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Rossini BC, Oliveira CAM, de Melo FAG, Bertaco VDA, de Astarloa JMD, Rosso JJ, Foresti F, Oliveira C. Highlighting Astyanax Species Diversity through DNA Barcoding. PLoS One 2016; 11:e0167203. [PMID: 27992537 PMCID: PMC5167228 DOI: 10.1371/journal.pone.0167203] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 11/10/2016] [Indexed: 11/18/2022] Open
Abstract
DNA barcoding has been used extensively to solve taxonomic questions and identify new species. Neotropical fishes are found in a wide variety of shapes and sizes, with a large number of species yet to be described, many of which are very difficult to identify. Characidae is the most species-rich family of the Characiformes, and many of its genera are affected by taxonomic uncertainties, including the widely-distributed, species-rich genus Astyanax. In this study, we present an extensive analysis of Astyanax covering almost its entire area of occurrence, based on DNA barcoding. The use of different approaches (ABGD, GMYC and BIN) to the clustering of the sequences revealed ample consistency in the results obtained by the initial cutoff value of 2% divergence for putative species in the Neighbor-Joining analysis using the Kimura-2-parameter model. The results indicate the existence of five Astyanax lineages. Some groups, such as that composed by the trans-Andean forms, are mostly composed of well-defined species, and in others a number of nominal species are clustered together, hampering the delimitation of species, which in many cases proved impossible. The results confirm the extreme complexity of the systematics of the genus Astyanax and show that DNA barcoding can be an useful tool to address these complexes questions.
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Affiliation(s)
- Bruno César Rossini
- Laboratório de Biologia e Genética de Peixes, Departamento de Morfologia, UNESP—Universidade Estadual Paulista, Botucatu, São Paulo, Brazil
- Instituto de Biotecnologia da UNESP, UNESP—Universidade Estadual Paulista, Botucatu, São Paulo, Brazil
- * E-mail:
| | - Carlos Alexandre Miranda Oliveira
- Universidade Estadual de Maringá, Programa de Pós-Graduação em Ecologia de Ambientes Aquáticos Continentais, Maringá, Paraná, Brazil
| | | | - Vinicius de Araújo Bertaco
- Museu de Ciências Naturais, Fundação Zoobotânica do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Juan M. Díaz de Astarloa
- Grupo de Biotaxonomía Morfológica y Molecular de Peces, Instituto de Investigaciones Marinas y Costeras, Universidad Nacional de Mar del Plata. Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Juan J. Rosso
- Grupo de Biotaxonomía Morfológica y Molecular de Peces, Instituto de Investigaciones Marinas y Costeras, Universidad Nacional de Mar del Plata. Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Fausto Foresti
- Laboratório de Biologia e Genética de Peixes, Departamento de Morfologia, UNESP—Universidade Estadual Paulista, Botucatu, São Paulo, Brazil
| | - Claudio Oliveira
- Laboratório de Biologia e Genética de Peixes, Departamento de Morfologia, UNESP—Universidade Estadual Paulista, Botucatu, São Paulo, Brazil
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Abstract
Host-parasite co-evolutionary studies can shed light on diversity and the processes that shape it. Molecular methods have proven to be an indispensable tool in this task, often uncovering unseen diversity. This study used two nuclear markers (18S rRNA and 28S rRNA) and one mitochondrial (cytochrome oxidase subunit I) marker to investigate the diversity of nematodes of the family Pharyngodonidae parasitizing New Zealand (NZ) lizards (lygosomine skinks and diplodactylid geckos) and to explore their co-evolutionary history. A Bayesian approach was used to infer phylogenetic relationships of the parasitic nematodes. Analyses revealed that nematodes parasitizing skinks, currently classified as Skrjabinodon, are more closely related to Spauligodon than to Skrjabinodon infecting NZ geckos. Genetic analyses also uncovered previously undetected diversity within NZ gecko nematodes and provided evidence for several provisionally cryptic species. We also examined the level of host-parasite phylogenetic congruence using a global-fit approach. Significant congruence was detected between gecko-Skrjabinodon phylogenies, but our results indicated that strict co-speciation is not the main co-evolutionary process shaping the associations between NZ skinks and geckos and their parasitic nematodes. However, further sampling is required to fully resolve co-phylogenetic patterns of diversification in this host-parasite system.
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Barreira AS, Lijtmaer DA, Tubaro PL. The multiple applications of DNA barcodes in avian evolutionary studies. Genome 2016; 59:899-911. [DOI: 10.1139/gen-2016-0086] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
DNA barcodes of birds are currently available for 41% of known species and for many different geographic areas; therefore, they are a rich data source to answer evolutionary questions. We review studies that have used DNA barcodes to investigate evolutionary processes in birds using diverse approaches. We also review studies that have investigated species in depth where taxonomy and DNA barcodes present inconsistencies. Species that showed low genetic interspecific divergence and lack of reciprocal monophyly either are the result of recent radiation and (or) hybridize, while species with large genetic splits in their COI sequences were determined to be more than one independent evolutionary unit. In addition, we review studies that employed large DNA barcode datasets to study the molecular evolution of mitochondrial genes and the biogeography of islands, continents, and even at a multi-continental scale. These studies showed that DNA barcodes offer high-quality data well beyond their main purpose of serving as a molecular tool for species identification.
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Affiliation(s)
- Ana S. Barreira
- División Ornitología, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” - CONICET, Avda. Ángel Gallardo 470, Ciudad Autónoma de Buenos Aires, C1405DJR, Argentina
- División Ornitología, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” - CONICET, Avda. Ángel Gallardo 470, Ciudad Autónoma de Buenos Aires, C1405DJR, Argentina
| | - Darío A. Lijtmaer
- División Ornitología, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” - CONICET, Avda. Ángel Gallardo 470, Ciudad Autónoma de Buenos Aires, C1405DJR, Argentina
- División Ornitología, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” - CONICET, Avda. Ángel Gallardo 470, Ciudad Autónoma de Buenos Aires, C1405DJR, Argentina
| | - Pablo L. Tubaro
- División Ornitología, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” - CONICET, Avda. Ángel Gallardo 470, Ciudad Autónoma de Buenos Aires, C1405DJR, Argentina
- División Ornitología, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” - CONICET, Avda. Ángel Gallardo 470, Ciudad Autónoma de Buenos Aires, C1405DJR, Argentina
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Asing, Ali ME, Abd Hamid SB, Hossain MAM, Mustafa S, Kader MA, Zaidul ISM. Lab-on-a-Chip-Based PCR-RFLP Assay for the Detection of Malayan Box Turtle (Cuora amboinensis) in the Food Chain and Traditional Chinese Medicines. PLoS One 2016; 11:e0163436. [PMID: 27716792 PMCID: PMC5055339 DOI: 10.1371/journal.pone.0163436] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 09/08/2016] [Indexed: 11/18/2022] Open
Abstract
The Malayan box turtle (Cuora amboinensis) (MBT) is a vulnerable and protected turtle species, but it is a lucrative item in the illegal wildlife trade because of its great appeal as an exotic food item and in traditional medicine. Although several polymerase chain reaction (PCR) assays to identify MBT by various routes have been documented, their applicability for forensic authentication remains inconclusive due to the long length of the amplicon targets, which are easily broken down by natural decomposition, environmental stresses or physiochemical treatments during food processing. To address this research gap, we developed, for the first time, a species-specific PCR-restriction fragment length polymorphism (RFLP) assay with a very short target length (120 bp) to detect MBT in the food chain; this authentication ensured better security and reliability through molecular fingerprints. The PCR-amplified product was digested with Bfa1 endonuclease, and distinctive restriction fingerprints (72, 43 and 5 bp) for MBT were found upon separation in a microfluidic chip-based automated electrophoresis system, which enhances the resolution of short oligos. The chances of any false negative identifications were eliminated through the use of a universal endogenous control for eukaryotes, and the limit of detection was 0.0001 ng DNA or 0.01% of the meat under admixed states. Finally, the optimized PCR-RFLP assay was validated for the screening of raw and processed commercial meatballs, burgers and frankfurters, which are very popular in most countries. The optimized PCR-RFLP assay was further used to screen MBT materials in 153 traditional Chinese medicines of 17 different brands and 62 of them were found MBT positive; wherein the ingredients were not declared in product labels. Overall, the novel assay demonstrated sufficient merit for use in any forensic and/or archaeological authentication of MBT, even under a state of decomposition.
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Affiliation(s)
- Asing
- Nanotechnology and Catalysis Research Center (NANOCAT), University of Malaya, Kuala Lumpur, Malaysia
| | - Md. Eaqub Ali
- Nanotechnology and Catalysis Research Center (NANOCAT), University of Malaya, Kuala Lumpur, Malaysia
- Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, Kuala Lumpur, Malaysia
| | - Sharifah Bee Abd Hamid
- Nanotechnology and Catalysis Research Center (NANOCAT), University of Malaya, Kuala Lumpur, Malaysia
| | - M. A. Motalib Hossain
- Nanotechnology and Catalysis Research Center (NANOCAT), University of Malaya, Kuala Lumpur, Malaysia
| | - Shuhaimi Mustafa
- Institute of Halal Products Research, University of Putra Malaysia, UPM Serdang, Selangor, Malaysia
| | - Md. Abdul Kader
- School of Aquaculture and Fisheries, University of Malaysia Terrenganu, Kuala Terrenganu, Terrenganu, Malaysia
| | - I. S. M. Zaidul
- Department of Pharmaceutical Technology, Faculty of Pharmacy, International Islamic University, Kuantan, Pahang, Malaysia
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Molecular Identification and Traceability of Illegal Trading in Lignobrycon myersi (Teleostei: Characiformes), a Threatened Brazilian Fish Species, Using DNA Barcode. ScientificWorldJournal 2016; 2016:9382613. [PMID: 27668281 PMCID: PMC5030449 DOI: 10.1155/2016/9382613] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 08/16/2016] [Accepted: 08/17/2016] [Indexed: 11/18/2022] Open
Abstract
Lignobrycon myersi is a threatened freshwater fish species and endemic of a few coastal rivers in northeastern Brazil. Even though the Brazilian laws prohibit the fisheries of threatened species, L. myersi is occasionally found in street markets, being highly appreciated by local population. In order to provide a reliable DNA barcode dataset for L. myersi, we compared mitochondrial sequences of cytochrome c oxidase subunit I (COI) from fresh, frozen, and salt-preserved specimens. Phylogenetically related species (Triportheus spp.) and other fish species (Astyanax fasciatus) commonly mixed with L. myersi in street markets were also included to test the efficiency of molecular identification. In spite of the differences in conservation processes and advanced deterioration of some commercial samples, high-quality COI sequences were obtained and effective in discriminating L. myersi specimens. In addition, while populations from Contas and Almada River basins seem to comprise a single evolutionary lineage, the specimens from Cachoeira River were genetically differentiated, indicating population structuring. Therefore, DNA barcoding has proved to be useful to trace the illegal trading of L. myersi and to manage threatened populations, which should focus on conservation of distinct genetic stocks and mitigation on human impacts along their range.
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Zhang X, Li N, Yao Y, Liang X, Qu X, Liu X, Zhu Y, Yang D, Sun W. Identification of Species in Tripterygium (Celastraceae) Based on DNA Barcoding. Biol Pharm Bull 2016; 39:1760-1766. [PMID: 27601081 DOI: 10.1248/bpb.b15-00956] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Species of genus Tripterygium (Celastraceae) have attracted much attention owing to their excellent effect on treating autoimmune and inflammatory diseases. However, due to high market demand causing overexploitation, natural populations of genus Tripterygium have rapidly declined. Tripterygium medicinal materials are mainly collected from the wild, making the quality of medicinal materials unstable. Additionally, identification of herbal materials from Tripterygium species and their adulterants is difficult based on morphological characters. Therefore, an accurate, convenient, and stability method is urgently needed. In this wok, we developed a DNA barcoding technique to distinguish T. wilfordii HOOK. f., T. hypoglaucum (LÉVL.) HUTCH, and T. regelii SPRAGUE et TAKEDA and their adulterants based on four uniform and standard DNA regions (internal transcribed spacer 2 (ITS2), matK, rbcL, and psbA-trnH). DNA was extracted from 26 locations of fresh leaves. Phylogenetic tree was constructed with Neighbor-Joining (NJ) method, while barcoding gap was analyzed to assess identification efficiency. Compared with the other DNA barcodes applied individually or in combination, ITS2+psbA-trnH was demonstrated as the optimal barcode. T. hypoglaucum and T. wilfordii can be considered as conspecific, while T. regelii was recognized as a separate species. Furthermore, identification of commercial Tripterygium samples was conducted using BLAST against GenBank and Species Identification System for Traditional Chinese Medicine. Our results indicated that DNA barcoding is a convenient, effective, and stability method to identify and distinguish Tripterygium and its adulterants, and could be applied as the quality control for Tripterygium medicinal preparations and monitoring of the medicinal herb trade in markets.
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The use of DNA barcode for identifying species of Oxysarcodexia Townsend (Diptera: Sarcophagidae): A preliminary survey. Acta Trop 2016; 161:73-8. [PMID: 27260665 DOI: 10.1016/j.actatropica.2016.05.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Revised: 05/28/2016] [Accepted: 05/30/2016] [Indexed: 11/23/2022]
Abstract
Oxysarcodexia is one of the Neotropical richest genera within the Sarcophagidae family. Medical, veterinary and forensic importance of these flies are due to their association with corpses, cases of myiasis in humans and domestic animals, and being pathogen carriers. Regarding morphological identification, molecular techniques, especially the DNA-based ones, arise as useful alternatives or complementary methodologies for species identification. Thus, in this study we aimed to investigate the potential of the COI marker (barcode region) to delimit Oxysarcodexia species in comparison with the morphological identification criteria. A COI fragment was amplified and the length of the sequences after alignment were of 648bp (149 parsimoniously informative variable sites). According to the Neighbor-Joining phylogenetic tree, specimens of the same morphological species were clustered in monophyletic clades (82-100% bootstrap branch support). Species-level resolution thus achieved was successful, despite low interspecific divergence (1.8-2.3%) and since interspecific variation was higher than intraspecific divergence (0.1-1.2%). Therefore, the use of COI barcode sequences supports differentiation and identification of the Oxysarcodexia species studied.
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58
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Ortiz D, Francke OF. Two DNA barcodes and morphology for multi-method species delimitation in Bonnetina tarantulas (Araneae: Theraphosidae). Mol Phylogenet Evol 2016; 101:176-193. [DOI: 10.1016/j.ympev.2016.05.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 04/07/2016] [Accepted: 05/01/2016] [Indexed: 12/13/2022]
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59
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Geary J, Camicioli E, Bubela T. DNA barcoding in the media: does coverage of cool science reflect its social context? Genome 2016; 59:738-50. [PMID: 27463361 DOI: 10.1139/gen-2015-0210] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Paul Hebert and colleagues first described DNA barcoding in 2003, which led to international efforts to promote and coordinate its use. Since its inception, DNA barcoding has generated considerable media coverage. We analysed whether this coverage reflected both the scientific and social mandates of international barcoding organizations. We searched newspaper databases to identify 900 English-language articles from 2003 to 2013. Coverage of the science of DNA barcoding was highly positive but lacked context for key topics. Coverage omissions pose challenges for public understanding of the science and applications of DNA barcoding; these included coverage of governance structures and issues related to the sharing of genetic resources across national borders. Our analysis provided insight into how barcoding communication efforts have translated into media coverage; more targeted communication efforts may focus media attention on previously omitted, but important topics. Our analysis is timely as the DNA barcoding community works to establish the International Society for the Barcode of Life.
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Affiliation(s)
- Janis Geary
- School of Public Health, University of Alberta, Edmonton, AB, Canada.,School of Public Health, University of Alberta, Edmonton, AB, Canada
| | - Emma Camicioli
- School of Public Health, University of Alberta, Edmonton, AB, Canada.,School of Public Health, University of Alberta, Edmonton, AB, Canada
| | - Tania Bubela
- School of Public Health, University of Alberta, Edmonton, AB, Canada.,School of Public Health, University of Alberta, Edmonton, AB, Canada
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60
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Thomas VG, Hanner RH, Borisenko AV. DNA-based identification of invasive alien species in relation to Canadian federal policy and law, and the basis of rapid-response management. Genome 2016; 59:1023-1031. [PMID: 27767334 DOI: 10.1139/gen-2016-0022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Managing invasive alien species in Canada requires reliable taxonomic identification as the basis of rapid-response management. This can be challenging, especially when organisms are small and lack morphological diagnostic features. DNA-based techniques, such as DNA barcoding, offer a reliable, rapid, and inexpensive toolkit for taxonomic identification of individual or bulk samples, forensic remains, and even environmental DNA. Well suited for this requirement, they could be more broadly deployed and incorporated into the operating policy and practices of Canadian federal departments and should be authorized under these agencies' articles of law. These include Fisheries and Oceans Canada, Canadian Food Inspection Agency, Transport Canada, Environment Canada, Parks Canada, and Health Canada. These efforts should be harmonized with the appropriate provisions of provincial jurisdictions, for example, the Ontario Invasive Species Act. This approach necessitates that a network of accredited, certified laboratories exists, and that updated DNA reference libraries are readily accessible. Harmonizing this approach is vital among Canadian federal agencies, and between the federal and provincial levels of government. Canadian policy and law must also be harmonized with that of the USA when detecting, and responding to, invasive species in contiguous lands and waters. Creating capacity in legislation for use of DNA-based identifications brings the authority to fund, train, deploy, and certify staff, and to refine further developments in this molecular technology.
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Affiliation(s)
- Vernon G Thomas
- a Department of Integrative Biology, College of Biological Science, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Robert H Hanner
- a Department of Integrative Biology, College of Biological Science, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Alex V Borisenko
- b Biodiversity Institute of Ontario, University of Guelph, Guelph, ON N1G 2W1, Canada
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61
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Dulla EL, Kathera C, Gurijala HK, Mallakuntla TR, Srinivasan P, Prasad V, Mopati RD, Jasti PK. Highlights of DNA Barcoding in identification of salient microorganisms like fungi. J Mycol Med 2016; 26:291-297. [PMID: 27402509 DOI: 10.1016/j.mycmed.2016.05.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 04/22/2016] [Accepted: 05/25/2016] [Indexed: 11/19/2022]
Abstract
Fungi, the second largest kingdom of eukaryotic life, are diverse and widespread. Fungi play a distinctive role in the production of different products on industrial scale, like fungal enzymes, antibiotics, fermented foods, etc., to give storage stability and improved health to meet major global challenges. To utilize algae perfectly for human needs, and to pave the way for getting a healthy relationship with fungi, it is important to identify them in a quick and robust manner with molecular-based identification system. So, there is a technique that aims to provide a well-organized method for species level identifications and to contribute powerfully to taxonomic and biodiversity research is DNA Barcoding. DNA Barcoding is generally achieved by the retrieval of a short DNA sequence - the 'barcode' - from a standard part of the genome and that barcode is then compared with a library of reference barcode sequences derived from individuals of known identity for identification.
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Affiliation(s)
- E L Dulla
- Department of Biotechnology, Sri Venkateswara University, Tirupati, Andhra Pradesh 517502, India
| | - C Kathera
- Jiangsu key laboratory for Molecular and Medicak Biotechnology, College of life sciences, Nanjing normal university, Nanjing, China
| | - H K Gurijala
- Department of Biotechnology, Sri Venkateswara University, Tirupati, Andhra Pradesh 517502, India; Department of Microbiology, Sri Venkateswara University, Tirupati, Andhra Pradesh 517502, India
| | - T R Mallakuntla
- Department of Microbiology, Sri Venkateswara University, Tirupati, Andhra Pradesh 517502, India
| | - P Srinivasan
- Department of Microbiology, Sri Venkateswara University, Tirupati, Andhra Pradesh 517502, India
| | - V Prasad
- Jiangsu key laboratory for Molecular and Medicak Biotechnology, College of life sciences, Nanjing normal university, Nanjing, China
| | - R D Mopati
- Department of Microbiology, Sri Venkateswara University, Tirupati, Andhra Pradesh 517502, India
| | - P K Jasti
- Department of Biotechnology, Sri Venkateswara University, Tirupati, Andhra Pradesh 517502, India.
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Aksöyek E, İbiş O, Özcan S, Moradi M, Tez C. DNA barcoding of three species (Canis aureus, Canis lupus and Vulpes vulpes) of Canidae. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:747-755. [PMID: 27180732 DOI: 10.1080/24701394.2016.1180512] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene have been used for DNA barcoding and determining the genetic diversity of mammal species. In the current study, our intention was to test the validity of COI barcodes for detecting genetic divergence and to reveal whether or not there is a genetic variation at this marker within canids. Three species (Canis aureus, Canis lupus and Vulpes vulpes) from the family Canidae were selected for DNA barcoding using samples collected from Iran and Turkey. All three species had unique barcoding sequences and none of the sequences were shared among these species. The mean sequence divergences within and among the species were 0.61% and 12.32%, respectively, which fell into the mean divergence ranges found in some mammal groups. The genetic diversity of these three canid species was relatively higher than that found in previously reported studies.
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Affiliation(s)
- Eren Aksöyek
- a Graduate School of Natural and Applied Sciences , Erciyes University , Kayseri , Turkey
| | - Osman İbiş
- b Department of Agricultural Biotechnology, Faculty of Agriculture , Erciyes University , Kayseri , Turkey.,c Genome and Stem Cell Center, GENKOK, Erciyes University , Kayseri , Turkey
| | - Servet Özcan
- c Genome and Stem Cell Center, GENKOK, Erciyes University , Kayseri , Turkey.,d Department of Biology, Faculty of Sciences , Erciyes University , Kayseri , Turkey
| | - Mohammad Moradi
- e Department of Biology, Faculty of Science , University of Zanjan , Zanjan , Iran
| | - Coşkun Tez
- d Department of Biology, Faculty of Sciences , Erciyes University , Kayseri , Turkey
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Elderkin CL, Clewing C, Wembo Ndeo O, Albrecht C. Molecular phylogeny and DNA barcoding confirm cryptic species in the African freshwater oysterEtheria ellipticaLamarck, 1807 (Bivalvia: Etheriidae). Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12734] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Curt L. Elderkin
- Department of Biology; The College of New Jersey; Ewing NJ 08638 USA
| | - Catharina Clewing
- Department of Animal Ecology and Systematics; Justus Liebig University Giessen; Heinrich-Buff-Ring 26-32 IFZ; 35392 Giessen Germany
| | - Oscar Wembo Ndeo
- Hydrobiological Department; Faculty of Sciences; University of Kisangani; Kisangani Oriental Province DR Congo
| | - Christian Albrecht
- Department of Animal Ecology and Systematics; Justus Liebig University Giessen; Heinrich-Buff-Ring 26-32 IFZ; 35392 Giessen Germany
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65
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Mishra P, Kumar A, Nagireddy A, Mani DN, Shukla AK, Tiwari R, Sundaresan V. DNA barcoding: an efficient tool to overcome authentication challenges in the herbal market. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:8-21. [PMID: 26079154 DOI: 10.1111/pbi.12419] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 04/28/2015] [Accepted: 05/16/2015] [Indexed: 05/21/2023]
Abstract
The past couple of decades have witnessed global resurgence of herbal-based health care. As a result, the trade of raw drugs has surged globally. Accurate and fast scientific identification of the plant(s) is the key to success for the herbal drug industry. The conventional approach is to engage an expert taxonomist, who uses a mix of traditional and modern techniques for precise plant identification. However, for bulk identification at industrial scale, the process is protracted and time-consuming. DNA barcoding, on the other hand, offers an alternative and feasible taxonomic tool box for rapid and robust species identification. For the success of DNA barcode, the barcode loci must have sufficient information to differentiate unambiguously between closely related plant species and discover new cryptic species. For herbal plant identification, matK, rbcL, trnH-psbA, ITS, trnL-F, 5S-rRNA and 18S-rRNA have been used as successful DNA barcodes. Emerging advances in DNA barcoding coupled with next-generation sequencing and high-resolution melting curve analysis have paved the way for successful species-level resolution recovered from finished herbal products. Further, development of multilocus strategy and its application has provided new vistas to the DNA barcode-based plant identification for herbal drug industry. For successful and acceptable identification of herbal ingredients and a holistic quality control of the drug, DNA barcoding needs to work harmoniously with other components of the systems biology approach. We suggest that for effectively resolving authentication challenges associated with the herbal market, DNA barcoding must be used in conjunction with metabolomics along with need-based transcriptomics and proteomics.
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Affiliation(s)
- Priyanka Mishra
- Department of Biology & Systematics, CSIR - Central Institute of Medicinal and Aromatic Plants, Research Centre, Bangalore, Karnataka, India
| | - Amit Kumar
- Department of Biology & Systematics, CSIR - Central Institute of Medicinal and Aromatic Plants, Research Centre, Bangalore, Karnataka, India
| | - Akshitha Nagireddy
- Department of Biology & Systematics, CSIR - Central Institute of Medicinal and Aromatic Plants, Research Centre, Bangalore, Karnataka, India
| | - Daya N Mani
- Herbal Medicinal Products Department, CSIR - Central Institute of Medicinal and Aromatic Plants, Lucknow, Uttar Pradesh, India
| | - Ashutosh K Shukla
- Biotechnology Division, CSIR - Central Institute of Medicinal and Aromatic Plants, Lucknow, Uttar Pradesh, India
| | - Rakesh Tiwari
- Publication Division, CSIR - Central Institute of Medicinal and Aromatic Plants, Lucknow, Uttar Pradesh, India
| | - Velusamy Sundaresan
- Department of Biology & Systematics, CSIR - Central Institute of Medicinal and Aromatic Plants, Research Centre, Bangalore, Karnataka, India
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Wang Y, Nansen C, Zhang Y. Integrative insect taxonomy based on morphology, mitochondrial DNA, and hyperspectral reflectance profiling. Zool J Linn Soc 2015. [DOI: 10.1111/zoj.12367] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Yang Wang
- Key Laboratory of Plant Protection Resources and Pest Management; Ministry of Education; Entomological Museum; Northwest A&F University; Yangling Shaanxi 712100 China
| | - Christian Nansen
- Department of Entomology and Nematology; UC Davis Briggs Hall; Room 367 Davis CA USA
| | - Yalin Zhang
- Key Laboratory of Plant Protection Resources and Pest Management; Ministry of Education; Entomological Museum; Northwest A&F University; Yangling Shaanxi 712100 China
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67
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Mohrbeck I, Raupach MJ, Martínez Arbizu P, Knebelsberger T, Laakmann S. High-Throughput Sequencing-The Key to Rapid Biodiversity Assessment of Marine Metazoa? PLoS One 2015; 10:e0140342. [PMID: 26479071 PMCID: PMC4610693 DOI: 10.1371/journal.pone.0140342] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Accepted: 09/24/2015] [Indexed: 02/03/2023] Open
Abstract
The applications of traditional morphological and molecular methods for species identification are greatly restricted by processing speed and on a regional or greater scale are generally considered unfeasible. In this context, high-throughput sequencing, or metagenetics, has been proposed as an efficient tool to document biodiversity. Here we evaluated the effectiveness of 454 pyrosequencing in marine metazoan community analysis using the 18S rDNA: V1-V2 region. Multiplex pyrosequencing of the V1-V2 region was used to analyze two pooled samples of DNA, one comprising 118 and the other 37 morphologically identified species, and one natural sample taken directly from a North Sea zooplankton community. A DNA reference library comprising all species represented in the pooled samples was created by Sanger sequencing, and this was then used to determine the optimal similarity threshold for species delineation. The optimal threshold was found at 99% species similarity, with 85% identification success. Pyrosequencing was able to identify between fewer species: 67% and 78% of the species in the two pooled samples. Also, a large number of sequences for three species that were not included in the pooled samples were amplified by pyrosequencing, suggesting preferential amplification of some genotypes and the sensitivity of this approach to even low levels of contamination. Conversely, metagenetic analysis of the natural zooplankton sample identified many more species (particularly gelatinous zooplankton and meroplankton) than morphological analysis of a formalin-fixed sample from the same sampling site, suggesting an increased level of taxonomic resolution with pyrosequencing. The study demonstrated that, based on the V1-V2 region, 454 sequencing does not provide accurate species differentiation and reliable taxonomic classification, as it is required in most biodiversity monitoring. The analysis of artificially prepared samples indicated that species detection in pyrosequencing datasets is complicated by potential PCR-based biases and that the V1-V2 marker is poorly resolved for some taxa.
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Affiliation(s)
- Inga Mohrbeck
- Department German Center for Marine Biodiversity Research, Senckenberg am Meer, Wilhelmshaven, Germany
| | - Michael J Raupach
- Department German Center for Marine Biodiversity Research, Senckenberg am Meer, Wilhelmshaven, Germany
| | - Pedro Martínez Arbizu
- Department German Center for Marine Biodiversity Research, Senckenberg am Meer, Wilhelmshaven, Germany
| | - Thomas Knebelsberger
- Department German Center for Marine Biodiversity Research, Senckenberg am Meer, Wilhelmshaven, Germany
| | - Silke Laakmann
- Department German Center for Marine Biodiversity Research, Senckenberg am Meer, Wilhelmshaven, Germany
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68
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Maranan JBD, Basiao ZU, Quilang JP. DNA barcoding of feral tilapias in Philippine lakes. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4302-4313. [PMID: 26457820 DOI: 10.3109/19401736.2015.1089478] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Tilapia (Oreochromis mossambicus) was first introduced to the Philippines in 1950 for aquaculture. Since then, other species of tilapia have been introduced to the country and some of them (mainly Oreochromis niloticus) have become established in lakes and other water bodies. In this study, DNA barcoding using the mitochondrial cytochrome c oxidase subunit I (COI) gene was done to assess the reliability of morphological identification and the degree of introgression among feral tilapias (Oreochromis spp.) in seven major Philippine lakes, namely Laguna de Bay, Lake Lanao, Taal Lake, Lake Mainit, Lake Naujan, Lake Bato, and Lake Buhi. Specimens were also collected from a private hatchery in Sual, Pangasinan to serve as reference. Morphological traits, Nucleotide BLAST (BLASTn), and Translated BLAST (BLASTx) analyses were used to classify the specimens. A Neighbor-Joining tree was constructed using the Kimura 2-Parameter method, incorporating 66 COI sequences generated from the study and 20 additional reference sequences obtained from GenBank. Three Oreochromis clusters were obtained and were classified as the O. niloticus group, O. mossambicus group, and O. aureus group, with bootstrap support values of 99%, 74%, and 99%, respectively. The mean K2P genetic distances within each group were 0.008%, 0.959%, and 0.086%, respectively. The clustering of COI sequences generated from this study corresponded with the results of the BLASTn analysis. Oreochromis hybrids were also found in all the lakes. The study highlights the usefulness of DNA barcoding for molecular identification and detection of introgressed individuals, with potential applications in management of feral stocks.
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Affiliation(s)
- Justin Bryan D Maranan
- a Molecular Population Genetics Laboratory, Institute of Biology, College of Science, University of the Philippines , Diliman , Quezon City , Philippines
| | - Zubaida U Basiao
- a Molecular Population Genetics Laboratory, Institute of Biology, College of Science, University of the Philippines , Diliman , Quezon City , Philippines
| | - Jonas P Quilang
- a Molecular Population Genetics Laboratory, Institute of Biology, College of Science, University of the Philippines , Diliman , Quezon City , Philippines
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69
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Lalis A, Leblois R, Liefried S, Ouarour A, Reddy Beeravolu C, Michaux J, Hamani A, Denys C, Nicolas V. New molecular data favour an anthropogenic introduction of the wood mouse (Apodemus sylvaticus
) in North Africa. J ZOOL SYST EVOL RES 2015. [DOI: 10.1111/jzs.12111] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Aude Lalis
- Institut de Systématique, Evolution; Biodiversité ISYEB UMR 7205 - CNRS MNHN UMPC EPHE; Muséum National d'Histoire Naturelle; Sorbonne Universités; Paris France
| | | | - Sohaib Liefried
- Laboratoire de Biologie et Santé; Faculté des Sciences; Université Abdelmalek Essaâdi; Tétouan Maroc
| | - Ali Ouarour
- Laboratoire de Biologie et Santé; Faculté des Sciences; Université Abdelmalek Essaâdi; Tétouan Maroc
| | | | - Johan Michaux
- Unité de génétique de la conservation; Institut de Botanique; Université de Liège (Sart Tilman); Liège Belgique
| | - Adel Hamani
- Laboratoire d'Ornithologie; Département de Zoologie; ENSA El Harrach; Alger Algeria
| | - Christiane Denys
- Institut de Systématique, Evolution; Biodiversité ISYEB UMR 7205 - CNRS MNHN UMPC EPHE; Muséum National d'Histoire Naturelle; Sorbonne Universités; Paris France
| | - Violaine Nicolas
- Institut de Systématique, Evolution; Biodiversité ISYEB UMR 7205 - CNRS MNHN UMPC EPHE; Muséum National d'Histoire Naturelle; Sorbonne Universités; Paris France
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70
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Gonçalves PFM, Oliveira-Marques AR, Matsumoto TE, Miyaki CY. DNA Barcoding Identifies Illegal Parrot Trade: Figure 1. J Hered 2015; 106 Suppl 1:560-4. [DOI: 10.1093/jhered/esv035] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
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71
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Kang TH, Lee KS, Lee HS. DNA Barcoding of the Korean Lymantria Hübner, 1819 (Lepidoptera: Erebidae: Lymantriinae) for Quarantine Inspection. JOURNAL OF ECONOMIC ENTOMOLOGY 2015; 108:1596-1611. [PMID: 26470300 DOI: 10.1093/jee/tov111] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 04/20/2015] [Indexed: 06/05/2023]
Abstract
DNA barcoding and morphological analyses of Korean Lymantria (Erebidae, Lepidoptera) were conducted for quarantine inspection. In DNA barcoding, Lymantria dispar identified through quarantine inspection was distinguished as three species, L. dispar asiatica, L. albescens, and L. xylina. Lymantria monacha, which is known as a single species in Korea, is revealed as containing three species, L. monacha, L. minomonis, and L. sugii. At the subspecies level, L. dispar dispar formed a single cluster, whereas L. d. asiatica and L. d. japonica formed a cluster containing both subspecies. In morphological re-examination on DNA barcoding results, L. dispar was distinguished from L. albescens by wing pattern, and from L. xylina by papillae anale. L. monacha and the related species were hard to be distinct from each other by using wing pattern, but it was easily distinct through comparison of genitalia. Therefore, DNA barcoding led to accurate identification in species level, but in subspecies level, only a taxon showing geographically far distance was discriminated from the others. These results may provide a taxonomic outline of the Korean Lymantria fauna and may be used as an identification reference for Lymantria species during quarantine inspection.
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Affiliation(s)
- Tae Hwa Kang
- Plant Quarantine Technology Center, Animal and Plant Quarantine Agency, 234-3, Mangpo-dong, Yeongtong-gu, Suwon-si, Gyeonggi-do, 443-400, Korea
| | - Kwang-Su Lee
- Department of Forest Science, Sangji University, 83, Sangjidae-gil, Wonju-si, Gangwon-do, 220-702, Korea
| | - Heung-Sik Lee
- Animal and Plant Quarantine Agency, Jongbu regional office, 129, Juan-ro, Nam-gu, Incheon, Korea.
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72
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Bhattacharya M, Sharma AR, Patra BC, Sharma G, Seo EM, Nam JS, Chakraborty C, Lee SS. DNA barcoding to fishes: current status and future directions. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2744-52. [PMID: 26057011 DOI: 10.3109/19401736.2015.1046175] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
DNA barcoding appears to be a promising approach for taxonomic identification, characterization, and discovery of newer species, facilitating biodiversity studies. It helps researchers to appreciate genetic and evolutionary associations by collection of molecular, morphological, and distributional data. Fish DNA barcoding, based on the sequencing of a uniform area of Cytochrome C Oxidase type I (COI) gene, has received significant interest as an accurate tool for species identification, authentication, and phylogenetic analysis. The aim of this review article was to investigate recent global status, approaches, and future direction of DNA barcoding in fisheries sectors. We have tried to highlight its possible impacts, complications, and validation issues at species levels for biodiversity analysis. Moreover, an effort has been put forward to understand issues related to various marker genes associated with barcode process as primer sequences and have concluded barcode promotion as an indispensable tool of molecular biology for the development of taxonomic support systems.
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Affiliation(s)
- Manojit Bhattacharya
- a Institute for Skeletal Aging & Orthopedic Surgery, Hallym University - Chuncheon Sacred Heart Hospital , Chuncheon-si , Korea .,b Aquaculture Research Unit, Department of Zoology , Vidyasagar University , Midnapore , West Bengal , India , and
| | - Ashish Ranjan Sharma
- a Institute for Skeletal Aging & Orthopedic Surgery, Hallym University - Chuncheon Sacred Heart Hospital , Chuncheon-si , Korea
| | - Bidhan Chandra Patra
- b Aquaculture Research Unit, Department of Zoology , Vidyasagar University , Midnapore , West Bengal , India , and
| | - Garima Sharma
- a Institute for Skeletal Aging & Orthopedic Surgery, Hallym University - Chuncheon Sacred Heart Hospital , Chuncheon-si , Korea
| | - Eun-Min Seo
- a Institute for Skeletal Aging & Orthopedic Surgery, Hallym University - Chuncheon Sacred Heart Hospital , Chuncheon-si , Korea
| | - Ju-Suk Nam
- a Institute for Skeletal Aging & Orthopedic Surgery, Hallym University - Chuncheon Sacred Heart Hospital , Chuncheon-si , Korea
| | - Chiranjib Chakraborty
- a Institute for Skeletal Aging & Orthopedic Surgery, Hallym University - Chuncheon Sacred Heart Hospital , Chuncheon-si , Korea .,c Department of Bio-informatics , School of Computer and Information Sciences, Galgotias University , Greater Noida , India
| | - Sang-Soo Lee
- a Institute for Skeletal Aging & Orthopedic Surgery, Hallym University - Chuncheon Sacred Heart Hospital , Chuncheon-si , Korea
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73
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Chen J, Jiang Z, Li C, Ping X, Cui S, Tang S, Chu H, Liu B. Identification of ungulates used in a traditional Chinese medicine with DNA barcoding technology. Ecol Evol 2015; 5:1818-25. [PMID: 26140198 PMCID: PMC4485963 DOI: 10.1002/ece3.1457] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Revised: 02/12/2015] [Accepted: 02/16/2015] [Indexed: 11/22/2022] Open
Abstract
Horns of Saiga antelope (Saiga tatarica) have always been an ingredient of “Lingyangjiao”, a traditional Chinese medicine (TCM). Persistent hunting for Saiga antelope has already threatened the survival of critical endangered populations in wild. To control the growing pressure, CITES and Chinese government have legislated for monitoring the trade of Saiga horns. However, similar ungulate horns are difficult to identify by their morphological characteristics, which has impeded the law enforcement. Besides Saiga antelope, other seven ungulate species which have similar horns are also sold and marked as “Lingyangjiao” in TCM markets to offset shortage of Saiga antelope horns. Such species are Gazella subgutturosa, Pantholops hodgsonii, Procapra picticaudata, Procapra gutturosa, Procapra przewalskii, Capra hircus, and Ovis aries. Our study aimed at implementing DNA barcoding technology to diagnose Saiga horns and the substitutes. We successfully extracted genomic DNA from horn samples. We recovered COI sequences of 644 bp with specific primers and 349 bp with nested PCR primers designed for degraded horn samples. The mean interspecific genetic distance of data set of the 644-bp full barcodes and the 349-bp mini-barcodes was 14.96% and 15.38%, respectively, and the mean intraspecific distance was 0.24% and 0.20%, respectively. Each species formed independent clades in neighbor-joining (NJ) phylogenetic tree of the two data sets with >99% supporting values, except P. gutturosa and P. przewalskii. The deep genetic distances gap and clear species clades in NJ tree of either full barcodes or mini-barcodes suggest that barcoding technology is an effective tool to diagnose Saiga horns and their substitutes. Barcoding diagnosis protocol developed here will simplify diagnosis of “Lingyangjiao” species and will facilitate conservation of endangered ungulates involved in TCM “Lingyangjiao” markets, especially the Saiga antelope.
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Affiliation(s)
- Jing Chen
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences Chaoyang District, No. 1 Beichen West Road, Beijing, 100101, China ; University of Chinese Academy of Sciences No. 19 (A) Yuquan Road, Beijing, 100049, China
| | - Zhigang Jiang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences Chaoyang District, No. 1 Beichen West Road, Beijing, 100101, China ; University of Chinese Academy of Sciences No. 19 (A) Yuquan Road, Beijing, 100049, China ; Endangered Species Scientific Commission of the People's Republic of China Chaoyang District, No. 1 Beichen West Road, Beijing, 100101, China
| | - Chunlin Li
- School of Resources and Environmental Engineering, Anhui University No. 111 Jiu Long Road, Hefei, 230601, Anhui Province, China
| | - Xiaoge Ping
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences Chaoyang District, No. 1 Beichen West Road, Beijing, 100101, China
| | - Shaopeng Cui
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences Chaoyang District, No. 1 Beichen West Road, Beijing, 100101, China ; University of Chinese Academy of Sciences No. 19 (A) Yuquan Road, Beijing, 100049, China
| | - Songhua Tang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences Chaoyang District, No. 1 Beichen West Road, Beijing, 100101, China
| | - Hongjun Chu
- Wildlife Conservation Office of Altay Prefecture 836500, Altay, Xinjiang, China
| | - Binwan Liu
- College of Wildlife Resources, Northeast Forestry University, No. 26 Hexing Road Xiangfang District Harbin, 150040, Heilongjiang Province, China
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74
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Irinyi L, Serena C, Garcia-Hermoso D, Arabatzis M, Desnos-Ollivier M, Vu D, Cardinali G, Arthur I, Normand AC, Giraldo A, da Cunha KC, Sandoval-Denis M, Hendrickx M, Nishikaku AS, de Azevedo Melo AS, Merseguel KB, Khan A, Parente Rocha JA, Sampaio P, da Silva Briones MR, e Ferreira RC, de Medeiros Muniz M, Castañón-Olivares LR, Estrada-Barcenas D, Cassagne C, Mary C, Duan SY, Kong F, Sun AY, Zeng X, Zhao Z, Gantois N, Botterel F, Robbertse B, Schoch C, Gams W, Ellis D, Halliday C, Chen S, Sorrell TC, Piarroux R, Colombo AL, Pais C, de Hoog S, Zancopé-Oliveira RM, Taylor ML, Toriello C, de Almeida Soares CM, Delhaes L, Stubbe D, Dromer F, Ranque S, Guarro J, Cano-Lira JF, Robert V, Velegraki A, Meyer W. International Society of Human and Animal Mycology (ISHAM)-ITS reference DNA barcoding database--the quality controlled standard tool for routine identification of human and animal pathogenic fungi. Med Mycol 2015; 53:313-37. [PMID: 25802363 DOI: 10.1093/mmy/myv008] [Citation(s) in RCA: 207] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 01/19/2015] [Indexed: 12/13/2022] Open
Abstract
Human and animal fungal pathogens are a growing threat worldwide leading to emerging infections and creating new risks for established ones. There is a growing need for a rapid and accurate identification of pathogens to enable early diagnosis and targeted antifungal therapy. Morphological and biochemical identification methods are time-consuming and require trained experts. Alternatively, molecular methods, such as DNA barcoding, a powerful and easy tool for rapid monophasic identification, offer a practical approach for species identification and less demanding in terms of taxonomical expertise. However, its wide-spread use is still limited by a lack of quality-controlled reference databases and the evolving recognition and definition of new fungal species/complexes. An international consortium of medical mycology laboratories was formed aiming to establish a quality controlled ITS database under the umbrella of the ISHAM working group on "DNA barcoding of human and animal pathogenic fungi." A new database, containing 2800 ITS sequences representing 421 fungal species, providing the medical community with a freely accessible tool at http://www.isham.org/ and http://its.mycologylab.org/ to rapidly and reliably identify most agents of mycoses, was established. The generated sequences included in the new database were used to evaluate the variation and overall utility of the ITS region for the identification of pathogenic fungi at intra-and interspecies level. The average intraspecies variation ranged from 0 to 2.25%. This highlighted selected pathogenic fungal species, such as the dermatophytes and emerging yeast, for which additional molecular methods/genetic markers are required for their reliable identification from clinical and veterinary specimens.
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Affiliation(s)
- Laszlo Irinyi
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Sydney Medical School-Westmead Hospital, Marie Bashir Institute for Infectious Diseases and Bioscurity, University of Sydney, Westmead Millennium Institute, Sydney, Australia
| | - Carolina Serena
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Sydney Medical School-Westmead Hospital, Marie Bashir Institute for Infectious Diseases and Bioscurity, University of Sydney, Westmead Millennium Institute, Sydney, Australia Unitat de Recerca, Hospital Joan XXIII, Institut de Investigacio Sanitaria Rovira I Virgili (IISPV), Universitat Rovira i Virgili, Tarragona, Spain
| | - Dea Garcia-Hermoso
- Institut Pasteur, National Reference Center for Invasive Mycoses and Antifungals, Molecular Mycology Unit; CNRS URA3012, Paris, France
| | - Michael Arabatzis
- Mycology Research Laboratory, Department of Microbiology, Medical School, the University of Athens Hellenic Collection of Pathogenic Fungi (UOA/HCPF), National and Kapodistrian University of Athens, Athens, Greece
| | - Marie Desnos-Ollivier
- Institut Pasteur, National Reference Center for Invasive Mycoses and Antifungals, Molecular Mycology Unit; CNRS URA3012, Paris, France
| | - Duong Vu
- CBS-KNAW, Fungal Biodiversity Centre, Utrecht, The Netherlands
| | - Gianluigi Cardinali
- Department of Pharmaceutical Sciences-Università degli Studi di Perugia, Perugia, Italy
| | - Ian Arthur
- Mycology Laboratory, Department of Microbiology and Infectious Diseases, PathWest Laboratory Medicine WA, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Anne-Cécile Normand
- Parasitology - Mycology, APHM, CHU Timone-Adultes, Marseille, France; Aix-Marseille University, UMR MD3 IP-TPT, Marseille, France
| | - Alejandra Giraldo
- Unitat de Microbiologia, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
| | - Keith Cassia da Cunha
- Unitat de Microbiologia, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
| | - Marcelo Sandoval-Denis
- Unitat de Microbiologia, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
| | - Marijke Hendrickx
- BCCM/IHEM, Biomedical fungi and yeasts collection, Scientific Institute of Public Health, Brussels, Belgium
| | - Angela Satie Nishikaku
- Laboratório Especial de Micologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Analy Salles de Azevedo Melo
- Laboratório Especial de Micologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | | | - Aziza Khan
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Sydney Medical School-Westmead Hospital, Marie Bashir Institute for Infectious Diseases and Bioscurity, University of Sydney, Westmead Millennium Institute, Sydney, Australia
| | - Juliana Alves Parente Rocha
- Universidade Federal de Goiás, Instituto de Ciências Biológicas, Laboratório de Biologia Molecular, Goiânia, Goiás, Brazil
| | - Paula Sampaio
- Centre of Molecular and Environmental Biology (CBMA), Biology Department, School of Sciences, University of Minho, Braga, Portugal
| | - Marcelo Ribeiro da Silva Briones
- Laboratório de Genômica e Biocomplexidade Evolutiva, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Renata Carmona e Ferreira
- Laboratório de Genômica e Biocomplexidade Evolutiva, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Mauro de Medeiros Muniz
- Instituto de Pesquisa Clínica Evandro Chagas (IPEC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
| | - Laura Rosio Castañón-Olivares
- Facultad de Medicina, Departamento de Microbiología y Parasitología (Unidad de Micología), Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Daniel Estrada-Barcenas
- Facultad de Medicina, Departamento de Microbiología y Parasitología (Unidad de Micología), Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Carole Cassagne
- Parasitology - Mycology, APHM, CHU Timone-Adultes, Marseille, France; Aix-Marseille University, UMR MD3 IP-TPT, Marseille, France
| | - Charles Mary
- Parasitology - Mycology, APHM, CHU Timone-Adultes, Marseille, France; Aix-Marseille University, UMR MD3 IP-TPT, Marseille, France
| | - Shu Yao Duan
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Sydney Medical School-Westmead Hospital, Marie Bashir Institute for Infectious Diseases and Bioscurity, University of Sydney, Westmead Millennium Institute, Sydney, Australia
| | - Fanrong Kong
- Centre for Infectious Diseases and Microbiology, Westmead Hospital, Westmead, NSW, Australia
| | - Annie Ying Sun
- School of Paediatrics and Reproductive Health, University of Adelaide, Adelaide, SA, Australia; Robinson Institute, University of Adelaide, Adelaide, SA, Australia
| | - Xianyu Zeng
- Centre for Infectious Diseases and Microbiology, Westmead Hospital, Westmead, NSW, Australia
| | - Zuotao Zhao
- Centre for Infectious Diseases and Microbiology, Westmead Hospital, Westmead, NSW, Australia
| | - Nausicaa Gantois
- BDEEP-EA4547, CIIL, Institut Pasteur de Lille, CHU de Lille, Université de Lille2, Lille, France
| | - Françoise Botterel
- Unité de Parasitologie - Mycologie, Dynamyc Team, CHU Henri Mondor, AP-HP, Créteil, France
| | - Barbara Robbertse
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Conrad Schoch
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Walter Gams
- CBS-KNAW, Fungal Biodiversity Centre, Utrecht, The Netherlands
| | - David Ellis
- Mycology and Infectious Diseases, SA Pathology, University of Adelaide, Adelaide, SA, Australia
| | - Catriona Halliday
- Centre for Infectious Diseases and Microbiology, Westmead Hospital, Westmead, NSW, Australia
| | - Sharon Chen
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Sydney Medical School-Westmead Hospital, Marie Bashir Institute for Infectious Diseases and Bioscurity, University of Sydney, Westmead Millennium Institute, Sydney, Australia Centre for Infectious Diseases and Microbiology, Westmead Hospital, Westmead, NSW, Australia
| | - Tania C Sorrell
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Sydney Medical School-Westmead Hospital, Marie Bashir Institute for Infectious Diseases and Bioscurity, University of Sydney, Westmead Millennium Institute, Sydney, Australia
| | - Renaud Piarroux
- Parasitology - Mycology, APHM, CHU Timone-Adultes, Marseille, France; Aix-Marseille University, UMR MD3 IP-TPT, Marseille, France
| | - Arnaldo L Colombo
- Laboratório Especial de Micologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Célia Pais
- Centre of Molecular and Environmental Biology (CBMA), Biology Department, School of Sciences, University of Minho, Braga, Portugal
| | - Sybren de Hoog
- CBS-KNAW, Fungal Biodiversity Centre, Utrecht, The Netherlands
| | | | - Maria Lucia Taylor
- Facultad de Medicina, Departamento de Microbiología y Parasitología (Unidad de Micología), Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Conchita Toriello
- Facultad de Medicina, Departamento de Microbiología y Parasitología (Unidad de Micología), Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Célia Maria de Almeida Soares
- Universidade Federal de Goiás, Instituto de Ciências Biológicas, Laboratório de Biologia Molecular, Goiânia, Goiás, Brazil
| | - Laurence Delhaes
- BDEEP-EA4547, CIIL, Institut Pasteur de Lille, CHU de Lille, Université de Lille2, Lille, France
| | - Dirk Stubbe
- BCCM/IHEM, Biomedical fungi and yeasts collection, Scientific Institute of Public Health, Brussels, Belgium
| | - Françoise Dromer
- Institut Pasteur, National Reference Center for Invasive Mycoses and Antifungals, Molecular Mycology Unit; CNRS URA3012, Paris, France
| | - Stéphane Ranque
- Parasitology - Mycology, APHM, CHU Timone-Adultes, Marseille, France; Aix-Marseille University, UMR MD3 IP-TPT, Marseille, France
| | - Josep Guarro
- Unitat de Microbiologia, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
| | - Jose F Cano-Lira
- Unitat de Microbiologia, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
| | - Vincent Robert
- CBS-KNAW, Fungal Biodiversity Centre, Utrecht, The Netherlands
| | - Aristea Velegraki
- Mycology Research Laboratory, Department of Microbiology, Medical School, the University of Athens Hellenic Collection of Pathogenic Fungi (UOA/HCPF), National and Kapodistrian University of Athens, Athens, Greece
| | - Wieland Meyer
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Sydney Medical School-Westmead Hospital, Marie Bashir Institute for Infectious Diseases and Bioscurity, University of Sydney, Westmead Millennium Institute, Sydney, Australia
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Harrup LE, Bellis GA, Balenghien T, Garros C. Culicoides Latreille (Diptera: Ceratopogonidae) taxonomy: current challenges and future directions. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2015; 30:249-266. [PMID: 25535946 PMCID: PMC4330985 DOI: 10.1016/j.meegid.2014.12.018] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 12/12/2014] [Accepted: 12/13/2014] [Indexed: 11/23/2022]
Abstract
Culicoides Latreille biting midges (Diptera: Ceratopogonidae) cause a significant biting nuisance to humans, livestock and equines, and are the biological vectors of a range of internationally important pathogens of both veterinary and medical importance. Despite their economic significance, the delimitation and identification of species and evolutionary relationships between species within this genus remains at best problematic. To date no phylogenetic study has attempted to validate the subgeneric classification of the genus and the monophyly of many of the subgenera remains doubtful. Many informal species groupings are also known to exist but few are adequately described, further complicating accurate identification. Recent contributions to Culicoides taxonomy at the species level have revealed a high correlation between morphological and molecular analyses although molecular analyses are revealing the existence of cryptic species. This review considers the methods for studying the systematics of Culicoides using both morphological and genetic techniques, with a view to understanding the factors limiting our current understanding of Culicoides biology and hence arbovirus epidemiology. In addition, we examine the global status of Culicoides identification, highlighting areas that are poorly addressed, including the potential implementation of emerging technologies.
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Affiliation(s)
- L E Harrup
- Vector-borne Viral Diseases Programme, The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, UK.
| | - G A Bellis
- University of Queensland, St Lucia, Brisbane, Qld, Australia
| | - T Balenghien
- Cirad, UMR15 CMAEE, 34398 Montpellier, France; INRA, UMR1309 CMAEE, 34398 Montpellier, France
| | - C Garros
- Cirad, UMR15 CMAEE, 34398 Montpellier, France; INRA, UMR1309 CMAEE, 34398 Montpellier, France
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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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Yu Z, Li Q, Kong L, Yu H. Utility of DNA barcoding for Tellinoidea: a comparison of distance, coalescent and character-based methods on multiple genes. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2015; 17:55-65. [PMID: 25107691 DOI: 10.1007/s10126-014-9596-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 07/18/2014] [Indexed: 06/03/2023]
Abstract
DNA barcoding has become a promising tool for rapid species identification using a short fragment of mitochondrial gene. Currently, an increasing number of analytical methods are available to assign DNA barcodes to taxa. The methods can be broadly divided into three main categories: (i) distance-based methods (the classical approach and the automatic barcode gap discovery (ABGD) approach), (ii) coalescent-based methods (the monophyly-based method and the general mixed Yule coalescent (GMYC) model) and (iii) the character-based method (CAOS). This study is set out to evaluate the availability of each method in barcoding Tellinoidea on the cytomchrome c oxidase subunit I (COI) and the 16 small-subunit ribosomal DNA (16S rDNA) genes. As a result, the character-based method was found to be the best in all cases, especially on a genus level. For distance-based methods, the elaborate one gained a success equal or greater than the basic one. The traditional coalescent-based method nicely delimited all of the tellinoideans on a species level. The GMYC model, which is the most radical, clearly inflated the number of species units by 34.6 % for COI gene and by 58.8 % for 16S gene. Thus, we conclude that CAOS better approximates a real barcode, and suggest the use of the ABGD method and the monophyly-based method for primary partitions. Additionally, COI gene may be more suitable as a standard barcode marker than 16S gene, particularly for tree-based methods.
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Affiliation(s)
- Zhenzhen Yu
- The Key Laboratory of Mariculture Ministry of Education, Ocean University of China, Qingdao, 266003, China
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Miller JA, Miller JH, Pham DS, Beentjes KK. Cyberdiversity: improving the informatic value of diverse tropical arthropod inventories. PLoS One 2014; 9:e115750. [PMID: 25541974 PMCID: PMC4277369 DOI: 10.1371/journal.pone.0115750] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 11/26/2014] [Indexed: 11/19/2022] Open
Abstract
In an era of biodiversity crisis, arthropods have great potential to inform conservation assessment and test hypotheses about community assembly. This is because their relatively narrow geographic distributions and high diversity offer high-resolution data on landscape-scale patterns of biodiversity. However, a major impediment to the more widespread application of arthropod data to a range of scientific and policy questions is the poor state of modern arthropod taxonomy, especially in the tropics. Inventories of spiders and other megadiverse arthropods from tropical forests are dominated by undescribed species. Such studies typically organize their data using morphospecies codes, which make it difficult for data from independent inventories to be compared and combined. To combat this shortcoming, we offer cyberdiversity, an online community-based approach for reconciling results of independent inventory studies where current taxonomic knowledge is incomplete. Participating scientists can upload images and DNA barcode sequences to dedicated databases and submit occurrence data and links to a web site (www.digitalSpiders.org). Taxonomic determinations can be shared with a crowdsourcing comments feature, and researchers can discover specimens of interest available for loan and request aliquots of genomic DNA extract. To demonstrate the value of the cyberdiversity framework, we reconcile data from three rapid structured inventories of spiders conducted in Vietnam with an independent inventory (Doi Inthanon, Thailand) using online image libraries. Species richness and inventory completeness were assessed using non-parametric estimators. Community similarity was evaluated using a novel index based on the Jaccard replacing observed with estimated values to correct for unobserved species. We use a distance-decay framework to demonstrate a rudimentary model of landscape-scale changes in community composition that will become increasingly informative as additional inventories participate. With broader adoption of the cyberdiversity approach, networks of information-sharing taxonomists can more efficiently and effectively address taxonomic impediments while elucidating landscape scale patterns of biodiversity.
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Affiliation(s)
- Jeremy A. Miller
- Department of Terrestrial Zoology, Naturalis Biodiversity Center, RA Leiden, The Netherlands
- Department of Entomology, California Academy of Sciences, Golden Gate Park, San Francisco, California, United States of America
- Plazi, Zinggstrasse 16, Bern, Switzerland
| | - Joshua H. Miller
- Department of Geology, University of Cincinnati, 500 Geology/Physics Building, Cincinnati, Ohio, United States of America
- University of Alaska Museum, Fairbanks, Alaska, United States of America
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, United States of America
| | - Dinh-Sac Pham
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, Cau Giay Dist, Ha Noi, Vietnam
| | - Kevin K. Beentjes
- Naturalis DNA Barcoding Facility, Naturalis Biodiversity Center, RA Leiden, The Netherlands
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Yan LJ, Liu J, Möller M, Zhang L, Zhang XM, Li DZ, Gao LM. DNA barcoding ofRhododendron(Ericaceae), the largest Chinese plant genus in biodiversity hotspots of the Himalaya-Hengduan Mountains. Mol Ecol Resour 2014; 15:932-44. [DOI: 10.1111/1755-0998.12353] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2014] [Revised: 11/22/2014] [Accepted: 11/26/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Li-Jun Yan
- Key Laboratory for Plant Diversity and Biogeography of East Asia; Kunming Institute of Botany; Chinese Academy of Sciences; Kunming 650201 Yunnan China
- Germplasm Bank of Wild Species; Kunming Institute of Botany; Chinese Academy of Sciences; Kunming 650201 Yunnan China
- University of Chinese Academy of Sciences; Beijing 100049 China
| | - Jie Liu
- Key Laboratory for Plant Diversity and Biogeography of East Asia; Kunming Institute of Botany; Chinese Academy of Sciences; Kunming 650201 Yunnan China
| | - Michael Möller
- Key Laboratory for Plant Diversity and Biogeography of East Asia; Kunming Institute of Botany; Chinese Academy of Sciences; Kunming 650201 Yunnan China
- Royal Botanic Garden Edinburgh; 20A Inverleith Row Edinburgh EH3 5LR UK
| | - Lin Zhang
- Key Laboratory for Plant Diversity and Biogeography of East Asia; Kunming Institute of Botany; Chinese Academy of Sciences; Kunming 650201 Yunnan China
- University of Chinese Academy of Sciences; Beijing 100049 China
| | - Xue-Mei Zhang
- Landscape and Horticultural College; Yunnan Agricultural University; Kunming 650201 Yunnan China
| | - De-Zhu Li
- Key Laboratory for Plant Diversity and Biogeography of East Asia; Kunming Institute of Botany; Chinese Academy of Sciences; Kunming 650201 Yunnan China
- Germplasm Bank of Wild Species; Kunming Institute of Botany; Chinese Academy of Sciences; Kunming 650201 Yunnan China
| | - Lian-Ming Gao
- Key Laboratory for Plant Diversity and Biogeography of East Asia; Kunming Institute of Botany; Chinese Academy of Sciences; Kunming 650201 Yunnan China
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80
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Chan A, Chiang LP, Hapuarachchi HC, Tan CH, Pang SC, Lee R, Lee KS, Ng LC, Lam-Phua SG. DNA barcoding: complementing morphological identification of mosquito species in Singapore. Parasit Vectors 2014; 7:569. [PMID: 25498759 PMCID: PMC4282734 DOI: 10.1186/s13071-014-0569-4] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Accepted: 11/25/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Taxonomy that utilizes morphological characteristics has been the gold standard method to identify mosquito species. However, morphological identification is challenging when the expertise is limited and external characters are damaged because of improper specimen handling. Therefore, we explored the applicability of mitochondrial cytochrome C oxidase subunit 1 (COI) gene-based DNA barcoding as an alternative tool to identify mosquito species. In the present study, we compared the morphological identification of mosquito specimens with their differentiation based on COI barcode, in order to establish a more reliable identification system for mosquito species found in Singapore. METHODS We analysed 128 adult mosquito specimens, belonging to 45 species of 13 genera. Phylogenetic trees were constructed for Aedes, Anopheles, Culex and other genera of mosquitoes and the distinctive clustering of different species was compared with their taxonomic identity. RESULTS The COI-based DNA barcoding achieved a 100% success rate in identifying the mosquito species. We also report COI barcode sequences of 16 mosquito species which were not available previously in sequence databases. CONCLUSIONS Our study utilised for the first time DNA barcoding to identify mosquito species in Singapore. COI-based DNA barcoding is a useful tool to complement taxonomy-based identification of mosquito species.
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Affiliation(s)
- Abigail Chan
- Environmental Health Institute, National Environment Agency, 11 Biopolis Way, Helios Block, #06-05/08, Singapore, 138667, Singapore.
| | - Lee-Pei Chiang
- Shizenature Pte Ltd, 3016, Eastech, Bedok North Avenue 4, #02-13, Singapore, 489947, Singapore.
| | - Hapuarachchige C Hapuarachchi
- Environmental Health Institute, National Environment Agency, 11 Biopolis Way, Helios Block, #06-05/08, Singapore, 138667, Singapore.
| | - Cheong-Huat Tan
- Environmental Health Institute, National Environment Agency, 11 Biopolis Way, Helios Block, #06-05/08, Singapore, 138667, Singapore.
| | - Sook-Cheng Pang
- Environmental Health Institute, National Environment Agency, 11 Biopolis Way, Helios Block, #06-05/08, Singapore, 138667, Singapore.
| | - Ruth Lee
- Environmental Health Institute, National Environment Agency, 11 Biopolis Way, Helios Block, #06-05/08, Singapore, 138667, Singapore.
| | - Kim-Sung Lee
- School of Life Sciences and Chemical Technology, Ngee Ann Polytechnic, 535, Clementi Road, Singapore, 599489, Singapore.
| | - Lee-Ching Ng
- Environmental Health Institute, National Environment Agency, 11 Biopolis Way, Helios Block, #06-05/08, Singapore, 138667, Singapore.
| | - Sai-Gek Lam-Phua
- Environmental Health Institute, National Environment Agency, 11 Biopolis Way, Helios Block, #06-05/08, Singapore, 138667, Singapore.
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81
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Carvalho-Batista A, Negri M, Pileggi LG, Castilho AL, Costa RC, Mantelatto FL. Inferring population connectivity across the range of distribution of the stiletto shrimp Artemesialonginaris Spence Bate, 1888 (Decapoda, Penaeidae) from DNA barcoding: implications for fishery management. Zookeys 2014:271-88. [PMID: 25561842 PMCID: PMC4283376 DOI: 10.3897/zookeys.457.6569] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 03/21/2014] [Indexed: 11/12/2022] Open
Abstract
Artemesialonginaris is a marine shrimp endemic to the southwestern Atlantic and distributed from Atafona, Rio de Janeiro (Brazil) to Rawson, Chubut (Argentina). In recent years, this species has become an important target of the commercial fishery as a consequence of the decline in the fishery of more traditional and profitable marine shrimps. In addition, phenotypic variations have been documented in populations along its distribution. Therefore, investigations on the genetics of the fishing stocks are necessary for the development of sustainable management strategies and for understanding the possible sources of these variations. The mitochondrial gene Cytochrome Oxidase I (COI) was used to search for evidence of genetic structure among the populations of Artemesialonginaris and to analyze the phylogenetic relationships among them. A total of 60 specimens were collected from seven different localities, covering its geographical range. The final alignment showed 53 haplotypes (48 individuals and 5 shared), with no biogeographical pattern. The low genetic divergence found, with a non-significant FST value, also suggests the absence of population structure for this gene. These findings indicate a continuous gene flow among the populations analyzed, suggesting that the phenotypic variation is a consequence of different environmental conditions among the localities.
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Affiliation(s)
- Abner Carvalho-Batista
- Laboratory of Biology of Marine and Fresh Water Shrimps, Faculty of Science, Department of Biological Sciences, São Paulo State University (UNESP), Bauru, São Paulo, Brazil
| | - Mariana Negri
- Laboratory of Bioecology and Crustacean Systematics, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto (FFCLRP), University of São Paulo (USP), Postgraduate Program in Comparative Biology, Ribeirão Preto, São Paulo, Brazil
| | - Leonardo G Pileggi
- Laboratory of Bioecology and Crustacean Systematics, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto (FFCLRP), University of São Paulo (USP), Postgraduate Program in Comparative Biology, Ribeirão Preto, São Paulo, Brazil
| | - Antonio L Castilho
- São Paulo State University (UNESP), Biosciences Institute of Botucatu, Zoology Department, Botucatu, Brazil
| | - Rogério C Costa
- Laboratory of Biology of Marine and Fresh Water Shrimps, Faculty of Science, Department of Biological Sciences, São Paulo State University (UNESP), Bauru, São Paulo, Brazil
| | - Fernando L Mantelatto
- Laboratory of Bioecology and Crustacean Systematics, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto (FFCLRP), University of São Paulo (USP), Postgraduate Program in Comparative Biology, Ribeirão Preto, São Paulo, Brazil
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Vogler RE, Beltramino AA, Peso JG, Rumi A. Threatened gastropods under the evolutionary genetic species concept: redescription and new species of the genusAylacostoma(Gastropoda: Thiaridae) from High Paraná River (Argentina-Paraguay). Zool J Linn Soc 2014. [DOI: 10.1111/zoj.12179] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Roberto E. Vogler
- Departamento de Biología; Facultad de Ciencias Exactas; Químicas y Naturales; Universidad Nacional de Misiones; Rivadavia 2370 N3300LDX Posadas Argentina
- National Science Agencies; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET); Argentina
| | - Ariel A. Beltramino
- National Science Agencies; Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT); Argentina
- División Zoología Invertebrados; Facultad de Ciencias Naturales y Museo; Universidad Nacional de La Plata; Paseo del Bosque s/n B1900FWA La Plata Argentina
| | - Juana G. Peso
- Departamento de Biología; Facultad de Ciencias Exactas; Químicas y Naturales; Universidad Nacional de Misiones; Rivadavia 2370 N3300LDX Posadas Argentina
| | - Alejandra Rumi
- National Science Agencies; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET); Argentina
- División Zoología Invertebrados; Facultad de Ciencias Naturales y Museo; Universidad Nacional de La Plata; Paseo del Bosque s/n B1900FWA La Plata Argentina
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83
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Vogler RE, Beltramino AA, Peso JG, Rumi A. Threatened gastropods under the evolutionary genetic species concept: redescription and new species of the genus Aylacostoma (Gastropoda: Thiaridae) from High Paraná River (Argentina–Paraguay). Zool J Linn Soc 2014. [DOI: 10.1111/zoj12179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Roberto E. Vogler
- Departamento de Biología, Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Rivadavia 2370, N3300LDX, Posadas, Argentina
- National Science Agencies, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Ariel A. Beltramino
- National Science Agencies, Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT), Argentina
- División Zoología Invertebrados, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, Paseo del Bosque s/n, B1900FWA, La Plata, Argentina
| | - Juana G. Peso
- Departamento de Biología, Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Rivadavia 2370, N3300LDX, Posadas, Argentina
| | - Alejandra Rumi
- National Science Agencies, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
- División Zoología Invertebrados, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, Paseo del Bosque s/n, B1900FWA, La Plata, Argentina
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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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85
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Status and prospects of DNA barcoding in medically important parasites and vectors. Trends Parasitol 2014; 30:582-91. [PMID: 25447202 DOI: 10.1016/j.pt.2014.09.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 09/18/2014] [Accepted: 09/19/2014] [Indexed: 11/23/2022]
Abstract
For over 10 years, DNA barcoding has been used to identify specimens and discern species. Its potential benefits in parasitology were recognized early, but its utility and uptake remain unclear. Here we review studies using DNA barcoding in parasites and vectors affecting humans and find that the technique is accurate (accords with author identifications based on morphology or other markers) in 94-95% of cases, although aspects of DNA barcoding (vouchering, marker implicated) have often been misunderstood. In a newly compiled checklist of parasites, vectors, and hazards, barcodes are available for 43% of all 1403 species and for more than half of 429 species of greater medical importance. This is encouraging coverage that would improve with an active campaign targeting parasites and vectors.
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Ferri G, Corradini B, Ferrari F, Santunione AL, Palazzoli F, Alu' M. Forensic botany II, DNA barcode for land plants: Which markers after the international agreement? Forensic Sci Int Genet 2014; 15:131-6. [PMID: 25457632 DOI: 10.1016/j.fsigen.2014.10.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 09/23/2014] [Accepted: 10/03/2014] [Indexed: 11/17/2022]
Abstract
The ambitious idea of using a short piece of DNA for large-scale species identification (DNA barcoding) is already a powerful tool for scientists and the application of this standard technique seems promising in a range of fields including forensic genetics. While DNA barcoding enjoyed a remarkable success for animal identification through cytochrome c oxidase I (COI) analysis, the attempts to identify a single barcode for plants remained a vain hope for a longtime. From the beginning, the Consortium for the Barcode of Life (CBOL) showed a lack of agreement on a core plant barcode, reflecting the diversity of viewpoints. Different research groups advocated various markers with divergent set of criteria until the recent publication by the CBOL-Plant Working Group. After a four-year effort, in 2009 the International Team concluded to agree on standard markers promoting a multilocus solution (rbcL and matK), with 70-75% of discrimination to the species level. In 2009 our group firstly proposed the broad application of DNA barcoding principles as a tool for identification of trace botanical evidence through the analysis of two chloroplast loci (trnH-psbA and trnL-trnF) in plant species belonging to local flora. Difficulties and drawbacks that were encountered included a poor coverage of species in specific databases and the lack of authenticated reference sequences for the selected markers. Successful preliminary results were obtained providing an approach to progressively identify unknown plant specimens to a given taxonomic rank, usable by any non-specialist botanist or in case of a shortage of taxonomic expertise. Now we considered mandatory to update and to compare our previous findings with the new selected plastid markers (matK+rbcL), taking into account forensic requirements. Features of all the four loci (the two previously analyzed trnH-psbA+trnL-trnF and matK+rbcL) were compared singly and in multilocus solutions to assess the most suitable combination for forensic botany. Based on obtained results, we recommend the adoption of a two-locus combination with rbcL+trnH-psbA plastid markers, which currently best satisfies forensic needs for botanical species identification.
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Affiliation(s)
- G Ferri
- Dipartimento di Medicina Diagnostica, Clinica e di Sanità Pubblica, Struttura Complessa di Medicina Legale, Università di Modena e Reggio Emilia, Italy.
| | - B Corradini
- Dipartimento di Medicina Diagnostica, Clinica e di Sanità Pubblica, Struttura Complessa di Medicina Legale, Università di Modena e Reggio Emilia, Italy
| | - F Ferrari
- Dipartimento di Medicina Diagnostica, Clinica e di Sanità Pubblica, Struttura Complessa di Medicina Legale, Università di Modena e Reggio Emilia, Italy
| | - A L Santunione
- Dipartimento di Medicina Diagnostica, Clinica e di Sanità Pubblica, Struttura Complessa di Medicina Legale, Università di Modena e Reggio Emilia, Italy
| | - F Palazzoli
- Dipartimento di Medicina Diagnostica, Clinica e di Sanità Pubblica, Struttura Complessa di Medicina Legale, Università di Modena e Reggio Emilia, Italy
| | - M Alu'
- Dipartimento di Medicina Diagnostica, Clinica e di Sanità Pubblica, Struttura Complessa di Medicina Legale, Università di Modena e Reggio Emilia, Italy
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87
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Wang YJ, Li ZH, Zhang SF, Varadínová Z, Jiang F, Kučerová Z, Stejskal V, Opit G, Cao Y, Li FJ. DNA barcoding of five common stored-product pest species of genus Cryptolestes (Coleoptera: Laemophloeidae). BULLETIN OF ENTOMOLOGICAL RESEARCH 2014; 104:671-678. [PMID: 24725375 DOI: 10.1017/s0007485314000224] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Several species of the genus Cryptolestes Ganglbauer, 1899 (Coleoptera: Laemophloeidae) are commonly found in stored products. In this study, five species of Cryptolestes, with almost worldwide distribution, were obtained from laboratories in China, Czech Republic and the USA: Cryptolestes ferrugineus (Stephens, 1831), Cryptolestes pusillus (Schönherr, 1817), Cryptolestes turcicus (Grouvelle, 1876), Cryptolestes pusilloides (Steel & Howe, 1952) and Cryptolestes capensis (Waltl, 1834). Molecular identification based on a 658 bp fragment from the mitochondrial DNA cytochrome c oxidase subunit I (COI) was adopted to overcome some problems of morphological identification of Cryptolestes species. The utility of COI sequences as DNA barcodes in discriminating the five Cryptolestes species was evaluated on adults and larvae by analysing Kimura 2-parameter distances, phylogenetic tree and haplotype networks. The results showed that molecular approaches based on DNA barcodes were able to accurately identify these species. This is the first study using DNA barcoding to identify Cryptolestes species and the gathered DNA sequences will complement the biological barcode database.
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Affiliation(s)
- Y J Wang
- Department of Entomology, College of Agriculture and Biotechnology,China Agricultural University,No. 2 Yuanmingyuan West Road, Beijing,China
| | - Z H Li
- Department of Entomology, College of Agriculture and Biotechnology,China Agricultural University,No. 2 Yuanmingyuan West Road, Beijing,China
| | - S F Zhang
- Institute of Animal and Plant Quarantine,Chinese Academy of Inspection and Quarantine,Beijing,China
| | - Z Varadínová
- Department of Zoology, Faculty of Science,Charles University in Prague,Viničná 7, Prague,Czech Republic
| | - F Jiang
- Department of Entomology, College of Agriculture and Biotechnology,China Agricultural University,No. 2 Yuanmingyuan West Road, Beijing,China
| | - Z Kučerová
- Department of Pest Control of Stored Products and Food Safety,Crop Research Institute,Drnovská 507, Prague,Czech Republic
| | - V Stejskal
- Department of Pest Control of Stored Products and Food Safety,Crop Research Institute,Drnovská 507, Prague,Czech Republic
| | - G Opit
- Department of Entomology and Plant Pathology,Oklahoma State University,Stillwater, OK,USA
| | - Y Cao
- Academy of State Administration of Grain,No. 11 Baiwanzhuang Street, Beijing,China
| | - F J Li
- Academy of State Administration of Grain,No. 11 Baiwanzhuang Street, Beijing,China
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88
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Alcantara SG, Yambot AV. DNA barcoding of commercially important Grouper species (Perciformes, Serranidae) in the Philippines. Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:3837-3845. [PMID: 25238110 DOI: 10.3109/19401736.2014.958672] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Fish identification is generally challenging because of their unpronounced and overlapping morphological characters which is true in grouper species. In the Philippines, an updated, reliable and accurate inventory of this high value commercial groupers has not been carried out previously. Using molecular tools in the identification and inventory of fish species in the country is confined to few laboratories and experts in the country. In this study, 27 species of the Serranidae family were identified from the grouper samples collected from major fish landing sites and markets in the Philippines. The grouper species were molecularly identified using the cytochrome c oxidase I (COI) sequences for DNA barcoding. The accuracy of the inferred species-level taxonomy based on COI is supported with high similarity search (98-100%) both in BOLD and BLAST, well-distributed genetic distance values and cohesive clustering in the Neighbor-Joining Tree. Aside from reinforcing the classical methodology of grouper identification in the country, this pioneering study on molecular identification of Philippine groupers constitutes a significant contribution to the DNA barcode library of Philippine marine fishes and to the global barcode entries in general, which can be used when dealing with grouper taxonomy, biodiversity, stock assessment and trade. The results reveal the different localities where the grouper species can be possibly sourced out in the country for trade and aquaculture purposes. Several of the grouper species are included in the IUCN Red List of Threatened Species. As a tool for conservation ecology, this study signals the implementation of sustainable fisheries management regulation to protect in particular those which are listed under the IUCN.
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Affiliation(s)
- Simon G Alcantara
- a Biotechnology and Analytical Laboratory , Central Luzon State University , Science City of Munoz , Nueva Ecija , Philippines.,b Molecular Biology and Biotechnology Laboratory , College of Fisheries, Central Luzon State University , Science City of Munoz , Nueva Ecija , Philippines , and.,c Freshwater Aquaculture Center, Central Luzon State University , Science City of Munoz , Nueva Ecija , Philippines
| | - Apolinario V Yambot
- a Biotechnology and Analytical Laboratory , Central Luzon State University , Science City of Munoz , Nueva Ecija , Philippines.,b Molecular Biology and Biotechnology Laboratory , College of Fisheries, Central Luzon State University , Science City of Munoz , Nueva Ecija , Philippines , and.,c Freshwater Aquaculture Center, Central Luzon State University , Science City of Munoz , Nueva Ecija , Philippines
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89
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Raupach MJ, Hendrich L, Küchler SM, Deister F, Morinière J, Gossner MM. Building-up of a DNA barcode library for true bugs (insecta: hemiptera: heteroptera) of Germany reveals taxonomic uncertainties and surprises. PLoS One 2014; 9:e106940. [PMID: 25203616 PMCID: PMC4159288 DOI: 10.1371/journal.pone.0106940] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 08/06/2014] [Indexed: 01/28/2023] Open
Abstract
During the last few years, DNA barcoding has become an efficient method for the identification of species. In the case of insects, most published DNA barcoding studies focus on species of the Ephemeroptera, Trichoptera, Hymenoptera and especially Lepidoptera. In this study we test the efficiency of DNA barcoding for true bugs (Hemiptera: Heteroptera), an ecological and economical highly important as well as morphologically diverse insect taxon. As part of our study we analyzed DNA barcodes for 1742 specimens of 457 species, comprising 39 families of the Heteroptera. We found low nucleotide distances with a minimum pairwise K2P distance <2.2% within 21 species pairs (39 species). For ten of these species pairs (18 species), minimum pairwise distances were zero. In contrast to this, deep intraspecific sequence divergences with maximum pairwise distances >2.2% were detected for 16 traditionally recognized and valid species. With a successful identification rate of 91.5% (418 species) our study emphasizes the use of DNA barcodes for the identification of true bugs and represents an important step in building-up a comprehensive barcode library for true bugs in Germany and Central Europe as well. Our study also highlights the urgent necessity of taxonomic revisions for various taxa of the Heteroptera, with a special focus on various species of the Miridae. In this context we found evidence for on-going hybridization events within various taxonomically challenging genera (e.g. Nabis Latreille, 1802 (Nabidae), Lygus Hahn, 1833 (Miridae), Phytocoris Fallén, 1814 (Miridae)) as well as the putative existence of cryptic species (e.g. Aneurus avenius (Duffour, 1833) (Aradidae) or Orius niger (Wolff, 1811) (Anthocoridae)).
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Affiliation(s)
- Michael J Raupach
- Molecular Taxonomy of Marine Organisms, German Center of Marine Biodiversity (DZMB), Senckenberg am Meer, Wilhelmshaven, Germany
| | - Lars Hendrich
- Sektion Insecta varia, Bavarian State Collection of Zoology (SNSB - ZSM), München, Germany
| | - Stefan M Küchler
- Department of Animal Ecology II, University of Bayreuth, Bayreuth, Germany
| | - Fabian Deister
- Molecular Taxonomy of Marine Organisms, German Center of Marine Biodiversity (DZMB), Senckenberg am Meer, Wilhelmshaven, Germany
| | - Jérome Morinière
- Taxonomic coordinator - Barcoding Fauna Bavarica, Bavarian State Collection of Zoology (SNSB - ZSM), München, Germany
| | - Martin M Gossner
- Terrestrial Ecology Research Group, Department of Ecology and Ecosystem Management, Technische Universität München, Freising-Weihenstephan, Germany
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90
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Yu Z, Li Q, Kong L. New insight into the phylogeny of Sinonovacula (Bivalvia: Solecurtidae) revealed by comprehensive DNA barcoding analyses of two mitochondrial genes. Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:1554-7. [PMID: 25186335 DOI: 10.3109/19401736.2014.953135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The present study was undertaken to clarify the genetic relationships of Sinonovacula through comprehensive DNA barcoding analyses of COI and 16S rRNA genes. For both genes, the K2P distances between individuals of Sinonovacula and individuals of other genera belonging to Tellinoidea were much bigger than those between Sinonovacula and genera of Solenoidea. On the Bayesian tree of combined data, Sinonovacula and Cultellus formed a well supports monophylic clade. An extremely high matching rate of CAs between Sinonovacula and the reference family Cultellidae was found. Thus, we suggest transferring Sinonovacula from Solecurtidae to Cultellidae, as a sister group of Cultellus.
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Affiliation(s)
- Zhenzhen Yu
- a Key Laboratory of Mariculture , Ministry of Education, Ocean University of China , Qingdao , China
| | - Qi Li
- a Key Laboratory of Mariculture , Ministry of Education, Ocean University of China , Qingdao , China
| | - Lingfeng Kong
- a Key Laboratory of Mariculture , Ministry of Education, Ocean University of China , Qingdao , China
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91
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DNA barcoding works in practice but not in (neutral) theory. PLoS One 2014; 9:e100755. [PMID: 24988408 PMCID: PMC4079456 DOI: 10.1371/journal.pone.0100755] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 05/30/2014] [Indexed: 11/19/2022] Open
Abstract
Background DNA barcode differences within animal species are usually much less than differences among species, making it generally straightforward to match unknowns to a reference library. Here we aim to better understand the evolutionary mechanisms underlying this usual “barcode gap” pattern. We employ avian barcode libraries to test a central prediction of neutral theory, namely, intraspecific variation equals 2 Nµ, where N is population size and µ is mutations per site per generation. Birds are uniquely suited for this task: they have the best-known species limits, are well represented in barcode libraries, and, most critically, are the only large group with documented census population sizes. In addition, we ask if mitochondrial molecular clock measurements conform to neutral theory prediction of clock rate equals µ. Results Intraspecific COI barcode variation was uniformly low regardless of census population size (n = 142 species in 15 families). Apparent outliers reflected lumping of reproductively isolated populations or hybrid lineages. Re-analysis of a published survey of cytochrome b variation in diverse birds (n = 93 species in 39 families) further confirmed uniformly low intraspecific variation. Hybridization/gene flow among species/populations was the main limitation to DNA barcode identification. Conclusions/Significance To our knowledge, this is the first large study of animal mitochondrial diversity using actual census population sizes and the first to test outliers for population structure. Our finding of universally low intraspecific variation contradicts a central prediction of neutral theory and is not readily accounted for by commonly proposed ad hoc modifications. We argue that the weight of evidence–low intraspecific variation and the molecular clock–indicates neutral evolution plays a minor role in mitochondrial sequence evolution. As an alternate paradigm consistent with empirical data, we propose extreme purifying selection, including at synonymous sites, limits variation within species and continuous adaptive selection drives the molecular clock.
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92
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Elzinga JA, Mappes J, Kaila L. Pre- and post-mating reproductive barriers drive divergence of five sympatric species of Naryciinae moths (Lepidoptera: Psychidae). Biol J Linn Soc Lond 2014. [DOI: 10.1111/bij.12281] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jelmer A. Elzinga
- Department of Biological and Environmental Science; University of Jyväskylä; PO Box 35 FI-40014 Jyväskylä Finland
| | - Johanna Mappes
- Department of Biological and Environmental Science; Centre of Excellence in Biological Interactions; University of Jyväskylä; PO Box 35 FI-40014 Jyväskylä Finland
| | - Lauri Kaila
- Finnish Museum of Natural History; Zoology Unit; University of Helsinki; P.O. Box 17 FI-00014 Helsinki Finland
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93
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Li M, Liu Q, Xi L, Liu Y, Zhu G, Zhao Y, Bu W. Testing the potential of proposed DNA barcoding markers in Nezara virudula and Nezara antennata when geographic variation and closely related species were considered. JOURNAL OF INSECT SCIENCE (ONLINE) 2014; 14:79. [PMID: 25373226 PMCID: PMC4212858 DOI: 10.1093/jis/14.1.79] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2012] [Accepted: 12/10/2013] [Indexed: 06/04/2023]
Abstract
The COI gene as the core of the DNA barcoding system for animals has received significant attention. The observed wide overlap between intraand interspecific sequence variability has led researchers to envisage the primary COI-based method. The sequences of 16S rDNA, COI, and Cyt b genes of Nezara virudula (L.) (Hemiptera: Pentatomidae) from 13 countries and the same sequences of N. antennata Scott were chosen as molecular markers to analyze the intraand interspecific relationships between the closely related species in this study. The results support that Cyt b gene may be a good candidate alongside COI, when the combined factors of geographic variation and closely related species are taken into account.
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Affiliation(s)
- Min Li
- Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University. 300387, Tianjin, China Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Qiang Liu
- Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University. 300387, Tianjin, China
| | - Li Xi
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Yang Liu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Gengping Zhu
- Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University. 300387, Tianjin, China
| | - Yanni Zhao
- Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University. 300387, Tianjin, China
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, 300071, China
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94
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Elliott TL, Jonathan Davies T. Challenges to barcoding an entire flora. Mol Ecol Resour 2014; 14:883-91. [PMID: 24813242 DOI: 10.1111/1755-0998.12277] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 04/12/2014] [Accepted: 04/20/2014] [Indexed: 12/01/2022]
Abstract
DNA barcodes are species-specific genetic markers that allow taxonomic identification of biological samples. The promise of DNA barcoding as a rapid molecular tool for conducting biodiversity inventories has catalysed renewed efforts to document and catalogue the diversity of life, parallel to the large-scale sampling conducted by Victorian naturalists. The unique contribution of DNA barcode data is in its ability to identify biotic material that would be impossible to classify using traditional taxonomic keys. However, the utility of DNA barcoding relies upon the construction of accurate barcode libraries that provide a reference database to match to unidentified samples. Whilst there has been much debate in the literature over the choice and efficacy of barcode markers, there has been little consideration of the practicalities of generating comprehensive barcode reference libraries for species-rich floras. Here, we discuss several challenges to the generation of such libraries and present a case study from a regional biodiversity hotspot in southern Quebec. We suggest that the key challenges include (i) collection of specimens for rare or ephemeral species, (ii) limited access to taxonomic expertise necessary for reliable identification of reference specimens and (iii) molecular challenges in amplifying and matching barcode data. To be most effective, we recommend that sampling must be both flexible and opportunistic and conducted across the entire growing season by expert taxonomists. We emphasize that the success of the global barcoding initiative will depend upon the close collaboration of taxonomists, plant collectors, and molecular biologists.
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Affiliation(s)
- Tammy L Elliott
- Department of Biology, McGill University, 1205 Docteur Penfield Avenue, Montreal, Quebec H3A 1B1, Canada
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95
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Jiang F, Jin Q, Liang L, Zhang AB, Li ZH. Existence of species complex largely reduced barcoding success for invasive species of Tephritidae: a case study inBactroceraspp. Mol Ecol Resour 2014; 14:1114-28. [DOI: 10.1111/1755-0998.12259] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Revised: 03/18/2014] [Accepted: 03/24/2014] [Indexed: 11/28/2022]
Affiliation(s)
- F. Jiang
- Department of Entomology; College of Agronomy and Biotechnology; China Agricultural University; Beijing 100193 China
| | - Q. Jin
- College of Life Sciences; Capital Normal University; Beijing 100048 China
| | - L. Liang
- Institute of Agro-Products Processing Engineering; Chinese Academy of Agricultural Engineering; Beijing 100125 China
| | - A. B. Zhang
- College of Life Sciences; Capital Normal University; Beijing 100048 China
| | - Z. H. Li
- Department of Entomology; College of Agronomy and Biotechnology; China Agricultural University; Beijing 100193 China
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96
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Aly SM. Reliability of long vs short COI markers in identification of forensically important flies. Croat Med J 2014; 55:19-26. [PMID: 24577823 PMCID: PMC3944415 DOI: 10.3325/cmj.2014.55.19] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Aim To compare the reliability of short and long cytochrome oxidase I gene fragment (COI) in identification of forensically important Diptera from Egypt and China. Methods We analyzed 50 specimens belonging to 18 species. The two investigated markers were amplified by polymerase chain reaction (PCR) followed by direct sequencing. Nucleotide sequence divergences were calculated using the Kimura two-parameter (K2P) distance model and neighbor-joining (NJ) phylogenetic trees. Results Although both tested fragments showed an overlap between intra and interspecific variations, long marker had greater completeness of monophyletic separation with high bootstrap support. Moreover, NJ tree based on the long fragment clustered species more in accordance with their taxonomic classification than that based on the short fragment. Conclusion In dipterous identification, it is recommended to use the long COI marker due to its greater reliability and safety.
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Affiliation(s)
- Sanaa M Aly
- Sanaa M. Aly, Department of Forensic Medicine and Clinical Toxicology, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt,
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97
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Sonet G, Jordaens K, Nagy ZT, Breman FC, De Meyer M, Backeljau T, Virgilio M. Adhoc: an R package to calculate ad hoc distance thresholds for DNA barcoding identification. Zookeys 2013:329-36. [PMID: 24453565 PMCID: PMC3890685 DOI: 10.3897/zookeys.365.6034] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 12/02/2013] [Indexed: 12/02/2022] Open
Abstract
Identification by DNA barcoding is more likely to be erroneous when it is based on a large distance between the query (the barcode sequence of the specimen to identify) and its best match in a reference barcode library. The number of such false positive identifications can be decreased by setting a distance threshold above which identification has to be rejected. To this end, we proposed recently to use an ad hoc distance threshold producing identifications with an estimated relative error probability that can be fixed by the user (e.g. 5%). Here we introduce two R functions that automate the calculation of ad hoc distance thresholds for reference libraries of DNA barcodes. The scripts of both functions, a user manual and an example file are available on the JEMU website (http://jemu.myspecies.info/computer-programs) as well as on the comprehensive R archive network (CRAN, http://cran.r-project.org).
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Affiliation(s)
- Gontran Sonet
- Royal Belgian Institute of Natural Sciences, OD Taxonomy and Phylogeny (JEMU), Vautierstraat 29, 1000 Brussels, Belgium
| | - Kurt Jordaens
- Royal Museum for Central Africa, Department of Biology (JEMU), Leuvensesteenweg 13, 3080 Tervuren, Belgium ; University of Antwerp, Evolutionary Ecology Group, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Zoltán T Nagy
- Royal Belgian Institute of Natural Sciences, OD Taxonomy and Phylogeny (JEMU), Vautierstraat 29, 1000 Brussels, Belgium
| | - Floris C Breman
- Royal Museum for Central Africa, Department of Biology (JEMU), Leuvensesteenweg 13, 3080 Tervuren, Belgium
| | - Marc De Meyer
- Royal Museum for Central Africa, Department of Biology (JEMU), Leuvensesteenweg 13, 3080 Tervuren, Belgium
| | - Thierry Backeljau
- Royal Belgian Institute of Natural Sciences, OD Taxonomy and Phylogeny (JEMU), Vautierstraat 29, 1000 Brussels, Belgium ; University of Antwerp, Evolutionary Ecology Group, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Massimiliano Virgilio
- Royal Museum for Central Africa, Department of Biology (JEMU), Leuvensesteenweg 13, 3080 Tervuren, Belgium
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98
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Betson M, Sousa-Figueiredo JC, Kabatereine NB, Stothard JR. New insights into the molecular epidemiology and population genetics of Schistosoma mansoni in Ugandan pre-school children and mothers. PLoS Negl Trop Dis 2013; 7:e2561. [PMID: 24349589 PMCID: PMC3861247 DOI: 10.1371/journal.pntd.0002561] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 10/14/2013] [Indexed: 12/22/2022] Open
Abstract
Significant numbers of pre-school children are infected with Schistosoma mansoni in sub-Saharan Africa and are likely to play a role in parasite transmission. However, they are currently excluded from control programmes. Molecular phylogenetic studies have provided insights into the evolutionary origins and transmission dynamics of S. mansoni, but there has been no research into schistosome molecular epidemiology in pre-school children. Here, we investigated the genetic diversity and population structure of S. mansoni in pre-school children and mothers living in lakeshore communities in Uganda and monitored for changes over time after praziquantel treatment. Parasites were sampled from children (<6 years) and mothers enrolled in the longitudinal Schistosomiasis Mothers and Infants Study at baseline and at 6-, 12- and 18-month follow-up surveys. 1347 parasites from 35 mothers and 45 children were genotyped by direct sequencing of the cytochrome c oxidase (cox1) gene. The cox1 region was highly diverse with over 230 unique sequences identified. Parasite populations were genetically differentiated between lakes and non-synonymous mutations were more diverse at Lake Victoria than Lake Albert. Surprisingly, parasite populations sampled from children showed a similar genetic diversity to those sampled from mothers, pointing towards a non-linear relationship between duration of exposure and accumulation of parasite diversity. The genetic diversity six months after praziquantel treatment was similar to pre-treatment diversity. Our results confirm the substantial genetic diversity of S. mansoni in East Africa and provide significant insights into transmission dynamics within young children and mothers, important information for schistosomiasis control programmes. Many pre-school children in sub-Saharan Africa are infected with the parasite Schistosoma mansoni, which causes intestinal schistosomiasis. However, there has been no work published on the molecular epidemiology of Schistosoma in children under six or the role that these children play in parasite transmission. We analysed the genetic structure of parasite populations collected from mothers and young children living on the shores of Lakes Albert and Victoria in Uganda. Parasite populations were different at the two lakes indicating that there is little flow of parasite genes between the lakes. We were surprised to discover a large amount of genetic variation in parasites sampled from both children and mothers, suggesting that genetic variation is not directly related to duration of exposure to infested water. In addition, we found some evidence that young children are involved in S. mansoni transmission. The substantial genetic variation of S. mansoni in young children suggests that these parasites could be operating as a source of a variety of genetic traits, including drug susceptibility. Overall our findings offer significant insights into population genetics of S. mansoni in pre-school children and their mothers and provide important information for effective control of intestinal schistosomiasis.
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Affiliation(s)
- Martha Betson
- Department of Production and Population Health, The Royal Veterinary College, Hatfield, Hertfordshire, United Kingdom
| | - Jose C. Sousa-Figueiredo
- Parasitology Department, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | - J. Russell Stothard
- Parasitology Department, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- * E-mail:
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Webster BL, Webster JP, Gouvras AN, Garba A, Lamine MS, Diaw OT, Seye MM, Tchuem Tchuenté LA, Simoonga C, Mubila L, Mwanga JR, Lwambo NJ, Kabatereine NB, Lange CN, Kariuki C, Mkoji GM, Rollinson D, Stothard JR. DNA 'barcoding' of Schistosoma mansoni across sub-Saharan Africa supports substantial within locality diversity and geographical separation of genotypes. Acta Trop 2013; 128:250-60. [PMID: 22935316 DOI: 10.1016/j.actatropica.2012.08.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Revised: 08/08/2012] [Accepted: 08/10/2012] [Indexed: 11/25/2022]
Abstract
Schistosoma mansoni is a widespread human helminth and causes intestinal schistosomiasis in 54 countries, mainly across Africa but also in Madagascar, the Arabian Peninsula and the neotropics. The geographical range of this parasite relies on the distribution of certain species of freshwater pulmonate snails of the genus Biomphalaria. Whilst S. mansoni is known to exhibit high population diversity the true extent of this diversity is still to be fully elucidated as sampling of this taxon progressively accrues. Here a DNA 'barcoding' approach is taken using sequence analysis of a 450bp region within the mitochondrial cox1 gene to assess the genetic diversity within a large number of S. mansoni larval stages collected from their natural human hosts across sub-Saharan Africa. Five hundred and sixty one individual parasite samples were examined from 22 localities and 14 countries. Considerable within-species diversity was found with 120 unique haplotypes splitting geographically into five discrete lineages. The highest diversity was found in East Africa with samples forming three of the five lineages. Less diversity was found in the Far and Central Western regions of Africa with haplotypes from the New World showing a close affinity to the Far Western African S. mansoni populations supporting the hypothesis of a colonisation of South America via the West African slave trade. The data are discussed in relation to parasite diversity and disease epidemiology.
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McNamara MKA, Miller TL, Cribb TH. Evidence for extensive cryptic speciation in trematodes of butterflyfishes (Chaetodontidae) of the tropical Indo-West Pacific. Int J Parasitol 2013; 44:37-48. [PMID: 24188934 DOI: 10.1016/j.ijpara.2013.09.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 09/13/2013] [Accepted: 09/17/2013] [Indexed: 10/26/2022]
Abstract
Molecular data from the cytochrome c oxidase subunit I (cox1) mitochondrial DNA gene and the second internal transcribed spacer (ITS2) nuclear rDNA region were used to test the current morphologically-based taxonomic hypothesis regarding species of Monorchiidae (Hurleytrematoides) from chaetodontid and tetraodontid fishes from six sites in the tropical Indo-West Pacific (TIWP): Heron and Lizard Islands off the Great Barrier Reef (GBR, Australia), Moorea (French Polynesia), New Caledonia, Ningaloo Reef (Australia) and Palau. The 16 morphospecies analysed differed from each other by a minimum of 55bp (9.1%) over the mitochondrial cox1 and 8bp (1.6%) over the ITS2 DNA regions. For two species, Hurleytrematoides loi and Hurleytrematoides sasali, specimens from the same host species in sympatry differed at levels comparable to those between pairs of distinct morphospecies for both cox1 and ITS2 sequences. We take this as evidence of the presence of combinations of cryptic species; however, we do not propose new species for these taxa because we lack identified morphological voucher specimens. For seven species, Hurleytrematoides coronatum, Hurleytrematoides deblocki, Hurleytrematoides faliexae, H. loi, Hurleytrematoides morandi, H. sasali and Hurleytrematoides sp. A, samples from some combinations of localities had base pair differences that were equal to or greater than differences between some pairs of distinct morphospecies for one or both cox1 and ITS2 sequences. For three species, H. coronatum, H. loi and H. morandi, one haplotype differed from every other haplotype by more than the morphospecies benchmark. In these cases morphological specimens could not be distinguished by morphology. These data suggest extensive cryptic richness in this genus. For the present we refrain from dividing any of the morphospecies. This is because there is a continuum of levels of intra- and interspecific genetic variation in this system, so that distinguishing the two would be largely arbitrary.
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Affiliation(s)
- M K A McNamara
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia.
| | - T L Miller
- School of Marine and Tropical Biology, James Cook University, PO Box 6811, Cairns, Queensland 4870, Australia
| | - T H Cribb
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
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