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deMaintenon M, Strong EE. Molecular phylogeny of Columbellidae (Gastropoda: Neogastropoda). PeerJ 2022; 10:e13996. [PMID: 36345482 PMCID: PMC9636871 DOI: 10.7717/peerj.13996] [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: 03/02/2022] [Accepted: 08/12/2022] [Indexed: 01/18/2023] Open
Abstract
The neogastropod family Columbellidae is a highly successful group of small, primarily epibenthic marine snails distributed worldwide and most abundant in the tropics. The great diversity of the group makes them attractive for studying evolutionary shifts in gastropod anatomy, morphology, ecology and diversity. The existing classification of the family has been based to a large degree on the morphology of the shell and radula. Indeed, membership in the family is traditionally confirmed using the unique morphology of the radula. To reconstruct columbellid phylogeny and assess monophyly of the group, we assembled a multilocus dataset including five mitochondrial and nuclear genes, for 70 species in 31 genera. Phylogenetic analyses using Bayesian inference and maximum likelihood are not well enough resolved to support a subfamilial classification, but do support the monophyly of the family and of several well-defined genera and supra-generic groupings. Two of the most diverse nominal genera, Mitrella and Anachis, are supported as highly polyphyletic. Overall, the resulting topologies indicate that the generic and subfamilial classification is in need of extensive revision but that phylogenomic data are needed to resolve columbellid relationships.
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Affiliation(s)
| | - Ellen E. Strong
- Department of Invertebrate Zoology, Smithsonian Institution, National Museum of Natural History, Washington, D.C., USA
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2
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Egger C, Neusser TP, Norenburg J, Leasi F, Buge B, Vannozzi A, Cunha RL, Cox CJ, Jörger KM. Uncovering the shell game with barcodes: diversity of meiofaunal Caecidae snails (Truncatelloidea, Caenogastropoda) from Central America. Zookeys 2020; 968:1-42. [PMID: 33005079 PMCID: PMC7511454 DOI: 10.3897/zookeys.968.52986] [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: 04/11/2020] [Accepted: 08/05/2020] [Indexed: 11/27/2022] Open
Abstract
Caecidae is a species-rich family of microsnails with a worldwide distribution. Typical for many groups of gastropods, caecid taxonomy is largely based on overt shell characters. However, identification of species using shell characteristics is problematic due to their rather uniform, tubular shells, the presence of different growth stages, and a high degree of intraspecific variability. In the present study, a first integrative approach to caecid taxonomy is provided using light-microscopic investigation with microsculptural analyses and multi-marker barcoding, in conjunction with molecular species delineation analyses (ABGD, haplotype networks, GMYC, and bPTP). In total 132 specimens of Caecum and Meioceras collected during several sampling trips to Central America were analyzed and delineated into a minimum of 19 species to discuss putative synonyms, and supplement the original descriptions. Molecular phylogenetic analyses suggest Meiocerasnitidum and M.cubitatum should be reclassified as Caecum, and the genus Meioceras might present a junior synonym of Caecum. Meiofaunal caecids morphologically resembling C.glabrum from the Northeast Atlantic are a complex of cryptic species with independent evolutionary origins, likely associated with multiple habitat shifts to the mesopsammic environment. Caecuminvisibile Egger & Jörger, sp. nov. is formally described based on molecular diagnostic characters. This first integrative approach towards the taxonomy of Caecidae increases the known diversity, reveals the need for a reclassification of the genus Caecum and serves as a starting point for a barcoding library of the family, thereby enabling further reliable identifications of these taxonomically challenging microsnails in future studies.
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Affiliation(s)
- Christina Egger
- SNSB-Zoologische Staatssammlung München, Münchhausenstr. 21, 81247 Munich, Germany SNSB-Zoologische Staatssammlung München Munich Germany.,CCMAR, Campus de Gambelas, Universidade do Algarve, 8005-139 Faro, Portugal Universidade do Algarve Faro Portugal
| | - Timea P Neusser
- LMU Munich, Biocenter, Dept. II, Großhaderner Str. 2, 82152 Planegg-Martinsried, Germany LMU Munich Munich Germany
| | - Jon Norenburg
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA National Museum of Natural History Washington, DC United States of America
| | - Francesca Leasi
- Department of Biology, Geology and Environmental Science. University of Tennessee at Chattanooga. 615 McCallie Ave. Chattanooga, TN 37403, USA University of Tennessee at Chattanooga Chattanooga United States of America
| | - Barbara Buge
- Muséum national d'Histoire naturelle, 55 Rue Buffon, 75231 Paris, France Muséum national d'Histoire naturelle Paris France
| | - Angelo Vannozzi
- Independent researcher, Via M.L. Longo 8, Rome, Italy Unaffiliated Rome Italy
| | - Regina L Cunha
- CCMAR, Campus de Gambelas, Universidade do Algarve, 8005-139 Faro, Portugal Universidade do Algarve Faro Portugal
| | - Cymon J Cox
- CCMAR, Campus de Gambelas, Universidade do Algarve, 8005-139 Faro, Portugal Universidade do Algarve Faro Portugal
| | - Katharina M Jörger
- SNSB-Zoologische Staatssammlung München, Münchhausenstr. 21, 81247 Munich, Germany SNSB-Zoologische Staatssammlung München Munich Germany
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3
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Kannan A, Rama Rao S, Ratnayeke S, Yow YY. The efficiency of universal mitochondrial DNA barcodes for species discrimination of Pomacea canaliculata and Pomacea maculata. PeerJ 2020; 8:e8755. [PMID: 32274263 PMCID: PMC7127494 DOI: 10.7717/peerj.8755] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 02/16/2020] [Indexed: 12/05/2022] Open
Abstract
Invasive apple snails, Pomacea canaliculata and P. maculata, have a widespread distribution globally and are regarded as devastating pests of agricultural wetlands. The two species are morphologically similar, which hinders species identification via morphological approaches and species-specific management efforts. Advances in molecular genetics may contribute effective diagnostic tools to potentially resolve morphological ambiguity. DNA barcoding has revolutionized the field of taxonomy by providing an alternative, simple approach for species discrimination, where short sections of DNA, the cytochrome c oxidase subunit I (COI) gene in particular, are used as ‘barcodes’ to delineate species boundaries. In our study, we aimed to assess the effectiveness of two mitochondrial markers, the COI and 16S ribosomal deoxyribonucleic acid (16S rDNA) markers for DNA barcoding of P. canaliculata and P. maculata. The COI and 16S rDNA sequences of 40 Pomacea specimens collected from six localities in Peninsular Malaysia were analyzed to assess their barcoding performance using phylogenetic methods and distance-based assessments. The results confirmed both markers were suitable for barcoding P. canaliculata and P. maculata. The phylogenies of the COI and 16S rDNA markers demonstrated species-specific monophyly and were largely congruent with the exception of one individual. The COI marker exhibited a larger barcoding gap (6.06–6.58%) than the 16S rDNA marker (1.54%); however, the magnitude of barcoding gap generated within the barcoding region of the 16S rDNA marker (12-fold) was bigger than the COI counterpart (approximately 9-fold). Both markers were generally successful in identifying P. canaliculata and P. maculata in the similarity-based DNA identifications. The COI + 16S rDNA concatenated dataset successfully recovered monophylies of P. canaliculata and P. maculata but concatenation did not improve individual datasets in distance-based analyses. Overall, although both markers were successful for the identification of apple snails, the COI molecular marker is a better barcoding marker and could be utilized in various population genetic studies of P. canaliculata and P. maculata.
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Affiliation(s)
- Adrian Kannan
- Department of Biological Sciences, School of Science & Technology, Sunway University, Selangor Darul Ehsan, Malaysia
| | - Suganiya Rama Rao
- Department of Biological Sciences, School of Science & Technology, Sunway University, Selangor Darul Ehsan, Malaysia
| | - Shyamala Ratnayeke
- Department of Biological Sciences, School of Science & Technology, Sunway University, Selangor Darul Ehsan, Malaysia
| | - Yoon-Yen Yow
- Department of Biological Sciences, School of Science & Technology, Sunway University, Selangor Darul Ehsan, Malaysia
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Mulcahy DG, Lee JL, Miller AH, Chand M, Thura MK, Zug GR. Filling the BINs of life: Report of an amphibian and reptile survey of the Tanintharyi (Tenasserim) Region of Myanmar, with DNA barcode data. Zookeys 2018:85-152. [PMID: 29780268 PMCID: PMC5958176 DOI: 10.3897/zookeys.757.24453] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 04/09/2018] [Indexed: 11/12/2022] Open
Abstract
Despite threats of species extinctions, taxonomic crises, and technological advances in genomics and natural history database informatics, we are still distant from cataloguing all of the species of life on earth. Amphibians and reptiles are no exceptions; in fact new species are described nearly every day and many species face possible extinction. The number of described species continues to climb as new areas of the world are explored and as species complexes are examined more thoroughly. The use of DNA barcoding provides a mechanism for rapidly estimating the number of species at a given site and has the potential to record all of the species of life on Earth. Though DNA barcoding has its caveats, it can be useful to estimate the number of species in a more systematic and efficient manner, to be followed in combination with more traditional, morphology-based identifications and species descriptions. Herein, we report the results of a voucher-based herpetological expedition to the Tanintharyi (Tenasserim) Region of Myanmar, enhanced with DNA barcode data. Our main surveys took place in the currently proposed Tanintharyi National Park. We combine our results with photographs and observational data from the Chaung-nauk-pyan forest reserve. Additionally, we provide the first checklist of amphibians and reptiles of the region, with species based on the literature and museum. Amphibians, anurans in particular, are one of the most poorly known groups of vertebrates in terms of taxonomy and the number of known species, particularly in Southeast Asia. Our rapid-assessment program combined with DNA barcoding and use of Barcode Index Numbers (BINs) of voucher specimens reveals the depth of taxonomic diversity in the southern Tanintharyi herpetofauna even though only a third of the potential amphibians and reptiles were seen. A total of 51 putative species (one caecilian, 25 frogs, 13 lizards, 10 snakes, and two turtles) were detected, several of which represent potentially undescribed species. Several of these species were detected by DNA barcode data alone. Furthermore, five species were recorded for the first time in Myanmar, two amphibians (Ichthyophis cf. kohtaoensis and Chalcorana eschatia) and three snakes (Ahaetulla mycterizans, Boiga dendrophila, and Boiga drapiezii).
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Affiliation(s)
- Daniel G Mulcahy
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, 10th & Constitution Ave., Washington, DC, 20013 USA
| | - Justin L Lee
- College of Computer, Mathematical and Natural Sciences, University of Maryland, College Park Maryland, 20742 USA
| | - Aryeh H Miller
- Department of Biology, University of North Carolina Asheville, Asheville, NC 28804 USA
| | - Mia Chand
- College of William & Mary, Williamsburg, Virginia, 23187 USA
| | - Myint Kyaw Thura
- Myanmar Environment Sustainable Conservation (MESC), Yangon, Myanmar
| | - George R Zug
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013 USA
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Inoue K, Hayes DM, Harris JL, Johnson NA, Morrison CL, Eackles MS, King TL, Jones JW, Hallerman EM, Christian AD, Randklev CR. The Pleurobemini (Bivalvia : Unionida) revisited: molecular species delineation using a mitochondrial DNA gene reveals multiple conspecifics and undescribed species. INVERTEBR SYST 2018. [DOI: 10.1071/is17059] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The Pleurobemini (Bivalvia: Unionida) represent approximately one-third of freshwater mussel diversity in North America. Species identification within this group is challenging due to morphological convergence and phenotypic plasticity. Accurate species identification, including characterisation of currently unrecognised taxa, is required to develop effective conservation strategies because many species in the group are imperiled. We examined 575 cox1 sequences from 110 currently recognised species (including 13 Fusconaia and 21 Pleurobema species) to understand phylogenetic relationships among pleurobemine species (mainly Fusconaia and Pleurobema) and to delineate species boundaries. The results of phylogenetic analyses showed no geographic structure within widespread species and illustrated a close relationship between Elliptio lanceolata and Parvaspina collina. Constraint tests supported monophyly of the genera Fusconaia and Pleurobema, including the subgenus P. (Sintoxia). Furthermore, results revealed multiple conspecifics, including P. hanleyianum and P. troschelianum, P. chattanoogaense and P. decisum, P. clava and P. oviforme, P. rubrum and P. sintoxia, F. askewi and F. lananensis, and F. cerina and F. flava. Species delimitation analyses identified three currently unrecognised taxa (two in Fusconaia and one in Pleurobema). Further investigation using additional genetic markers and other lines of evidence (e.g. morphology, life history, ecology) are necessary before any taxonomic changes are formalised.
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Kocher A, Thoisy B, Catzeflis F, Huguin M, Valière S, Zinger L, Bañuls A, Murienne J. Evaluation of short mitochondrial metabarcodes for the identification of Amazonian mammals. Methods Ecol Evol 2017. [DOI: 10.1111/2041-210x.12729] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Arthur Kocher
- CNRS, University Toulouse III Paul Sabatier, ENFA, UMR5174 EDB (Laboratoire Evolution et Diversité Biologique) Toulouse France
- UMR MIVEGEC (IRD 224 – CNRS 5290 – Université de Montpellier) 911 Avenue Agropolis F34394 Montpellier France
| | - Benoit Thoisy
- Institut Pasteur de la Guyane 23 avenue Pasteur 97300 Cayenne French Guiana
- Association Kwata 16 avenue Pasteur 97300 Cayenne French Guiana
| | - François Catzeflis
- Institut des Sciences de l'Evolution, Case Courrier 064, CNRS UMR‐5554, Université Montpellier‐2 Place E. Bataillon F‐34095 Montpellier France
| | - Mailis Huguin
- Institut Pasteur de la Guyane 23 avenue Pasteur 97300 Cayenne French Guiana
- Association Kwata 16 avenue Pasteur 97300 Cayenne French Guiana
| | - Sophie Valière
- GeT–PlaGe, Genotoul, INRA Auzeville 31326 Castanet‐Tolosan France
| | - Lucie Zinger
- CNRS, University Toulouse III Paul Sabatier, ENFA, UMR5174 EDB (Laboratoire Evolution et Diversité Biologique) Toulouse France
| | - Anne‐Laure Bañuls
- UMR MIVEGEC (IRD 224 – CNRS 5290 – Université de Montpellier) 911 Avenue Agropolis F34394 Montpellier France
| | - Jérôme Murienne
- CNRS, University Toulouse III Paul Sabatier, ENFA, UMR5174 EDB (Laboratoire Evolution et Diversité Biologique) Toulouse France
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7
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Layton KKS, Corstorphine EA, Hebert PDN. Exploring Canadian Echinoderm Diversity through DNA Barcodes. PLoS One 2016; 11:e0166118. [PMID: 27870868 PMCID: PMC5117606 DOI: 10.1371/journal.pone.0166118] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 10/24/2016] [Indexed: 11/19/2022] Open
Abstract
DNA barcoding has proven an effective tool for species identification in varied groups of marine invertebrates including crustaceans, molluscs, polychaetes and echinoderms. In this study, we further validate its utility by analyzing almost half of the 300 species of Echinodermata known from Canadian waters. COI sequences from 999 specimens were assigned to 145 BINs. In most cases, species discrimination was straightforward due to the large difference (25-fold) between mean intra- (0.48%) and inter- (12.0%) specific divergence. Six species were flagged for further taxonomic investigation because specimens assigned to them fell into two or three discrete sequence clusters. The potential influence of larval dispersal capacity and glacial events on patterns of genetic diversity is discussed for 19 trans-oceanic species. Although additional research is needed to clarify biogeographic patterns and resolve taxonomic questions, this study represents an important step in the assembly of a DNA barcode library for all Canadian echinoderms, a valuable resource for future biosurveillance programs.
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Affiliation(s)
- Kara K. S. Layton
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, ON, N1G 2W1, Canada
- * E-mail:
| | - Erin A. Corstorphine
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, ON, N1G 2W1, Canada
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Sun S, Li Q, Kong L, Yu H, Zheng X, Yu R, Dai L, Sun Y, Chen J, Liu J, Ni L, Feng Y, Yu Z, Zou S, Lin J. DNA barcoding reveal patterns of species diversity among northwestern Pacific molluscs. Sci Rep 2016; 6:33367. [PMID: 27640675 PMCID: PMC5027561 DOI: 10.1038/srep33367] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 08/25/2016] [Indexed: 11/26/2022] Open
Abstract
This study represents the first comprehensive molecular assessment of northwestern Pacific molluscs. In total, 2801 DNA barcodes belonging to 569 species from China, Japan and Korea were analyzed. An overlap between intra- and interspecific genetic distances was present in 71 species. We tested the efficacy of this library by simulating a sequence-based specimen identification scenario using Best Match (BM), Best Close Match (BCM) and All Species Barcode (ASB) criteria with three threshold values. BM approach returned 89.15% true identifications (95.27% when excluding singletons). The highest success rate of congruent identifications was obtained with BCM at 0.053 threshold. The analysis of our barcode library together with public data resulted in 582 Barcode Index Numbers (BINs), 72.2% of which was found to be concordantly with morphology-based identifications. The discrepancies were divided in two groups: sequences from different species clustered in a single BIN and conspecific sequences divided in one more BINs. In Neighbour-Joining phenogram, 2,320 (83.0%) queries fromed 355 (62.4%) species-specific barcode clusters allowing their successful identification. 33 species showed paraphyletic and haplotype sharing. 62 cases are represented by deeply diverged lineages. This study suggest an increased species diversity in this region, highlighting taxonomic revision and conservation strategy for the cryptic complexes.
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Affiliation(s)
- Shao’e Sun
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Hong Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Xiaodong Zheng
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Ruihai Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Lina Dai
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Yan Sun
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Jun Chen
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Jun Liu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Lehai Ni
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Yanwei Feng
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Zhenzhen Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Shanmei Zou
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Jiping Lin
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
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9
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Li XF, Han C, Zhong CR, Xu JQ, Huang JR. Identification of Sphaeroma terebrans via morphology and the mitochondrial cytochrome c oxidase subunit I (COI) gene. Zool Res 2016; 37:307-12. [PMID: 27686791 DOI: 10.13918/j.issn.2095-8137.2016.5.307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
Sphaeroma terebrans, a wood-boring isopoda, is distributed worldwide in tropical and subtropical mangroves. The taxonomy of S. terebrans is usually based on morphological characteristics, with its molecular identification still poorly understood. The number of teeth on the uropodal exopod and the length of the propodus of the seventh pereopod are considered as the major morphological characteristics in S. terebrans, which can cause difficulty in regards to accurate identification. In this study, we identified S. terebrans via molecular and morphological data. Furthermore, the validity of the mitochondrial cytochrome c oxidase subunit I (COI) gene as a DNA barcode for the identification of genus Sphaeroma, including species S. terebrans, S. retrolaeve, and S. serratum, was examined. The mitochondrial COI gene sequences of all specimens were sequenced and analysed. The interspecific Kimura 2-parameter distances were higher than intraspecific distances and no intraspecific-interspecific distance overlaps were observed. In addition, genetic distance and nucleotide diversity (π) exhibited no differences within S. terebrans. Our results revealed that the mitochondrial COI gene can serve as a valid DNA barcode for the identification of S. terebrans. Furthermore, the number of teeth on the uropodal exopod and the length of the propodus of the seventh pereopod were found to be unreliable taxonomic characteristics for S. terebrans.
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Affiliation(s)
- Xiu-Feng Li
- School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Chong Han
- School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Cai-Rong Zhong
- Management Bureau of Dongzhaigang Mangrove Natural Reserve, Haikou 571129, China
| | - Jun-Qiu Xu
- School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Jian-Rong Huang
- School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China.
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10
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Shelton AO, O'Donnell JL, Samhouri JF, Lowell N, Williams GD, Kelly RP. A framework for inferring biological communities from environmental DNA. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2016; 26:1645-1659. [PMID: 27755698 DOI: 10.1890/15-1733.1] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 01/17/2016] [Accepted: 01/28/2016] [Indexed: 06/06/2023]
Abstract
Environmental DNA (eDNA), genetic material recovered from an environmental medium such as soil, water, or feces, reflects the membership of the ecological community present in the sampled environment. As such, eDNA is a potentially rich source of data for basic ecology, conservation, and management, because it offers the prospect of quantitatively reconstructing whole ecological communities from easily obtained samples. However, like all sampling methods, eDNA sequencing is subject to methodological limitations that can generate biased descriptions of ecological communities. Here, we demonstrate parallels between eDNA sampling and traditional sampling techniques, and use these parallels to offer a statistical structure for framing the challenges faced by eDNA and for illuminating the gaps in our current knowledge. Although the current state of knowledge on some of these steps precludes a full estimate of biomass for each taxon in a sampled eDNA community, we provide a map that illustrates potential methods for bridging these gaps. Additionally, we use an original data set to estimate the relative abundances of taxon-specific template DNA prior to PCR, given the abundance of DNA sequences recovered post-PCR-and-sequencing, a critical step in the chain of eDNA inference. While we focus on the use of eDNA samples to determine the relative abundance of taxa within a community, our approach also applies to single-taxon applications (including applications using qPCR), studies of diversity, and studies focused on occurrence. By grounding inferences about eDNA community composition in a rigorous statistical framework, and by making these inferences explicit, we hope to improve the inferential potential for the emerging field of community-level eDNA analysis.
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Affiliation(s)
- Andrew Olaf Shelton
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, 98112, USA.
| | - James Lawrence O'Donnell
- School of Marine and Environmental Affairs, University of Washington, 3707 Brooklyn Avenue NE, Seattle, Washington, 98105, USA
| | - Jameal F Samhouri
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, 98112, USA
| | - Natalie Lowell
- School of Marine and Environmental Affairs, University of Washington, 3707 Brooklyn Avenue NE, Seattle, Washington, 98105, USA
| | - Gregory D Williams
- Pacific States Marine Fisheries Commission, Under Contract to Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, 98112, USA
| | - Ryan P Kelly
- School of Marine and Environmental Affairs, University of Washington, 3707 Brooklyn Avenue NE, Seattle, Washington, 98105, USA
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11
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Trivedi S, Aloufi AA, Ansari AA, Ghosh SK. Role of DNA barcoding in marine biodiversity assessment and conservation: An update. Saudi J Biol Sci 2016; 23:161-71. [PMID: 26980996 PMCID: PMC4778524 DOI: 10.1016/j.sjbs.2015.01.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 12/09/2014] [Accepted: 01/05/2015] [Indexed: 12/18/2022] Open
Abstract
More than two third area of our planet is covered by oceans and assessment of marine biodiversity is a challenging task. With the increasing global population, there is a tendency to exploit marine resources for food, energy and other requirements. This puts pressure on the fragile marine environment and necessitates sustainable conservation efforts. Marine species identification using traditional taxonomical methods is often burdened with taxonomic controversies. Here we discuss the comparatively new concept of DNA barcoding and its significance in marine perspective. This molecular technique can be useful in the assessment of cryptic species which is widespread in marine environment and linking the different life cycle stages to the adult which is difficult to accomplish in the marine ecosystem. Other advantages of DNA barcoding include authentication and safety assessment of seafood, wildlife forensics, conservation genetics and detection of invasive alien species (IAS). Global DNA barcoding efforts in the marine habitat include MarBOL, CeDAMar, CMarZ, SHARK-BOL, etc. An overview on DNA barcoding of different marine groups ranging from the microbes to mammals is revealed. In conjugation with newer and faster techniques like high-throughput sequencing, DNA barcoding can serve as an effective modern tool in marine biodiversity assessment and conservation.
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Affiliation(s)
- Subrata Trivedi
- Department of Biology, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Abdulhadi A. Aloufi
- Department of Biology, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Abid A. Ansari
- Department of Biology, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Sankar K. Ghosh
- Department of Biotechnology, Assam University, Silchar 788011, Assam, India
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Dang NX, Sun FH, Lv YY, Zhao BH, Wang JC, Murphy RW, Wang WZ, Li JT. DNA barcoding and the identification of tree frogs (Amphibia: Anura: Rhacophoridae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2574-84. [PMID: 26004249 DOI: 10.3109/19401736.2015.1041113] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The DNA barcoding gene COI (cytochrome c oxidase subunit I) effectively identifies many species. Herein, we barcoded 172 individuals from 37 species belonging to nine genera in Rhacophoridae to test if the gene serves equally well to identify species of tree frogs. Phenetic neighbor joining and phylogenetic Bayesian inference were used to construct phylogenetic trees, which resolved all nine genera as monophyletic taxa except for Rhacophorus, two new matrilines for Liuixalus, and Polypedates leucomystax species complex. Intraspecific genetic distances ranged from 0.000 to 0.119 and interspecific genetic distances ranged from 0.015 to 0.334. Within Rhacophorus and Kurixalus, the intra- and interspecific genetic distances did not reveal an obvious barcode gap. Notwithstanding, we found that COI sequences unambiguously identified rhacophorid species and helped to discover likely new cryptic species via the synthesis of genealogical relationships and divergence patterns. Our results supported that COI is an effective DNA barcoding marker for Rhacophoridae.
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Affiliation(s)
- Ning-Xin Dang
- a Chengdu Institute of Biology, Chinese Academy of Sciences , Chengdu , China .,b College of Life Sciences, Sichuan University , Chengdu , China
| | - Feng-Hui Sun
- c School of Medical Laboratory Science, Chengdu Medical College , Chengdu , China
| | - Yun-Yun Lv
- a Chengdu Institute of Biology, Chinese Academy of Sciences , Chengdu , China
| | - Bo-Han Zhao
- a Chengdu Institute of Biology, Chinese Academy of Sciences , Chengdu , China .,b College of Life Sciences, Sichuan University , Chengdu , China
| | - Ji-Chao Wang
- d Department of Tropical Animal and Plant Ecology , College of Life Sciences, Hainan Normal University , Haikou , China
| | - Robert W Murphy
- e Department of Conservation Biology , Royal Ontario Museum , Toronto , Ontario , Canada , and
| | - Wen-Zhi Wang
- f State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences , Kunming , China
| | - Jia-Tang Li
- a Chengdu Institute of Biology, Chinese Academy of Sciences , Chengdu , China
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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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Hubert N, Hanner R. DNA Barcoding, species delineation and taxonomy: a historical perspective. ACTA ACUST UNITED AC 2015. [DOI: 10.1515/dna-2015-0006] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractDNA barcoding is a system designed to provide species identification by using standardized gene regions as internal species tag. Foreseen since its earlier development as a solution to speed up the pace of species discovery, DNA barcoding has established as a mature field of biodiversity sciences filing the conceptual gap between traditional taxonomy and different fields of molecular systematics. Initially proposed as a tool for species identification, DNA barcoding has also been applied in taxonomy routines for automated species delineation. Species identification and species delineation, however, should be considered as distinct activities relying on different theoretical and methodological backgrounds. The aim of the present review is to provide an overview of the use of DNA sequences in taxonomy, since the earliest development of molecular taxonomy until the development of DNA barcoding. We further present the differences between procedures of species identification and species delineation and highlight how DNA barcoding proposed a new paradigm that helps promote more sustainable practices in taxonomy.
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Gaubert P, Njiokou F, Olayemi A, Pagani P, Dufour S, Danquah E, Nutsuakor MEK, Ngua G, Missoup AD, Tedesco PA, Dernat R, Antunes A. Bushmeat genetics: setting up a reference framework for the DNA typing of African forest bushmeat. Mol Ecol Resour 2014; 15:633-51. [DOI: 10.1111/1755-0998.12334] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 09/17/2014] [Accepted: 09/19/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Philippe Gaubert
- Institut des Sciences de l'Evolution de Montpellier - UM2-CNRS-IRD; Université Montpellier 2; Place Eugène Bataillon - CC 64 34095 Montpellier Cedex 05 France
| | - Flobert Njiokou
- Laboratoire de Parasitologie et d'Ecologie; Faculté des Sciences; Université de Yaoundé I; BP 812 Yaoundé Cameroon
| | - Ayodeji Olayemi
- Natural History Museum; Obafemi Awolowo University; Ho 220005 Ile-Ife Osun State Nigeria
| | - Paolo Pagani
- Dutch Wildlife Health Centre; Faculty of Veterinary Medicine; Yalelaan 1 3584 CL Utrecht The Netherlands
| | | | - Emmanuel Danquah
- Department of Wildlife and Range Management; Faculty of Renewable Natural Resources; Kwame Nkrumah University of Science and Technology; University Post Office; Kumasi Ghana
| | - Mac Elikem K. Nutsuakor
- Department of Wildlife and Range Management; Faculty of Renewable Natural Resources; Kwame Nkrumah University of Science and Technology; University Post Office; Kumasi Ghana
| | - Gabriel Ngua
- Amigos de la Naturaleza y del Desarrollo de Guinea Ecuatorial (ANDEGE); Barrió Ukomba, S/N Bata Equatorial Guinea
| | - Alain-Didier Missoup
- Biologie de l'Evolution - Mammalogie; Département de Biologie des Organismes Animaux; Faculté des Sciences; Université de Douala; BP 24157 Douala Cameroon
| | - Pablo A. Tedesco
- Département Milieux et Peuplements Aquatiques; Muséum National d'Histoire Naturelle; UMR Biologie des ORganismes et des Ecosystèmes Aquatiques (UMR BOREA IRD 207-CNRS 7208-UPMC-MNHN); 43 rue Cuvier FR-75231 Paris Cedex France
| | - Rémy Dernat
- Institut des Sciences de l'Evolution - CNRS UMR 5554; Plateforme Bioinformatique LabEx; Université Montpellier 2; Place Eugène Bataillon 34095 Montpellier Cedex 05 France
| | - Agostinho Antunes
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental; Universidade do Porto; Rua dos Bragas, 177 4050-123 Porto Portugal
- Departamento de Biologia; Faculdade de Ciências; Universidade do Porto; Rua do Campo Alegre 4169-007 Porto Portugal
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16
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Puillandre N, Bouchet P, Duda TF, Kauferstein S, Kohn AJ, Olivera BM, Watkins M, Meyer C. Molecular phylogeny and evolution of the cone snails (Gastropoda, Conoidea). Mol Phylogenet Evol 2014; 78:290-303. [PMID: 24878223 PMCID: PMC5556946 DOI: 10.1016/j.ympev.2014.05.023] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 05/08/2014] [Accepted: 05/16/2014] [Indexed: 11/26/2022]
Abstract
We present a large-scale molecular phylogeny that includes 320 of the 761 recognized valid species of the cone snails (Conus), one of the most diverse groups of marine molluscs, based on three mitochondrial genes (COI, 16S rDNA and 12S rDNA). This is the first phylogeny of the taxon to employ concatenated sequences of several genes, and it includes more than twice as many species as the last published molecular phylogeny of the entire group nearly a decade ago. Most of the numerous molecular phylogenies published during the last 15years are limited to rather small fractions of its species diversity. Bayesian and maximum likelihood analyses are mostly congruent and confirm the presence of three previously reported highly divergent lineages among cone snails, and one identified here using molecular data. About 85% of the species cluster in the single Large Major Clade; the others are divided between the Small Major Clade (∼12%), the Conus californicus lineage (one species), and a newly defined clade (∼3%). We also define several subclades within the Large and Small major clades, but most of their relationships remain poorly supported. To illustrate the usefulness of molecular phylogenies in addressing specific evolutionary questions, we analyse the evolution of the diet, the biogeography and the toxins of cone snails. All cone snails whose feeding biology is known inject venom into large prey animals and swallow them whole. Predation on polychaete worms is inferred as the ancestral state, and diet shifts to molluscs and fishes occurred rarely. The ancestor of cone snails probably originated from the Indo-Pacific; rather few colonisations of other biogeographic provinces have probably occurred. A new classification of the Conidae, based on the molecular phylogeny, is published in an accompanying paper.
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Affiliation(s)
- N Puillandre
- Muséum National d'Histoire Naturelle, Département Systématique et Evolution, ISyEB Institut (UMR 7205 CNRS/UPMC/MNHN/EPHE), 43, Rue Cuvier, 75231 Paris, France.
| | - P Bouchet
- Muséum National d'Histoire Naturelle, Département Systématique et Evolution, ISyEB Institut (UMR 7205 CNRS/UPMC/MNHN/EPHE), 55, Rue Buffon, 75231 Paris, France.
| | - T F Duda
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, 1109 Geddes Avenue, Ann Arbor, MI 48109, USA; Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panama.
| | - S Kauferstein
- Institute of Legal Medicine, University of Frankfurt, Kennedyallee 104, D-60596 Frankfurt, Germany.
| | - A J Kohn
- Department of Biology, Box 351800, University of Washington, Seattle, WA 98195, USA.
| | - B M Olivera
- Department of Biology, University of Utah, 257 South 1400 East, Salt Lake City, UT 84112, USA.
| | - M Watkins
- Department of Pathology, University of Utah, 257 South 1400 East, Salt Lake City, UT 84112, USA.
| | - C Meyer
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA.
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Kulsantiwong J, Prasopdee S, Ruangsittichai J, Ruangjirachuporn W, Boonmars T, Viyanant V, Pierossi P, Hebert PDN, Tesana S. DNA barcode identification of freshwater snails in the family Bithyniidae from Thailand. PLoS One 2013; 8:e79144. [PMID: 24223896 PMCID: PMC3817070 DOI: 10.1371/journal.pone.0079144] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 09/19/2013] [Indexed: 12/16/2022] Open
Abstract
Freshwater snails in the family Bithyniidae are the first intermediate host for Southeast Asian liver fluke (Opisthorchis viverrini), the causative agent of opisthorchiasis. Unfortunately, the subtle morphological characters that differentiate species in this group are not easily discerned by non-specialists. This is a serious matter because the identification of bithyniid species is a fundamental prerequisite for better understanding of the epidemiology of this disease. Because DNA barcoding, the analysis of sequence diversity in the 5’ region of the mitochondrial COI gene, has shown strong performance in other taxonomic groups, we decided to test its capacity to resolve 10 species/ subspecies of bithyniids from Thailand. Our analysis of 217 specimens indicated that COI sequences delivered species-level identification for 9 of 10 currently recognized species. The mean intraspecific divergence of COI was 2.3% (range 0-9.2 %), whereas sequence divergences between congeneric species averaged 8.7% (range 0-22.2 %). Although our results indicate that DNA barcoding can differentiate species of these medically-important snails, we also detected evidence for the presence of one overlooked species and one possible case of synonymy.
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Affiliation(s)
- Jutharat Kulsantiwong
- Food-Borne Parasite Research Group, Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Sattrachai Prasopdee
- Food-Borne Parasite Research Group, Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Jiraporn Ruangsittichai
- Department of Medical Entomology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Wipaporn Ruangjirachuporn
- Food-Borne Parasite Research Group, Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Thidarut Boonmars
- Food-Borne Parasite Research Group, Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Vithoon Viyanant
- Center of Excellence for Research in Biomedical Sciences, and Thailand Center of Excellence on Drug Discovery and Development, Thammasat University, Klongluang, Pathumthani, Thailand
| | - Paola Pierossi
- Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Paul D. N. Hebert
- Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Smarn Tesana
- Food-Borne Parasite Research Group, Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- * E-mail:
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18
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Ruiter DE, Boyle EE, Zhou X. DNA barcoding facilitates associations and diagnoses for Trichoptera larvae of the Churchill (Manitoba, Canada) area. BMC Ecol 2013; 13:5. [PMID: 23425021 PMCID: PMC3691766 DOI: 10.1186/1472-6785-13-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Accepted: 09/24/2012] [Indexed: 11/10/2022] Open
Abstract
Background The North American Trichoptera larvae are poorly known at the species level, despite their importance in the understanding of freshwater fauna and critical use in biomonitoring. This study focused on morphological diagnoses for larvae occurring in the Churchill, Manitoba area, representing the largest larval association effort for the caddisflies at any given locality thus far. The current DNA barcode reference library of Trichoptera (available on the Barcode of Life Data Systems) was utilized to provide larval-adult associations. Results The present study collected an additional 23 new species records for the Churchill area, increasing the total Trichoptera richness to 91 species. We were able to associate 62 larval taxa, comprising 68.1% of the Churchill area Trichoptera taxa. This endeavor to identify immature life stage for the caddisflies enabled the development of morphological diagnoses, production of photographs and an appropriate taxonomic key to facilitate larval species analyses in the area. Conclusions The use of DNA for associations of unknown larvae with known adults proved rapid and successful. This method should accelerate the state-of-knowledge for North American Trichoptera larvae as well as other taxonomic lineages. The morphological analysis should be useful for determination of material from the Churchill area.
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Affiliation(s)
- David E Ruiter
- Department of Integrative Biology, University of Guelph, 50 Stone Rd. E, Guelph, ON N1G 2 W1, Canada
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19
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Keskin E, Atar HH. DNA barcoding commercially important aquatic invertebrates of Turkey. ACTA ACUST UNITED AC 2013; 24:440-50. [PMID: 23387292 DOI: 10.3109/19401736.2012.762576] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
DNA barcoding was used in order to identify aquatic invertebrates sampled from fisheries bycatch and discards. A total of 440 unique cytochrome c oxidase sub unit I (COI) barcodes were generated for 22 species from three important phyla (Arthropoda, Cnidaria, and Mollusca). All the species were sequenced and submitted to GenBank and Barcode of Life Database (BOLD) databases using 654 bp-long fragment of mitochondrial COI gene. Two of them (Pontastacus leptodactylus and Rapana bezoar) were first records of the species for the BOLD database and six of them (Carcinus aestuarii, Loligo vulgaris, Melicertus kerathurus, Nephrops norvegicus, Scyllarides latus, and Scyllarus arctus) were first standard (>648 bp) COI barcode records for the GenBank database. COI barcodes were analyzed for nucleotide composition, nucleotide pair frequencies, and Kimura's two-parameter genetic distance. Mean genetic distance among species was found increasing at higher taxonomic levels. Neighbor-joining trees generated were congruent with morphometric-based taxonomic classification. Findings of this study clearly demonstrate that DNA barcodes could be used as an efficient molecular tool in identification of not only target species from fisheries but also bycatch and discard species, and so it could provide us leverage for a better understanding in monitoring and management of fisheries and biodiversity.
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Affiliation(s)
- Emre Keskin
- Department of Fisheries and Aquaculture, Agricultural Faculty, Ankara University, Dıs¸kapı, Ankara, Turkey.
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20
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Molecular identification of genus Scylla (Decapoda: Portunidae) based on DNA barcoding and polymerase chain reaction. BIOCHEM SYST ECOL 2012. [DOI: 10.1016/j.bse.2011.12.016] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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21
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PUILLANDRE N, BOUCHET P, BOISSELIER‐DUBAYLE M, BRISSET J, BUGE B, CASTELIN M, CHAGNOUX S, CHRISTOPHE T, CORBARI L, LAMBOURDIÈRE J, LOZOUET P, MARANI G, RIVASSEAU A, SILVA N, TERRYN Y, TILLIER S, UTGE J, SAMADI S. New taxonomy and old collections: integrating DNA barcoding into the collection curation process. Mol Ecol Resour 2012; 12:396-402. [DOI: 10.1111/j.1755-0998.2011.03105.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- N. PUILLANDRE
- UMR 7138, Muséum National d’Histoire Naturelle, Departement Systematique et Evolution, 43, Rue Cuvier, 75231 Paris, France
| | - P. BOUCHET
- UMR 7138, Muséum National d’Histoire Naturelle, Departement Systematique et Evolution, 55, Rue Buffon, 75231 Paris, France
| | - M.‐C. BOISSELIER‐DUBAYLE
- UMR 7138, Muséum National d’Histoire Naturelle, Departement Systematique et Evolution, 43, Rue Cuvier, 75231 Paris, France
| | - J. BRISSET
- UMR 7138, Muséum National d’Histoire Naturelle, Departement Systematique et Evolution, 43, Rue Cuvier, 75231 Paris, France
| | - B. BUGE
- Muséum National d’Histoire Naturelle, Direction des Collections, 55, rue de Buffon, 75005 Paris
| | - M. CASTELIN
- UMR 7138, Muséum National d’Histoire Naturelle, Departement Systematique et Evolution, 43, Rue Cuvier, 75231 Paris, France
| | - S. CHAGNOUX
- Muséum National d’Histoire Naturelle, Division des Systèmes d’Information, 57, Rue Cuvier, 75231 Paris, France
| | - T. CHRISTOPHE
- UMR 7138, Muséum National d’Histoire Naturelle, Departement Systematique et Evolution, 43, Rue Cuvier, 75231 Paris, France
| | - L. CORBARI
- UMR 7138, Muséum National d’Histoire Naturelle, Departement Systematique et Evolution, 43, Rue Cuvier, 75231 Paris, France
| | - J. LAMBOURDIÈRE
- UMS 2700, Museum National d’Histoire Naturelle, Departement Systematique et Evolution, 43, Rue Cuvier, 75231 Paris, France
| | - P. LOZOUET
- Muséum National d’Histoire Naturelle, Direction des Collections, 55, rue de Buffon, 75005 Paris
| | - G. MARANI
- UMR 7138, Muséum National d’Histoire Naturelle, Departement Systematique et Evolution, 55, Rue Buffon, 75231 Paris, France
| | - A. RIVASSEAU
- UMR 7138, Muséum National d’Histoire Naturelle, Departement Systematique et Evolution, 43, Rue Cuvier, 75231 Paris, France
| | - N. SILVA
- Muséum National d’Histoire Naturelle, Division des Systèmes d’Information, 57, Rue Cuvier, 75231 Paris, France
| | - Y. TERRYN
- NaturalArt, Kapiteinstraat 27, 9000 Gent, Belgium
| | - S. TILLIER
- UMR 7138, Muséum National d’Histoire Naturelle, Departement Systematique et Evolution, 43, Rue Cuvier, 75231 Paris, France
| | - J. UTGE
- UMS 2700, Museum National d’Histoire Naturelle, Departement Systematique et Evolution, 43, Rue Cuvier, 75231 Paris, France
| | - S. SAMADI
- UMR 7138, Muséum National d’Histoire Naturelle, Departement Systematique et Evolution, 43, Rue Cuvier, 75231 Paris, France
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XIA YUN, GU HAI, PENG RUI, CHEN QIN, ZHENG YU, MURPHY ROBERTW, ZENG XIAO. COI is better than 16S rRNA for DNA barcoding Asiatic salamanders (Amphibia: Caudata: Hynobiidae). Mol Ecol Resour 2011; 12:48-56. [DOI: 10.1111/j.1755-0998.2011.03055.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- YUN XIA
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- Graduate University of Chinese Academy of Sciences, Beijing, 100049, China
| | - HAI‐FENG GU
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- Graduate University of Chinese Academy of Sciences, Beijing, 100049, China
| | - RUI PENG
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - QIN CHEN
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - YU‐CHI ZHENG
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - ROBERT W. MURPHY
- State Key Laboratory of Genetic Resources and Evolution, 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, Ontario M5S 2C6, Canada
| | - XIAO‐MAO ZENG
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
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23
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Matzen da Silva J, Creer S, dos Santos A, Costa AC, Cunha MR, Costa FO, Carvalho GR. Systematic and evolutionary insights derived from mtDNA COI barcode diversity in the Decapoda (Crustacea: Malacostraca). PLoS One 2011; 6:e19449. [PMID: 21589909 PMCID: PMC3093375 DOI: 10.1371/journal.pone.0019449] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Accepted: 04/06/2011] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Decapods are the most recognizable of all crustaceans and comprise a dominant group of benthic invertebrates of the continental shelf and slope, including many species of economic importance. Of the 17635 morphologically described Decapoda species, only 5.4% are represented by COI barcode region sequences. It therefore remains a challenge to compile regional databases that identify and analyse the extent and patterns of decapod diversity throughout the world. METHODOLOGY/PRINCIPAL FINDINGS We contributed 101 decapod species from the North East Atlantic, the Gulf of Cadiz and the Mediterranean Sea, of which 81 species represent novel COI records. Within the newly-generated dataset, 3.6% of the species barcodes conflicted with the assigned morphological taxonomic identification, highlighting both the apparent taxonomic ambiguity among certain groups, and the need for an accelerated and independent taxonomic approach. Using the combined COI barcode projects from the Barcode of Life Database, we provide the most comprehensive COI data set so far examined for the Order (1572 sequences of 528 species, 213 genera, and 67 families). Patterns within families show a general predicted molecular hierarchy, but the scale of divergence at each taxonomic level appears to vary extensively between families. The range values of mean K2P distance observed were: within species 0.285% to 1.375%, within genus 6.376% to 20.924% and within family 11.392% to 25.617%. Nucleotide composition varied greatly across decapods, ranging from 30.8 % to 49.4 % GC content. CONCLUSIONS/SIGNIFICANCE Decapod biological diversity was quantified by identifying putative cryptic species allowing a rapid assessment of taxon diversity in groups that have until now received limited morphological and systematic examination. We highlight taxonomic groups or species with unusual nucleotide composition or evolutionary rates. Such data are relevant to strategies for conservation of existing decapod biodiversity, as well as elucidating the mechanisms and constraints shaping the patterns observed.
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Affiliation(s)
- Joana Matzen da Silva
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Environment Centre for Wales, Bangor University, Bangor, Wales, United Kingdom.
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Abstract
More than 230,000 known species representing 31 metazoan phyla populate the world's oceans. Perhaps another 1,000,000 or more species remain to be discovered. There is reason for concern that species extinctions may out-pace discovery, especially in diverse and endangered marine habitats such as coral reefs. DNA barcodes (i.e., short DNA sequences for species recognition and discrimination) are useful tools to accelerate species-level analysis of marine biodiversity and to facilitate conservation efforts. This review focuses on the usual barcode region for metazoans: a approximately 648 base-pair region of the mitochondrial cytochrome c oxidase subunit I (COI) gene. Barcodes have also been used for population genetic and phylogeographic analysis, identification of prey in gut contents, detection of invasive species, forensics, and seafood safety. More controversially, barcodes have been used to delimit species boundaries, reveal cryptic species, and discover new species. Emerging frontiers are the use of barcodes for rapid and increasingly automated biodiversity assessment by high-throughput sequencing, including environmental barcoding and the use of barcodes to detect species for which formal identification or scientific naming may never be possible.
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Affiliation(s)
- Ann Bucklin
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut 06340, USA.
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25
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SANTOS ANAMC, BESNARD GUILLAUME, QUICKE DONALDLJ. Applying DNA barcoding for the study of geographical variation in host–parasitoid interactions. Mol Ecol Resour 2010; 11:46-59. [DOI: 10.1111/j.1755-0998.2010.02889.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- ANA M. C. SANTOS
- Division of Biology, Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK
- Universidade dos Açores, Dep. de Ciências Agrárias – CITA‐A (Azorean Biodiversity Group), Terra‐Chã, 9700‐851 Angra do Heroísmo, Portugal
| | - GUILLAUME BESNARD
- Division of Biology, Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK
| | - DONALD L. J. QUICKE
- Division of Biology, Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK
- Department of Entomology, Natural History Museum, Cromwell Road, London SW7 5BD, UK
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