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Šedo O, Roblíčková A, Ježek F, Gintar P, Kameník J, Zdráhal Z. Discriminatory power of MALDI-TOF MS protein profiling analysis of pork meat and meat products. Food Chem 2024; 449:139155. [PMID: 38608601 DOI: 10.1016/j.foodchem.2024.139155] [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: 12/18/2023] [Revised: 03/08/2024] [Accepted: 03/25/2024] [Indexed: 04/14/2024]
Abstract
Forty different sample preparation methods were tested to obtain the most informative MALDI-TOF MS protein profiles of pork meat. Extraction by 25% formic acid with the assistance of zirconia-silica beads followed by defatting by methanol:chloroform mixture (1:1, v/v) and deposition by using the layer-by-layer method was determined as the optimum sample preparation protocol. The discriminatory power of the method was then examined on samples of pork meat and meat products. The method was able to discriminate between selected salami based on the production method and brand and was able to monitor the ripening process in salami. However, it was not able to differentiate between different brands of pork ham or closely located parts of pork meat. In the latter case, a more comprehensive analysis using LC-MS/MS was used to assess the differences in protein abundance and their relation to the outputs of MALDI - TOF MS profiling.
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Affiliation(s)
- Ondrej Šedo
- Masaryk University, Central European Institute of Technology, Kamenice 5, 625 00 Brno, Czech Republic.
| | - Alena Roblíčková
- Masaryk University, Central European Institute of Technology, Kamenice 5, 625 00 Brno, Czech Republic
| | - František Ježek
- University of Veterinary Sciences Brno, Faculty of Veterinary Hygiene and Ecology, Palackého tř. 1946/1, 612 42 Brno, Czech Republic.
| | - Petr Gintar
- Masaryk University, Central European Institute of Technology, Kamenice 5, 625 00 Brno, Czech Republic; Masaryk University, Faculty of Science, National Centre for Biomolecular Research, Kamenice 5, 625 00 Brno, Czech Republic.
| | - Josef Kameník
- University of Veterinary Sciences Brno, Faculty of Veterinary Hygiene and Ecology, Palackého tř. 1946/1, 612 42 Brno, Czech Republic.
| | - Zbyněk Zdráhal
- Masaryk University, Central European Institute of Technology, Kamenice 5, 625 00 Brno, Czech Republic; Masaryk University, Faculty of Science, National Centre for Biomolecular Research, Kamenice 5, 625 00 Brno, Czech Republic.
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2
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Míč R, Řehulková E, Šimková A, Razanabolana JR, Seifertová M. New species of Dermoergasilus Ho & Do, 1982 (Copepoda: Cyclopoida: Ergasilidae) parasitizing endemic cichlid Paretroplus polyactis (Bleeker) in Madagascar. Parasitology 2024; 151:319-336. [PMID: 38239098 PMCID: PMC11007281 DOI: 10.1017/s0031182024000088] [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: 10/20/2023] [Revised: 01/09/2024] [Accepted: 01/09/2024] [Indexed: 02/13/2024]
Abstract
Dermoergasilus madagascarensis n. sp. is described from the gills of Paretroplus polyactis, an endemic cichlid fish in Madagascar, using a combined morphological (light microscopy and SEM) and molecular approach (partial 18S rDNA, 28S rDNA, and COI sequences). The new species is characterized mainly by possessing: (i) roughly pentagonal cephalosome; (ii) antennal endopodal segments covered with slightly inflated membrane; (iii) maxillule bearing 2 equally long outer setae and a minute inner seta; (iv) interpodal sternites of swimming legs ornamented with 3–4 rows of spinules; (v) genital segment and first abdominal somite both barrel-shaped; and (vi) a caudal ramus projecting into a digitiform process with inconspicuous terminal seta and bearing 3 terminal setae. The obtained DNA sequences of Malagasy species represent the first molecular data for species of Dermoergasilus. The 28S rDNA phylogeny showed the affiliation of D. madagascarensis n. sp. to Ergasilidae and its sister relationship with cosmopolitan Ergasilus sieboldi von Nordmann, 1832. The first checklist for all species of Dermoergasilus is provided.
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Affiliation(s)
- Robert Míč
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
| | - Eva Řehulková
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
| | - Andrea Šimková
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
| | - Jeanne Rasamy Razanabolana
- Department of Animal Biology, Faculty of Science, University of Antananarivo, BP 906 Antananarivo 101, Madagascar
| | - Mária Seifertová
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
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3
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Rossel S, Peters J, Charzinski N, Eichsteller A, Laakmann S, Neumann H, Martínez Arbizu P. A universal tool for marine metazoan species identification: towards best practices in proteomic fingerprinting. Sci Rep 2024; 14:1280. [PMID: 38218969 PMCID: PMC10787734 DOI: 10.1038/s41598-024-51235-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 01/02/2024] [Indexed: 01/15/2024] Open
Abstract
Proteomic fingerprinting using MALDI-TOF mass spectrometry is a well-established tool for identifying microorganisms and has shown promising results for identification of animal species, particularly disease vectors and marine organisms. And thus can be a vital tool for biodiversity assessments in ecological studies. However, few studies have tested species identification across different orders and classes. In this study, we collected data from 1246 specimens and 198 species to test species identification in a diverse dataset. We also evaluated different specimen preparation and data processing approaches for machine learning and developed a workflow to optimize classification using random forest. Our results showed high success rates of over 90%, but we also found that the size of the reference library affects classification error. Additionally, we demonstrated the ability of the method to differentiate marine cryptic-species complexes and to distinguish sexes within species.
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Affiliation(s)
- Sven Rossel
- Senckenberg am Meer, German Centre for Marine Biodiversity Research (DZMB), 26382, Wilhelmshaven, Germany.
| | - Janna Peters
- German Centre for Marine Biodiversity Research (DZMB), Senckenberg am Meer, 20146, Hamburg, Germany
| | - Nele Charzinski
- Marine Biodiversity Research, Institute of Biology and Environmental Sciences, Carl von Ossietzky University Oldenburg, 26129, Oldenburg, Germany
| | - Angelina Eichsteller
- Senckenberg am Meer, German Centre for Marine Biodiversity Research (DZMB), 26382, Wilhelmshaven, Germany
- Marine Biodiversity Research, Institute of Biology and Environmental Sciences, Carl von Ossietzky University Oldenburg, 26129, Oldenburg, Germany
| | - Silke Laakmann
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), 26129, Oldenburg, Germany
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, 27570, Bremerhaven, Germany
| | - Hermann Neumann
- Institute for Sea Fisheries, Thuenen Institute, 27572, Bremerhaven, Germany
| | - Pedro Martínez Arbizu
- Senckenberg am Meer, German Centre for Marine Biodiversity Research (DZMB), 26382, Wilhelmshaven, Germany
- Marine Biodiversity Research, Institute of Biology and Environmental Sciences, Carl von Ossietzky University Oldenburg, 26129, Oldenburg, Germany
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4
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Chien HJ, Zheng YF, Wang WC, Kuo CY, Hsu YM, Lai CC. Determination of adulteration, geographical origins, and species of food by mass spectrometry. MASS SPECTROMETRY REVIEWS 2023; 42:2273-2323. [PMID: 35652168 DOI: 10.1002/mas.21780] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 04/07/2022] [Accepted: 04/12/2022] [Indexed: 06/15/2023]
Abstract
Food adulteration, mislabeling, and fraud, are rising global issues. Therefore, a number of precise and reliable analytical instruments and approaches have been proposed to ensure the authenticity and accurate labeling of food and food products by confirming that the constituents of foodstuffs are of the kind and quality claimed by the seller and manufacturer. Traditional techniques (e.g., genomics-based methods) are still in use; however, emerging approaches like mass spectrometry (MS)-based technologies are being actively developed to supplement or supersede current methods for authentication of a variety of food commodities and products. This review provides a critical assessment of recent advances in food authentication, including MS-based metabolomics, proteomics and other approaches.
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Affiliation(s)
- Han-Ju Chien
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan
| | - Yi-Feng Zheng
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan
| | - Wei-Chen Wang
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan
| | - Cheng-Yu Kuo
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan
| | - Yu-Ming Hsu
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan
| | - Chien-Chen Lai
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan
- Graduate Institute of Chinese Medical Science, China Medical University, Taichung, Taiwan
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
- Ph.D. Program in Translational Medicine, National Chung Hsing University, Taichung, Taiwan
- Rong Hsing Research Center For Translational Medicine, National Chung Hsing University, Taichung, Taiwan
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5
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Two New Phyllopodopsyllus Species (Harpacticoida, Tetragonicipitidae) from Korea. DIVERSITY 2023. [DOI: 10.3390/d15010097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Three species of the genus Phyllopodopsyllus T. Scott, 1906 (Copepoda: Harpacticoida: Tetragonicipitidae) were reported from the intertidal sand of Jeju Island and Busan in Korea, Phyllopdopsyllus kitazimai Karanovic, 2017, Phyllopodopsyllus saywakimi sp. nov. and Phyllopodopsyllus similis sp. nov. The latter two were described here. Phyllopodopsyllus saywakimi sp. nov. collected from only Udo, Jeju is similar to a Pacific species from Costa Rica, Phyllopodopsyllus ancylus Mielke, 1992. However, P. saywakimi sp. nov. differs from the Costa Rica species in the body size, the number of armatures on the antenna, the length ratio of endo- and exopod of the mandible, and the chaetotaxy of the fifth female pereiopod and the sixth male pereiopod. The second new species, P. similis sp. nov., found in Busan and several localities of Jeju, significantly resembles the species complex related to Phyllopodopsyllus aegypticus Nicholls, 1944, which is widely distributed in the Indian, Pacific, and Atlantic oceans. P. similis sp. nov. can be distinguished from the P. aegypticus complex by the body size, the shape of the rostrum, the type of armatures, the length ratio of rami and armatures, and the chaetotaxy of the female P5. In addition to the species descriptions, partial fragments of small and large subunit ribosomal RNA genes, cytochrome b, and cytochrome c oxidase subunit I were provided. Using molecular markers, a phylogenetic analysis was also performed to estimate the relationships among the three Korean species of Phyllopodopsyllus for the first time.
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Alshehri E, Alotaibi M, Al-Quraishy S, Abdel-Gaber R. Morphological and mitochondrial approaches of Hatschekia sargi (Copepoda: Hatschekiidae) as a parasite of Epinephelus chlorostigma. Mol Biol Rep 2023; 50:1-9. [PMID: 36201103 DOI: 10.1007/s11033-022-07901-4] [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: 07/15/2022] [Revised: 08/13/2022] [Accepted: 08/22/2022] [Indexed: 02/01/2023]
Abstract
Little information is available until now about the copepods infecting different fish species. Therefore, this study aimed to provide light on siphonostomatoids infecting Epinephelus chlorostigma. Twenty fish specimens were taken from the Red Sea coast (Jeddah, Saudi Arabia), and ectoparasitic copepods were investigated. Light microscopy and molecular tools were used to examine copepods isolated from fish. Parasitological indexes were calculated and showed that 60% of the examined fish were infected with a mean intensity of 12 parasite/fish. Morphological examination revealed that this copepod species is characterized by all unique features of the genus Hatschekia with special reference to Hatschekia sargi. The taxonomic position of the recovered species in the Hatschekiidae family within Siphonostomatoida was confirmed using phylogenetic analysis based on partial mitochondrial cytochrome c oxidase subunit I (mt COI) gene sequences. The mt COI gene query revealed that the recovered Hatschekia species is closely related to Hatschekia maculatus (gb| JQ664005.1). This study discovers a new host for Hatschekia species isolated from Saudi Arabia and conducts the first genomic investigation of the mt COI gene.
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Affiliation(s)
- Eman Alshehri
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Monirah Alotaibi
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Saleh Al-Quraishy
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Rewaida Abdel-Gaber
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia.
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Pu K, Qiu J, Li J, Huang W, Lai X, Liu C, Lin Y, Ng KM. MALDI-TOF MS Protein Profiling Combined with Multivariate Analysis for Identification and Quantitation of Beef Adulteration. FOOD ANAL METHOD 2022. [DOI: 10.1007/s12161-022-02403-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Geburzi JC, Heuer N, Homberger L, Kabus J, Moesges Z, Ovenbeck K, Brandis D, Ewers C. An environmental gradient dominates ecological and genetic differentiation of marine invertebrates between the North and Baltic Sea. Ecol Evol 2022; 12:e8868. [PMID: 35600684 PMCID: PMC9121054 DOI: 10.1002/ece3.8868] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 04/07/2022] [Accepted: 04/08/2022] [Indexed: 12/14/2022] Open
Abstract
Environmental gradients have emerged as important barriers to structuring populations and species distributions. We set out to test whether the strong salinity gradient from the marine North Sea to the brackish Baltic Sea in northern Europe represents an ecological and genetic break, and to identify life history traits that correlate with the strength of this break. We accumulated mitochondrial cytochrome oxidase subunit 1 sequence data, and data on the distribution, salinity tolerance, and life history for 28 species belonging to the Cnidaria, Crustacea, Echinodermata, Mollusca, Polychaeta, and Gastrotricha. We included seven non‐native species covering a broad range of times since introduction, in order to gain insight into the pace of adaptation and differentiation. We calculated measures of genetic diversity and differentiation across the environmental gradient, coalescent times, and migration rates between North and Baltic Sea populations, and analyzed correlations between genetic and life history data. The majority of investigated species is either genetically differentiated and/or adapted to the lower salinity conditions of the Baltic Sea. Species exhibiting population structure have a range of patterns of genetic diversity in comparison with the North Sea, from lower in the Baltic Sea to higher in the Baltic Sea, or equally diverse in North and Baltic Sea. Two of the non‐native species showed signs of genetic differentiation, their times since introduction to the Baltic Sea being about 80 and >700 years, respectively. Our results indicate that the transition from North Sea to Baltic Sea represents a genetic and ecological break: The diversity of genetic patterns points toward independent trajectories in the Baltic compared with the North Sea, and ecological differences with regard to salinity tolerance are common. The North Sea–Baltic Sea region provides a unique setting to study evolutionary adaptation during colonization processes at different stages by jointly considering native and non‐native species.
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Affiliation(s)
- Jonas C. Geburzi
- Mangrove Ecology Leibniz Centre for Tropical Marine Research (ZMT) Bremen Germany
- Department of Organismic and Evolutionary Biology Museum of Comparative Zoology Harvard University Cambridge Massachusetts USA
- Zoological Museum Kiel University Kiel Germany
| | - Nele Heuer
- Zoological Museum Kiel University Kiel Germany
| | | | - Jana Kabus
- Zoological Museum Kiel University Kiel Germany
- Department Aquatic Ecotoxicology Institute of Ecology Diversity and Evolution Goethe University Frankfurt am Main Frankfurt am Main Germany
| | - Zoe Moesges
- Zoological Museum Kiel University Kiel Germany
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9
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Paulus E, Brix S, Siebert A, Martínez Arbizu P, Rossel S, Peters J, Svavarsson J, Schwentner M. Recent speciation and hybridization in Icelandic deep-sea isopods: An integrative approach using genomics and proteomics. Mol Ecol 2021; 31:313-330. [PMID: 34676606 DOI: 10.1111/mec.16234] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 10/06/2021] [Accepted: 10/11/2021] [Indexed: 02/06/2023]
Abstract
The crustacean marine isopod species Haploniscus bicuspis (Sars, 1877) shows circum-Icelandic distribution in a wide range of environmental conditions and along well-known geographic barriers, such as the Greenland-Iceland-Faroe (GIF) Ridge. We wanted to explore population genetics, phylogeography and cryptic speciation as well as investigate whether previously described, but unaccepted subspecies have any merit. Using the same set of specimens, we combined mitochondrial COI sequences, thousands of nuclear loci (ddRAD), and proteomic profiles, plus selected morphological characters using confocal laser scanning microscopy (CLSM). Five divergent genetic lineages were identified by COI and ddRAD, two south and three north of the GIF Ridge. Assignment of populations to the three northern lineages varied and detailed analyses revealed hybridization and gene flow between them, suggesting a single northern species with a complex phylogeographic history. No apparent hybridization was observed among lineages south of the GIF Ridge, inferring the existence of two more species. Differences in proteomic profiles between the three putative species were minimal, implying an ongoing or recent speciation process. Population differentiation was high, even among closely associated populations, and higher in mitochondrial COI than nuclear ddRAD loci. Gene flow is apparently male-biased, leading to hybrid zones and instances of complete exchange of the local nuclear genome through immigrating males. This study did not confirm the existence of subspecies defined by male characters, which probably instead refer to different male developmental stages.
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Affiliation(s)
- Eva Paulus
- University of Groningen, Groningen, The Netherlands.,Senckenberg am Meer, German Centre for Marine Biodiversity Research (DZMB), Hamburg, Germany
| | - Saskia Brix
- Senckenberg am Meer, German Centre for Marine Biodiversity Research (DZMB), Hamburg, Germany
| | - Annabelle Siebert
- Senckenberg am Meer, German Centre for Marine Biodiversity Research (DZMB), Hamburg, Germany.,Center of Natural History (CeNak), Universität Hamburg, Hamburg, Germany
| | - Pedro Martínez Arbizu
- Senckenberg am Meer, German Centre for Marine Biodiversity Research (DZMB), Wilhelmshaven, Germany
| | - Sven Rossel
- Senckenberg am Meer, German Centre for Marine Biodiversity Research (DZMB), Wilhelmshaven, Germany
| | - Janna Peters
- Senckenberg am Meer, German Centre for Marine Biodiversity Research (DZMB), Wilhelmshaven, Germany
| | - Jörundur Svavarsson
- Department of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
| | - Martin Schwentner
- Center of Natural History (CeNak), Universität Hamburg, Hamburg, Germany.,Naturhistorisches Museum Wien, Vienna, Austria
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10
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Novel attempt at discrimination of a bullet-shaped siphonophore (Family Diphyidae) using matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-ToF MS). Sci Rep 2021; 11:19077. [PMID: 34561535 PMCID: PMC8463557 DOI: 10.1038/s41598-021-98724-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 09/14/2021] [Indexed: 02/08/2023] Open
Abstract
One major difficulty in identifying the gelatinous bodied bullet-shaped Siphonophore, Diphyids, is that their shape is deformed following ethanol fixation. Ethanol often is preferred over other fixatives, since samples fixed in ethanol can be used for molecular studies that can supplement morphological findings. To overcome this problem, we obtained protein mass spectra of ten species of Diphyidae found in the waters of the Kuroshio Current (Northwest Pacific and South Coast of South Korea) to test whether MALDI-ToF MS could be used as a methodology for species identification. In addition, a number of morphological characteristics that can be used with ethanol-treated samples was summarized. Concatenated phylogenetic analysis was also performed to determine the phylogenetic relationship by obtaining partial sequences of four genes (mtCOI, 16S rRNA, 18S rRNA, and ITS regions). Based on our integrative analysis, MALDI-ToF MS was evaluated as a potentially fast, inexpensive, and accurate tool for species identification along with conventional morphological and DNA barcoding for Diphyidae.
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Renz J, Markhaseva EL, Laakmann S, Rossel S, Martinez Arbizu P, Peters J. Proteomic fingerprinting facilitates biodiversity assessments in understudied ecosystems: A case study on integrated taxonomy of deep sea copepods. Mol Ecol Resour 2021; 21:1936-1951. [PMID: 33900025 DOI: 10.1111/1755-0998.13405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 03/30/2021] [Accepted: 04/13/2021] [Indexed: 11/26/2022]
Abstract
Accurate and reliable biodiversity estimates of marine zooplankton are a prerequisite to understand how changes in diversity can affect whole ecosystems. Species identification in the deep sea is significantly impeded by high numbers of new species and decreasing numbers of taxonomic experts, hampering any assessment of biodiversity. We used in parallel morphological, genetic, and proteomic characteristics of specimens of calanoid copepods from the abyssal South Atlantic to test if proteomic fingerprinting can accelerate estimating biodiversity. We cross-validated the respective molecular discrimination methods with morphological identifications to establish COI and proteomic reference libraries, as they are a pre-requisite to assign taxonomic information to the identified molecular species clusters. Due to the high number of new species only 37% of the individuals could be assigned to species or genus level morphologically. COI sequencing was successful for 70% of the specimens analysed, while proteomic fingerprinting was successful for all specimens examined. Predicted species richness based on morphological and molecular methods was 42 morphospecies, 56 molecular operational taxonomic units (MOTUs) and 79 proteomic operational taxonomic units (POTUs), respectively. Species diversity was predicted based on proteomic profiles using hierarchical cluster analysis followed by application of the variance ratio criterion for identification of species clusters. It was comparable to species diversity calculated based on COI sequence distances. Less than 7% of specimens were misidentified by proteomic profiles when compared with COI derived MOTUs, indicating that unsupervised machine learning using solely proteomic data could be used for quickly assessing species diversity.
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Affiliation(s)
- Jasmin Renz
- German Centre for Marine Biodiversity Research (DZMB), Senckenberg Research Institute, Hamburg, Germany
| | - Elena L Markhaseva
- Laboratory of Marine Research, Zoological Institute of the Russian Academy of Sciences, St. Petersburg, Russia
| | - Silke Laakmann
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Oldenburg, Germany.,Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany
| | - Sven Rossel
- German Centre for Marine Biodiversity Research (DZMB), Senckenberg Research Institute, Wilhelmshaven, Germany.,Marine Biodiversity Research, Institute for Biology and Environmental Sciences, Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Pedro Martinez Arbizu
- German Centre for Marine Biodiversity Research (DZMB), Senckenberg Research Institute, Wilhelmshaven, Germany.,Marine Biodiversity Research, Institute for Biology and Environmental Sciences, Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Janna Peters
- German Centre for Marine Biodiversity Research (DZMB), Senckenberg Research Institute, Hamburg, Germany
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12
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Mercado-Salas NF, Khodami S, Martínez Arbizu P. Copepods and ostracods associated with bromeliads in the Yucatán Peninsula, Mexico. PLoS One 2021; 16:e0248863. [PMID: 33735283 PMCID: PMC7971893 DOI: 10.1371/journal.pone.0248863] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 03/05/2021] [Indexed: 11/18/2022] Open
Abstract
A substantial fraction of the freshwater available in the Neotropical forests is enclosed within the rosettes of bromeliads that form small aquatic islands within a terrestrial landscape. These aquatic oases provide shelter, water, nutrients and resting of aggregation sites for several aquatic organisms, among them crustaceans. However, in comparison with the multitude of studies on open aquatic systems, our knowledge on crustaceans inhabiting semi-terrestrial habitats and phytotelmata is limited and their presence in such environments is poorly understood. The present study was carried out in two natural protected areas of the Yucatán Peninsula aiming to understand the diversity and dispersal strategies of crustaceans living in bromeliads. Sediment and water contained in four species of bromeliads have been collected in order to understand the diversity and dispersal strategies of crustaceans living in such habitats. From a total of 238 bromeliads surveyed, 55% were colonized by crustaceans. Sixteen copepod, three ostracod and one branchiopod species were recorded during this study, however only seven species are considered as true bromeliad inhabitants. Different degrees of association between crustaceans and bromeliad species were assessed with an indicator species analysis, where significant associations were found for all crustaceans. We found significant differences between bromeliad species and reserves and their associated fauna. In order to analyze the genetic diversity of this fauna, we sequenced several individuals of each species with two genetic markers (18S rRNA and COI mtDNA). Bayesian analyses and the Generalized Mixed Yule Coalescent method (GMYC), delimited 7 well supported species. A comparison of the dispersal strategies used by different species, including passive dispersal, phoretic behavior and active dispersal, is included. This study stresses the need of studying meiofauna of phytotelms, which could be used as an indicator of local diversity in Neotropical forests.
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Affiliation(s)
- Nancy F. Mercado-Salas
- Senckenberg am Meer Wilhelmshaven, German Centre for Marine Biodiversity Research, Südstrand, Wilhelmshaven, Germany
| | - Sahar Khodami
- Senckenberg am Meer Wilhelmshaven, German Centre for Marine Biodiversity Research, Südstrand, Wilhelmshaven, Germany
| | - Pedro Martínez Arbizu
- Senckenberg am Meer Wilhelmshaven, German Centre for Marine Biodiversity Research, Südstrand, Wilhelmshaven, Germany
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13
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Kim J, Nam E, Lee W. Quinquelaophonte enormis sp. nov., a new interstitial copepod (Harpacticoida: Laophontidae) from Korea. PeerJ 2020; 8:e10007. [PMID: 33024639 PMCID: PMC7518157 DOI: 10.7717/peerj.10007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 08/31/2020] [Indexed: 11/20/2022] Open
Abstract
We collected an undescribed laophontid copepod from a coarse sand habitat on the east coast of Korea and named it Quinquelaophonte enormissp. nov. We compared the detailed morphological characteristics of the new species with those of congeneric species. Among them, the new species shows a superficial resemblance to the Californian species Quinquelaophonte longifurcataLang, 1965. However, the two species are easily distinguishable by the setation of the syncoxa on the maxilliped and the fourth swimming leg. The new species has the variable setation on the second to fourth swimming legs. The variations appear among individuals or between the left and right rami of a pair of legs in a single specimen. Although complex chaetotaxical polymorphism occur in this new species, we used myCOI and Cytb to confirm that the new species is not a species complex. Also, partial sequences of 18S and 28S ribosomal RNA genes were used to analyze the position of the new species within the family Laophontidae. The new speciesis the fourteenth Quinquelaophonte species in the world and the second species in Korea.
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Affiliation(s)
- Jaehyun Kim
- Department of Life Science, Hanyang University, Seoul, South Korea
| | - Eunjung Nam
- Animal Resources Division, National Institute of Biological Resources, Incheon, South Korea
| | - Wonchoel Lee
- Department of Life Science, Hanyang University, Seoul, South Korea
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Wilke T, Renz J, Hauffe T, Delicado D, Peters J. Proteomic Fingerprinting Discriminates Cryptic Gastropod Species. MALACOLOGIA 2020. [DOI: 10.4002/040.063.0113] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Thomas Wilke
- Department of Animal Ecology and Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 26 (IFZ), D-35392 Giessen, Germany
| | - Jasmin Renz
- Senckenberg Research Institute, German Center for Marine Biodiversity Research (DZMB), Südstrand 44, D-26382 Wilhelmshaven, Germany
| | - Torsten Hauffe
- Department of Animal Ecology and Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 26 (IFZ), D-35392 Giessen, Germany
| | - Diana Delicado
- Department of Animal Ecology and Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 26 (IFZ), D-35392 Giessen, Germany
| | - Janna Peters
- Senckenberg Research Institute, German Center for Marine Biodiversity Research (DZMB), Südstrand 44, D-26382 Wilhelmshaven, Germany
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15
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Guo Q, Li D, Zhai Y, Gu Z. CCPRD: A Novel Analytical Framework for the Comprehensive Proteomic Reference Database Construction of NonModel Organisms. ACS OMEGA 2020; 5:15370-15384. [PMID: 32637811 PMCID: PMC7331046 DOI: 10.1021/acsomega.0c01278] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/09/2020] [Indexed: 06/11/2023]
Abstract
Protein reference databases are a critical part of producing efficient proteomic analyses. However, the method for constructing clean, efficient, and comprehensive protein reference databases of nonmodel organisms is lacking. Existing methods either do not have contamination control procedures, or these methods rely on a three-frame and/or six-frame translation that sharply increases the search space and the need for computational resources. Herein, we propose a framework for constructing a customized comprehensive proteomic reference database (CCPRD) from draft genomes and deep sequencing transcriptomes. Its effectiveness is demonstrated by incorporating the proteomes of nematocysts from endoparasitic cnidarian: myxozoans. By applying customized contamination removal procedures, contaminations in omic data were successfully identified and removed. This is an effective method that does not result in overdecontamination. This can be shown by comparing the CCPRD MS results with an artificially contaminated database and another database with removed contaminations in genomes and transcriptomes added back. CCPRD outperformed traditional frame-based methods by identifying 35.2-50.7% more peptides and 35.8-43.8% more proteins, with a maximum of 84.6% in size reduction. A BUSCO analysis showed that the CCPRD maintained a relatively high level of completeness compared to traditional methods. These results confirm the superiority of the CCPRD over existing methods in peptide and protein identification numbers, database size, and completeness. By providing a general framework for generating the reference database, the CCPRD, which does not need a high-quality genome, can potentially be applied to nonmodel organisms and significantly contribute to proteomic research.
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Affiliation(s)
- Qingxiang Guo
- Department of Aquatic
Animal Medicine, College of Fisheries, Huazhong
Agricultural University, Wuhan, Hubei Province 430070, PR China
- Hubei Engineering Technology Research
Center for Aquatic Animal Diseases Control and Prevention, Wuhan 430070, PR China
| | - Dan Li
- Department of Aquatic
Animal Medicine, College of Fisheries, Huazhong
Agricultural University, Wuhan, Hubei Province 430070, PR China
- Hubei Engineering Technology Research
Center for Aquatic Animal Diseases Control and Prevention, Wuhan 430070, PR China
| | - Yanhua Zhai
- Department of Aquatic
Animal Medicine, College of Fisheries, Huazhong
Agricultural University, Wuhan, Hubei Province 430070, PR China
- Hubei Engineering Technology Research
Center for Aquatic Animal Diseases Control and Prevention, Wuhan 430070, PR China
| | - Zemao Gu
- Department of Aquatic
Animal Medicine, College of Fisheries, Huazhong
Agricultural University, Wuhan, Hubei Province 430070, PR China
- Hubei Engineering Technology Research
Center for Aquatic Animal Diseases Control and Prevention, Wuhan 430070, PR China
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16
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Khodami S, Mercado-Salas NF, Martìnez Arbizu P. Genus level molecular phylogeny of Aegisthidae Gisbrecht, 1893 (Copepoda: Harpacticoida) reveals morphological adaptations to deep-sea and plagic habitats. BMC Evol Biol 2020; 20:36. [PMID: 32171237 PMCID: PMC7071595 DOI: 10.1186/s12862-020-1594-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 02/05/2020] [Indexed: 11/10/2022] Open
Abstract
Background The family Aegisthidae is known as typical component of deep-sea hyperbenthic waters that gradually colonized other marine environments. The phylogenetic relationships within this family have been examined here including hyperbenthic, planktonic, benthic forms and two associated Aegisthidae species. Results Ninety four specimens belong to 14 genera were studied using 18S and 28S rRNA and COI mtDNA. Bayesian analysis supports the monophyly of 10 genera whereas Andromastax, Jamstecia, Nudivorax and Aegisthus revealed to be paraphyletic. The first offshoot of the phylogenetic tree is a clade consists of the undescribed genus Aegisthidae gen.1 sister to the two monophyletic genera Cerviniella and Hase, whereas the other Cerviniinae members (represented by Cervinia and Expansicervinia) assemble a monophylum, sister to the hyperbenthic and planktonic aegisthid genera, resulting in the paraphyly of the subfamily Cerviniinae. Hence, we defined the new subfamily Cerviniellinae subfam. nov. encompassing the three benthic genera Cerviniella, Hase and Eucanuella. The subfamily Cerviniinae has been re-defined to include Cervinia, Expansicervinia and Paracerviniella. Members of the subfamily Pontostratiotinae were clustered into two clades, one consists of the genus Stratiopontotes sister to an undescribed genus + Cerviniopsis and Siphonis. The second contains Pontostratiotes sister to the members of the planktonic subfamily Aegisthinae, resulting in the paraphyly of the Pontostratiotinae. Therefore, the Pontostratiotinae has been re-defined to include only members of the genus Pontostratiotes; whereas the subfamily Cerviniopseinae has been re-erected and re-defined containing Stratiopontotes, Cerviniopsis, Siphonis, Aegisthidae gen. 2, Herdmaniopsis, Hemicervinia and Tonpostratiotes. Within this subfamily, the associated Siphonis clusters as sister to the Cerviniopsis represents an example of convergent evolution in which the possession of a stylet-like mandible and an oral cone reminiscent of the Siphonostomatoida. The planktonic Aegisthus, Andromastax, Jamstecia, Nudivorax and Scabrantenna confirm the monophylom Aegisthinae, sister to the Pontostratiotinae. Conclusions Our DNA based phylogeny reveals the deep-sea origin of Aegisthidae by placing benthic Aegisthidae gen.1 and Cerviniellinae subfam. nov. as the most basal lineages. Secondary adaptations to hyperbenthic and planktonic realms, as well as associated lifestyle were discovered here by the derived positions of Pontostratiotinae, Aegisthinae and Siphonis respectively.
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Affiliation(s)
- Sahar Khodami
- Senckenberg am Meer, German Centre for Marine Biodiversity Research, Südstrand 44, 26382, Wilhelmshaven, Germany.
| | - Nancy F Mercado-Salas
- Senckenberg am Meer, German Centre for Marine Biodiversity Research, Südstrand 44, 26382, Wilhelmshaven, Germany
| | - Pedro Martìnez Arbizu
- Senckenberg am Meer, German Centre for Marine Biodiversity Research, Südstrand 44, 26382, Wilhelmshaven, Germany
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Rajpoot A, Bahuguna A, Kumar VP. Molecular study of globally threatened turtle species (families Trionychidae and Geoemydidae) of Uttarakhand and their relationship with other Indian populations: A wildlife forensic and conservation genetic approach. FORENSIC SCIENCE INTERNATIONAL: REPORTS 2019. [DOI: 10.1016/j.fsir.2019.100039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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18
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Scheifler M, Ruiz-Rodríguez M, Sanchez-Brosseau S, Magnanou E, Suzuki MT, West N, Duperron S, Desdevises Y. Characterization of ecto- and endoparasite communities of wild Mediterranean teleosts by a metabarcoding approach. PLoS One 2019; 14:e0221475. [PMID: 31504055 PMCID: PMC6736230 DOI: 10.1371/journal.pone.0221475] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 08/07/2019] [Indexed: 02/01/2023] Open
Abstract
Next-generation sequencing methods are increasingly used to identify eukaryotic, unicellular and multicellular symbiont communities within hosts. In this study, we analyzed the non-specific reads obtained during a metabarcoding survey of the bacterial communities associated to three different tissues collected from 13 wild Mediterranean teleost fish species. In total, 30 eukaryotic genera were identified as putative parasites of teleosts, associated to skin mucus, gills mucus and intestine: 2 ascomycetes, 4 arthropods, 2 cnidarians, 7 nematodes, 10 platyhelminthes, 4 apicomplexans, 1 ciliate as well as one order in dinoflagellates (Syndiniales). These results highlighted that (1) the metabarcoding approach was able to uncover a large spectrum of symbiotic organisms associated to the fish species studied, (2) symbionts not yet identified in several teleost species were putatively present, (3) the parasitic diversity differed markedly across host species and (4) in most cases, the distribution of known parasitic genera within tissues is in accordance with the literature. The current work illustrates the large insights that can be gained by making maximum use of data from a metabarcoding approach.
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Affiliation(s)
- Mathilde Scheifler
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, Observatoire Océanologique, Banyuls/Mer, France
| | - Magdalena Ruiz-Rodríguez
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, Observatoire Océanologique, Banyuls/Mer, France
| | - Sophie Sanchez-Brosseau
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, Observatoire Océanologique, Banyuls/Mer, France
| | - Elodie Magnanou
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, Observatoire Océanologique, Banyuls/Mer, France
| | - Marcelino T. Suzuki
- Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes, LBBM Observatoire Océanologique, Banyuls/Mer, France
| | - Nyree West
- Sorbonne Université, CNRS, Observatoire Océanologique de Banyuls, Banyuls/Mer, France
| | - Sébastien Duperron
- CNRS, Muséum National d’Histoire Naturelle, Molécules de Communication et Adaptation des Micro-organismes, UMR7245 MCAM, Muséum National d’Histoire Naturelle, Paris, France
| | - Yves Desdevises
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, Observatoire Océanologique, Banyuls/Mer, France
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Rossel S, Martínez Arbizu P. Revealing higher than expected diversity of Harpacticoida (Crustacea:Copepoda) in the North Sea using MALDI-TOF MS and molecular barcoding. Sci Rep 2019; 9:9182. [PMID: 31235850 PMCID: PMC6591307 DOI: 10.1038/s41598-019-45718-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 05/29/2019] [Indexed: 11/09/2022] Open
Abstract
The North Sea is one of the most extensively studied marine regions of the world. Hence, large amounts of molecular data for species identification are available in public repositories, and expectations to find numerous new species in this well-known region are rather low. However, molecular reference data for harpacticoid copepods from this area in particular but also for this group in general is scarce. By assessing COI barcodes and MALDI-TOF mass spectra for this group of small crustaceans, it was discovered that there is a huge unknown diversity in this area. In total, COI sequences for 548 specimens from 115 species of harpacticoid copepods are presented. Over 19% of these were new to science and ten MOTUs were found to be part of cryptic species complexes. MALDI-TOF mass spectra were assessed for 622 specimens from 75 species. Because results were in concordance with species delimitation by COI barcoding and also enabled recognition of possible cryptic species, the discriminative power of this technique for biodiversity assessments is highlighted. Findings imply, species diversity in this group may be largely underestimated and total species number can be expected to be much higher than previously assumed.
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Affiliation(s)
- S Rossel
- Senckenberg Research Institute, German Centre for Marine Biodiversity Research (DZMB), Südstrand 44, 26382, Wilhelmshaven, Germany. .,Marine Biodiversity Research, Institute for Biology and Environmental Sciences, Carl von Ossietzky University Oldenburg, Oldenburg, Germany.
| | - P Martínez Arbizu
- Senckenberg Research Institute, German Centre for Marine Biodiversity Research (DZMB), Südstrand 44, 26382, Wilhelmshaven, Germany.,Marine Biodiversity Research, Institute for Biology and Environmental Sciences, Carl von Ossietzky University Oldenburg, Oldenburg, Germany
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20
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Khodami S, Mercado-Salas NF, Tang D, Martinez Arbizu P. Molecular evidence for the retention of the Thaumatopsyllidae in the order Cyclopoida (Copepoda) and establishment of four suborders and two families within the Cyclopoida. Mol Phylogenet Evol 2019; 138:43-52. [PMID: 31125659 DOI: 10.1016/j.ympev.2019.05.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 05/06/2019] [Accepted: 05/20/2019] [Indexed: 11/16/2022]
Abstract
The classification of the Thaumatopsyllidae within the Copepoda has been an issue of ongoing discussion since the discovery of Thaumatopsyllus paradoxus G.O. Sars, 1913 from the Norwegian coast. The family has been formally placed in the Monstrilloida, the Cyclopoida and even in its own order, the Thaumatopsylloida, based on different morphological criteria. We examined for the first time, the phylogenetic position of the Thaumatopsyllidae using gene sequences of 28S and 18S rRNA, as well as COI mtDNA, obtained from two thaumatopsyllid species occurring off the coast of southern California. We also fortuitously explored the phylogenetic relationships of the Cyclopoida in more detail than Khodami et al. (2017) by including a wider sample of key families such as the Erebonasteridae and Gisellinidae. Both Maximum Likelihood and Bayesian analyses revealed the Thaumatopsyllidae is nested in the Cyclopoida and is related to the marine Speleoithonidae. In addition, 16 families of the Cyclopoida are supported to be monophyletic, but surprisingly, the Cyclopidae is paraphyletic. The Cyclopicinidae is the first monophyletic offshoot of the cyclopoid tree, followed by two derived clades. The first clade contains a monophylum consisting of the Schminkepinellidae + Giselinidae which is sister to a clade including the monophyletic Erebonasteridae and all other poecilostome families. The second clade is divided into two main, well-supported family clusters. One includes the Cyclopidae encompassing two subfamilies (Eucylopinae and Cyclopinae), but unexpectedly the parasitic Lernaeidae cluster as a sister-group to the brackish water Halicyclops (subfamily Halicyclopinae) and the Euryteinae is the sister to all the rest of Cyclopidae s. l., making the Cyclopidae paraphyletic. To resolve this conundrum, we erected two families, Euryteidae and Halicyclopidae. The Cyclopidae s. str. retains the subfamilies Eucyclopinae and Cyclopinae, although our phylogeny does not support the reciprocal monophyly of these subfamilies. Our results support the gradual invasion of fresh water by the four families in this cluster. The highly supported monophyletic marine Euryteidae is the first offshoot followed by the brackish-water, free-living Halicyclopidae and the freshwater, parasitic Lernaeidae. The Cyclopidae fulfilled the colonization of freshwater bodies. The other clade of families comprises 12 monophyletic families recovered by our analysis, including the Pterinopsyllidae (at first offshoot), the Smirnovipinidae sister to the Hemicyclopinidae + Psammocyclopinidae, the Thaumatopsyllidae + Speleoithonidae, an undescribed family sister to the Archinotodelphyidae + Notodelphyidae and the Cyclopinidae sister to the Oithonidae + Cyclopettidae. We propose suborder ranks for each of the four main phylogenetic subdivisions of the Cyclopoida. These are named Cyclopicinida, Ergasilida, Cyclopida and Oithonida after the type genus of the oldest described family in the respective group.
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Affiliation(s)
- Sahar Khodami
- Senckenberg am Meer, German Centre for Marine Biodiversity Research, Südstrand 44, 26382 Wilhelmshaven, Germany.
| | - Nancy F Mercado-Salas
- Senckenberg am Meer, German Centre for Marine Biodiversity Research, Südstrand 44, 26382 Wilhelmshaven, Germany
| | - Danny Tang
- Laboratory, Monitoring, and Compliance Division, Orange County Sanitation District, 10844 Ellis Avenue, Fountain Valley, CA 92708-7018, USA
| | - Pedro Martinez Arbizu
- Senckenberg am Meer, German Centre for Marine Biodiversity Research, Südstrand 44, 26382 Wilhelmshaven, Germany
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21
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Jørgensen TS, Petersen B, Petersen HCB, Browne PD, Prost S, Stillman JH, Hansen LH, Hansen BW. The Genome and mRNA Transcriptome of the Cosmopolitan Calanoid Copepod Acartia tonsa Dana Improve the Understanding of Copepod Genome Size Evolution. Genome Biol Evol 2019; 11:1440-1450. [PMID: 30918947 PMCID: PMC6526698 DOI: 10.1093/gbe/evz067] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/26/2019] [Indexed: 11/14/2022] Open
Abstract
Members of the crustacean subclass Copepoda are likely the most abundant metazoans worldwide. Pelagic marine species are critical in converting planktonic microalgae to animal biomass, supporting oceanic food webs. Despite their abundance and ecological importance, only six copepod genomes are publicly available, owing to a number of factors including large genome size, repetitiveness, GC-content, and small animal size. Here, we report the seventh representative copepod genome and the first genome and the first transcriptome from the calanoid copepod species Acartia tonsa Dana, which is among the most numerous mesozooplankton in boreal coastal and estuarine waters. The ecology, physiology, and behavior of A. tonsa have been studied extensively. The genetic resources contributed in this work will allow researchers to link experimental results to molecular mechanisms. From PCR-free whole genome sequence and mRNA Illumina data, we assemble the largest copepod genome to date. We estimate that A. tonsa has a total genome size of 2.5 Gb including repetitive elements we could not resolve. The nonrepetitive fraction of the genome assembly is estimated to be 566 Mb. Our DNA sequencing-based analyses suggest there is a 14-fold difference in genome size between the six members of Copepoda with available genomic information. This finding complements nucleus staining genome size estimations, where 100-fold difference has been reported within 70 species. We briefly analyze the repeat structure in the existing copepod whole genome sequence data sets. The information presented here confirms the evolution of genome size in Copepoda and expands the scope for evolutionary inferences in Copepoda by providing several levels of genetic information from a key planktonic crustacean species.
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Affiliation(s)
- Tue Sparholt Jørgensen
- Department of Science and Environment, Roskilde University, Denmark
- Department of Environmental Science – Environmental Microbiology and Biotechnology, Aarhus University, Roskilde, Denmark
| | - Bent Petersen
- Natural History Museum of Denmark, University of Copenhagen, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | | | - Patrick Denis Browne
- Department of Environmental Science – Environmental Microbiology and Biotechnology, Aarhus University, Roskilde, Denmark
| | - Stefan Prost
- Department of Integrative Biology and Evolution, Research Institute of Wildlife Ecology, University of Veterinary Medicine, Vienna, Austria
- Department of Integrative Biology, University of California, Berkeley
- National Zoological Garden, South African National Biodiversity Institute, Pretoria, South Africa
| | - Jonathon H Stillman
- Department of Integrative Biology, University of California, Berkeley
- Estuary and Ocean Science Center, San Francisco State University, Tiburon, California
| | - Lars Hestbjerg Hansen
- Department of Environmental Science – Environmental Microbiology and Biotechnology, Aarhus University, Roskilde, Denmark
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Laakmann S, Markhaseva EL, Renz J. Do molecular phylogenies unravel the relationships among the evolutionary young “Brafordian” families (Copepoda; Calanoida)? Mol Phylogenet Evol 2019; 130:330-345. [DOI: 10.1016/j.ympev.2018.10.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 10/19/2018] [Accepted: 10/22/2018] [Indexed: 10/28/2022]
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Renz J, Markhaseva EL, Laakmann S. The phylogeny of Ryocalanoidea (Copepoda, Calanoida) based on morphology and a multi-gene analysis with a description of new ryocalanoidean species. Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zly069] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Two new species of ryocalanoid copepods (Crustacea: Calanoida), Ryocalanus squamatus sp. nov. and Yrocalanus kurilensis sp. nov. are described together with a female of Ryocalanus infelix Tanaka, 1956, type species for the genus Ryocalanus Tanaka, 1956, from abyssal depths in the Kurile-Kamchatka trench. The new species can be assigned to the superfamily Ryocalanoidea based on the segmentation and armature of the swimming legs and the modification of the male right antennule. A new interpretation of the fusions of segments in the male right antennule of Ryocalanus shows the marked differences between the ryocalanoidean genera. The status of Ryocalanoidea within the Calanoida is discussed based on morphology and a first molecular multi-gene analysis with cytochrome oxidase subunit I, cytochrome b, nuclear ribosomal 18S and 28S rDNA and internal transcribed spacer 2. This analysis supports the close interrelationship between Ryocalanoidea and Spinocalanoidea. The monophyletic status of Ryocalanoidea could not be retrieved in the phylogenetic analysis, as specimens of Yrocalanus formed a clade within Spinocalanoidea. The inconclusive results between morphological and molecular analyses are discussed with a proposition to keep the current system until more males of taxa belonging to the Spinocalanoidea are discovered, as the male antennule plays a crucial role in the interpretation of relationships between Ryocalanoidea and Spinocalanoidea.
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Affiliation(s)
- Jasmin Renz
- German Centre for Marine Biodiversity Research (DZMB), Senckenberg am Meer, Hamburg, Germany
| | - Elena L Markhaseva
- Laboratory of Marine Research, Zoological Institute, Russian Academy of Sciences, St. Petersburg, Russia
| | - Silke Laakmann
- German Centre for Marine Biodiversity Research (DZMB), Senckenberg am Meer, Wilhelmshaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Oldenburg, Germany
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Metabarcoding of marine environmental DNA based on mitochondrial and nuclear genes. Sci Rep 2018; 8:14822. [PMID: 30287908 PMCID: PMC6172225 DOI: 10.1038/s41598-018-32917-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 09/17/2018] [Indexed: 11/17/2022] Open
Abstract
We establish the new approach of environmental DNA (eDNA) analyses for the North Sea. Our study uses a multigene approach, including the mitochondrial cytochrome-c-oxidase subunit I (COI) gene for analyzing species composition and the nuclear hypervariable region V8 of 18S rDNA for analyzing supraspecific biodiversity. A new minibarcode primer (124 bp) was created on the basis of a metazoan COI barcode library with 506 species and tested in silico, in vitro, and in situ. We applied high throughput sequencing to filtrates of 23 near-bottom water samples taken at three seasons from 14 stations. The set of COI primers allowed amplification of mitochondrial minibarcodes for diverse metazoan phyla and the differentiation at the species level for more than 99% of the specimens in the dataset. Our results revealed that the number of sequences is not consistent with proportions in the given DNA mixture. Altogether, environmental sequences could be assigned to 114 species and to 12 metazoan phyla. A spatial distribution of taxa recovered by eDNA was congruent with known distributions. Finally, the successful detection of species and biodiversity depends on a comprehensive sequence reference database. Our study offers a powerful tool for future biodiversity research, including the detection of nonnative species.
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Maas AE, Blanco-Bercial L, Lo A, Tarrant AM, Timmins-Schiffman E. Variations in Copepod Proteome and Respiration Rate in Association with Diel Vertical Migration and Circadian Cycle. THE BIOLOGICAL BULLETIN 2018; 235:30-42. [PMID: 30160998 DOI: 10.1086/699219] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The diel vertical migration of zooplankton is a process during which individuals spend the night in surface waters and retreat to depth during the daytime, with substantial implications for carbon transport and the ecology of midwater ecosystems. The physiological consequences of this daily pattern have, however, been poorly studied beyond investigations of speed and the energetic cost of swimming. Many other processes are likely influenced, such as fuel use, energetic trade-offs, underlying diel (circadian) rhythms, and antioxidant responses. Using a new reference transcriptome, proteomic analyses were applied to compare the physiological state of a migratory copepod, Pleuromamma xiphias, immediately after arriving to the surface at night and six hours later. Oxygen consumption was monitored semi-continuously to explore underlying cyclical patterns in metabolic rate under dark-dark conditions. The proteomic analysis suggests a distinct shift in physiology that reflects migratory exertion and changes in metabolism. These proteomic analyses are supported by the respiration experiments, which show an underlying cycle in metabolic rate, with a peak at dawn. This project generates molecular tools (transcriptome and proteome) that will allow for more detailed understanding of the underlying physiological processes that influence and are influenced by diel vertical migration. Further, these studies suggest that P. xiphias is a tractable model for continuing investigations of circadian and diel vertical migration influences on plankton physiology. Previous studies did not account for this cyclic pattern of respiration and may therefore have unrepresented respiratory carbon fluxes from copepods by about 24%.
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Key Words
- ACN, acetonitrile
- ANOSIM, analysis of similarity
- BATS, Bermuda Atlantic Time Series
- BUSCO, Benchmarking Universal Single-Copy Orthologs
- DM, dry mass
- DVM, diel vertical migration
- FFT-NLLS, fast Fourier transform non-linear least squares
- GO, gene ontology
- MESA, maximum entropy spectral analysis
- NAD+, oxidized nicotinamide adenine dinucleotide
- NAD, nicotinamide adenine dinucleotide
- NADH, reduced nicotinamide adenine dinucleotide
- NMDS, non-metric multidimensional scaling
- NSAF, normalized spectral abundance factor
- RT, room temperature
- TTP, Trans Proteomic Pipeline
- nr, non-redundant database
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Rossel S, Martínez Arbizu P. Automatic specimen identification of Harpacticoids (Crustacea:Copepoda) using Random Forest and
MALDI
‐
TOF
mass spectra, including a post hoc test for false positive discovery. Methods Ecol Evol 2018. [DOI: 10.1111/2041-210x.13000] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Sven Rossel
- Senckenberg am MeerGerman Centre for Marine Biodiversity Research (DZMB) Wilhelmshaven Germany
- AG Marine BiodiversitätFKV‐IBUUniversität Oldenburg Oldenburg Germany
| | - Pedro Martínez Arbizu
- Senckenberg am MeerGerman Centre for Marine Biodiversity Research (DZMB) Wilhelmshaven Germany
- AG Marine BiodiversitätFKV‐IBUUniversität Oldenburg Oldenburg Germany
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27
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Kumar VP, Shukla M, Rajpoot A, Thakur M, Nigam P, Kumar D, Mehta AK, Goyal SP. DNA barcoding as a tool for robust identification of cervids of India and its utility in wildlife forensics. MITOCHONDRIAL DNA PART B-RESOURCES 2018; 3:250-255. [PMID: 33474133 PMCID: PMC7800678 DOI: 10.1080/23802359.2018.1438858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA barcoding has become a popular method of choice for identification of specimen based on molecular techniques. Here, we present preliminary findings on generating robust DNA barcode library of Cervids of India. The dataset comprising the DNA barcode library of seven deer species included in the genus Cervus, Axis and Muntiacus classified under family Cervidae. Mitochondrial Cytochrome C Oxidase subunit I gene of ca. 710 bp accepted widely as DNA barcode region, was used for generating species specific signature from 31 known samples of seven Indian deer species. Expectedly, the NJ tree clustered three genera i.e. Cervus, Axis and Muntiacus of Cervids of India into three clades. Further, the intra- and interspecies distances based on Kimura 2 parameter model also supported the results. The average intra- and interspecies sequence divergence were 0.011 (±0.09) and 0.65 (±0.14), respectively. The present study has exhibited that DNA barcoding has discriminating power to delineate boundaries among the closely related species. The data generated are of high importance to the law enforcement agencies in effective identification of species in wildlife offence cases. The similar approach can be utilized for generating DNA barcodes for other Indian mammals for making effective management and conservation action decisions.
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Affiliation(s)
- Ved P Kumar
- Wildlife Forensic Cell, Wildlife Institute of India, Dehradun, Uttarakhand, India.,Department of Zoology, Veer Kunwar Singh University, Arrah, Bihar, India
| | - Malay Shukla
- Wildlife Forensic Cell, Wildlife Institute of India, Dehradun, Uttarakhand, India.,Institute of Forensic Science, Gujarat Forensic Sciences University, Gandhinagar, Gujarat, India
| | - Ankita Rajpoot
- Molecular Systematics Laboratory, Zoological Survey of India, Northern Regional Centre, Dehradun, Uttarakhand, India
| | - Mukesh Thakur
- Molecular Systematics Division,Centre for DNA Taxonomy, Zoological Survey of India, Kolkata, India
| | - Parag Nigam
- Wildlife Forensic Cell, Wildlife Institute of India, Dehradun, Uttarakhand, India
| | - Dhyanendra Kumar
- Department of Zoology, Veer Kunwar Singh University, Arrah, Bihar, India
| | - Anil Kumar Mehta
- Institute of Forensic Science, Gujarat Forensic Sciences University, Gandhinagar, Gujarat, India
| | - Surendra P Goyal
- Department of Zoology, Veer Kunwar Singh University, Arrah, Bihar, India
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28
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Spielmann G, Huber I, Maggipinto M, Haszprunar G, Busch U, Pavlovic M. Comparison of five preparatory protocols for fish species identification using MALDI-TOF MS. Eur Food Res Technol 2017. [DOI: 10.1007/s00217-017-2983-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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29
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Stahl A, Schröder U. Development of a MALDI-TOF MS-Based Protein Fingerprint Database of Common Food Fish Allowing Fast and Reliable Identification of Fraud and Substitution. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:7519-7527. [PMID: 28745053 DOI: 10.1021/acs.jafc.7b02826] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Fish substitution and fish fraud are widely observed in the global food market. To detect and prevent substitution, DNA-based methods do not always meet the demand of being time- and cost-efficient; therefore, methodology improvements are needed. The use of species-specific protein patterns, as determined by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry, has recently improved species identification of prokaryotes both time- and cost-wise. We used the method to establish a database containing protein patterns of common food fish prone to substitution. The database currently comprises 54 fish species. Aspects such as the sensitivity of identification on the species level and the impact of bacterial contamination of fish filets are assessed. Most database entries are characterized by low intraspecies but high interspecies variability. Hitherto, 118 validation samples were successfully determined. The results presented herein underline the potential and reliability of eukaryotic species identification via MALDI-TOF mass spectrometry.
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Affiliation(s)
- Antje Stahl
- Intertek Food Services GmbH , Olof-Palme-Straße 8, 28719 Bremen, Germany
| | - Uwe Schröder
- Intertek Food Services GmbH , Olof-Palme-Straße 8, 28719 Bremen, Germany
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30
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Williams LG, Karl SA, Rice S, Simon C. Molecular identification of polydorid polychaetes (Annelida: Spionidae): is there a quick way to identify pest and alien species? AFRICAN ZOOLOGY 2017. [DOI: 10.1080/15627020.2017.1313131] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Lee-Gavin Williams
- Department of Botany and Zoology, Stellenbosch University, Stellenbosch, South Africa
| | - Stephen A Karl
- University of Hawai‘i at Mānoa, Hawai‘i Institute of Marine Biology, Kāne‘ohe, Hawai‘i, USA
| | - Stanley Rice
- Department of Biology, University of Tampa, Tampa, Florida, USA
| | - Carol Simon
- Department of Botany and Zoology, Stellenbosch University, Stellenbosch, South Africa
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31
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Vasquez AA, Hudson PL, Fujimoto M, Keeler K, Armenio PM, Ram JL. Eurytemora carolleeae in the Laurentian Great Lakes revealed by phylogenetic and morphological analysis. JOURNAL OF GREAT LAKES RESEARCH 2016; 42:802-811. [PMID: 27713595 PMCID: PMC5047287 DOI: 10.1016/j.jglr.2016.04.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
In the Laurentian Great Lakes, specimens of Eurytemora have been reported as E. affinis since its invasion in the late 1950s. During an intensive collection of aquatic invertebrates for morphological and molecular identification in Western Lake Erie in 2012-2013, several specimens of Eurytemora were collected. Analysis of these specimens identified them as the recently described species E. carolleeae Alekseev and Souissi 2011. This result led us to assess E. carolleeae's identifying features, geographic distribution and historical presence in the Laurentian Great Lakes in view of its recent description in 2011. Cytochrome oxidase I (COI) DNA sequences of Eurytemora specimens were identified as closer (2 - 4% different) to recently described E. carolleeae than to most Eurytemora affinis sequences (14% different). Eurytemora from other areas of the Great Lakes and from North American rivers as far west as South Dakota (Missouri River) and east to Delaware (Christina River) also keyed to E. carolleeae. Morphological analysis of archival specimens from 1962 and from all the Great Lakes were identified as E. carolleeae. Additionally, Eurytemora drawings in previous publications from studies in the Holarctic region were reassessed to determine if these specimens were E. carolleeae. Additional morphological characters that may distinguish the North American E. carolleeae from other taxa are also described. We conclude that E. carolleeae is the correct name for the species of Eurytemora that has inhabited the Great Lakes since its invasion, as established by both morphological and COI sequence comparisons to reference keys and sequence databases in present and archival specimens.
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Affiliation(s)
- Adrian A. Vasquez
- Department of Physiology, Wayne State University School of Medicine, 5374 Scott Hall, 540 E. Canfield St., Detroit, MI, 48201, USA
| | - Patrick L. Hudson
- US Geological Survey, Great Lakes Science Center, 1451 Green Road, Ann Arbor, MI 48105, USA
| | - Masanori Fujimoto
- Department of Physiology, Wayne State University School of Medicine, 5374 Scott Hall, 540 E. Canfield St., Detroit, MI, 48201, USA
| | - Kevin Keeler
- US Geological Survey, Great Lakes Science Center, 1451 Green Road, Ann Arbor, MI 48105, USA
| | - Patricia M. Armenio
- US Geological Survey, Great Lakes Science Center, 1451 Green Road, Ann Arbor, MI 48105, USA
| | - Jeffrey L. Ram
- Department of Physiology, Wayne State University School of Medicine, 5374 Scott Hall, 540 E. Canfield St., Detroit, MI, 48201, USA
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32
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DNA Barcoding of Metazoan Zooplankton Copepods from South Korea. PLoS One 2016; 11:e0157307. [PMID: 27383475 PMCID: PMC4934703 DOI: 10.1371/journal.pone.0157307] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 05/30/2016] [Indexed: 12/03/2022] Open
Abstract
Copepods, small aquatic crustaceans, are the most abundant metazoan zooplankton and outnumber every other group of multicellular animals on earth. In spite of ecological and biological importance in aquatic environment, their morphological plasticity, originated from their various lifestyles and their incomparable capacity to adapt to a variety of environments, has made the identification of species challenging, even for expert taxonomists. Molecular approaches to species identification have allowed rapid detection, discrimination, and identification of cryptic or sibling species based on DNA sequence data. We examined sequence variation of a partial mitochondrial cytochrome C oxidase I gene (COI) from 133 copepod individuals collected from the Korean Peninsula, in order to identify and discriminate 94 copepod species covering six copepod orders of Calanoida, Cyclopoida, Harpacticoida, Monstrilloida, Poecilostomatoida and Siphonostomatoida. The results showed that there exists a clear gap with ca. 20 fold difference between the averages of within-specific sequence divergence (2.42%) and that of between-specific sequence divergence (42.79%) in COI, suggesting the plausible utility of this gene in delimitating copepod species. The results showed, with the COI barcoding data among 94 copepod species, that a copepod species could be distinguished from the others very clearly, only with four exceptions as followings: Mesocyclops dissimilis–Mesocyclops pehpeiensis (0.26% K2P distance in percent) and Oithona davisae–Oithona similis (1.1%) in Cyclopoida, Ostrincola japonica–Pseudomyicola spinosus (1.5%) in Poecilostomatoida, and Hatschekia japonica–Caligus quadratus (5.2%) in Siphonostomatoida. Thus, it strongly indicated that COI may be a useful tool in identifying various copepod species and make an initial progress toward the construction of a comprehensive DNA barcode database for copepods inhabiting the Korean Peninsula.
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Aarbakke ONS, Fevolden SE, Weydmann A. Relative summer abundances and distribution of Pseudocalanus spp. (Copepoda: Calanoida) adults in relation to environmental variables in the Nordic Seas and Svalbard fjords. Polar Biol 2016. [DOI: 10.1007/s00300-016-1923-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Trivedi S, Aloufi AA, Ansari AA, Ghosh SK. Role of DNA barcoding in marine biodiversity assessment and conservation: An update. Saudi J Biol Sci 2016; 23:161-71. [PMID: 26980996 PMCID: PMC4778524 DOI: 10.1016/j.sjbs.2015.01.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 12/09/2014] [Accepted: 01/05/2015] [Indexed: 12/18/2022] Open
Abstract
More than two third area of our planet is covered by oceans and assessment of marine biodiversity is a challenging task. With the increasing global population, there is a tendency to exploit marine resources for food, energy and other requirements. This puts pressure on the fragile marine environment and necessitates sustainable conservation efforts. Marine species identification using traditional taxonomical methods is often burdened with taxonomic controversies. Here we discuss the comparatively new concept of DNA barcoding and its significance in marine perspective. This molecular technique can be useful in the assessment of cryptic species which is widespread in marine environment and linking the different life cycle stages to the adult which is difficult to accomplish in the marine ecosystem. Other advantages of DNA barcoding include authentication and safety assessment of seafood, wildlife forensics, conservation genetics and detection of invasive alien species (IAS). Global DNA barcoding efforts in the marine habitat include MarBOL, CeDAMar, CMarZ, SHARK-BOL, etc. An overview on DNA barcoding of different marine groups ranging from the microbes to mammals is revealed. In conjugation with newer and faster techniques like high-throughput sequencing, DNA barcoding can serve as an effective modern tool in marine biodiversity assessment and conservation.
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Affiliation(s)
- Subrata Trivedi
- Department of Biology, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Abdulhadi A. Aloufi
- Department of Biology, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Abid A. Ansari
- Department of Biology, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Sankar K. Ghosh
- Department of Biotechnology, Assam University, Silchar 788011, Assam, India
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35
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Albaina A, Aguirre M, Abad D, Santos M, Estonba A. 18S rRNA V9 metabarcoding for diet characterization: a critical evaluation with two sympatric zooplanktivorous fish species. Ecol Evol 2016; 6:1809-24. [PMID: 27087935 PMCID: PMC4801955 DOI: 10.1002/ece3.1986] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 12/23/2015] [Accepted: 01/03/2016] [Indexed: 01/26/2023] Open
Abstract
The potential of the 18S rRNA V9 metabarcoding approach for diet assessment was explored using MiSeq paired‐end (PE; 2 × 150 bp) technology. To critically evaluate the method′s performance with degraded/digested DNA, the diets of two zooplanktivorous fish species from the Bay of Biscay, European sardine (Sardina pilchardus) and European sprat (Sprattus sprattus), were analysed. The taxonomic resolution and quantitative potential of the 18S V9 metabarcoding was first assessed both in silico and with mock and field plankton samples. Our method was capable of discriminating species within the reference database in a reliable way providing there was at least one variable position in the 18S V9 region. Furthermore, it successfully discriminated diet between both fish species, including habitat and diel differences among sardines, overcoming some of the limitations of traditional visual‐based diet analysis methods. The high sensitivity and semi‐quantitative nature of the 18S V9 metabarcoding approach was supported by both visual microscopy and qPCR‐based results. This molecular approach provides an alternative cost and time effective tool for food‐web analysis.
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Affiliation(s)
- Aitor Albaina
- Laboratory of Genetics Department of Genetics, Physical Anthropology & Animal Physiology University of the Basque Country (UPV/EHU) Leioa 48940 Spain
| | - Mikel Aguirre
- Laboratory of Genetics Department of Genetics, Physical Anthropology & Animal Physiology University of the Basque Country (UPV/EHU) Leioa 48940 Spain
| | - David Abad
- Laboratory of Genetics Department of Genetics, Physical Anthropology & Animal Physiology University of the Basque Country (UPV/EHU) Leioa 48940 Spain
| | - María Santos
- Marine Research Division AZTI Tecnalia Herrera Kaia Portualdea z/g P.O. Box 20110 Pasaia Gipuzkoa Spain
| | - Andone Estonba
- Laboratory of Genetics Department of Genetics, Physical Anthropology & Animal Physiology University of the Basque Country (UPV/EHU) Leioa 48940 Spain
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Raupach MJ, Barco A, Steinke D, Beermann J, Laakmann S, Mohrbeck I, Neumann H, Kihara TC, Pointner K, Radulovici A, Segelken-Voigt A, Wesse C, Knebelsberger T. The Application of DNA Barcodes for the Identification of Marine Crustaceans from the North Sea and Adjacent Regions. PLoS One 2015; 10:e0139421. [PMID: 26417993 PMCID: PMC4587929 DOI: 10.1371/journal.pone.0139421] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 09/14/2015] [Indexed: 12/02/2022] Open
Abstract
During the last years DNA barcoding has become a popular method of choice for molecular specimen identification. Here we present a comprehensive DNA barcode library of various crustacean taxa found in the North Sea, one of the most extensively studied marine regions of the world. Our data set includes 1,332 barcodes covering 205 species, including taxa of the Amphipoda, Copepoda, Decapoda, Isopoda, Thecostraca, and others. This dataset represents the most extensive DNA barcode library of the Crustacea in terms of species number to date. By using the Barcode of Life Data Systems (BOLD), unique BINs were identified for 198 (96.6%) of the analyzed species. Six species were characterized by two BINs (2.9%), and three BINs were found for the amphipod species Gammarus salinus Spooner, 1947 (0.4%). Intraspecific distances with values higher than 2.2% were revealed for 13 species (6.3%). Exceptionally high distances of up to 14.87% between two distinct but monophyletic clusters were found for the parasitic copepod Caligus elongatus Nordmann, 1832, supporting the results of previous studies that indicated the existence of an overlooked sea louse species. In contrast to these high distances, haplotype-sharing was observed for two decapod spider crab species, Macropodia parva Van Noort & Adema, 1985 and Macropodia rostrata (Linnaeus, 1761), underlining the need for a taxonomic revision of both species. Summarizing the results, our study confirms the application of DNA barcodes as highly effective identification system for the analyzed marine crustaceans of the North Sea and represents an important milestone for modern biodiversity assessment studies using barcode sequences.
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Affiliation(s)
- Michael J. Raupach
- German Center of Marine Biodiversity (DZMB), Senckenberg am Meer, Wilhelmshaven, Niedersachsen, Germany
- * E-mail:
| | - Andrea Barco
- German Center of Marine Biodiversity (DZMB), Senckenberg am Meer, Wilhelmshaven, Niedersachsen, Germany
| | - Dirk Steinke
- Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Jan Beermann
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Biologische Anstalt Helgoland, Helgoland, Schleswig-Holstein, Germany
| | - Silke Laakmann
- German Center of Marine Biodiversity (DZMB), Senckenberg am Meer, Wilhelmshaven, Niedersachsen, Germany
| | - Inga Mohrbeck
- German Center of Marine Biodiversity (DZMB), Senckenberg am Meer, Wilhelmshaven, Niedersachsen, Germany
| | - Hermann Neumann
- Department for Marine Research, Senckenberg am Meer, Wilhelmshaven, Niedersachsen, Germany
| | - Terue C. Kihara
- German Center of Marine Biodiversity (DZMB), Senckenberg am Meer, Wilhelmshaven, Niedersachsen, Germany
| | - Karin Pointner
- German Center of Marine Biodiversity (DZMB), Senckenberg am Meer, Wilhelmshaven, Niedersachsen, Germany
| | - Adriana Radulovici
- Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Alexandra Segelken-Voigt
- Animal Biodiversity and Evolutionary Biology, Institute for Biology and Environmental Sciences, V. School of Mathematics and Science, Carl von Ossietzky University Oldenburg, Oldenburg, Niedersachsen, Germany
| | - Christina Wesse
- German Center of Marine Biodiversity (DZMB), Senckenberg am Meer, Wilhelmshaven, Niedersachsen, Germany
| | - Thomas Knebelsberger
- German Center of Marine Biodiversity (DZMB), Senckenberg am Meer, Wilhelmshaven, Niedersachsen, Germany
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The application of “-omics” technologies for the classification and identification of animals. ORG DIVERS EVOL 2015. [DOI: 10.1007/s13127-015-0234-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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39
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Siriwut W, Edgecombe GD, Sutcharit C, Panha S. The Centipede Genus Scolopendra in Mainland Southeast Asia: Molecular Phylogenetics, Geometric Morphometrics and External Morphology as Tools for Species Delimitation. PLoS One 2015; 10:e0135355. [PMID: 26270342 PMCID: PMC4536039 DOI: 10.1371/journal.pone.0135355] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Accepted: 07/21/2015] [Indexed: 12/31/2022] Open
Abstract
Seven Scolopendra species from the Southeast Asian mainland delimited based on standard external morphological characters represent monophyletic groups in phylogenetic trees inferred from concatenated sequences of three gene fragments (cytochrome c oxidase subunit 1, 16S rRNA and 28S rRNA) using Maximum likelihood and Bayesian inference. Geometric morphometric description of shape variation in the cephalic plate, forcipular coxosternite, and tergite of the ultimate leg-bearing segment provides additional criteria for distinguishing species. Colouration patterns in some Scolopendra species show a high degree of fit to phylogenetic trees at the population level. The most densely sampled species, Scolopendra dehaani Brandt, 1840, has three subclades with allopatric distributions in mainland SE Asia. The molecular phylogeny of S. pinguis Pocock, 1891, indicated ontogenetic colour variation among its populations. The taxonomic validation of S. dawydoffi Kronmüller, 2012, S. japonica Koch, 1878, and S. dehaani Brandt, 1840, each a former subspecies of S. subspinipes Leach, 1814 sensu Lewis, 2010, as full species was supported by molecular information and additional morphological data. Species delimitation in these taxonomically challenging animals is facilitated by an integrative approach that draws on both morphology and molecular phylogeny.
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Affiliation(s)
- Warut Siriwut
- Biological Sciences Program, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Animal Systematics Research Unit, Department of Biology, Chulalongkorn University, Bangkok, Thailand
| | - Gregory D. Edgecombe
- Department of Earth Sciences, The Natural History Museum, London, United Kingdom
| | - Chirasak Sutcharit
- Animal Systematics Research Unit, Department of Biology, Chulalongkorn University, Bangkok, Thailand
| | - Somsak Panha
- Animal Systematics Research Unit, Department of Biology, Chulalongkorn University, Bangkok, Thailand
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Barco A, Raupach MJ, Laakmann S, Neumann H, Knebelsberger T. Identification of North Sea molluscs with DNA barcoding. Mol Ecol Resour 2015; 16:288-97. [DOI: 10.1111/1755-0998.12440] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 06/09/2015] [Accepted: 06/17/2015] [Indexed: 12/18/2022]
Affiliation(s)
- Andrea Barco
- GEOMAR-Helmholtz Centre for Ocean Research Kiel; Düsternbrooker Weg 20 24105 Kiel Germany
- German Centre for Marine Biodiversity Research (DZMB); Senckenberg am Meer; Südstrand 44 26382 Wilhelmshaven Germany
| | - Michael J. Raupach
- German Centre for Marine Biodiversity Research (DZMB); Senckenberg am Meer; Südstrand 44 26382 Wilhelmshaven Germany
| | - Silke Laakmann
- German Centre for Marine Biodiversity Research (DZMB); Senckenberg am Meer; Südstrand 44 26382 Wilhelmshaven Germany
| | - Hermann Neumann
- German Centre for Marine Biodiversity Research (DZMB); Senckenberg am Meer; Südstrand 44 26382 Wilhelmshaven Germany
| | - Thomas Knebelsberger
- German Centre for Marine Biodiversity Research (DZMB); Senckenberg am Meer; Südstrand 44 26382 Wilhelmshaven Germany
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Wu S, Xiong J, Yu Y. Taxonomic resolutions based on 18S rRNA genes: a case study of subclass copepoda. PLoS One 2015; 10:e0131498. [PMID: 26107258 PMCID: PMC4479608 DOI: 10.1371/journal.pone.0131498] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Accepted: 06/01/2015] [Indexed: 01/20/2023] Open
Abstract
Biodiversity studies are commonly conducted using 18S rRNA genes. In this study, we compared the inter-species divergence of variable regions (V1-9) within the copepod 18S rRNA gene, and tested their taxonomic resolutions at different taxonomic levels. Our results indicate that the 18S rRNA gene is a good molecular marker for the study of copepod biodiversity, and our conclusions are as follows: 1) 18S rRNA genes are highly conserved intra-species (intra-species similarities are close to 100%); and could aid in species-level analyses, but with some limitations; 2) nearly-whole-length sequences and some partial regions (around V2, V4, and V9) of the 18S rRNA gene can be used to discriminate between samples at both the family and order levels (with a success rate of about 80%); 3) compared with other regions, V9 has a higher resolution at the genus level (with an identification success rate of about 80%); and 4) V7 is most divergent in length, and would be a good candidate marker for the phylogenetic study of Acartia species. This study also evaluated the correlation between similarity thresholds and the accuracy of using nuclear 18S rRNA genes for the classification of organisms in the subclass Copepoda. We suggest that sample identification accuracy should be considered when a molecular sequence divergence threshold is used for taxonomic identification, and that the lowest similarity threshold should be determined based on a pre-designated level of acceptable accuracy.
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Affiliation(s)
- Shu Wu
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jie Xiong
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Yuhe Yu
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- * E-mail:
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Shoemaker KM, Moisander PH. Microbial diversity associated with copepods in the North Atlantic subtropical gyre. FEMS Microbiol Ecol 2015; 91:fiv064. [DOI: 10.1093/femsec/fiv064] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2015] [Indexed: 01/21/2023] Open
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Zagoskin MV, Lazareva VI, Grishanin AK, Mukha DV. Phylogenetic information content of Copepoda ribosomal DNA repeat units: ITS1 and ITS2 impact. BIOMED RESEARCH INTERNATIONAL 2014; 2014:926342. [PMID: 25215300 PMCID: PMC4151598 DOI: 10.1155/2014/926342] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 07/08/2014] [Accepted: 07/08/2014] [Indexed: 11/17/2022]
Abstract
The utility of various regions of the ribosomal repeat unit for phylogenetic analysis was examined in 16 species representing four families, nine genera, and two orders of the subclass Copepoda (Crustacea). Fragments approximately 2000 bp in length containing the ribosomal DNA (rDNA) 18S and 28S gene fragments, the 5.8S gene, and the internal transcribed spacer regions I and II (ITS1 and ITS2) were amplified and analyzed. The DAMBE (Data Analysis in Molecular Biology and Evolution) software was used to analyze the saturation of nucleotide substitutions; this test revealed the suitability of both the 28S gene fragment and the ITS1/ITS2 rDNA regions for the reconstruction of phylogenetic trees. Distance (minimum evolution) and probabilistic (maximum likelihood, Bayesian) analyses of the data revealed that the 28S rDNA and the ITS1 and ITS2 regions are informative markers for inferring phylogenetic relationships among families of copepods and within the Cyclopidae family and associated genera. Split-graph analysis of concatenated ITS1/ITS2 rDNA regions of cyclopoid copepods suggested that the Mesocyclops, Thermocyclops, and Macrocyclops genera share complex evolutionary relationships. This study revealed that the ITS1 and ITS2 regions potentially represent different phylogenetic signals.
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Affiliation(s)
- Maxim V. Zagoskin
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkin Street. 3, Moscow 119991, Russia
| | - Valentina I. Lazareva
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok 152742, Russia
| | - Andrey K. Grishanin
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok 152742, Russia
- Dubna International University for Nature, Society and Man, Universitetskaya Street 19, Dubna 141980, Russia
| | - Dmitry V. Mukha
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkin Street. 3, Moscow 119991, Russia
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Blanco-Bercial L, Cornils A, Copley N, Bucklin A. DNA barcoding of marine copepods: assessment of analytical approaches to species identification. PLOS CURRENTS 2014; 6:ecurrents.tol.cdf8b74881f87e3b01d56b43791626d2. [PMID: 24987576 PMCID: PMC4073882 DOI: 10.1371/currents.tol.cdf8b74881f87e3b01d56b43791626d2] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
More than 2,500 species of copepods (Class Maxillopoda; Subclass Copepoda) occur in the marine planktonic environment. The exceptional morphological conservation of the group, with numerous sibling species groups, makes the identification of species challenging, even for expert taxonomists. Molecular approaches to species identification have allowed rapid detection, discrimination, and identification of species based on DNA sequencing of single specimens and environmental samples. Despite the recent development of diverse genetic and genomic markers, the barcode region of the mitochondrial cytochrome c oxidase subunit I (COI) gene remains a useful and - in some cases - unequaled diagnostic character for species-level identification of copepods. This study reports 800 new barcode sequences for 63 copepod species not included in any previous study and examines the reliability and resolution of diverse statistical approaches to species identification based upon a dataset of 1,381 barcode sequences for 195 copepod species. We explore the impact of missing data (i.e., species not represented in the barcode database) on the accuracy and reliability of species identifications. Among the tested approaches, the best close match analysis resulted in accurate identification of all individuals to species, with no errors (false positives), and out-performed automated tree-based or BLAST based analyses. This comparative analysis yields new understanding of the strengths and weaknesses of DNA barcoding and confirms the value of DNA barcodes for species identification of copepods, including both individual specimens and bulk samples. Continued integrative morphological-molecular taxonomic analysis is needed to produce a taxonomically-comprehensive database of barcode sequences for all species of marine copepods.
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Affiliation(s)
| | - Astrid Cornils
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhavn, Germany
| | - Nancy Copley
- Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Ann Bucklin
- University of Connecticut, Groton, Connecticut, USA
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Cornils A, Held C. Evidence of cryptic and pseudocryptic speciation in the Paracalanus parvus species complex (Crustacea, Copepoda, Calanoida). Front Zool 2014; 11:19. [PMID: 24581044 PMCID: PMC3948017 DOI: 10.1186/1742-9994-11-19] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 02/20/2014] [Indexed: 11/17/2022] Open
Abstract
Introduction Many marine planktonic crustaceans such as copepods have been considered as widespread organisms. However, the growing evidence for cryptic and pseudo-cryptic speciation has emphasized the need of re-evaluating the status of copepod species complexes in molecular and morphological studies to get a clearer picture about pelagic marine species as evolutionary units and their distributions. This study analyses the molecular diversity of the ecologically important Paracalanus parvus species complex. Its seven currently recognized species are abundant and also often dominant in marine coastal regions worldwide from temperate to tropical oceans. Results COI and Cytochrome b sequences of 160 specimens of the Paracalanus parvus complex from all oceans were obtained. Furthermore, 42 COI sequences from GenBank were added for the genetic analyses. Thirteen distinct molecular operational taxonomic units (MOTU) and two single sequences were revealed with cladistic analyses (Maximum Likelihood, Bayesian Inference), of which seven were identical with results from species delimitation methods (barcode gaps, ABDG, GMYC, Rosenberg’s P(AB)). In total, 10 to 12 putative species were detected and could be placed in three categories: (1) temperate geographically isolated, (2) warm-temperate to tropical wider spread and (3) circumglobal warm-water species. Conclusions The present study provides evidence of cryptic or pseudocryptic speciation in the Paracalanus parvus complex. One major insight is that the species Paracalanus parvus s.s. is not panmictic, but may be restricted in its distribution to the northeastern Atlantic.
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Affiliation(s)
- Astrid Cornils
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Am Alten Hafen 26, D-27568 Bremerhaven, Germany.
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Palomares-Rius JE, Cantalapiedra-Navarrete C, Castillo P. Cryptic species in plant-parasitic nematodes. NEMATOLOGY 2014. [DOI: 10.1163/15685411-00002831] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
This paper summarises the current knowledge concerning cryptic species of plant-parasitic nematode and briefly reviews the different methods available for their detection and characterisation. Cryptic species represent an important component of biodiversity, such speciation being common among plant-parasitic nematodes and occurring in diverse groups with different life history traits, including the spiral, virus vector, root-lesion and false root-knot nematodes. Cryptic species are important for a number of reasons, including food security, quarantine, non-chemical management technologies and species conservation, and should not be ignored. The magnitude of the phenomenon is largely unknown, but the available data on plant-parasitic nematodes demonstrate that reliance on morphology alone for species delimitation seriously underestimates the total number of taxa. Future research should focus on appropriately designed case studies using combined approaches, including large-scale, whole sample analyses by next-generation sequencing or proteomics in order to be able to answer the many questions that still remain.
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Affiliation(s)
- Juan E. Palomares-Rius
- Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Alameda del Obispo s/n, Apdo. 4084, 14080 Córdoba, Campus de Excelencia Internacional Agroalimentario, ceiA3, Spain
| | - Carolina Cantalapiedra-Navarrete
- Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Alameda del Obispo s/n, Apdo. 4084, 14080 Córdoba, Campus de Excelencia Internacional Agroalimentario, ceiA3, Spain
| | - Pablo Castillo
- Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Alameda del Obispo s/n, Apdo. 4084, 14080 Córdoba, Campus de Excelencia Internacional Agroalimentario, ceiA3, Spain
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