmark
| | - Gitte Petersen
- Evolutionary Genomics Section, Natural History Museum of Denmark, Sølvgade 83S, Copenhagen, DK-1307, Denmark
| | - Anna K. Jäger
- Natural Products Research, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, Copenhagen, DK-2100, Denmark
| | - Nina Rønsted
- Evolutionary Genomics Section, Natural History Museum of Denmark, Sølvgade 83S, Copenhagen, DK-1307, Denmark
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20
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Lu L, Ge D, Chesters D, Ho SYW, Ma Y, Li G, Wen Z, Wu Y, Wang J, Xia L, Liu J, Guo T, Zhang X, Zhu C, Yang Q, Liu Q. Molecular phylogeny and the underestimated species diversity of the endemic white-bellied rat (Rodentia: Muridae:Niviventer) in Southeast Asia and China. ZOOL SCR 2015. [DOI: 10.1111/zsc.12117] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Liang Lu
- State Key Laboratory for Infectious Disease Prevention and Control; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases; National Institute for Communicable Disease Control and Prevention; Chinese Center for Disease Control and Prevention; Beijing 102206 China
| | - Deyan Ge
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beichen West Road, Chaoyang District Beijing 100101 China
| | - Douglas Chesters
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beichen West Road, Chaoyang District Beijing 100101 China
| | - Simon Y. W. Ho
- School of Biological Sciences; University of Sydney; Sydney NSW 2006 Australia
| | - Ying Ma
- Qinghai Institute for Endemic Disease Prevention and Control; Qinghai 811602 China
| | - Guichang Li
- State Key Laboratory for Infectious Disease Prevention and Control; National Institute for Communicable Disease Control and Prevention; Chinese Center for Disease Control and Prevention; Beijing 102206 China
| | - Zhixin Wen
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beichen West Road, Chaoyang District Beijing 100101 China
| | - Yongjie Wu
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beichen West Road, Chaoyang District Beijing 100101 China
| | - Jun Wang
- State Key Laboratory for Infectious Disease Prevention and Control; National Institute for Communicable Disease Control and Prevention; Chinese Center for Disease Control and Prevention; Beijing 102206 China
| | - Lin Xia
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beichen West Road, Chaoyang District Beijing 100101 China
| | - Jingli Liu
- State Key Laboratory for Infectious Disease Prevention and Control; National Institute for Communicable Disease Control and Prevention; Chinese Center for Disease Control and Prevention; Beijing 102206 China
| | - Tianyu Guo
- Institute of Health Quarantine; Chinese Academy of Inspection and Quarantine; Beijing 100020 China
| | - Xiaolong Zhang
- Institute of Health Quarantine; Chinese Academy of Inspection and Quarantine; Beijing 100020 China
| | - Chaodong Zhu
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beichen West Road, Chaoyang District Beijing 100101 China
| | - Qisen Yang
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beichen West Road, Chaoyang District Beijing 100101 China
| | - Qiyong Liu
- State Key Laboratory for Infectious Disease Prevention and Control; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases; National Institute for Communicable Disease Control and Prevention; Chinese Center for Disease Control and Prevention; Beijing 102206 China
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21
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Deharveng L, Bedos A, Daugeron C, Villemant C, Judson MLI. Organization, usefulness and limitations of an ATBI (All Taxa Biodiversity Inventory): the inventory of terrestrial invertebrates in the Mercantour National Park. ZOOSYSTEMA 2015. [DOI: 10.5252/z2015n1a1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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22
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Aznar-Cormano L, Brisset J, Chan TY, Corbari L, Puillandre N, Utge J, Zbinden M, Zuccon D, Samadi S. An improved taxonomic sampling is a necessary but not sufficient condition for resolving inter-families relationships in Caridean decapods. Genetica 2015; 143:195-205. [DOI: 10.1007/s10709-014-9807-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2014] [Accepted: 12/10/2014] [Indexed: 12/28/2022]
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23
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Cowart DA, Pinheiro M, Mouchel O, Maguer M, Grall J, Miné J, Arnaud-Haond S. Metabarcoding is powerful yet still blind: a comparative analysis of morphological and molecular surveys of seagrass communities. PLoS One 2015; 10:e0117562. [PMID: 25668035 PMCID: PMC4323199 DOI: 10.1371/journal.pone.0117562] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 12/27/2014] [Indexed: 11/26/2022] Open
Abstract
In the context of the sixth wave of extinction, reliable surveys of biodiversity are increasingly needed to infer the cause and consequences of species and community declines, identify early warning indicators of tipping points, and provide reliable impact assessments before engaging in activities with potential environmental hazards. DNA metabarcoding has emerged as having potential to provide speedy assessment of community structure from environmental samples. Here we tested the reliability of metabarcoding by comparing morphological and molecular inventories of invertebrate communities associated with seagrasses through estimates of alpha and beta diversity, as well as the identification of the most abundant taxa. Sediment samples were collected from six Zostera marina seagrass meadows across Brittany, France. Metabarcoding surveys were performed using both mitochondrial (Cytochrome Oxidase I) and nuclear (small subunit 18S ribosomal RNA) markers, and compared to morphological inventories compiled by a long-term benthic monitoring network. A sampling strategy was defined to enhance performance and accuracy of results by preventing the dominance of larger animals, boosting statistical support through replicates, and using two genes to compensate for taxonomic biases. Molecular barcodes proved powerful by revealing a remarkable level of diversity that vastly exceeded the morphological survey, while both surveys identified congruent differentiation of the meadows. However, despite the addition of individual barcodes of common species into taxonomic reference databases, the retrieval of only 36% of these species suggest that the remaining were either not present in the molecular samples or not detected by the molecular screening. This finding exemplifies the necessity of comprehensive and well-curated taxonomic reference libraries and multi-gene surveys. Overall, results offer methodological guidelines and support for metabarcoding as a powerful and repeatable method of characterizing communities, while also presenting suggestions for improvement, including implementation of pilot studies prior to performing full "blind" metabarcoding assessments to optimize sampling and amplification protocols.
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Affiliation(s)
- Dominique A. Cowart
- IFREMER (Institut Français de Recherche pour l’Exploitation de la MER), Unité Environnement Profond, Département des Ressources physiques et Ecosystèmes de Fond de mer (REM), B.P. 70, 29280, Plouzané, France
| | - Miguel Pinheiro
- University of St. Andrews, Medical and Biological Sciences Building, North Haugh, St. Andrews, Fife, KY16 9TF, United Kingdom
| | - Olivier Mouchel
- IFREMER (Institut Français de Recherche pour l’Exploitation de la MER), Unité Environnement Profond, Département des Ressources physiques et Ecosystèmes de Fond de mer (REM), B.P. 70, 29280, Plouzané, France
| | - Marion Maguer
- Institut Universitaire Européen de la Mer (IUEM), Technopôle Brest-Iroiserue Dumont d’Urville, 29280, Plouzané, France
| | - Jacques Grall
- Institut Universitaire Européen de la Mer (IUEM), Technopôle Brest-Iroiserue Dumont d’Urville, 29280, Plouzané, France
| | - Jacques Miné
- Total Exploration & Production, Direction HSE, 2 Place Jean Millier, 92078, Paris la Défense, France
| | - Sophie Arnaud-Haond
- IFREMER (Institut Français de Recherche pour l’Exploitation de la MER), Unité Environnement Profond, Département des Ressources physiques et Ecosystèmes de Fond de mer (REM), B.P. 70, 29280, Plouzané, France
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24
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Pompanon F, Samadi S. Next generation sequencing for characterizing biodiversity: promises and challenges. Genetica 2015; 143:133-8. [PMID: 25613325 DOI: 10.1007/s10709-015-9816-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2014] [Accepted: 01/09/2015] [Indexed: 01/22/2023]
Abstract
DNA barcoding approaches are used to describe biodiversity by analysing specimens or environmental samples in taxonomic, phylogenetic and ecological studies. While sharing data among these disciplines would be highly valuable, this remains difficult because of contradictory requirements. The properties making a DNA barcode efficient for specimen identification or species delimitation are hardly reconcilable with those required for a powerful analysis of degraded DNA from environmental samples. The use of next generation sequencing methods open up the way towards the development of new markers (e.g., multilocus barcodes) that would overcome such limitations. However, several challenges should be taken up for coordinating actions at the interface between taxonomy, ecology, molecular biology and bioinformatics in order to develop methods and protocols compatible with both taxonomic and ecological studies.
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Affiliation(s)
- François Pompanon
- Laboratoire d'Ecologie Alpine, Univ. Grenoble Alpes, 38000, Grenoble, France,
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25
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Collins RA, Cruickshank RH. Known knowns, known unknowns, unknown unknowns and unknown knowns in DNA barcoding: a comment on Dowton et al. Syst Biol 2014; 63:1005-9. [PMID: 25116917 DOI: 10.1093/sysbio/syu060] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Rupert A Collins
- Laboratório de Evolução e Genética Animal, Departamento de Biologia, Universidade Federal do Amazonas, Av. Rodrigo Otávio, Manaus, Amazonas, Brazil and Department of Ecology, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, Canterbury, New Zealand
| | - Robert H Cruickshank
- Laboratório de Evolução e Genética Animal, Departamento de Biologia, Universidade Federal do Amazonas, Av. Rodrigo Otávio, Manaus, Amazonas, Brazil and Department of Ecology, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, Canterbury, New Zealand
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26
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Gippoliti S, Amori G, Castiglia R, Colangelo P, Capanna E. The relevance of Italian museum collections for research and conservation: the case of mammals. RENDICONTI LINCEI-SCIENZE FISICHE E NATURALI 2014. [DOI: 10.1007/s12210-014-0304-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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27
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Abstract
Taxonomy is the science that explores, describes, names, and classifies all organisms. In this introductory chapter, we highlight the major historical steps in the elaboration of this science that provides baseline data for all fields of biology and plays a vital role for society but is also an independent, complex, and sound hypothesis-driven scientific discipline.In a first part, we underline that plant taxonomy is one of the earliest scientific disciplines that emerged thousands of years ago, even before the important contributions of Greeks and Romans (e.g., Theophrastus, Pliny the Elder, and Dioscorides). In the fifteenth to sixteenth centuries, plant taxonomy benefited from the Great Navigations, the invention of the printing press, the creation of botanic gardens, and the use of the drying technique to preserve plant specimens. In parallel with the growing body of morpho-anatomical data, subsequent major steps in the history of plant taxonomy include the emergence of the concept of natural classification, the adoption of the binomial naming system (with the major role of Linnaeus) and other universal rules for the naming of plants, the formulation of the principle of subordination of characters, and the advent of the evolutionary thought. More recently, the cladistic theory (initiated by Hennig) and the rapid advances in DNA technologies allowed to infer phylogenies and to propose true natural, genealogy-based classifications.In a second part, we put the emphasis on the challenges that plant taxonomy faces nowadays. The still very incomplete taxonomic knowledge of the worldwide flora (the so-called taxonomic impediment) is seriously hampering conservation efforts that are especially crucial as biodiversity enters its sixth extinction crisis. It appears mainly due to insufficient funding, lack of taxonomic expertise, and lack of communication and coordination. We then review recent initiatives to overcome these limitations and to anticipate how taxonomy should and could evolve. In particular, the use of molecular data has been era-splitting for taxonomy and may allow an accelerated pace of species discovery. We examine both strengths and limitations of such techniques in comparison to morphology-based investigations, we give broad recommendations on the use of molecular tools for plant taxonomy, and we highlight the need for an integrative taxonomy based on evidence from multiple sources.
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28
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Ardura A, Planes S, Garcia-Vazquez E. Applications of DNA barcoding to fish landings: authentication and diversity assessment. Zookeys 2013; 365:49-65. [PMID: 24453550 PMCID: PMC3890670 DOI: 10.3897/zookeys.365.6409] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Accepted: 10/23/2013] [Indexed: 11/24/2022] Open
Abstract
DNA barcoding methodologies are being increasingly applied not only for scientific purposes but also for diverse real-life uses. Fisheries assessment is a potential niche for DNA barcoding, which serves for species authentication and may also be used for estimating within-population genetic diversity of exploited fish. Analysis of single-sequence barcodes has been proposed as a shortcut for measuring diversity in addition to the original purpose of species identification. Here we explore the relative utility of different mitochondrial sequences (12S rDNA, COI, cyt b, and D-Loop) for application as barcodes in fisheries sciences, using as case studies two marine and two freshwater catches of contrasting diversity levels. Ambiguous catch identification from COI and cyt b was observed. In some cases this could be attributed to duplicated names in databases, but in others it could be due to mitochondrial introgression between closely related species that may obscure species assignation from mtDNA. This last problem could be solved using a combination of mitochondrial and nuclear genes. We suggest to simultaneously analyze one conserved and one more polymorphic gene to identify species and assess diversity in fish catches.
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Affiliation(s)
- Alba Ardura
- University of Oviedo, Department of Functional Biology. C/ Julian Claveria s/n. 33006-Oviedo, Spain
| | - Serge Planes
- USR 3278 CNRS – EPHE. Centre de Recherche Insulaire et Observatoire de l’Environnement (CRIOBE) BP 1013 - 98 729, Papetoai, Moorea, Polynésie française
- Centre de Biologie et d’Ecologie Tropicale et Méditerranéenne, Université de Perpignan, 52 Av. Paul Alduy - 66860 Perpignan cedex, France
| | - Eva Garcia-Vazquez
- University of Oviedo, Department of Functional Biology. C/ Julian Claveria s/n. 33006-Oviedo, Spain
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29
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Fišer Pečnikar Ž, Buzan EV. 20 years since the introduction of DNA barcoding: from theory to application. J Appl Genet 2013; 55:43-52. [PMID: 24203863 DOI: 10.1007/s13353-013-0180-y] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Revised: 10/14/2013] [Accepted: 10/15/2013] [Indexed: 01/29/2023]
Abstract
Traditionally, taxonomic identification has relied upon morphological characters. In the last two decades, molecular tools based on DNA sequences of short standardised gene fragments, termed DNA barcodes, have been developed for species discrimination. The most common DNA barcode used in animals is a fragment of the cytochrome c oxidase (COI) mitochondrial gene, while for plants, two chloroplast gene fragments from the RuBisCo large subunit (rbcL) and maturase K (matK) genes are widely used. Information gathered from DNA barcodes can be used beyond taxonomic studies and will have far-reaching implications across many fields of biology, including ecology (rapid biodiversity assessment and food chain analysis), conservation biology (monitoring of protected species), biosecurity (early identification of invasive pest species), medicine (identification of medically important pathogens and their vectors) and pharmacology (identification of active compounds). However, it is important that the limitations of DNA barcoding are understood and techniques continually adapted and improved as this young science matures.
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Affiliation(s)
- Živa Fišer Pečnikar
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, 6000, Koper, Slovenia,
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30
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Henrich CJ, Beutler JA. Matching the power of high throughput screening to the chemical diversity of natural products. Nat Prod Rep 2013; 30:1284-98. [PMID: 23925671 PMCID: PMC3801163 DOI: 10.1039/c3np70052f] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Covering up to 2013. Application of high throughput screening technologies to natural product samples demands alterations in assay design as well as sample preparation in order to yield meaningful hit structures at the end of the campaign.
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Affiliation(s)
- Curtis J. Henrich
- Basic Science Program, SAIC-Frederick, Inc. Frederick National Lab
- Molecular Targets Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702 USA
| | - John A. Beutler
- Molecular Targets Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702 USA
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31
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Osmundson TW, Robert VA, Schoch CL, Baker LJ, Smith A, Robich G, Mizzan L, Garbelotto MM. Filling gaps in biodiversity knowledge for macrofungi: contributions and assessment of an herbarium collection DNA barcode sequencing project. PLoS One 2013; 8:e62419. [PMID: 23638077 PMCID: PMC3640088 DOI: 10.1371/journal.pone.0062419] [Citation(s) in RCA: 118] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 03/22/2013] [Indexed: 11/19/2022] Open
Abstract
Despite recent advances spearheaded by molecular approaches and novel technologies, species description and DNA sequence information are significantly lagging for fungi compared to many other groups of organisms. Large scale sequencing of vouchered herbarium material can aid in closing this gap. Here, we describe an effort to obtain broad ITS sequence coverage of the approximately 6000 macrofungal-species-rich herbarium of the Museum of Natural History in Venice, Italy. Our goals were to investigate issues related to large sequencing projects, develop heuristic methods for assessing the overall performance of such a project, and evaluate the prospects of such efforts to reduce the current gap in fungal biodiversity knowledge. The effort generated 1107 sequences submitted to GenBank, including 416 previously unrepresented taxa and 398 sequences exhibiting a best BLAST match to an unidentified environmental sequence. Specimen age and taxon affected sequencing success, and subsequent work on failed specimens showed that an ITS1 mini-barcode greatly increased sequencing success without greatly reducing the discriminating power of the barcode. Similarity comparisons and nonmetric multidimensional scaling ordinations based on pairwise distance matrices proved to be useful heuristic tools for validating the overall accuracy of specimen identifications, flagging potential misidentifications, and identifying taxa in need of additional species-level revision. Comparison of within- and among-species nucleotide variation showed a strong increase in species discriminating power at 1-2% dissimilarity, and identified potential barcoding issues (same sequence for different species and vice-versa). All sequences are linked to a vouchered specimen, and results from this study have already prompted revisions of species-sequence assignments in several taxa.
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Affiliation(s)
- Todd W. Osmundson
- Forest Pathology and Mycology Laboratory, Department of Environmental Science, Policy and Management, University of California, Berkeley, California, United States of America
| | - Vincent A. Robert
- Centraalbureau voor Schimmelcultures, CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands
| | - Conrad L. Schoch
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Lydia J. Baker
- Forest Pathology and Mycology Laboratory, Department of Environmental Science, Policy and Management, University of California, Berkeley, California, United States of America
| | - Amy Smith
- Forest Pathology and Mycology Laboratory, Department of Environmental Science, Policy and Management, University of California, Berkeley, California, United States of America
| | | | - Luca Mizzan
- Venice Museum of Natural History, Venice, Italy
| | - Matteo M. Garbelotto
- Forest Pathology and Mycology Laboratory, Department of Environmental Science, Policy and Management, University of California, Berkeley, California, United States of America
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32
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Cryptic diversity with wide salinity tolerance in the putative euryhalineTestudinella clypeata(Rotifera, Monogononta). Zool J Linn Soc 2013. [DOI: 10.1111/zoj.12020] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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33
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Young MK, McKelvey KS, Pilgrim KL, Schwartz MK. DNA
barcoding at riverscape scales: assessing biodiversity among fishes of the genus
C
ottus
(
T
eleostei) in northern
R
ocky
M
ountain streams. Mol Ecol Resour 2013; 13:583-95. [DOI: 10.1111/1755-0998.12091] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 01/24/2013] [Accepted: 02/06/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Michael K. Young
- U.S. Forest Service Rocky Mountain Research Station 800 East Beckwith Avenue Missoula MT 59801 USA
| | - Kevin S. McKelvey
- U.S. Forest Service Rocky Mountain Research Station 800 East Beckwith Avenue Missoula MT 59801 USA
| | - Kristine L. Pilgrim
- U.S. Forest Service Rocky Mountain Research Station 800 East Beckwith Avenue Missoula MT 59801 USA
| | - Michael K. Schwartz
- U.S. Forest Service Rocky Mountain Research Station 800 East Beckwith Avenue Missoula MT 59801 USA
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Murphy RW, Crawford AJ, Bauer AM, Che J, Donnellan SC, Fritz U, Haddad CF, Nagy ZT, Poyarkov NA, Vences M, Wang W, Zhang Y. Cold Code: the global initiative to
DNA
barcode amphibians and nonavian reptiles. Mol Ecol Resour 2012. [DOI: 10.1111/1755-0998.12050] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Robert W. Murphy
- State Key Laboratory of Genetic Resources and Evolution State, and Yunnan Laboratory of Molecular Biology of Domestic Animals Kunming Institute of Zoology Chinese Academy of Sciences Kunming 650223 China
- Centre for Biodiversity and Conservation Biology Royal Ontario Museum 100 Queen's Park Toronto Canada M5S 2C6
| | - Andrew J. Crawford
- Department of Biological Sciences Universidad de los Andes A.A. 4976 Bogotá Colombia
- Smithsonian Tropical Research Institute Apartado 0843‐03092 Panamá Republic of Panama
| | - Aaron M. Bauer
- Department of Biology Villanova University 800 Lancaster Avenue Villanova PA 19085‐1699 USA
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution State, and Yunnan Laboratory of Molecular Biology of Domestic Animals Kunming Institute of Zoology Chinese Academy of Sciences Kunming 650223 China
| | - Stephen C. Donnellan
- Evolutionary Biology Unit South Australian Museum North Terrace Adelaide SA 5000 Australia
| | - Uwe Fritz
- Museum of Zoology Koenigsbruecker Landstr. 159 Dresden 01109 Germany
| | - Célio F.B. Haddad
- Departmento de Zoologia Instituto de Biociências Universidade Estadual Paulista Av. 24 A 1515 Rio Claro 13506‐900 São Paulo Brazil
| | - Zoltán T. Nagy
- Joint Experimental Molecular Unit Royal Belgian Institute of Natural Sciences Brussels Belgium
| | - Nikolay A. Poyarkov
- Department of Vertebrate Zoology Moscow MV Lomonosov State University Moscow 119991 Russia
| | - Miguel Vences
- Zoological Institute Technical University of Braunschweig Mendelssohnstr. 4 Braunschweig 38106 Germany
| | - Wen‐zhi Wang
- State Key Laboratory of Genetic Resources and Evolution State, and Yunnan Laboratory of Molecular Biology of Domestic Animals Kunming Institute of Zoology Chinese Academy of Sciences Kunming 650223 China
| | - Ya‐ping Zhang
- State Key Laboratory of Genetic Resources and Evolution State, and Yunnan Laboratory of Molecular Biology of Domestic Animals Kunming Institute of Zoology Chinese Academy of Sciences Kunming 650223 China
- Laboratory for Conservation and Utilization of Bio‐resources Yunnan University Kunming 650091 China
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35
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Zuccon D, Brisset J, Corbari L, Puillandre N, Utge J, Samadi S. An optimised protocol for barcoding museum collections of decapod crustaceans: a case-study for a 10 - 40-years-old collection. INVERTEBR SYST 2012. [DOI: 10.1071/is12027] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The sequencing of the crustacean collection of the MNHN, Paris, constitutes a promising yet very challenging barcoding project. For the collection’s crustacean specimens preserved in ethanol, some of which were collected up to 40 years ago, the conventional COI barcoding procedure of amplification with Folmer primers failed for more than half of the specimens (58%, n = 1920). We hypothesised that this failure may have been due to incompatible mismatches between the crustaceans targeted and the Folmer primer sequences and/or the amount of degradation of the DNA extracted from museum specimens. The comparison of the Folmer primers against the COI sequences from GenBank complete decapod mitochondrial genomes revealed that the annealing regions were, in fact, rather conserved, suggesting that the amplification failures were due more likely to the low quality of the DNA isolated. Using an alignment of all available decapod sequences we designed two internal primers in the middle of the barcoding COI region and also selected two additional external primers to be used as alternative to the standard Folmer primers. Using a two-overlapping-fragments amplification strategy and different primer combinations, our new protocol significantly increased the amplification success rate of the collection material from 42% with the Folmer primers to 84%, recovering an additional 364 complete barcodes and 443 minibarcodes (i.e. fragments of less than 400 base pairs), and expanding the species coverage from 254 to 397 barcoded crustaceans.
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