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Nakagawa K, Ogino K, Katoh TK, Kono N. Species identification of livefood flightless fly ( Torinido-shoujoubae) through DNA barcoding. Ecol Evol 2024; 14:e11622. [PMID: 38979002 PMCID: PMC11229428 DOI: 10.1002/ece3.11622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 05/28/2024] [Accepted: 06/10/2024] [Indexed: 07/10/2024] Open
Abstract
Torinido-shoujoubae, as it is called in Japanese, is a flightless Drosophila sp. that is sold commercially in Japan. This Drosophila sp. is often used as feeds for model organisms such as reptiles and spiders. There is no scientific name provided for the fruit fly that is known as Torinido-shoujoubae, as well as any historical background or data behind this species. There has been a previous study that was conducted through morphological characteristics analysis of the body as well as the male copulatory organ and has been estimated as Drosophila hydei. The objective of this study was to determine the species of this unidentified fly known as Torinido-shoujoubae based on a molecular evidence with a DNA barcoding. Samples were purchased from four separate suppliers to examine whether there are any differences between them. COI regions were amplified using PCR and the sequenced results were aligned against two databases, NCBI and BOLD. Torinido-shoujoubae samples provided from all suppliers were confirmed to be D. hydei.
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Affiliation(s)
- Koh Nakagawa
- Institute for Advanced Biosciences Keio University Tsuruoka Yamagata Japan
| | - Kaoru Ogino
- Institute for Advanced Biosciences Keio University Tsuruoka Yamagata Japan
- Faculty of Environment and Information Studies Keio University Fujisawa Kanagawa Japan
| | - Takehiro K Katoh
- Department of Biological Sciences Tokyo Metropolitan University Hachioji Tokyo Japan
| | - Nobuaki Kono
- Institute for Advanced Biosciences Keio University Tsuruoka Yamagata Japan
- Faculty of Environment and Information Studies Keio University Fujisawa Kanagawa Japan
- Graduate School of Media and Governance Keio University Fujisawa Kanagawa Japan
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Gajski D, Wolff JO, Melcher A, Weber S, Prost S, Krehenwinkel H, Kennedy SR. Facilitating taxonomy and phylogenetics: An informative and cost-effective protocol integrating long amplicon PCRs and third-generation sequencing. Mol Phylogenet Evol 2024; 192:107988. [PMID: 38072140 DOI: 10.1016/j.ympev.2023.107988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/22/2023] [Accepted: 12/07/2023] [Indexed: 12/31/2023]
Abstract
Phylogenetic inference has become a standard technique in integrative taxonomy and systematics, as well as in biogeography and ecology. DNA barcodes are often used for phylogenetic inference, despite being strongly limited due to their low number of informative sites. Also, because current DNA barcodes are based on a fraction of a single, fast-evolving gene, they are highly unsuitable for resolving deeper phylogenetic relationships due to saturation. In recent years, methods that analyse hundreds and thousands of loci at once have improved the resolution of the Tree of Life, but these methods require resources, experience and molecular laboratories that most taxonomists do not have. This paper introduces a PCR-based protocol that produces long amplicons of both slow- and fast-evolving unlinked mitochondrial and nuclear gene regions, which can be sequenced by the affordable and portable ONT MinION platform with low infrastructure or funding requirements. As a proof of concept, we inferred a phylogeny of a sample of 63 spider species from 20 families using our proposed protocol. The results were overall consistent with the results from approaches based on hundreds and thousands of loci, while requiring just a fraction of the cost and labour of such approaches, making our protocol accessible to taxonomists worldwide.
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Affiliation(s)
- Domagoj Gajski
- Department of Biogeography, Faculty of Spatial and Environmental Sciences, University of Trier, Universitätsring 15, Trier 54296, Germany; Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno 611 37, Czech Republic
| | - Jonas O Wolff
- Evolutionary Biomechanics, Zoological Institute and Museum, University of Greifswald, Loitzer Str. 26, Greifswald 17489, Germany; School of Natural Sciences, Macquarie University, NSW 2109, Sydney, Australia
| | - Anja Melcher
- Department of Biogeography, Faculty of Spatial and Environmental Sciences, University of Trier, Universitätsring 15, Trier 54296, Germany
| | - Sven Weber
- Department of Biogeography, Faculty of Spatial and Environmental Sciences, University of Trier, Universitätsring 15, Trier 54296, Germany
| | - Stefan Prost
- Ecology and Genetics Research Unit, University of Oulu, Pentti Kaiteran katu 1, Linnanmaa, Finland
| | - Henrik Krehenwinkel
- Department of Biogeography, Faculty of Spatial and Environmental Sciences, University of Trier, Universitätsring 15, Trier 54296, Germany
| | - Susan R Kennedy
- Department of Biogeography, Faculty of Spatial and Environmental Sciences, University of Trier, Universitätsring 15, Trier 54296, Germany.
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Wang W, Chen B, Ma R, Qiao M, Fu Y. The DNA barcode identification of Dalbergia odorifera T. Chen and Dalbergia tonkinensis Prain. BMC PLANT BIOLOGY 2023; 23:546. [PMID: 37936056 PMCID: PMC10629101 DOI: 10.1186/s12870-023-04513-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 10/04/2023] [Indexed: 11/09/2023]
Abstract
BACKGROUND Dalbergia odorifera is a precious tree species with unique economic and medicinal values, which is difficult to distinguish from Dalbergia tonkinensis by traditional identification methods such as morphological characteristics and wood structure characteristics. It has been demonstrated that the identification of tree species can be effectively achieved using DNA barcoding, but there is a lack of study of the combined sequences used as DNA barcodes in the two tree species. In this study, 10 single sequences and 4 combined sequences were selected for analysis, and the identification effect of each sequence was evaluated by the distance-based method, BLAST-based search, character-based method, and tree-based method. RESULTS Among the single sequences and the combined sequences, the interspecies distance of trnH-psbA and ITS2 + trnH-psbA was greater than the intraspecies distance, and there was no overlap in their frequency distribution plots. The results of the Wilcoxon signed-rank test for the interspecies distance of each sequence showed that the interspecies differences of the single sequences except trnL-trnF, trnH-psbA, and ycf3 were significantly smaller than those of the combined sequences. The results of BLAST analysis showed that trnH-psbA could accurately identify D. odorifera and D. tonkinensis at the species level. In the character-based method, single sequences of trnL-trnF, trnH-psbA with all the combined sequences can be used for the identification of D. odorifera and D. tonkinensis. In addition, the neighbor-joining (NJ) trees constructed based on trnH-psbA and ITS2 + trnH-psbA were able to cluster D. odorifera and D. tonkinensis on two clades. CONCLUSIONS The results showed that the character-based method with the BLOG algorithm was the most effective among all the evaluation methods, and the combined sequences can improve the ability to identify tree species compared with single sequences. Finally, the trnH-psbA and ITS2 + trnH-psbA were proposed as DNA barcodes to identify D. odorifera and D. tonkinensis.
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Affiliation(s)
- Weijie Wang
- Guangxi Key Laboratory of Forest Ecology and Conservation, Key Laboratory of National Forestry and Grassland Administration on Cultivation of Fast-Growing Timber in Central South China, College of Forestry, Guangxi University, Nanning, 530004, China
| | - Baixu Chen
- Guangxi Key Laboratory of Forest Ecology and Conservation, Key Laboratory of National Forestry and Grassland Administration on Cultivation of Fast-Growing Timber in Central South China, College of Forestry, Guangxi University, Nanning, 530004, China
| | - Ruoke Ma
- Guangxi Key Laboratory of Forest Ecology and Conservation, Key Laboratory of National Forestry and Grassland Administration on Cultivation of Fast-Growing Timber in Central South China, College of Forestry, Guangxi University, Nanning, 530004, China
| | - Mengji Qiao
- Guangxi Key Laboratory of Forest Ecology and Conservation, Key Laboratory of National Forestry and Grassland Administration on Cultivation of Fast-Growing Timber in Central South China, College of Forestry, Guangxi University, Nanning, 530004, China.
| | - Yunlin Fu
- Guangxi Key Laboratory of Forest Ecology and Conservation, Key Laboratory of National Forestry and Grassland Administration on Cultivation of Fast-Growing Timber in Central South China, College of Forestry, Guangxi University, Nanning, 530004, China.
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Hadj-Henni L, Millot C, Lehrter V, Augot D. Wing morphometrics of biting midges (Diptera: Culicoides) of veterinary importance in Madagascar. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 114:105494. [PMID: 37640128 DOI: 10.1016/j.meegid.2023.105494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/23/2023] [Accepted: 08/25/2023] [Indexed: 08/31/2023]
Abstract
Biting midges are vectors of arboviruses such as bluetongue virus, bovine ephemeral fever virus, Akabane virus, African horse sickness virus, epizootic haemorrhagic disease virus and Schmallenberg virus. Fast and accurate identification of biting midges is crucial in the study of Culicoides-borne diseases. Morphological identification of biting midges has revealed the presence of cryptic species. A total of 20 species are reported in Madagascar. In this study, we assessed wing morphometric analysis for identification of seven species namely C. dubitatus Kremer, Rebholtz-Hirtzel and Delécolle, C. enderleini Cornet and Brunhes, C. kibatiensis Goetghebuer, C. miombo Meiswinkel, C. moreli Clastrier, C. nevilli Cornet and Brunhes, and C. zuluensis de Meillon. Culicoides enderleini, C. miombo, C. moreli, C. nevilli and C. zuluensis are vectors diseases. A molecular approach, based on the cytochrome oxidase I gene (Cox1), was used for species delimitation. The molecular analysis presented seven different clades grouped two-by-two according to morphological characters. A total of 179 wing images were digitised. We found morphometric variation among seven species based on 11 landmarks and two outlines. Wing shape variation plots showed that species overlapped with species belonging to the same group. The cross-validation revealed a relatively high percentage of correct classification in most species, ranging from 91.3% to 100% for landmarks; 60% to 82.6% for outlines-1 and 77.1% to 91.3% for outlines-2. Our study suggests that wing geometric morphometric analysis is a robust tool for reliable "Moka Fohy" identification in Madagascar. This inexpensive and simple method is a precise supplement to morphological identification, with reaches the accuracy of Cox1 barcoding.
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Affiliation(s)
- Leila Hadj-Henni
- Usc Vecpar-ANSES LSA, EA 7510, SFR Cap Santé, Université de Reims Champagne-Ardenne, 51 rue Cognacq-Jay, 51096 Reims Cedex, France
| | - Christine Millot
- Usc Vecpar-ANSES LSA, EA 7510, SFR Cap Santé, Université de Reims Champagne-Ardenne, 51 rue Cognacq-Jay, 51096 Reims Cedex, France.
| | - Véronique Lehrter
- Unité BioSpecT, EA7506, Université de Reims Champagne-Ardenne, Reims, France
| | - Denis Augot
- Usc Vecpar-ANSES LSA, EA 7510, SFR Cap Santé, Université de Reims Champagne-Ardenne, 51 rue Cognacq-Jay, 51096 Reims Cedex, France; ANSES, INRAe, ENVA, UMR-BIPAR, Laboratoire de Santé Animale, 14 rue Pierre et Marie Curie, 94701 Maisons-Alfort Cedex, France.
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Santos Rampasso A, O'Grady PM. Standardized terminology and visual atlas of the external morphology and terminalia for the genus Scaptomyza (Diptera: Drosophilidae). Fly (Austin) 2021; 16:37-61. [PMID: 34641736 PMCID: PMC8525988 DOI: 10.1080/19336934.2021.1969220] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The genus Scaptomyza is one of the two Drosophilidae genera with Hawaiian endemic species. This genus is an excellent model for biogeographic studies since it is distributed throughout the majority of continents, including continental islands, the Hawaiian Islands, and many other remote oceanic islands. This genus currently comprises 273 described species, 148 of which are endemic to the Hawaiian Islands. However, most descriptions were published before efforts to standardizing the morphological terminology across the Diptera were made in the 1980’s. Since research groups developed their own set of terminologies independently, without considering homologies, multiple terms have been used to refer to the same characters. This is especially true for the male terminalia, which have remarkable modifications within the family Drosophilidae. We reviewed the Scaptomyza literature, in addition to other studies across the Drosophilidae and Diptera, compiled the English synonyms, and provided a visual atlas of each body part, indicating how to recognize the morphological characters. The goal of the present study is to facilitate species identification and propose preferred terms to be adopted for future Scaptomyza descriptions.
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Kimprasit T, Nunome M, Iida K, Murakami Y, Wong ML, Wu CH, Kobayashi R, Hengjan Y, Takemae H, Yonemitsu K, Kuwata R, Shimoda H, Si L, Sohn JH, Asakawa S, Ichiyanagi K, Maeda K, Oh HS, Mizutani T, Kimura J, Iida A, Hondo E. Dispersal history of Miniopterus fuliginosus bats and their associated viruses in east Asia. PLoS One 2021; 16:e0244006. [PMID: 33444317 PMCID: PMC7808576 DOI: 10.1371/journal.pone.0244006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 12/02/2020] [Indexed: 12/23/2022] Open
Abstract
In this study, we examined the role of the eastern bent-winged bat (Miniopterus fuliginosus) in the dispersion of bat adenovirus and bat alphacoronavirus in east Asia, considering their gene flows and divergence times (based on deep-sequencing data), using bat fecal guano samples. Bats in China moved to Jeju Island and/or Taiwan in the last 20,000 years via the Korean Peninsula and/or Japan. The phylogenies of host mitochondrial D-loop DNA was not significantly congruent with those of bat adenovirus (m2XY = 0.07, p = 0.08), and bat alphacoronavirus (m2XY = 0.48, p = 0.20). We estimate that the first divergence time of bats carrying bat adenovirus in five caves studied (designated as K1, K2, JJ, N2, and F3) occurred approximately 3.17 million years ago. In contrast, the first divergence time of bat adenovirus among bats in the 5 caves was estimated to be approximately 224.32 years ago. The first divergence time of bats in caves CH, JJ, WY, N2, F1, F2, and F3 harboring bat alphacoronavirus was estimated to be 1.59 million years ago. The first divergence time of bat alphacoronavirus among the 7 caves was estimated to be approximately 2,596.92 years ago. The origin of bat adenovirus remains unclear, whereas our findings suggest that bat alphacoronavirus originated in Japan. Surprisingly, bat adenovirus and bat alphacoronavirus appeared to diverge substantially over the last 100 years, even though our gene-flow data indicate that the eastern bent-winged bat serves as an important natural reservoir of both viruses.
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Affiliation(s)
- Thachawech Kimprasit
- Laboratory of Animal Morphology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Mitsuo Nunome
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Keisuke Iida
- Laboratory of Animal Morphology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | | | - Min-Liang Wong
- Department of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Chung-Hsin Wu
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Ryosuke Kobayashi
- Laboratory of Animal Morphology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Yupadee Hengjan
- Laboratory of Animal Morphology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Hitoshi Takemae
- Laboratory of Animal Morphology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Kenzo Yonemitsu
- Laboratory of Veterinary Microbiology, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Ryusei Kuwata
- Laboratory of Veterinary Microbiology, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Hiroshi Shimoda
- Laboratory of Veterinary Microbiology, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Lifan Si
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, Henan, China
| | - Joon-Hyuk Sohn
- Laboratory of Anatomy and Cell Biology and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, Korea
| | - Susumu Asakawa
- Laboratory of Soil Biology and Chemistry, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Kenji Ichiyanagi
- Laboratory of Genome and Epigenome Dynamics, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Ken Maeda
- Laboratory of Veterinary Microbiology, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Hong-Shik Oh
- Institute of Science Education, Jeju National University, Jeju, Korea
| | - Tetsuya Mizutani
- Research and Education Center for Prevention of Global Infectious Diseases of Animals, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Junpei Kimura
- Laboratory of Anatomy and Cell Biology and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, Korea
| | - Atsuo Iida
- Laboratory of Animal Morphology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Eiichi Hondo
- Laboratory of Animal Morphology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
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Identification of some Egyptian leafhopper species (Hemiptera: Cicadellidae) using DNA barcoding. Biologia (Bratisl) 2020. [DOI: 10.2478/s11756-019-00384-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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8
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A protocol for fast identification of larval tephritid flies with a community-wide COI reference bank. CONSERV GENET RESOUR 2019. [DOI: 10.1007/s12686-019-01120-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Gemmellaro MD, Hamilton GC, Ware JL. Review of Molecular Identification Techniques for Forensically Important Diptera. JOURNAL OF MEDICAL ENTOMOLOGY 2019; 56:887-902. [PMID: 31173634 DOI: 10.1093/jme/tjz040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Indexed: 06/09/2023]
Abstract
The medico-legal section of forensic entomology focuses on the analysis of insects associated with a corpse. Such insects are identified, and their life history characteristics are evaluated to provide information related to the corpse, such as postmortem interval and time of colonization. Forensically important insects are commonly identified using dichotomous keys, which rely on morphological characteristics. Morphological identifications can pose a challenge as local keys are not always available and can be difficult to use, especially when identifying juvenile stages. If a specimen is damaged, certain keys cannot be used for identification. In contrast, molecular identification can be a better instrument to identify forensically important insects, regardless of life stage or specimen completeness. Despite more than 20 yr since the first use of molecular data for the identification of forensic insects, there is little overlap in gene selection or phylogenetic methodology among studies, and this inconsistency reduces efficiency. Several methods such as genetic distance, reciprocal monophyly, or character-based methods have been implemented in forensic identification studies. It can be difficult to compare the results of studies that employ these different methods. Here we present a comprehensive review of the published results for the molecular identification of Diptera of forensic interest, with an emphasis on evaluating variation among studies in gene selection and phylogenetic methodology.
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Affiliation(s)
| | | | - Jessica L Ware
- Department of Entomology, Rutgers University, New Brunswick, NJ
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He T, Jiao L, Wiedenhoeft AC, Yin Y. Machine learning approaches outperform distance- and tree-based methods for DNA barcoding of Pterocarpus wood. PLANTA 2019; 249:1617-1625. [PMID: 30825008 DOI: 10.1007/s00425-019-03116-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 02/20/2019] [Indexed: 05/10/2023]
Abstract
Machine-learning approaches (MLAs) for DNA barcoding outperform distance- and tree-based methods on identification accuracy and cost-effectiveness to arrive at species-level identification of wood. DNA barcoding is a promising tool to combat illegal logging and associated trade, and the development of reliable and efficient analytical methods is essential for its extensive application in the trade of wood and in the forensics of natural materials more broadly. In this study, 120 DNA sequences of four barcodes (ITS2, matK, ndhF-rpl32, and rbcL) generated in our previous study and 85 downloaded from National Center for Biotechnology Information (NCBI) were collected to establish a reference data set for six commercial Pterocarpus woods. MLAs (BLOG, BP-neural network, SMO and J48) were compared with distance- (TaxonDNA) and tree-based (NJ tree) methods based on identification accuracy and cost-effectiveness across these six species, and also were applied to discriminate the CITES-listed species Pterocarpus santalinus from its anatomically similar species P. tinctorius for forensic identification. MLAs provided higher identification accuracy (30.8-100%) than distance- (15.1-97.4%) and tree-based methods (11.1-87.5%), with SMO performing the best among the machine learning classifiers. The two-locus combination ITS2 + matK when using SMO classifier exhibited the highest resolution (100%) with the fewest barcodes for discriminating the six Pterocarpus species. The CITES-listed species P. santalinus was discriminated successfully from P. tinctorius using MLAs with a single barcode, ndhF-rpl32. This study shows that MLAs provided higher identification accuracy and cost-effectiveness for forensic application over other analytical methods in DNA barcoding of Pterocarpus wood.
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Affiliation(s)
- Tuo He
- Department of Wood Anatomy and Utilization, Chinese Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing, 100091, China
- Wood Collections (WOODPEDIA), Chinese Academy of Forestry, Beijing, 100091, China
- Forest Products Laboratory, Center for Wood Anatomy Research, USDA Forest Service, Madison, WI, 53726, USA
- Department of Botany, University of Wisconsin, Madison, WI, 53706, USA
| | - Lichao Jiao
- Department of Wood Anatomy and Utilization, Chinese Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing, 100091, China
- Wood Collections (WOODPEDIA), Chinese Academy of Forestry, Beijing, 100091, China
| | - Alex C Wiedenhoeft
- Forest Products Laboratory, Center for Wood Anatomy Research, USDA Forest Service, Madison, WI, 53726, USA
- Department of Botany, University of Wisconsin, Madison, WI, 53706, USA
- Department of Forestry and National Resources, Purdue University, West Lafayette, IN, 47907, USA
- Ciências Biológicas (Botânica), Univesidade Estadual Paulista, Botucatu, São Paulo, Brazil
| | - Yafang Yin
- Department of Wood Anatomy and Utilization, Chinese Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing, 100091, China.
- Wood Collections (WOODPEDIA), Chinese Academy of Forestry, Beijing, 100091, China.
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11
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Luhur A, Klueg KM, Zelhof AC. Generating and working with Drosophila cell cultures: Current challenges and opportunities. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2018; 8:e339. [PMID: 30561900 DOI: 10.1002/wdev.339] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 10/30/2018] [Accepted: 11/21/2018] [Indexed: 12/26/2022]
Abstract
The use of Drosophila cell cultures has positively impacted both fundamental and biomedical research. The most widely used cell lines: Schneider, Kc, the CNS and imaginal disc lines continue to be the choice for many applications. Drosophila cell lines provide a homogenous source of cells suitable for biochemical experimentations, transcriptomics, functional genomics, and biomedical applications. They are amenable to RNA interference and serve as a platform for high-throughput screens to identify relevant candidate genes or drugs for any biological process. Currently, CRISPR-based functional genomics are also being developed for Drosophila cell lines. Even though many uniquely derived cell lines exist, cell genetic techniques such the transgenic UAS-GAL4-based RasV12 oncogene expression, CRISPR-Cas9 editing and recombination mediated cassette exchange are likely to drive the establishment of many more lines from specific tissues, cells, or genotypes. However, the pace of creating new lines is hindered by several factors inherent to working with Drosophila cell cultures: single cell cloning, optimal media formulations and culture conditions capable of supporting lines from novel tissue sources or genotypes. Moreover, even though many Drosophila cell lines are morphologically and transcriptionally distinct it may be necessary to implement a standard for Drosophila cell line authentication, ensuring the identity and purity of each cell line. Altogether, recent advances and a standardized authentication effort should improve the utility of Drosophila cell cultures as a relevant model for fundamental and biomedical research. This article is categorized under: Technologies > Analysis of Cell, Tissue, and Animal Phenotypes.
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Affiliation(s)
- Arthur Luhur
- Department of Biology, Drosophila Genomics Resource Center, Indiana University Bloomington, Bloomington, Indiana
| | - Kristin M Klueg
- Department of Biology, Drosophila Genomics Resource Center, Indiana University Bloomington, Bloomington, Indiana
| | - Andrew C Zelhof
- Department of Biology, Drosophila Genomics Resource Center, Indiana University Bloomington, Bloomington, Indiana
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12
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Kang W, Eldfjell Y, Fromm B, Estivill X, Biryukova I, Friedländer MR. miRTrace reveals the organismal origins of microRNA sequencing data. Genome Biol 2018; 19:213. [PMID: 30514392 PMCID: PMC6280396 DOI: 10.1186/s13059-018-1588-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 11/15/2018] [Indexed: 12/27/2022] Open
Abstract
We present here miRTrace, the first algorithm to trace microRNA sequencing data back to their taxonomic origins. This is a challenge with profound implications for forensics, parasitology, food control, and research settings where cross-contamination can compromise results. miRTrace accurately (> 99%) assigns real and simulated data to 14 important animal and plant groups, sensitively detects parasitic infection in mammals, and discovers the primate origin of single cells. Applying our algorithm to over 700 public datasets, we find evidence that over 7% are cross-contaminated and present a novel solution to clean these computationally, even after sequencing has occurred. miRTrace is freely available at https://github.com/friedlanderlab/mirtrace .
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Affiliation(s)
- Wenjing Kang
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Yrin Eldfjell
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Bastian Fromm
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Xavier Estivill
- Genetics and Genomics Department, Sidra Medicine, Doha, Qatar
| | - Inna Biryukova
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Marc R Friedländer
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.
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Doysabas KCC, Oba M, Furuta M, Iida K, Omatsu T, Furuya T, Okada T, Sutummaporn K, Shimoda H, Wong ML, Wu CH, Ohmori Y, Kobayashi R, Hengjan Y, Yonemitsu K, Kuwata R, Kim YK, Han SH, Sohn JH, Han SH, Suzuki K, Kimura J, Maeda K, Oh HS, Endoh D, Mizutani T, Hondo E. Encephalomyocarditis virus is potentially derived from eastern bent-wing bats living in East Asian countries. Virus Res 2018; 259:62-67. [PMID: 30391400 PMCID: PMC7114854 DOI: 10.1016/j.virusres.2018.10.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 10/19/2018] [Accepted: 10/30/2018] [Indexed: 12/22/2022]
Abstract
EMCV genome was widely found in fecal guanos in Taiwanese, Korean, and Japanese caves. Miniopterus fuliginosus is the main source of the fecal guano. It is possible that Miniopterus fuliginosus is one of the natural hosts of EMCV in East Asia.
Bats are reservoir hosts of many zoonotic viruses and identification of viruses that they carry is important. This study aimed to use high throughput screening to identify the viruses in fecal guano of Taiwanese insectivorous bats caves in order to obtain more information on bat-derived pathogenic viruses in East Asia. Guano samples were collected from two caves in Taiwan, pooled, and then subjected to Multiplex PCR-based next generation sequencing for viral identification. Subsequently, encephalomyocarditis virus (EMCV) sequence was detected and confirmed by reverse transcription PCR. EMCV is considered as rodent virus and thus, animal species identification through cytochrome oxidase I (COI) barcoding was further done to identify the viral source. Finally, determination of distribution and verification of the presence of EMCV in guano obtained from Japanese and South Korean caves was also done. We concluded that the guano collected was not contaminated with the excrement of rodents which were reported and presumed to live in Taiwan. Also, EMCV genome fragments were found in guanos of Japanese and South Korean caves. It is possible that the eastern bent-wing bat (Miniopterus fuliginosus) is one of the natural hosts of EMCV in East Asia.
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Affiliation(s)
- Karla Cristine C Doysabas
- Laboratory of Animal Morphology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Mami Oba
- Laboratory of Veterinary Microbiology, Cooperative Department of Veterinary Medicine, Tokyo University of Agriculture and Technology, Japan
| | - Masaya Furuta
- Laboratory of Animal Morphology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Keisuke Iida
- Laboratory of Animal Morphology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Tsutomu Omatsu
- Laboratory of Veterinary Microbiology, Cooperative Department of Veterinary Medicine, Tokyo University of Agriculture and Technology, Japan
| | - Tetsuya Furuya
- Laboratory of Veterinary Microbiology, Cooperative Department of Veterinary Medicine, Tokyo University of Agriculture and Technology, Japan
| | - Takashi Okada
- Department of Pediatric Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Kripitch Sutummaporn
- Laboratory of Veterinary Microbiology, Cooperative Department of Veterinary Medicine, Tokyo University of Agriculture and Technology, Japan
| | | | | | | | - Yasushige Ohmori
- Laboratory of Animal Morphology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Ryosuke Kobayashi
- Laboratory of Animal Morphology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Yupadee Hengjan
- Laboratory of Animal Morphology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | | | | | - Yoo-Kyung Kim
- Institute of Science Education, Jeju National University, Jeju, South Korea
| | - Sang-Hyun Han
- Institute of Science Education, Jeju National University, Jeju, South Korea
| | - Joon-Hyuk Sohn
- Laboratory of Veterinary Anatomy and Cell Biology and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, South Korea
| | - Sang-Hoon Han
- Natural Institute of Biological Resources, South Korea
| | | | - Junpei Kimura
- Laboratory of Veterinary Anatomy and Cell Biology and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, South Korea
| | - Ken Maeda
- Yamaguchi University, Yamaguchi, Japan
| | - Hong-Shik Oh
- Institute of Science Education, Jeju National University, Jeju, South Korea
| | - Daiji Endoh
- Department of Veterinary Radiology, School of Veterinary Medicine, Rakuno Gakuen University, 582 Midorimachi, Bunkyodai, Ebetsu-shi 069-8501, Japan
| | - Tetsuya Mizutani
- Laboratory of Veterinary Microbiology, Cooperative Department of Veterinary Medicine, Tokyo University of Agriculture and Technology, Japan
| | - Eiichi Hondo
- Laboratory of Animal Morphology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan.
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Abstract
Understanding phylogenetic relationships among taxa is key to designing and implementing comparative analyses. The genus Drosophila, which contains over 1600 species, is one of the most important model systems in the biological sciences. For over a century, one species in this group, Drosophila melanogaster, has been key to studies of animal development and genetics, genome organization and evolution, and human disease. As whole-genome sequencing becomes more cost-effective, there is increasing interest in other members of this morphologically, ecologically, and behaviorally diverse genus. Phylogenetic relationships within Drosophila are complicated, and the goal of this paper is to provide a review of the recent taxonomic changes and phylogenetic relationships in this genus to aid in further comparative studies.
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15
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Lu J, Zhang Y, Chen H. Integrative taxonomy of the genus Pseudostegana (Diptera, Drosophilidae) from China, with descriptions of eleven new species. PeerJ 2018; 6:e5160. [PMID: 30202640 PMCID: PMC6129143 DOI: 10.7717/peerj.5160] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 06/14/2018] [Indexed: 11/20/2022] Open
Abstract
The genus Pseudostegana (Okada, 1978) currently contains thirty-nine described species. A number of Pseudostegana were collected from the fieldwork in southwestern China from 2010 to 2017. Eleven new species were discovered and are described from southwestern China: Pseudostegana alpina Zhang & Chen, sp. nov.; Pseudostegana amnicola Zhang & Chen, sp. nov.; Pseudostegana amoena Zhang & Chen, sp. nov.; Pseudostegana mailangang Zhang & Chen, sp. nov.; Pseudostegana meiduo Zhang & Chen, sp. nov.; Pseudostegana meiji Zhang & Chen, sp. nov.; Pseudostegana mystica Zhang & Chen, sp. nov.; Pseudostegana stictiptrata Zhang & Chen, sp. nov.; Pseudostegana stigmatptera Zhang & Chen, sp. nov.; Pseudostegana ximalaya Zhang & Chen, sp. nov. and Pseudostegana zhuoma Zhang & Chen, sp. nov. A key to all Chinese Pseudostegana species based on morphological characters is provided. Two mitochondrial loci (COI and ND2) and one nuclear locus (28S rRNA) were sequenced for the Pseudostegana specimens, and Bayesian and RAxML concatenated analyses were run. Molecular species delimitation is performed using the distance-based automatic barcode gap discovery (ABGD) method. Molecular data support the morphological characteristics observed among these Chinese species and confirm the new species as being distinctly different.
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Affiliation(s)
- Jinming Lu
- Department of Entomology, South China Agricultural University, Guangzhou, Guangdong, China
| | - Yuan Zhang
- Department of Entomology, South China Agricultural University, Guangzhou, Guangdong, China
| | - Hongwei Chen
- Department of Entomology, South China Agricultural University, Guangzhou, Guangdong, China
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16
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Rosas U, Menendez F, Cornejo R, Canales R, Velez-Zuazo X. Fish DNA barcoding around large marine infrastructure for improved biodiversity assessment and monitoring. Mitochondrial DNA A DNA Mapp Seq Anal 2018; 29:1174-1179. [PMID: 29373939 DOI: 10.1080/24701394.2018.1431225] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Accurate species-level identification is pivotal for environmental assessments and monitoring. The PERU LNG terminal is composed of large marine infrastructure located on the central coast of Peru. Since construction, taxonomically challenging species such as drum fishes (Sciaenidae) have been attracted to the new hard-bottom habitat. We conducted a DNA barcoding study to investigate fish diversity and constructed a DNA barcode reference library. We examined 56 vouchered specimens and identified 24 unique species. Intra- and interspecific divergence estimates ranged between 0 and 0.64% and 11 and 35.5%, respectively. We assessed the efficiency of the reference library to identify 29 non-vouchered specimens. We had 82.5% efficiency by using both our reference library (n = 17) and GenBank (n = 24). We highlight the importance of implementing molecular barcoding for complementing biodiversity assessments in marine environments. This study represents a first step towards generating a comprehensive DNA barcode reference library for marine fishes in Peru.
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Affiliation(s)
- Ulises Rosas
- a Center for Conservation and Sustainability, Smithsonian Conservation Biology Institute, National Zoological Park , Washington , DC , USA.,b Departamento de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos , Lima , Peru
| | - Francisco Menendez
- a Center for Conservation and Sustainability, Smithsonian Conservation Biology Institute, National Zoological Park , Washington , DC , USA
| | - Rodolfo Cornejo
- c Instituto del Mar del Peru (IMARPE) , Callao , Peru.,d Facultad de Oceanografía, Pesquería, Alimentarias y Acuicultura , Universidad Nacional Federico Villarreal , Miraflores , Peru
| | - Remy Canales
- b Departamento de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos , Lima , Peru
| | - Ximena Velez-Zuazo
- a Center for Conservation and Sustainability, Smithsonian Conservation Biology Institute, National Zoological Park , Washington , DC , USA
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17
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Dawkins KL, Furse JM, Wild CH, Hughes JM. A novel genus and cryptic species harboured within the monotypic freshwater crayfish genus Tenuibranchiurus Riek, 1951 (Decapoda: Parastacidae). PeerJ 2017; 5:e3310. [PMID: 28560095 PMCID: PMC5445942 DOI: 10.7717/peerj.3310] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 04/13/2017] [Indexed: 11/20/2022] Open
Abstract
Identifying species groups is an important yet difficult task, with there being no single accepted definition as to what constitutes a species, nor a set of criteria by which they should be delineated. Employing the General Lineage Concept somewhat circumvents these issues, as this concept allows multiple concordant lines of evidence to be used as support for species delimitation, where a species is defined as any independently evolving lineage. Genetically diverse groups have previously been identified within the monotypic parastacid genus Tenuibranchiurus Riek, 1951, but no further investigation of this diversity has previously been undertaken. Analysis of two mitochondrial DNA gene regions has previously identified two highly divergent groups within this taxon, representing populations from Queensland (Qld) and New South Wales (NSW), respectively. Additional testing within this study of both mitochondrial and nuclear DNA through species discovery analyses identified genetically diverse groups within these regions, which were further supported by lineage validation methods. The degree of genetic differentiation between Qld and NSW populations supports the recognition of two genera; with Qld retaining the original genus name Tenuibranchiurus, and NSW designated as Gen. nov. until a formal description is completed. Concordance between the species discovery and lineage validation methods supports the presence of six species within Tenuibranchiurus and two within Gen. nov. The recognition of additional species removes the monotypy of the genus, and the methods used can improve species identification within groups of organisms with taxonomic problems and cryptic diversity.
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Affiliation(s)
- Kathryn L Dawkins
- Australian Rivers Institute, Griffith University, Gold Coast, Queensland, Australia
| | - James M Furse
- Environmental Futures Research Institute, Griffith University, Gold Coast, Queensland, Australia.,Miyazaki International College, Miyazaki, Japan
| | - Clyde H Wild
- Environmental Futures Research Institute, Griffith University, Gold Coast, Queensland, Australia
| | - Jane M Hughes
- Australian Rivers Institute, Griffith University, Nathan, Queensland, Australia
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18
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Kang L, Zhang S, Wu C, Liu X, Xu MY, Jiang L. Molecular phylogeny of Loliginidae inferred from mitochondrial DNA sequence variation. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:600-605. [PMID: 28531368 DOI: 10.1080/24701394.2017.1325482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Loliginidae includes many economically important species in trophic systems worldwide. Here, we investigated genetic relationships and diversity in this family. Sequence comparisons and phylogenetic analyses revealed considerable variations between mitochondrial 16 S rRNA gene and cytochrome coxidase subunit I gene among nine Loliginid species. We identified three similar non-coding regions in eight Loliginid species, but not in Sepioteuthislessoniana. We detected a single extended termination-associated sequence and three conserved sequence blocks among these eight species. Our results suggest that Loliginidae forms a major lineage, with S. lessoniana located at the most basal position and forming an individual clade as sister to the remaining species. Loligobeka, Loliolusjaponica, Loliolusuyii, Loligochinensis, Loligoedulis, Loligoduvauceli, Loligobleekeri, and Loligoopalescensare clustered into a monophyletic group. We identified repetitive elements and repeat numbers in the control regions.
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Affiliation(s)
- Lisen Kang
- a National Engineering Research Center of Marine Facilities Aquaculture, College of Marine Science , Zhejiang Ocean University , Zhoushan , China
| | - Shuyi Zhang
- a National Engineering Research Center of Marine Facilities Aquaculture, College of Marine Science , Zhejiang Ocean University , Zhoushan , China
| | - Changwen Wu
- a National Engineering Research Center of Marine Facilities Aquaculture, College of Marine Science , Zhejiang Ocean University , Zhoushan , China
| | - Xiaoxu Liu
- a National Engineering Research Center of Marine Facilities Aquaculture, College of Marine Science , Zhejiang Ocean University , Zhoushan , China
| | - Mei Ying Xu
- a National Engineering Research Center of Marine Facilities Aquaculture, College of Marine Science , Zhejiang Ocean University , Zhoushan , China
| | - Lihua Jiang
- a National Engineering Research Center of Marine Facilities Aquaculture, College of Marine Science , Zhejiang Ocean University , Zhoushan , China
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19
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Species evolution and quality evaluation of four Coptis herbal medicinal materials in Southwest China. 3 Biotech 2017; 7:62. [PMID: 28444606 DOI: 10.1007/s13205-017-0679-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 02/27/2017] [Indexed: 01/08/2023] Open
Abstract
Coptis herbs, which are important herbal medicinal materials, are the dried rhizomes of various plants. In China's herbal market, drying herbs can severely influence morphological markers such as shape, color, and odor, which make consumers difficult to precisely identify the herbs and effectively evaluate the quality. Here, we present the phylogenetic analysis of four Coptis herbal medicinal materials based on internal transcribed spacer sequences. C. chinensis, C. omeiensis, C. deltoidea and C. teeta constituted a monophyletic group. In this group, C. omeiensis and C. deltoidea cluster together, and they form the sister group with C. teeta, and C. chinensis locate the outermost of C. omeiensis, C. deltoidea and C. teeta. At the same time, the HPLC-DAD method was applied to simultaneously analyze main alkaloids from seventeen different samples. On the basis of the robust phylogenetic topology, the parsimony reconstructions of six effective medicinal constituents were implemented to elucidate the evolutionary history in Coptis herbs, and thus evaluate the herbal quality. The results showed that C. chinensis had been considered to be the best herb, not only the high content in single constituent but also in total alkaloids. In addition, all the samples from seventeen habitats were considered as qualified herbs, and they could meet the requirements of national quality standards for Coptis herbs in China.
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20
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Liu ZF, Ci XQ, Li L, Li HW, Conran JG, Li J. DNA barcoding evaluation and implications for phylogenetic relationships in Lauraceae from China. PLoS One 2017; 12:e0175788. [PMID: 28414813 PMCID: PMC5393608 DOI: 10.1371/journal.pone.0175788] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 04/01/2017] [Indexed: 11/18/2022] Open
Abstract
Lauraceae are an important component of tropical and subtropical forests and have major ecological and economic significance. Owing to lack of clear-cut morphological differences between genera and species, this family is an ideal case for testing the efficacy of DNA barcoding in the identification and discrimination of species and genera. In this study, we evaluated five widely recommended plant DNA barcode loci matK, rbcL, trnH–psbA, ITS2 and the entire ITS region for 409 individuals representing 133 species, 12 genera from China. We tested the ability of DNA barcoding to distinguish species and as an alternative tool for correcting species misidentification. We also used the rbcL+matK+trnH–psbA+ITS loci to investigate the phylogenetic relationships of the species examined. Among the gene regions and their combinations, ITS was the most efficient for identifying species (57.5%) and genera (70%). DNA barcoding also had a positive role for correcting species misidentification (10.8%). Furthermore, based on the results of the phylogenetic analyses, Chinese Lauraceae species formed three supported monophyletic clades, with the Cryptocarya group strongly supported (PP = 1.00, BS = 100%) and the clade including the Persea group, Laureae and Cinnamomum also receiving strong support (PP = 1.00, BS = 98%), whereas the Caryodaphnopsis–Neocinnamomum received only moderate support (PP = 1.00 and BS = 85%). This study indicates that molecular barcoding can assist in screening difficult to identify families like Lauraceae, detecting errors of species identification, as well as helping to reconstruct phylogenetic relationships. DNA barcoding can thus help with large-scale biodiversity inventories and rare species conservation by improving accuracy, as well as reducing time and costs associated with species identification.
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Affiliation(s)
- Zhi-Fang Liu
- Plant Phylogenetics and Conservation Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, P. R. China
- University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Xiu-Qin Ci
- Plant Phylogenetics and Conservation Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, P. R. China
- University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Lang Li
- Plant Phylogenetics and Conservation Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, P. R. China
| | - Hsi-Wen Li
- Herbarium (KUN), Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, P. R. China
| | - John G. Conran
- Australian Centre for Evolutionary Biology and Biodiversity & Sprigg Geobiology Centre, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Jie Li
- Plant Phylogenetics and Conservation Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, P. R. China
- * E-mail:
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21
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Sarswat M, Dewan S, Fartyal RS. Mitochondrial DNA sequence variation in Drosophilid species (Diptera: Drosophilidae) along altitudinal gradient from Central Himalayan region of India. J Genet 2017; 95:357-67. [PMID: 27350680 DOI: 10.1007/s12041-016-0646-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Central Himalayan region of India encompasses varied ecological habitats ranging from near tropics to the mid-elevation forests dominated by cool-temperate taxa. In past, we have reported several new records and novel species from Uttarakhand state of India. Here, we assessed genetic variations in three mitochondrial genes, namely, 16S rRNA, cytochrome c oxidase subunit I and cytochrome c oxidase subunit II (COI and COII) in 26 drosophilid species collected along altitudinal transect from 550 to 2700 m above mean sea level. In the present study, overall 543 sequences were generated, 82 for 16S rRNA, 238 for COI, 223 for COII with 21, 47 and 45 mitochondrial haplotypes for 16S rRNA, COI and COII genes, respectively. Almost all species were represented by 2-3 unique mitochondrial haplotypes, depicting a significant impact of environmental heterogeneity along altitudinal gradient on genetic diversity. Also for the first time, molecular data of some rare species like Drosophila mukteshwarensis, Liodrosophila nitida, Lordiphosa parantillaria, Lordiphosa ayarpathaensis, Scaptomyza himalayana, Scaptomyza tistai, Zaprionus grandis and Stegana minuta are provided to public domains through this study.
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Affiliation(s)
- Manisha Sarswat
- Cytogenetics and Molecular Systematics Laboratory, UGC-SAP Department of Zoology and Biotechnology, HNB Garhwal University, Garhwal 246 174, India.
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22
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Yassin A. Drosophila yakuba mayottensis, a new model for the study of incipient ecological speciation. Fly (Austin) 2017; 11:37-45. [PMID: 27560369 DOI: 10.1080/19336934.2016.1221550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
A full understanding of how ecological factors drive the fixation of genetic changes during speciation is obscured by the lack of appropriate models with clear natural history and powerful genetic toolkits. In a recent study, we described an early stage of ecological speciation in a population of the generalist species Drosophila yakuba (melanogaster subgroup) on the island of Mayotte (Indian Ocean). On this island, flies are strongly associated with the toxic fruits of noni (Morinda citrifolia) and show a partial degree of pre-zygotic reproductive isolation. Here, I mine the nuclear and mitochondrial genomes and provide a full morphological description of this population. Only 29 nuclear sites (< 4 × 10-7 of the genome) are fixed in this population and absent from 3 mainland populations and the closest relative D. santomea, but no mitochondrial or morphological character distinguish Mayotte flies from the mainland. This result indicates that physiological and behavioral traits may evolve faster than morphology at the early stages of speciation. Based on these differences, the Mayotte population is designated as a new subspecies, Drosophila yakuba mayottensis subsp. nov., and its strong potential in understanding the genetics of speciation and plant-insect interactions is discussed.
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Affiliation(s)
- Amir Yassin
- a Laboratory of Genetics , University of Wisconsin-Madison , Madison , WI , USA
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23
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Zou S, Li Q. Pay Attention to the Overlooked Cryptic Diversity in Existing Barcoding Data: the Case of Mollusca with Character-Based DNA Barcoding. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2016; 18:327-335. [PMID: 26899167 DOI: 10.1007/s10126-016-9692-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 01/28/2016] [Indexed: 06/05/2023]
Abstract
With the global biodiversity crisis, DNA barcoding aims for fast species identification and cryptic species diversity revelation. For more than 10 years, large amounts of DNA barcode data have been accumulating in publicly available databases, most of which were conducted by distance or tree-building methods that have often been argued, especially for cryptic species revelation. In this context, overlooked cryptic diversity may exist in the available barcoding data. The character-based DNA barcoding, however, has a good chance for detecting the overlooked cryptic diversity. In this study, marine mollusk was as the ideal case for detecting the overlooked potential cryptic species from existing cytochrome c oxidase I (COI) sequences with character-based DNA barcode. A total of 1081 COI sequences of mollusks, belonging to 176 species of 25 families of Gastropoda, Cephalopoda, and Lamellibranchia, were conducted by character analysis. As a whole, the character-based barcoding results were consistent with previous distance and tree-building analysis for species discrimination. More importantly, quite a number of species analyzed were divided into distinct clades with unique diagnostical characters. Based on the concept of cryptic species revelation of character-based barcoding, these species divided into separate taxonomic groups might be potential cryptic species. The detection of the overlooked potential cryptic diversity proves that the character-based barcoding mode possesses more advantages of revealing cryptic biodiversity. With the development of DNA barcoding, making the best use of barcoding data is worthy of our attention for species conservation.
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Affiliation(s)
- Shanmei Zou
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
- Jiangsu Provincial Key Laboratory of Marine Biology, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China.
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24
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Zou S, Fei C, Song J, Bao Y, He M, Wang C. Combining and Comparing Coalescent, Distance and Character-Based Approaches for Barcoding Microalgaes: A Test with Chlorella-Like Species (Chlorophyta). PLoS One 2016; 11:e0153833. [PMID: 27092945 PMCID: PMC4841637 DOI: 10.1371/journal.pone.0153833] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 03/13/2016] [Indexed: 01/19/2023] Open
Abstract
Several different barcoding methods of distinguishing species have been advanced, but which method is the best is still controversial. Chlorella is becoming particularly promising in the development of second-generation biofuels. However, the taxonomy of Chlorella-like organisms is easily confused. Here we report a comprehensive barcoding analysis of Chlorella-like species from Chlorella, Chloroidium, Dictyosphaerium and Actinastrum based on rbcL, ITS, tufA and 16S sequences to test the efficiency of traditional barcoding, GMYC, ABGD, PTP, P ID and character-based barcoding methods. First of all, the barcoding results gave new insights into the taxonomic assessment of Chlorella-like organisms studied, including the clear species discrimination and resolution of potentially cryptic species complexes in C. sorokiniana, D. ehrenbergianum and C. Vulgaris. The tufA proved to be the most efficient barcoding locus, which thus could be as potential "specific barcode" for Chlorella-like species. The 16S failed in discriminating most closely related species. The resolution of GMYC, PTP, P ID, ABGD and character-based barcoding methods were variable among rbcL, ITS and tufA genes. The best resolution for species differentiation appeared in tufA analysis where GMYC, PTP, ABGD and character-based approaches produced consistent groups while the PTP method over-split the taxa. The character analysis of rbcL, ITS and tufA sequences could clearly distinguish all taxonomic groups respectively, including the potentially cryptic lineages, with many character attributes. Thus, the character-based barcoding provides an attractive complement to coalescent and distance-based barcoding. Our study represents the test that proves the efficiency of multiple DNA barcoding in species discrimination of microalgaes.
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Affiliation(s)
- Shanmei Zou
- Jiangsu Provincial Key Laboratory of Marine Biology, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Cong Fei
- Jiangsu Provincial Key Laboratory of Marine Biology, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Jiameng Song
- Jiangsu Provincial Key Laboratory of Marine Biology, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Yachao Bao
- Jiangsu Provincial Key Laboratory of Marine Biology, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Meilin He
- Jiangsu Provincial Key Laboratory of Marine Biology, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Changhai Wang
- Jiangsu Provincial Key Laboratory of Marine Biology, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing 210095, PR China
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25
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Paknia O, Bergmann T, Hadrys H. Some ‘ant’swers: Application of a layered barcode approach to problems in ant taxonomy. Mol Ecol Resour 2015; 15:1262-74. [DOI: 10.1111/1755-0998.12395] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 02/03/2015] [Accepted: 02/18/2015] [Indexed: 11/26/2022]
Affiliation(s)
- Omid Paknia
- Institut für Tierökologie und Zellbiologie; Stiftung Tierärztliche Hochschule Hannover; Hannover Germany
| | - Tjard Bergmann
- Institut für Tierökologie und Zellbiologie; Stiftung Tierärztliche Hochschule Hannover; Hannover Germany
| | - Heike Hadrys
- Institut für Tierökologie und Zellbiologie; Stiftung Tierärztliche Hochschule Hannover; Hannover Germany
- EEB; Yale University; New Haven Connecticut 06511 USA
- Sackler Institute for Comparative Genomics; American Museum of Natural History; New York New York 10024 USA
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26
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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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27
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An K, Cao H, Wang X, Chen H. The subgenusAshima(Diptera, Drosophildae,Phortica) from China, with DNA barcoding and descriptions of three new species. SYST BIODIVERS 2014. [DOI: 10.1080/14772000.2014.968235] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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28
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Čandek K, Kuntner M. DNA barcoding gap: reliable species identification over morphological and geographical scales. Mol Ecol Resour 2014; 15:268-77. [DOI: 10.1111/1755-0998.12304] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Revised: 07/06/2014] [Accepted: 07/16/2014] [Indexed: 12/23/2022]
Affiliation(s)
- Klemen Čandek
- Institute of Biology; Scientific Research Centre of the Slovenian Academy of Sciences and Arts; Novi Trg 2 1000 Ljubljana Slovenia
| | - Matjaž Kuntner
- Institute of Biology; Scientific Research Centre of the Slovenian Academy of Sciences and Arts; Novi Trg 2 1000 Ljubljana Slovenia
- Centre for Behavioural Ecology and Evolution; College of Life Sciences; Hubei University; 368 Youyi Road 430062 Wuhan China
- Department of Entomology; National Museum of Natural History; Smithsonian Institution; PO Box 37012 Washington DC 20013-7012 USA
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29
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Liu XF, Yang CH, Han HL, Ward RD, Zhang AB. Identifying species of moths (Lepidoptera) from Baihua Mountain, Beijing, China, using DNA barcodes. Ecol Evol 2014; 4:2472-87. [PMID: 25360280 PMCID: PMC4203292 DOI: 10.1002/ece3.1110] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2013] [Revised: 04/19/2014] [Accepted: 04/23/2014] [Indexed: 12/28/2022] Open
Abstract
DNA barcoding has become a promising means for the identification of organisms of all life-history stages. Currently, distance-based and tree-based methods are most widely used to define species boundaries and uncover cryptic species. However, there is no universal threshold of genetic distance values that can be used to distinguish taxonomic groups. Alternatively, DNA barcoding can deploy a "character-based" method, whereby species are identified through the discrete nucleotide substitutions. Our research focuses on the delimitation of moth species using DNA-barcoding methods. We analyzed 393 Lepidopteran specimens belonging to 80 morphologically recognized species with a standard cytochrome c oxidase subunit I (COI) sequencing approach, and deployed tree-based, distance-based, and diagnostic character-based methods to identify the taxa. The tree-based method divided the 393 specimens into 79 taxa (species), and the distance-based method divided them into 84 taxa (species). Although the diagnostic character-based method found only 39 so-identifiable species in the 80 species, with a reduction in sample size the accuracy rate substantially improved. For example, in the Arctiidae subset, all 12 species had diagnostics characteristics. Compared with traditional morphological method, molecular taxonomy performed well. All three methods enable the rapid delimitation of species, although they have different characteristics and different strengths. The tree-based and distance-based methods can be used for accurate species identification and biodiversity studies in large data sets, while the character-based method performs well in small data sets and can also be used as the foundation of species-specific biochips.
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Affiliation(s)
- Xiao F Liu
- College of Life Sciences, Capital Normal UniversityBeijing, 100048, China
| | - Cong H Yang
- College of Life Sciences, Capital Normal UniversityBeijing, 100048, China
| | - Hui L Han
- School of Forestry, Experiment Center, Northeast Forestry UniversityHaerbin, 150040, China
| | - Robert D Ward
- Wealth from Oceans Flagship, CSIRO Marine and Atmospheric ResearchGPO Box 1538, Hobart, Tasmania, 7001, Australia
| | - Ai-bing Zhang
- College of Life Sciences, Capital Normal UniversityBeijing, 100048, China
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30
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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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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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Porter TM, Gibson JF, Shokralla S, Baird DJ, Golding GB, Hajibabaei M. Rapid and accurate taxonomic classification of insect (class Insecta) cytochrome
c
oxidase subunit 1 (
COI
)
DNA
barcode sequences using a naïve Bayesian classifier. Mol Ecol Resour 2014. [PMCID: PMC4282328 DOI: 10.1111/1755-0998.12240] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Current methods to identify unknown insect (class Insecta) cytochrome c oxidase (COI barcode) sequences often rely on thresholds of distances that can be difficult to define, sequence similarity cut-offs, or monophyly. Some of the most commonly used metagenomic classification methods do not provide a measure of confidence for the taxonomic assignments they provide. The aim of this study was to use a naïve Bayesian classifier (Wang et al.Applied and Environmental Microbiology, 2007; 73: 5261) to automate taxonomic assignments for large batches of insect COI sequences such as data obtained from high-throughput environmental sequencing. This method provides rank-flexible taxonomic assignments with an associated bootstrap support value, and it is faster than the blast-based methods commonly used in environmental sequence surveys. We have developed and rigorously tested the performance of three different training sets using leave-one-out cross-validation, two field data sets, and targeted testing of Lepidoptera, Diptera and Mantodea sequences obtained from the Barcode of Life Data system. We found that type I error rates, incorrect taxonomic assignments with a high bootstrap support, were already relatively low but could be lowered further by ensuring that all query taxa are actually present in the reference database. Choosing bootstrap support cut-offs according to query length and summarizing taxonomic assignments to more inclusive ranks can also help to reduce error while retaining the maximum number of assignments. Additionally, we highlight gaps in the taxonomic and geographic representation of insects in public sequence databases that will require further work by taxonomists to improve the quality of assignments generated using any method.
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Affiliation(s)
- Teresita M. Porter
- McMaster University Department of Biology 1280 Main Street West Hamilton ON Canada L8S 4K1
| | - Joel F. Gibson
- Biodiversity Institute of Ontario & Department of Integrative Biology University of Guelph 50 Stone Road East Guelph ON Canada N1G 2W1
| | - Shadi Shokralla
- Biodiversity Institute of Ontario & Department of Integrative Biology University of Guelph 50 Stone Road East Guelph ON Canada N1G 2W1
| | - Donald J. Baird
- Environment Canada at Canadian Rivers Institute Department of Biology University of New Brunswick Fredericton NB Canada E3B 6E1
| | - G. Brian Golding
- McMaster University Department of Biology 1280 Main Street West Hamilton ON Canada L8S 4K1
| | - Mehrdad Hajibabaei
- Biodiversity Institute of Ontario & Department of Integrative Biology University of Guelph 50 Stone Road East Guelph ON Canada N1G 2W1
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Jörger KM, Schrödl M. How to describe a cryptic species? Practical challenges of molecular taxonomy. Front Zool 2013; 10:59. [PMID: 24073641 PMCID: PMC4015967 DOI: 10.1186/1742-9994-10-59] [Citation(s) in RCA: 180] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 09/03/2013] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Molecular methods of species delineation are rapidly developing and widely considered as fast and efficient means to discover species and face the 'taxonomic impediment' in times of biodiversity crisis. So far, however, this form of DNA taxonomy frequently remains incomplete, lacking the final step of formal species description, thus enhancing rather than reducing impediments in taxonomy. DNA sequence information contributes valuable diagnostic characters and -at least for cryptic species - could even serve as the backbone of a taxonomic description. To this end solutions for a number of practical problems must be found, including a way in which molecular data can be presented to fulfill the formal requirements every description must meet. Multi-gene barcoding and a combined molecular species delineation approach recently revealed a radiation of at least 12 more or less cryptic species in the marine meiofaunal slug genus Pontohedyle (Acochlidia, Heterobranchia). All identified candidate species are well delimited by a consensus across different methods based on mitochondrial and nuclear markers. RESULTS The detailed microanatomical redescription of Pontohedyle verrucosa provided in the present paper does not reveal reliable characters for diagnosing even the two major clades identified within the genus on molecular data. We thus characterize three previously valid Pontohedyle species based on four genetic markers (mitochondrial cytochrome c oxidase subunit I, 16S rRNA, nuclear 28S and 18S rRNA) and formally describe nine cryptic new species (P. kepii sp. nov., P. joni sp. nov., P. neridae sp. nov., P. liliae sp. nov., P. wiggi sp. nov., P. wenzli sp. nov., P. peteryalli sp. nov., P. martynovi sp. nov., P. yurihookeri sp. nov.) applying molecular taxonomy, based on diagnostic nucleotides in DNA sequences of the four markers. Due to the minute size of the animals, entire specimens were used for extraction, consequently the holotype is a voucher of extracted DNA ('DNA-type'). We used the Character Attribute Organization System (CAOS) to determine diagnostic nucleotides, explore the dependence on input data and data processing, and aim for maximum traceability in our diagnoses for future research. Challenges, pitfalls and necessary considerations for applied DNA taxonomy are critically evaluated. CONCLUSIONS To describe cryptic species traditional lines of evidence in taxonomy need to be modified. DNA sequence information, for example, could even serve as the backbone of a taxonomic description. The present contribution demonstrates that few adaptations are needed to integrate into traditional taxonomy novel diagnoses based on molecular data. The taxonomic community is encouraged to join the discussion and develop a quality standard for molecular taxonomy, ideally in the form of an automated final step in molecular species delineation procedures.
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Affiliation(s)
- Katharina M Jörger
- Mollusca Section, SNSB-Bavarian State Collection of Zoology, Münchhausenstr 21, 81247 München, Germany
- Department Biology II, Ludwig-Maximilians-University, Großhaderner Str. 2, 82152 Planegg-Martinsried, Germany
| | - Michael Schrödl
- Mollusca Section, SNSB-Bavarian State Collection of Zoology, Münchhausenstr 21, 81247 München, Germany
- Department Biology II, Ludwig-Maximilians-University, Großhaderner Str. 2, 82152 Planegg-Martinsried, Germany
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Pfeiler E, Richmond MP, Riesgo-Escovar JR, Tellez-Garcia AA, Johnson S, Markow TA. Genetic differentiation, speciation, and phylogeography of cactus flies (Diptera: Neriidae:Odontoloxozus) from Mexico and south-western USA. Biol J Linn Soc Lond 2013. [DOI: 10.1111/bij.12133] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Edward Pfeiler
- Unidad Guaymas; Centro de Investigación en Alimentación y Desarrollo, A.C.; Apartado Postal 284; Guaymas; Sonora; CP 85480; México
| | | | - Juan R. Riesgo-Escovar
- Departamento de Neurobiología del Desarrollo y Neurofisiología; Instituto de Neurobiología; Universidad Nacional Autónoma de México; Querétaro; C.P. 76230; México
| | - Aldo A. Tellez-Garcia
- Departamento de Neurobiología del Desarrollo y Neurofisiología; Instituto de Neurobiología; Universidad Nacional Autónoma de México; Querétaro; C.P. 76230; México
| | - Sarah Johnson
- Division of Biological Sciences; University of California; San Diego; La Jolla; CA; 92093; USA
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Bergmann T, Rach J, Damm S, DeSalle R, Schierwater B, Hadrys H. The potential of distance-based thresholds and character-based DNA barcoding for defining problematic taxonomic entities by CO1 and ND1. Mol Ecol Resour 2013; 13:1069-81. [DOI: 10.1111/1755-0998.12125] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 04/09/2013] [Indexed: 11/28/2022]
Affiliation(s)
- T. Bergmann
- ITZ Ecology & Evolution; TiHo Hannover; Bünteweg 17d; D-30559; Hannover; Germany
| | - J. Rach
- ITZ Ecology & Evolution; TiHo Hannover; Bünteweg 17d; D-30559; Hannover; Germany
| | - S. Damm
- ITZ Ecology & Evolution; TiHo Hannover; Bünteweg 17d; D-30559; Hannover; Germany
| | - R. DeSalle
- American Museum of Natural History; The Sackler Institute for Comparative Genomics; New York; NY; 10024; USA
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Hassel K, Segreto R, Ekrem T. Restricted variation in plant barcoding markers limits identification in closely related bryophyte species. Mol Ecol Resour 2013; 13:1047-57. [PMID: 23368628 DOI: 10.1111/1755-0998.12074] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2012] [Revised: 12/18/2012] [Accepted: 12/22/2012] [Indexed: 11/26/2022]
Abstract
Species-level identification and delimitation of bryophytes using the proposed general barcode markers for land plants has been challenging. Bryophyta (mosses) is the second most species-rich group of land plants after angiosperms, and it is thus of great importance to find useful barcoding regions also for this group of plants. We investigated how the plastid regions atpF-atpH, rbcL and trnH-psbA and the nuclear ITS2 region performed as barcode markers on closely related bryophyte taxa of selected moss (Bartramia, Distichium, Fissidens, Meesia and Syntrichia) and liverwort (Blepharostoma) genera from boreal and arctic regions. We also evaluated how sequencing success of herbarium specimens is related to length of the sequenced fragment, specimen age and taxonomic group. Sequencing success was higher for shorter fragments and younger herbarium specimens, but was lower than expected in the genera Distichium and Fissidens, indicating imperfect universality of the primers used. None of the studied DNA barcode regions showed a consistent barcode gap across the studied genera. As a single locus, the region atpF-atpH performed slightly better than rbcL and ITS2 and much better than trnH-psbA in terms of grouping conspecific sequences in monophyletic groups. This marker also gave a higher percentage of correct hits when conducting blast searches on a local database of identified sequences. Concatenated data sets of two and three markers grouped more conspecific sequences in monophyletic groups, but the improvement was not great compared with atpF-atpH alone. A discussion of recent studies testing barcode regions for bryophytes is given. We conclude that atpF-atpH, rbcL and ITS2 are to be the most promising barcode markers for mosses.
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Affiliation(s)
- Kristian Hassel
- Systematics and Evolution Group, Museum of Natural History and Archaeology, Norwegian University of Science and Technology, NO-7491, Trondheim, Norway
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37
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Robe LJ, Machado S, Bartholomei-Santos ML. The DNA barcoding and the caveats with respect to its application to some species of Palaemonidae (Crustacea, Decapoda). Zoolog Sci 2012; 29:714-24. [PMID: 23030345 DOI: 10.2108/zsj.29.714] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
DNA-barcoding has recently attracted considerable attention due to its potential utility in aiding in species identification and discovery through the use of a short standardized sequence of mitochondrial DNA. Nevertheless, despite the fact that this technology has been proven a useful tool in several animal taxa, it also demonstrated limitations that may hinder correct application. Thus, its validity needs to be empirically evaluated in each taxonomic category before forward implementation. As the use of DNA barcoding within Palaemonidae may be of special interest, given its great interspecific morphological conservatism associated with considerable intraspecific morphological variation, we analyze here the potential of this technology in distinguishing and recovering some taxonomic boundaries within this family. We asked whether two GenBank-retrieved sets of COI sequences encompassing the conventional Barcode and Jerry-Pat regions possess the desired properties of reciprocal monophyly among species, and existence of a barcoding gap between intra- and interspecific variations, after performing a careful analysis of numt (nuclear mitochondrial DNA) contamination. These analyses revealed nine non-monophyletic species, with some cases of divergent intraspecific sequences, contrasted with interspecific similarity attained in others. Moreover, we were unable to identify any barcoding gap between intraspecific and interspecific divergences within Palaemonidae, although a threshold of 0.18 substitutions per site would differentiate intraspecific and congeneric divergences in 95% of the cases for the barcoding region. A fraction of the overlap could be certainly attributed to artifacts related to poor taxonomy, but even from this perspective DNA barcoding studies may help to uncover previously disregarded taxonomic and evolutionary issues.
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Affiliation(s)
- Lizandra J Robe
- Programa de Pós-Graduação em Biodiversidade Animal, Centro de Ciências Naturais e Exatas, Universidade Federal de Santa Maria (UFSM), Av. Roraima, 1000, Santa Maria (RS), 97105-900, Brazil.
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Zou S, Li Q, Kong L. Monophyly, distance and character-based multigene barcoding reveal extraordinary cryptic diversity in Nassarius: a complex and dangerous community. PLoS One 2012; 7:e47276. [PMID: 23071774 PMCID: PMC3469534 DOI: 10.1371/journal.pone.0047276] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Accepted: 09/10/2012] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Correct identification and cryptic biodiversity revelation for marine organisms are pressing since the marine life is important in maintaining the balance of ecological system and is facing the problem of biodiversity crisis or food safety. DNA barcoding has been proved successful to provide resolution beyond the boundaries of morphological information. Nassarius, the common mudsnail, plays an important role in marine environment and has problem in food safety, but the classification of it is quite confused because of the complex morphological diversity. METHODOLOGY/PRINCIPAL FINDINGS Here we report a comprehensive barcoding analysis of 22 Nassarius species. We integrated the mitochondrial and nuclear sequences and the morphological characters to determine 13 Nassarius species studied and reveal four cryptic species and one pair synonyms. Distance, monophyly, and character-based barcoding methods were employed. CONCLUSIONS/SIGNIFICANCE Such successful identification and unexpected cryptic discovery is significant for Nassarius in food safety and species conversation and remind us to pay more attention to the hidden cryptic biodiversity ignored in marine life. Distance, monophyly, and character-based barcoding methods are all very helpful in identification but the character-based method shows some advantages.
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Affiliation(s)
- Shanmei Zou
- Key Laboratory of Mariculture Ministry of Education, Ocean University of China, Qingdao, China
| | - Qi Li
- Key Laboratory of Mariculture Ministry of Education, Ocean University of China, Qingdao, China
| | - Lingfeng Kong
- Key Laboratory of Mariculture Ministry of Education, Ocean University of China, Qingdao, China
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DUPUIS JULIANR, ROE AMANDAD, SPERLING FELIXAH. Multi-locus species delimitation in closely related animals and fungi: one marker is not enough. Mol Ecol 2012; 21:4422-36. [DOI: 10.1111/j.1365-294x.2012.05642.x] [Citation(s) in RCA: 232] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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40
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DNA Barcoding and Molecular Phylogeny of Drosophila lini and Its Sibling Species. INTERNATIONAL JOURNAL OF EVOLUTIONARY BIOLOGY 2012; 2012:329434. [PMID: 22518333 PMCID: PMC3296172 DOI: 10.1155/2012/329434] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Accepted: 10/27/2011] [Indexed: 11/23/2022]
Abstract
Drosophila lini and its two sibling species, D. ohnishii and D. ogumai, are hardly distinguishable from one another in morphology. These species are more or less reproductively isolated. The mitochondrial ND2 and COI-COII and the nuclear ITS1-ITS2 regions were sequenced to seek for the possibility of DNA barcoding and to reconstruct the phylogeny of them. The character-based approach for DNA barcoding detected some diagnostic nucleotides only for monophyletic D. ogumai, but no informative sites for the other two very closely species, D. lini and D. ohnishii, of which strains intermingled in the molecular phylogenetic trees. Thus, this study provides another case of limited applicability of DNA barcoding in species delineation, as in other cases of related Drosophila species. The molecular phylogenetic tree inferred from the concatenated sequences strongly supported the monophyly of the cluster of the three species, that is, the lini clade. We propose some hypotheses of evolutionary events in this clade.
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41
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van Velzen R, Weitschek E, Felici G, Bakker FT. DNA barcoding of recently diverged species: relative performance of matching methods. PLoS One 2012; 7:e30490. [PMID: 22272356 PMCID: PMC3260286 DOI: 10.1371/journal.pone.0030490] [Citation(s) in RCA: 124] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Accepted: 12/22/2011] [Indexed: 12/23/2022] Open
Abstract
Recently diverged species are challenging for identification, yet they are frequently of special interest scientifically as well as from a regulatory perspective. DNA barcoding has proven instrumental in species identification, especially in insects and vertebrates, but for the identification of recently diverged species it has been reported to be problematic in some cases. Problems are mostly due to incomplete lineage sorting or simply lack of a 'barcode gap' and probably related to large effective population size and/or low mutation rate. Our objective was to compare six methods in their ability to correctly identify recently diverged species with DNA barcodes: neighbor joining and parsimony (both tree-based), nearest neighbor and BLAST (similarity-based), and the diagnostic methods DNA-BAR, and BLOG. We analyzed simulated data assuming three different effective population sizes as well as three selected empirical data sets from published studies. Results show, as expected, that success rates are significantly lower for recently diverged species (∼75%) than for older species (∼97%) (P<0.00001). Similarity-based and diagnostic methods significantly outperform tree-based methods, when applied to simulated DNA barcode data (P<0.00001). The diagnostic method BLOG had highest correct query identification rate based on simulated (86.2%) as well as empirical data (93.1%), indicating that it is a consistently better method overall. Another advantage of BLOG is that it offers species-level information that can be used outside the realm of DNA barcoding, for instance in species description or molecular detection assays. Even though we can confirm that identification success based on DNA barcoding is generally high in our data, recently diverged species remain difficult to identify. Nevertheless, our results contribute to improved solutions for their accurate identification.
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Affiliation(s)
- Robin van Velzen
- Biosystematics Group, Wageningen University, Wageningen, The Netherlands.
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Delsinne T, Sonet G, Nagy ZT, Wauters N, Jacquemin J, Leponce M. High species turnover of the ant genus Solenopsis (Hymenoptera : Formicidae) along an altitudinal gradient in the Ecuadorian Andes, indicated by a combined DNA sequencing and morphological approach. INVERTEBR SYST 2012. [DOI: 10.1071/is12030] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Solenopsis is a widespread ant genus and the identification of its species is notoriously difficult. Hence, investigation of their distribution along elevational gradients is challenging. Our aims were (1) to test the complementarity of the morphological and DNA barcoding approaches for Solenopsis species identification, and (2) to assess species diversity and distribution along an altitudinal gradient in the Ecuadorian Andes. Ants were collected in five localities between 1000 and 3000 m above sea level. In total, 24 morphospecies were identified along the gradient and 14 of them were barcoded. Seven morphospecies were confirmed by the molecular approach. Three others, occurring sympatrically and possessing clear diagnostic characters, showed low genetic divergence. Representatives of a further four morphospecies were split into nine clusters by COI and nuclear wingless genetic markers, suggesting the existence of cryptic species. Examination of gynes revealed potential diagnostic characters for morphological discrimination. Solenopsis species were found up to an altitudinal record of 3000 m. Most morphospecies (20 of 24) were found at a single elevation. Our results suggest a high species turnover along the gradient, and point to the use of morphological and DNA barcoding approaches as necessary for differentiating among Solenopsis species.
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Zou S, Li Q, Kong L, Yu H, Zheng X. Comparing the usefulness of distance, monophyly and character-based DNA barcoding methods in species identification: a case study of neogastropoda. PLoS One 2011; 6:e26619. [PMID: 22039517 PMCID: PMC3200347 DOI: 10.1371/journal.pone.0026619] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2011] [Accepted: 09/29/2011] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND DNA barcoding has recently been proposed as a promising tool for the rapid species identification in a wide range of animal taxa. Two broad methods (distance and monophyly-based methods) have been used. One method is based on degree of DNA sequence variation within and between species while another method requires the recovery of species as discrete clades (monophyly) on a phylogenetic tree. Nevertheless, some issues complicate the use of both methods. A recently applied new technique, the character-based DNA barcode method, however, characterizes species through a unique combination of diagnostic characters. METHODOLOGY/PRINCIPAL FINDINGS Here we analyzed 108 COI and 102 16S rDNA sequences of 40 species of Neogastropoda from a wide phylogenetic range to assess the performance of distance, monophyly and character-based methods of DNA barcoding. The distance-based method for both COI and 16S rDNA genes performed poorly in terms of species identification. Obvious overlap between intraspecific and interspecific divergences for both genes was found. The "10× rule" threshold resulted in lumping about half of distinct species for both genes. The neighbour-joining phylogenetic tree of COI could distinguish all species studied. However, the 16S rDNA tree could not distinguish some closely related species. In contrast, the character-based barcode method for both genes successfully identified 100% of the neogastropod species included, and performed well in discriminating neogastropod genera. CONCLUSIONS/SIGNIFICANCE This present study demonstrates the effectiveness of the character-based barcoding method for species identification in different taxonomic levels, especially for discriminating the closely related species. While distance and monophyly-based methods commonly use COI as the ideal gene for barcoding, the character-based approach can perform well for species identification using relatively conserved gene markers (e.g., 16S rDNA in this study). Nevertheless, distance and monophyly-based methods, especially the monophyly-based method, can still be used to flag species.
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Affiliation(s)
- Shanmei Zou
- Key Laboratory of Mariculture Ministry of Education Ocean University of China, Qingdao, China
| | - Qi Li
- Key Laboratory of Mariculture Ministry of Education Ocean University of China, Qingdao, China
| | - Lingfeng Kong
- Key Laboratory of Mariculture Ministry of Education Ocean University of China, Qingdao, China
| | - Hong Yu
- Key Laboratory of Mariculture Ministry of Education Ocean University of China, Qingdao, China
| | - Xiaodong Zheng
- Key Laboratory of Mariculture Ministry of Education Ocean University of China, Qingdao, China
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Reid BN, LE M, McCord WP, Iverson JB, Georges A, Bergmann T, Amato G, Desalle R, Naro-Maciel E. Comparing and combining distance-based and character-based approaches for barcoding turtles. Mol Ecol Resour 2011; 11:956-67. [PMID: 21635698 DOI: 10.1111/j.1755-0998.2011.03032.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Molecular barcoding can serve as a powerful tool in wildlife forensics and may prove to be a vital aid in conserving organisms that are threatened by illegal wildlife trade, such as turtles (Order Testudines). We produced cytochrome oxidase subunit one (COI) sequences (650 bp) for 174 turtle species and combined these with publicly available sequences for 50 species to produce a data set representative of the breadth of the order. Variability within the barcode region was assessed, and the utility of both distance-based and character-based methods for species identification was evaluated. For species in which genetic material from more than one individual was available (n = 69), intraspecific divergences were 1.3% on average, although divergences greater than the customary 2% barcode threshold occurred within 15 species. High intraspecific divergences could indicate species with a high degree of internal genetic structure or possibly even cryptic species, although introgression is also probable in some of these taxa. Divergences between species of the same genus were 6.4% on average; however, 49 species were <2% divergent from congeners. Low levels of interspecific divergence could be caused by recent evolutionary radiations coupled with the low rates of mtDNA evolution previously observed in turtles. Complementing distance-based barcoding with character-based methods for identifying diagnostic sets of nucleotides provided better resolution in several cases where distance-based methods failed to distinguish species. An online identification engine was created to provide character-based identifications. This study constitutes the first comprehensive barcoding effort for this seriously threatened order.
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Affiliation(s)
- B N Reid
- Department of Forest and Wildlife Ecology, University of Wisconsin, 1630 Linden Drive, Madison, WI 53706, USA.
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Evaluating DNA barcoding criteria using African duiker antelope (Cephalophinae) as a test case. CONSERV GENET 2011. [DOI: 10.1007/s10592-011-0220-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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The origin of the Tibetan Mastiff and species identification of Canis based on mitochondrial cytochrome c oxidase subunit I (COI) gene and COI barcoding. Animal 2011; 5:1868-73. [DOI: 10.1017/s1751731111001042] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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