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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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2
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Alqudah AA. Phylogenetic analysis and genetic similarities of Phyllidia spp. by comparing the nucleotide sequence of 16S rRNA and cytochrome c genes. BRAZ J BIOL 2023; 84:e272732. [PMID: 37493707 DOI: 10.1590/1519-6984.272732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 06/01/2023] [Indexed: 07/27/2023] Open
Abstract
Phyllidiid nudibranchs are brightly colored gastropod molluscs, frequently encountered in coral reefs of the tropical Indo-Pacific. This study aimed to identify the phylogenetic similarities among the Phyllidia spp. The phylogenetic similarities among all the available Phyllidia spp. were studied by comparing the nucleotide sequence of 16s rRNA and cytochrome c genes (cox I). Sequences were retrieved from NCBI databases and aligned by using Geneious software. A phylogenetic tree was constructed for the retrieved sequences of Phyllidia spp. by using the neighbor-joining method on MEGA software and the pairwise distances were also calculated. The similarities among nucleotide sequences of 16s rRNA showed that the P. elegans, and P. haegeli had the highest similarities (99.92%) and the lowest similarities (99.14%) among P. haegeli and P. picta. While nucleotide sequences of cox I showed the highest similarities (99.90%) between P. elegans and P. ocellata, and the P. varicosa had the lowest similarities 99.74% with P. koehleri and P. larryi. The molecular phylogenetic analysis based on mitochondrial marker indicated a close relation between P. elegans and P. alyta in both cox I and 16s rRNA phylogenetic tree. The phylogenetic tree of 16s rRNA gene shows the P. ocellata is closely related to the clade of species P. exquisita. The available phylogenetic analysis could be useful in further studies of Phyllidiidae within Nudibranchia.
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Affiliation(s)
- A A Alqudah
- Tafila Technical University, Department of Applied Biology, Tafila, Jordan
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Korshunova T, Grøtan VV, Johnson KB, Bakken T, Picton BE, Martynov A. Similar Ones Are Not Related and Vice Versa—New Dendronotus Taxa (Nudibranchia: Dendronotidae) from the North Atlantic Ocean Provide a Platform for Discussion of Global Marine Biodiversity Patterns. DIVERSITY 2023. [DOI: 10.3390/d15040504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Abstract
One new species of the genus Dendronotus (Nudibranchia: Dendronotidae) is described from Norway and Northern Ireland, as well as from the adjacent North Sea, and one new subspecies of Dendronotus arcticus is described from Norway by applying a combination of fine-scale morphological and molecular phylogenetic data. The present case demonstrates multilevel morphological and molecular similarities and differences considering on the one hand a grouping of three similar looking sympatric taxa (D. yrjargul, D. arcticus gartensis n. subsp. and D. keatleyae n. sp.), and on the other hand two different looking apparently allopatric subspecies (D. arcticus arcticus and D. arcticus gartensis n. subsp.). The type species of the genus, D. frondosus, which is the commonest dendronotid in Norway and the United Kingdom, consistently demonstrates substantial molecular and fine-scale morphological differences from D. keatleyae n. sp. The present study, apart from providing purely taxonomic information, also provides new data for a broad discussion of global biodiversity patterns.
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Affiliation(s)
| | | | | | - Torkild Bakken
- NTNU University Museum, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Bernard E. Picton
- National Museums Northern Ireland, Holywood BT18 0EU, UK
- Marine Laboratory, Queen’s University Belfast, Belfast BT22 1PF, Northern Ireland, UK
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Rizzo L, Minichino R, Virgili R, Tanduo V, Osca D, Manfredonia A, Consoli P, Colloca F, Crocetta F. Benthic litter in the continental slope of the Gulf of Naples (central-western Mediterranean Sea) hosts limited fouling communities but facilitates molluscan spawning. MARINE POLLUTION BULLETIN 2022; 181:113915. [PMID: 35868237 DOI: 10.1016/j.marpolbul.2022.113915] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 06/30/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Seafloor pollution by benthic litter is an emerging phenomenon, although debris colonization by biota remains largely unexplored. We characterized the litter of the continental slope (~400-600 m) of the Gulf of Naples (Mediterranean) and investigated its fouling biota through integrative taxonomic approaches. Plastic pieces (82 %) with land-based origin (96 %) and limited sizes (10-20 cm) were the items most commonly encountered, suggesting a transfer to deep waters through floating and sinking. The majority of the items were not fouled, and the debris hosted an impoverished biota, leading to hypothesize that benthic litter supports wide communities only in shallow waters. Higher colonization rates were observed for gastropod and cephalopod eggs with no preference for materials and sizes, suggesting that even small pieces of soft plastic provide a spawning habitat for molluscs and affect species' connectivity in the deep-sea ecosystem. Holistic approaches are necessary to evaluate interactions between litter and biota.
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Affiliation(s)
- Lucia Rizzo
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, I-80121 Napoli, Italy; Institute of Sciences of Food Production, National Research Council, Via Monteroni, I-73025 Lecce, Italy.
| | - Riccardo Minichino
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, I-80121 Napoli, Italy
| | - Riccardo Virgili
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, I-80121 Napoli, Italy
| | - Valentina Tanduo
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, I-80121 Napoli, Italy
| | - David Osca
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, I-80121 Napoli, Italy
| | - Alessandro Manfredonia
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, I-80121 Napoli, Italy
| | - Pierpaolo Consoli
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Pace, Contrada Porticatello 29, I-98167 Messina, Italy
| | - Francesco Colloca
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Via Po 25c, I-00198 Roma, Italy
| | - Fabio Crocetta
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, I-80121 Napoli, Italy.
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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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Chetoui I, Baraket G, Tir M, Lekired A, Boussaid M, Cafsi ME, Denis F. Molecular signature of phylogenetic relationships and demographic history of Tunisian Mactra stultorum: Evidence from mitochondrial and nuclear DNA data. ZOOLOGY 2021; 151:125989. [PMID: 35007841 DOI: 10.1016/j.zool.2021.125989] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 12/16/2021] [Accepted: 12/20/2021] [Indexed: 11/25/2022]
Abstract
The genetic structure of Mactra stultorum is inferred from partial sequence of a mitochondrial cox1gene and of the internal transcribed spacer region ITS1. The samples with two colors of shell (white and brown) were collected from three sites belonging to the Tunisian coasts: Kalaât El Andalous (KA) and Soliman (SM) and Gabes (GM)). The phylogenetic trees obtained from the 2 markers are similar and subdivided samples into 3 distinct clades; clade (1) regrouped GM, clade (2) regrouped KS (KS contains samples from SM and KAa) and clade (3) is formed by KAb. Using the external sequences from genbank, it can be suggested that M. stultorum from the three clades KS, GM and KAb are three subspecies. The two sympatric M. stultorum from KA (KAa and KAb) appear to be genetically isolated showing a high genetic distance and no common haplotypes where the shell color serves for segregating marker. A total of 29 and 18 haplotypes were detected in the examined cox1 and ITS1 regions, respectively. Our study revealed higher levels of genetic diversity for ITS1 compared to cox1. For both markers, significant clinal changes in haplotypes frequencies between the north and the south populations supported by the absence of common haplotypes were observed. The demographic history of M. stultorum populations has been assessed using neutral tests and mismatch distribution for cox1 marker. A unimodal curve of the Mismatch's distribution and negative significant neutral tests suggested a recent sudden demographic expansion for GM.
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Affiliation(s)
- Imene Chetoui
- Laboratoire d'Ecologie, Biologie et Physiologie des Organismes Aquatiques, Département de Biologie, Faculté des Sciences de Tunis El Manar, Université de Tunis El Manar.Farhat Hached Tunis, B.P. n° 94 - ROMMANA 1068, Tunisie.
| | - Ghada Baraket
- Faculté des Sciences de Tunis El Manar, Université de Tunis El Manar. Farhat Hached Tunis, B.P. n° 94 - ROMMANA 1068, Tunisie
| | - Mariem Tir
- Laboratoire d'Ecologie, Biologie et Physiologie des Organismes Aquatiques, Département de Biologie, Faculté des Sciences de Tunis El Manar, Université de Tunis El Manar.Farhat Hached Tunis, B.P. n° 94 - ROMMANA 1068, Tunisie
| | - Abdelmalek Lekired
- Laboratory of Microorganisms and Active Biomolecules, MBA-LR03ES03, Faculty of Sciences of Tunis, University of Tunis El Manar, Farhat Hached Tunis, B.P. n° 94 - ROMMANA 1068, Tunisia
| | - Mohamed Boussaid
- Laboratoire de biotechnologie Végétale, Institut National des Sciences Appliquées de Technologie, centre urbain Nord B.PN°676, 1080, Tunis cedex, Tunisie
| | - M'hamed El Cafsi
- Laboratoire d'Ecologie, Biologie et Physiologie des Organismes Aquatiques, Département de Biologie, Faculté des Sciences de Tunis El Manar, Université de Tunis El Manar.Farhat Hached Tunis, B.P. n° 94 - ROMMANA 1068, Tunisie
| | - Francoise Denis
- FRE BOREA, Muséum National d'Histoire Naturelle, Place de la Croix, Concarneau, 29900, France; Laboratoire Mer Molécule Santé, EA 2160, Le Mans Université, avenue O.-Messiaen, 72085, Le Mans Cedex 9, France
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7
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Attiná N, Núñez Bustos EO, Lijtmaer DA, Hebert PDN, Tubaro PL, Lavinia PD. Genetic variation in neotropical butterflies is associated with sampling scale, species distributions, and historical forest dynamics. Mol Ecol Resour 2021; 21:2333-2349. [PMID: 34097821 DOI: 10.1111/1755-0998.13441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 05/27/2021] [Accepted: 06/01/2021] [Indexed: 11/26/2022]
Abstract
Previous studies of butterfly diversification in the Neotropics have focused on Amazonia and the tropical Andes, while southern regions of the continent have received little attention. To address the gap in knowledge about the Lepidoptera of temperate South America, we analysed over 3000 specimens representing nearly 500 species from Argentina for a segment of the mitochondrial cytochrome c oxidase subunit I (COI) gene. Representing 42% of the country's butterfly fauna, collections targeted species from the Atlantic and Andean forests, and biodiversity hotspots that were previously connected but are now isolated. We assessed COI effectiveness for species discrimination and identification and how its performance was affected by geographic distances and taxon coverage. COI data also allowed to study patterns of genetic variation across Argentina, particularly between populations in the Atlantic and Andean forests. Our results show that COI discriminates species well, but that identification success is reduced on average by ~20% as spatial and taxonomic coverage rises. We also found that levels of genetic variation are associated with species' spatial distribution type, a pattern which might reflect differences in their dispersal and colonization abilities. In particular, intraspecific distance between populations in the Atlantic and Andean forests was significantly higher in species with disjunct distributions than in those with a continuous range. All splits between lineages in these forests dated to the Pleistocene, but divergence dates varied considerably, suggesting that historical connections between the Atlantic and Andean forests have differentially affected their shared butterfly fauna. Our study supports the fact that large-scale assessments of mitochondrial DNA variation are a powerful tool for evolutionary studies.
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Affiliation(s)
- Natalí Attiná
- Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" (MACN-CONICET), Buenos Aires, Argentina
| | - Ezequiel O Núñez Bustos
- Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" (MACN-CONICET), Buenos Aires, Argentina
| | - Darío A Lijtmaer
- Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" (MACN-CONICET), Buenos Aires, Argentina
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Pablo L Tubaro
- Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" (MACN-CONICET), Buenos Aires, Argentina
| | - Pablo D Lavinia
- Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" (MACN-CONICET), Buenos Aires, Argentina.,Universidad Nacional de Río Negro. CIT Río Negro (UNRN-CONICET). Sede Atlántica, Viedma, Río Negro, Viedma, Argentina
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8
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Ge Y, Xia C, Wang J, Zhang X, Ma X, Zhou Q. The efficacy of DNA barcoding in the classification, genetic differentiation, and biodiversity assessment of benthic macroinvertebrates. Ecol Evol 2021; 11:5669-5681. [PMID: 34026038 PMCID: PMC8131818 DOI: 10.1002/ece3.7470] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 02/26/2021] [Accepted: 03/05/2021] [Indexed: 11/19/2022] Open
Abstract
Macroinvertebrates have been recognized as key ecological indicators of aquatic environment and are the most commonly used approaches for water quality assessment. However, species identification of macroinvertebrates (especially of aquatic insects) proves to be very difficult due to the lack of taxonomic expertise in some regions and can become time-consuming. In this study, we evaluated the feasibility of DNA barcoding for the classification of benthic macroinvertebrates and investigated the genetic differentiation in seven orders (Insecta: Ephemeroptera, Plecoptera, Trichoptera, Diptera, Hemiptera, Coleoptera, and Odonata) from four large transboundary rivers of northwest China and further explored its potential application to biodiversity assessment. A total of 1,144 COI sequences, belonging to 176 species, 112 genera, and 53 families were obtained and analyzed. The barcoding gap analysis showed that COI gene fragment yielded significant intra- and interspecific divergences and obvious barcoding gaps. NJ phylogenetic trees showed that all species group into monophyletic species clusters whether from the same population or not, except two species (Polypedilum. laetum and Polypedilum. bullum). The distance-based (ABGD) and tree-based (PTP and MPTP) methods were utilized for grouping specimens into Operational Taxonomic Units (OTUs) and delimiting species. The ABGD, PTP, and MPTP analysis were divided into 177 (p = .0599), 197, and 195 OTUs, respectively. The BIN analysis generated 186 different BINs. Overall, our study showed that DNA barcoding offers an effective framework for macroinvertebrate species identification and sheds new light on the biodiversity assessment of local macroinvertebrates. Also, the construction of DNA barcode reference library of benthic macroinvertebrates in Eurasian transboundary rivers provides a solid backup for bioassessment studies of freshwater habitats using modern high-throughput technologies in the near future.
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Affiliation(s)
- Yihao Ge
- Key Laboratory of Freshwater Animal BreedingMinistry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of FisheriesHuazhong Agricultural UniversityWuhanChina
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic BeltMinistry of EducationWuhanChina
- The Key Laboratory of Aquatic Biodiversity and ConservationInstitute of HydrobiologyChinese Academy of SciencesWuhanChina
| | - Chengxing Xia
- Key Laboratory of Freshwater Animal BreedingMinistry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of FisheriesHuazhong Agricultural UniversityWuhanChina
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic BeltMinistry of EducationWuhanChina
| | - Jun Wang
- Key Laboratory of Freshwater Animal BreedingMinistry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of FisheriesHuazhong Agricultural UniversityWuhanChina
- The Key Laboratory of Aquatic Biodiversity and ConservationInstitute of HydrobiologyChinese Academy of SciencesWuhanChina
| | - Xiujie Zhang
- Key Laboratory of Freshwater Animal BreedingMinistry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of FisheriesHuazhong Agricultural UniversityWuhanChina
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic BeltMinistry of EducationWuhanChina
| | - Xufa Ma
- Key Laboratory of Freshwater Animal BreedingMinistry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of FisheriesHuazhong Agricultural UniversityWuhanChina
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic BeltMinistry of EducationWuhanChina
| | - Qiong Zhou
- Key Laboratory of Freshwater Animal BreedingMinistry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of FisheriesHuazhong Agricultural UniversityWuhanChina
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic BeltMinistry of EducationWuhanChina
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9
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DNA Barcoding of Marine Mollusks Associated with Corallina officinalis Turfs in Southern Istria (Adriatic Sea). DIVERSITY 2021. [DOI: 10.3390/d13050196] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Presence of mollusk assemblages was studied within red coralligenous algae Corallina officinalis L. along the southern Istrian coast. C. officinalis turfs can be considered a biodiversity reservoir, as they shelter numerous invertebrate species. The aim of this study was to identify mollusk species within these settlements using DNA barcoding as a method for detailed identification of mollusks. Nine locations and 18 localities with algal coverage range above 90% were chosen at four research areas. From 54 collected samples of C. officinalis turfs, a total of 46 mollusk species were identified. Molecular methods helped identify 16 gastropod, 14 bivalve and one polyplacophoran species. COI sequences for two bivalve species (Musculus cf. costulatus (Risso, 1826) and Gregariella semigranata (Reeve, 1858)) and seven gastropod species (Megastomia winfriedi Peñas & Rolán, 1999, Eatonina sp. Thiele, 1912, Eatonina cossurae (Calcara, 1841), Crisilla cf. maculata (Monterosato, 1869), Alvania cf. carinata (da Costa, 1778), Vitreolina antiflexa (Monterosato, 1884) and Odostomia plicata (Montagu, 1803)) represent new BINs in BOLD database. This study contributes to new findings related to the high biodiversity of mollusks associated with widespread C. officinalis settlements along the southern coastal area of Istria.
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Raupach MJ, Hannig K, Morinière J, Hendrich L. A DNA barcode library for ground beetles of Germany: the genus Pterostichus Bonelli, 1810 and allied taxa (Insecta, Coleoptera, Carabidae). Zookeys 2020; 980:93-117. [PMID: 33192140 PMCID: PMC7642132 DOI: 10.3897/zookeys.980.55979] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/04/2020] [Indexed: 11/12/2022] Open
Abstract
Species of the ground beetle genus Pterostichus Bonelli, 1810 are some of the most common carabids in Europe. This publication provides a first comprehensive DNA barcode library for this genus and allied taxa including Abax Bonelli, 1810, Molops Bonelli, 1810, Poecilus Bonelli, 1810, and Stomis Clairville, 1806 for Germany and Central Europe in general. DNA barcodes were analyzed from 609 individuals that represent 51 species, including sequences from previous studies as well as more than 198 newly generated sequences. The results showed a 1:1 correspondence between BIN and traditionally recognized species for 44 species (86%), whereas two (4%) species were characterized by two BINs. Three BINs were found for one species (2%), while one BIN for two species was revealed for two species pairs (8%). Low interspecific distances with maximum pairwise K2P values below 2.2% were found for four species pairs. Haplotype sharing was found for two closely related species pairs: Pterostichusadstrictus Eschscholtz, 1823/Pterostichusoblongopunctatus (Fabricius, 1787) and Pterostichusnigrita Paykull, 1790/Pterostichusrhaeticus Heer, 1837. In contrast to this, high intraspecific sequence divergences with values above 2.2% were shown for three species (Molopspiceus (Panzer, 1793), Pterostichuspanzeri (Panzer, 1805), Pterostichusstrenuus (Panzer, 1793)). Summarizing the results, the present DNA barcode library does not only allow the identification of most of the analyzed species, but also provides valuable information for alpha-taxonomy as well as for ecological and evolutionary research. This library represents another step in building a comprehensive DNA barcode library of ground beetles as part of modern biodiversity research.
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Affiliation(s)
- Michael J Raupach
- Sektion Hemiptera, Bavarian State Collection of Zoology (SNSB - ZSM), Münchhausenstraße 21, 81247 München, Germany
| | | | - Jérome Morinière
- AIM - Advanced Identification Methods GmbH, Spinnereistraße 11, 04179 Leipzig
| | - Lars Hendrich
- Sektion Insecta varia, Bavarian State Collection of Zoology (SNSB - ZSM), Münchhausenstraße 21, 81247 München, Germany
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11
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Franco‐Sierra ND, Díaz‐Nieto JF. Rapid mitochondrial genome sequencing based on Oxford Nanopore Sequencing and a proxy for vertebrate species identification. Ecol Evol 2020; 10:3544-3560. [PMID: 32274008 PMCID: PMC7141017 DOI: 10.1002/ece3.6151] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 02/09/2020] [Accepted: 02/12/2020] [Indexed: 02/06/2023] Open
Abstract
Molecular information is crucial for species identification when facing challenging morphology-based specimen identifications. The use of DNA barcodes partially solves this problem, but in some cases when PCR is not an option (i.e., primers are not available, problems in reaction standardization), amplification-free approaches could be an optimal alternative. Recent advances in DNA sequencing, like the MinION device from Oxford Nanopore Technologies (ONT), allow to obtain genomic data with low laboratory and technical requirements, and at a relatively low cost. In this study, we explore ONT sequencing for molecular species identification from a total DNA sample obtained from a neotropical rodent and we also test the technology for complete mitochondrial genome reconstruction via genome skimming. We were able to obtain "de novo" the complete mitogenome of a specimen from the genus Melanomys (Cricetidae: Sigmodontinae) with average depth coverage of 78X using ONT-only data and by combining multiple assembly routines. Our pipeline for an automated species identification was able to identify the sample using unassembled sequence data (raw) in a reasonable computing time, which was substantially reduced when a priori information related to the organism identity was known. Our findings suggest ONT sequencing as a suitable candidate to solve species identification problems in metazoan nonmodel organisms and generate complete mtDNA datasets.
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Affiliation(s)
- Nicolás D. Franco‐Sierra
- Grupo de investigación en Biodiversidad, Evolución y Conservación (BEC)Departamento de Ciencias Biológicas, Escuela de CienciasUniversidad EAFITMedellínColombia
| | - Juan F. Díaz‐Nieto
- Grupo de investigación en Biodiversidad, Evolución y Conservación (BEC)Departamento de Ciencias Biológicas, Escuela de CienciasUniversidad EAFITMedellínColombia
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12
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Ran K, Li Q, Qi L, Li W, Kong L. Molecular identification of Cerithiidae (Mollusca: Gastropod) in Hainan island, China. Mitochondrial DNA A DNA Mapp Seq Anal 2020; 31:57-63. [PMID: 32054368 DOI: 10.1080/24701394.2020.1726898] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
A number of same species of Cerithiidae are morphologically unlike, whereas most of species in the same genus are morphologically similar and just exhibit subtle differences. It is difficult to identify them by morphological methods alone. DNA barcoding is a modern molecular technique that can be used to identify species accurately, and is particularly helpful when distinguishing morphologically similar species. In order to identify species of Cerithiidae using DNA barcoding technology based on mitochondrial cytochrome oxidase subunit I (COI) and 16S ribosomal RNA (16S rRNA) genes, this study calculated intraspecific and interspecific genetic distance and constructed the phylogenetic trees. A total of 80 COI and 16S rRNA barcode sequences were obtained from 10 species and 3 genera. Some unknown specimens were further identified and a cryptic species may exist in Cerithium traillii, showing that DNA barcoding technology has the potential to discover new species and cryptic species. The phylogenetic trees revealed that all of the cerithiids could converge upon a monophyly with high support values and two genera (Cerithium and Clypeomorus) maybe support the reclassification. It is necessary for traditional morphological methods to combine with the DNA barcoding for classification and identification of Cerithiidae.
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Affiliation(s)
- Ke Ran
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Lu Qi
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
| | - Weidong Li
- College of Life Sciences and Ecology, Hainan Tropical Ocean University, Sanya, China
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
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13
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Wall-Palmer D, Hegmann M, Goetze E, Peijnenburg KT. Resolving species boundaries in the Atlanta brunnea species group (Gastropoda, Pterotracheoidea). Zookeys 2019; 899:59-84. [PMID: 31871402 PMCID: PMC6923281 DOI: 10.3897/zookeys.899.38892] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 10/29/2019] [Indexed: 12/22/2022] Open
Abstract
Atlantid heteropods are a family of holoplanktonic marine gastropods that occur primarily in tropical and subtropical latitudes. Atlantids bear a delicate aragonitic shell (<14 mm) and live in the upper ocean, where ocean acidification and ocean warming have a pronounced effect. Therefore, atlantids are likely to be sensitive to these ocean changes. However, we lack sufficiently detailed information on atlantid taxonomy and biogeography, which is needed to gain a deeper understanding of the consequences of a changing ocean. To date, atlantid taxonomy has mainly relied on morphometrics and shell ornamentation, but recent molecular work has highlighted hidden diversity. This study uses an integrated approach in a global analysis of biogeography, variation in shell morphology and molecular phylogenies based on three genes (CO1, 28S and 18S) to resolve the species boundaries within the Atlanta brunnea group. Results identify a new species, Atlanta vanderspoeli, from the Equatorial and South Pacific Ocean, and suggest that individuals of A. brunnea living in the Atlantic Ocean are an incipient species. Our results provide an important advance in atlantid taxonomy and will enable identification of these species in future studies of living and fossil plankton.
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Affiliation(s)
- Deborah Wall-Palmer
- Marine Biodiversity Group, Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The NetherlandsNaturalis Biodiversity CenterLeidenNetherlands
| | - Mona Hegmann
- Marine Biodiversity Group, Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The NetherlandsNaturalis Biodiversity CenterLeidenNetherlands
- Institute for Biosciences, University of Rostock, Albert Einstein Straβe 3, 18059 Rostock, GermanyUniversity of RostockRostockGermany
| | - Erica Goetze
- Department of Oceanography, University of Hawaii at Manoa, 1000 Pope Road, Honolulu, Hawaii, 96822, USAUniversity of Hawaii at ManoaHawaiiUnited States of America
| | - Katja T.C.A. Peijnenburg
- Marine Biodiversity Group, Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The NetherlandsNaturalis Biodiversity CenterLeidenNetherlands
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, P. O. Box 942480 1090 GE Amsterdam, The NetherlandsUniversity of AmsterdamAmsterdamNetherlands
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14
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Weigand H, Beermann AJ, Čiampor F, Costa FO, Csabai Z, Duarte S, Geiger MF, Grabowski M, Rimet F, Rulik B, Strand M, Szucsich N, Weigand AM, Willassen E, Wyler SA, Bouchez A, Borja A, Čiamporová-Zaťovičová Z, Ferreira S, Dijkstra KDB, Eisendle U, Freyhof J, Gadawski P, Graf W, Haegerbaeumer A, van der Hoorn BB, Japoshvili B, Keresztes L, Keskin E, Leese F, Macher JN, Mamos T, Paz G, Pešić V, Pfannkuchen DM, Pfannkuchen MA, Price BW, Rinkevich B, Teixeira MAL, Várbíró G, Ekrem T. DNA barcode reference libraries for the monitoring of aquatic biota in Europe: Gap-analysis and recommendations for future work. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 678:499-524. [PMID: 31077928 DOI: 10.1016/j.scitotenv.2019.04.247] [Citation(s) in RCA: 166] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 04/16/2019] [Accepted: 04/16/2019] [Indexed: 05/21/2023]
Abstract
Effective identification of species using short DNA fragments (DNA barcoding and DNA metabarcoding) requires reliable sequence reference libraries of known taxa. Both taxonomically comprehensive coverage and content quality are important for sufficient accuracy. For aquatic ecosystems in Europe, reliable barcode reference libraries are particularly important if molecular identification tools are to be implemented in biomonitoring and reports in the context of the EU Water Framework Directive (WFD) and the Marine Strategy Framework Directive (MSFD). We analysed gaps in the two most important reference databases, Barcode of Life Data Systems (BOLD) and NCBI GenBank, with a focus on the taxa most frequently used in WFD and MSFD. Our analyses show that coverage varies strongly among taxonomic groups, and among geographic regions. In general, groups that were actively targeted in barcode projects (e.g. fish, true bugs, caddisflies and vascular plants) are well represented in the barcode libraries, while others have fewer records (e.g. marine molluscs, ascidians, and freshwater diatoms). We also found that species monitored in several countries often are represented by barcodes in reference libraries, while species monitored in a single country frequently lack sequence records. A large proportion of species (up to 50%) in several taxonomic groups are only represented by private data in BOLD. Our results have implications for the future strategy to fill existing gaps in barcode libraries, especially if DNA metabarcoding is to be used in the monitoring of European aquatic biota under the WFD and MSFD. For example, missing species relevant to monitoring in multiple countries should be prioritized for future collaborative programs. We also discuss why a strategy for quality control and quality assurance of barcode reference libraries is needed and recommend future steps to ensure full utilisation of metabarcoding in aquatic biomonitoring.
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Affiliation(s)
- Hannah Weigand
- Musée National d'Histoire Naturelle, 25 Rue Münster, 2160 Luxembourg, Luxembourg.
| | - Arne J Beermann
- University of Duisburg-Essen, Faculty of Biology, Aquatic Ecosystem Research, Universitaetsstr. 5, 45141 Essen, Germany.
| | - Fedor Čiampor
- Slovak Academy of Sciences, Plant Science and Biodiversity Centre, Zoology Lab, Dúbravská cesta 9, 84523 Bratislava, Slovakia.
| | - Filipe O Costa
- Centre of Molecular and Environmental Biology (CBMA), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710--057 Braga, Portugal.
| | - Zoltán Csabai
- University of Pécs, Faculty of Sciences, Department of Hydrobiology, Ifjúság útja 6, H7624 Pécs, Hungary.
| | - Sofia Duarte
- Centre of Molecular and Environmental Biology (CBMA), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710--057 Braga, Portugal.
| | - Matthias F Geiger
- Zoologisches Forschungsmuseum Alexander Koenig, Leibniz Institute for Animal Biodiversity, Adenauerallee 160, 53113 Bonn, Germany.
| | - Michał Grabowski
- University of Lodz, Faculty of Biology and Environmental Protection, Department of Invertebrate Zoology and Hydrobiology, Banacha 12/16, 90-237 Łódź, Poland.
| | - Frédéric Rimet
- INRA, Université Savoie Mont Blanc, UMR Carrtel, FR-74200 Thonon-les-Bains, France.
| | - Björn Rulik
- Zoologisches Forschungsmuseum Alexander Koenig, Leibniz Institute for Animal Biodiversity, Adenauerallee 160, 53113 Bonn, Germany.
| | - Malin Strand
- Swedish University of Agricultural Sciences, Swedish Species Information Centre, Uppsala, Sweden.
| | | | - Alexander M Weigand
- Musée National d'Histoire Naturelle, 25 Rue Münster, 2160 Luxembourg, Luxembourg; University of Duisburg-Essen, Faculty of Biology, Aquatic Ecosystem Research, Universitaetsstr. 5, 45141 Essen, Germany.
| | - Endre Willassen
- University of Bergen, University Museum of Bergen, NO-5007 Bergen, Norway.
| | - Sofia A Wyler
- info fauna - Centre Suisse de Cartographie de la Faune (CSCF), Avenue de Bellevaux 51, 2000 Neuchâtel, Switzerland.
| | - Agnès Bouchez
- INRA, Université Savoie Mont Blanc, UMR Carrtel, FR-74200 Thonon-les-Bains, France.
| | - Angel Borja
- AZTI - Marine Research Division, Herrera Kaia, Portualdea z/g, 20110 Pasaia, Gipuzkoa, Spain.
| | - Zuzana Čiamporová-Zaťovičová
- Slovak Academy of Sciences, Plant Science and Biodiversity Centre, Zoology Lab, Dúbravská cesta 9, 84523 Bratislava, Slovakia.
| | - Sónia Ferreira
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | | | - Ursula Eisendle
- University of Salzburg, Department of Biosciences, Hellbrunnerstraße 34, 5020 Salzburg, Austria.
| | - Jörg Freyhof
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), 12587 Berlin, Germany.
| | - Piotr Gadawski
- University of Lodz, Faculty of Biology and Environmental Protection, Department of Invertebrate Zoology and Hydrobiology, Banacha 12/16, 90-237 Łódź, Poland.
| | - Wolfram Graf
- University of Natural Resources and Life Sciences, Vienna, Institute of Hydrobiology and Aquatic Ecosystem Management (IHG), Gregor-Mendel-Straße 33/DG, 1180 Vienna, Austria.
| | - Arne Haegerbaeumer
- Bielefeld University, Department of Animal Ecology, Konsequenz 45, 33615 Bielefeld, Germany.
| | | | - Bella Japoshvili
- Ilia State University, Institute of Zoology, ⅗ Cholokashvili ave, 0179 Tbilisi, Georgia.
| | - Lujza Keresztes
- Babeș-Bolyai University, Faculty of Biology and Geology, Center of Systems Biology, Biodiversity and Bioresources, Cliniclor 5-7, 400006 Cluj Napoca, Romania
| | - Emre Keskin
- Ankara University, Agricultural Faculty, Department of Fisheries and Aquaculture, Evolutionary Genetics Laboratory (eGL), Ankara, Turkey.
| | - Florian Leese
- University of Duisburg-Essen, Faculty of Biology, Aquatic Ecosystem Research, Universitaetsstr. 5, 45141 Essen, Germany.
| | - Jan N Macher
- Naturalis Biodiversity Center, PO Box 9517, 2300 RA Leiden, the Netherlands.
| | - Tomasz Mamos
- University of Lodz, Faculty of Biology and Environmental Protection, Department of Invertebrate Zoology and Hydrobiology, Banacha 12/16, 90-237 Łódź, Poland.
| | - Guy Paz
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, Haifa 31080, Israel.
| | - Vladimir Pešić
- University of Montenegro, Department of Biology, Cetinjski put bb., 20000 Podgorica, Montenegro
| | | | | | | | - Buki Rinkevich
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, Haifa 31080, Israel.
| | - Marcos A L Teixeira
- Centre of Molecular and Environmental Biology (CBMA), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710--057 Braga, Portugal
| | - Gábor Várbíró
- MTA Centre for Ecological Research, Danube Research Institute, Department of Tisza River Research, Bem square 18/C, H4026 Debrecen, Hungary.
| | - Torbjørn Ekrem
- Norwegian University of Science and Technology, NTNU University Museum, Department of Natural History, NO-7491 Trondheim, Norway.
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15
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Magnúsdóttir H, Pálsson S, Westfall KM, Jónsson ZO, Goodall J, Örnólfsdóttir EB. Revised phylogeography of the common whelk Buccinum undatum (Gastropoda: Buccinidae) across the North Atlantic. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz060] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
AbstractThe purpose of this study was to revisit the mitochondrial genetic divergence of North Atlantic populations of the subtidal gastropod Buccinum undatum, because previous mitochondrial DNA (mtDNA) analysis by Pálsson et al. (2014) included 16S ribosomal RNA sequences that were incorrectly assigned to the species. In the present study, population mtDNA variation is now assessed using COI sequences obtained from previous research (Pálsson et al., 2014) and, to increase the geographical cover of the study, data from recently assembled transcriptomes of 96 Icelandic whelks (Jónsson et al., 2019) and GenBank are also used. To estimate the mtDNA divergence in B. undatum across the North Atlantic, two species screening indices were used: automatic barcode gap discovey (ABGD; Puillandre et al., 2012a) and species screening threshold index (SSTI; Witt et al., 2006). Phylogenetic reconstruction revealed monophyletic Eastern and Western North Atlantic whelk lineages, which diverged early in the Pleistocene glaciation (2.1 Mya), followed by a subsequent divergence event between Greenlandic and Canadian populations at 1.3 Mya. Species screening indices, ABGD and SSTI, indicated cryptic speciation or allopatric divergence. Genetic distances between populations from the two continents were similar to or greater than interspecific genetic distances across several North Pacific and North Atlantic Buccinum species.
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Affiliation(s)
- Hildur Magnúsdóttir
- Faculty of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
- Department of Aquaculture and Fish Biology, Hólar University College, Sauðárkrókur, Iceland
| | - Snæbjörn Pálsson
- Faculty of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
| | - Kristen Marie Westfall
- Faculty of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
- Vör – Marine Research Centre in Breiðafjörður, Ólafsvík, Iceland
| | - Zophonías O Jónsson
- Faculty of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
| | - Jake Goodall
- Faculty of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
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16
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Hofmann EP, Nicholson KE, Luque-Montes IR, Köhler G, Cerrato-Mendoza CA, Medina-Flores M, Wilson LD, Townsend JH. Cryptic Diversity, but to What Extent? Discordance Between Single-Locus Species Delimitation Methods Within Mainland Anoles (Squamata: Dactyloidae) of Northern Central America. Front Genet 2019; 10:11. [PMID: 30804976 PMCID: PMC6378269 DOI: 10.3389/fgene.2019.00011] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 01/11/2019] [Indexed: 01/10/2023] Open
Abstract
Single-locus molecular barcoding is a useful method for identifying overlooked and undescribed biodiversity, providing the groundwork for further systematic study and taxonomic investigation. A variety of methods for delimiting species from barcoding libraries have been developed and applied, allowing for rapid estimates of species diversity in a broad range of taxa. However, tree-based and distance-based analyses can infer different group assignments, potentially over- or underestimating the number of putative species groups. Here, we explore diversity of mainland species of anole lizards from the Chortís Block biogeographical province of northern Central America using a DNA barcoding approach, generating and analyzing cytochrome oxidase subunit I (COI) sequences for over 400 samples assignable to 33 of 38 (86.8%) native and one introduced mainland species. We subsequently tested the effects different models of nucleotide substitution, different species-delimitation algorithms, and reducing our dataset had on species delimitation estimates. We performed of two distance-based (ABGD, RESL) and three tree-based (bPTP, mPTP, GMYC) analyses on both the full dataset and a dataset consisting only of unique halotypes. From 34 nominal taxa, analyses of the full dataset recovered between 34 and 64 operational taxonomic units (OTUs), while analyses of the reduced dataset inferred between 36 and 59. Reassigning individuals to either mPTP-inferred or ABGD clustered (7.2% threshold) groups improved the detection of a barcoding gap across three different models of nucleotide substitution, removing overlap between intra- and interspecific distances. Our results highlight the underestimated diversity of mainland Chortís Block anoles, but the lack of congruence between analyses demonstrates the importance of considering multiple analytical methods when dealing with single-locus datasets. We recommend future studies consider the effects of different models of nucleotide substitution on proposed barcoding gaps, as well as the effect reducing a dataset to unique haplotypes may have on proposed diversity estimates.
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Affiliation(s)
- Erich P. Hofmann
- Department of Biology, Indiana University of Pennsylvania, Indiana, PA, United States
- Department of Biological Sciences, Clemson University, Clemson, SC, United States
| | - Kirsten E. Nicholson
- Department of Biology, Central Michigan University, Mount Pleasant, MI, United States
| | | | - Gunther Köhler
- Senckenberg Forschungsinstitut und Naturmuseum, Frankfurt, Germany
| | - César A. Cerrato-Mendoza
- Federación Hondureña de Deportes de Montaña Y Escalada, Departamento de Francisco Morazán, Tegucigalpa, Honduras
| | - Melissa Medina-Flores
- Federación Hondureña de Deportes de Montaña Y Escalada, Departamento de Francisco Morazán, Tegucigalpa, Honduras
| | - Larry David Wilson
- Centro Zamorano de Biodiversidad, Escuela Agrícola Panamericana Zamorano, Departamento de Francisco Morazán, Tegucigalpa, Honduras
| | - Josiah H. Townsend
- Department of Biology, Indiana University of Pennsylvania, Indiana, PA, United States
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17
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Ren F, Wang Y, Xu Z, Li Y, Xin T, Zhou J, Qi Y, Wei X, Yao H, Song J. DNA barcoding of Corydalis, the most taxonomically complicated genus of Papaveraceae. Ecol Evol 2019; 9:1934-1945. [PMID: 30847083 PMCID: PMC6392370 DOI: 10.1002/ece3.4886] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 11/02/2018] [Accepted: 12/06/2018] [Indexed: 02/06/2023] Open
Abstract
The genus Corydalis is recognized as one of the most taxonomically challenging plant taxa. It is mainly distributed in the Himalaya-Hengduan Mountains, a global biodiversity hotspot. To date, no effective solution for species discrimination and taxonomic assignment in Corydalis has been developed. In this study, five nuclear and chloroplast DNA regions, ITS, ITS2, matK, rbcL, and psbA-trnH, were preliminarily assessed based on their ability to discriminate Corydalis to eliminate inefficient regions, and the three regions showing good performance (ITS, ITS2 and matK) were then evaluated in 131 samples representing 28 species of 11 sections of four subgenera in Corydalis using three analytical methods (NJ, ML, MP tree; K2P-distance and BLAST). The results showed that the various approaches exhibit different species identification power and that BLAST shows the best performance among the tested approaches. A comparison of different barcodes indicated that among the single barcodes, ITS (65.2%) exhibited the highest identification success rate and that the combination of ITS + matK (69.6%) provided the highest species resolution among all single barcodes and their combinations. Three Pharmacopoeia-recorded medicinal plants and their materia medica were identified successfully based on the ITS and ITS2 regions. In the phylogenetic analysis, the sections Thalictrifoliae, Sophorocapnos, Racemosae, Aulacostigma, and Corydalis formed well-supported separate lineages. We thus hypothesize that the five sections should be classified as an independent subgenus and that the genus should be divided into three subgenera. In this study, DNA barcoding provided relatively high species discrimination power, indicating that it can be used for species discrimination in this taxonomically complicated genus and as a potential tool for the authentication of materia medica belonging to Corydalis.
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Affiliation(s)
- Feng‐Ming Ren
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
- Chongqing Institute of Medicinal Plant Cultivation, Research and Utilization on Characteristic Biological Resources of Sichuan and Chongqing Co‐construction LabChinese Medicine Breeding and Evaluation Engineering Technology Research Center of ChongqingChongqingChina
| | - Ying‐Wei Wang
- Beijing Botanical Garden, Institute of BotanyChinese Academy of SciencesBeijingChina
| | - Zhi‐Chao Xu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
| | - Ying Li
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
| | - Tian‐Yi Xin
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
| | - Jian‐Guo Zhou
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
| | - Yao‐Dong Qi
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
| | - Xue‐Ping Wei
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
| | - Hui Yao
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
| | - Jing‐Yuan Song
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
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18
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An Antarctic flock under the Thorson's rule: Diversity and larval development of Antarctic Velutinidae (Mollusca: Gastropoda). Mol Phylogenet Evol 2018; 132:1-13. [PMID: 30502396 DOI: 10.1016/j.ympev.2018.11.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 11/22/2018] [Accepted: 11/22/2018] [Indexed: 11/22/2022]
Abstract
In most marine gastropods, the duration of the larval phase is a key feature, strongly influencing species distribution and persistence. Antarctic lineages, in agreement with Thorson's rule, generally show a short pelagic developmental phase (or lack it completely), with very few exceptions. Among them is the ascidian-feeding gastropod family Velutinidae, a quite understudied group. Based on a multilocus (COI, 16S, 28S and ITS2) dataset for 182 specimens collected in Antarctica and other regions worldwide, we investigated the actual Antarctic velutinid diversity, inferred their larval development, tested species genetic connectivity and produced a first phylogenetic framework of the family. We identified 15 Antarctic Molecular Operational Taxonomic Units (MOTUs), some of which represented undescribed species, which show two different types of larval shell, indicating different duration of the Pelagic Larval Phase (PLD). Antarctic velutinids stand as an independent lineage, sister to the rest of the family, with extensive hidden diversity likely produced by rapid radiation. Our phylogenetic framework indicates that this Antarctic flock underwent repeated events of pelagic phase shortening, in agreement with Thorson's rule, yielding species with restricted geographic ranges.
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19
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Spielmann G, Diedrich J, Haszprunar G, Busch U, Huber I. Comparison of three DNA marker regions for identification of food relevant crustaceans of the order Decapoda. Eur Food Res Technol 2018. [DOI: 10.1007/s00217-018-3199-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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20
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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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21
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Wang JD, Wang WZ, Lin ZL, Ali A, Fu HY, Huang MT, Gao SJ, Wang R. DNA Barcoding for Identification of Sugarcane Borers in China. NEOTROPICAL ENTOMOLOGY 2018; 47:362-368. [PMID: 28965311 DOI: 10.1007/s13744-017-0560-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 09/03/2017] [Indexed: 06/07/2023]
Abstract
Sugarcane borers are economically damaging insects with species that vary in distribution patterns both geographically and temporally, and vary based on ecological niche. Currently, identification of sugarcane borers is mostly based on morphological characters. However, morphological identification requires taxonomic expertise. An alternative method to identify sugarcane borers is the use of molecular data. DNA barcoding based on partial cytochrome c oxidase subunit 1 (COI) sequences has proven to be a useful tool for rapid and accurate species determination in many insect taxa. This study was conducted to test the effectiveness of DNA barcodes to discriminate among sugarcane borer species in China. Partial sequences of the COI gene (709 bp) were obtained from six species collected from different geographic areas. Results showed that the pairwise intraspecies genetic distance was < 0.02, whereas the interspecies genetic distance ranged from 0.117 to 0.182. Results from a neighbor-joining tree showed that the six sugarcane borer species were certainly separated. These results suggested that the partial COI sequences had high barcoding resolution in discriminating among sugarcane borer species. Our study emphasized the use of DNA barcodes for identification of the analyzed sugarcane borer species and represents an important step for building a comprehensive barcode library for sugarcane borers in China.
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Affiliation(s)
- J- D Wang
- National Engineering Research Center for Sugarcane, Fujian Agricultural and Forestry Univ, Fuzhou, Fujian, 350002, China.
| | - W- Z Wang
- National Engineering Research Center for Sugarcane, Fujian Agricultural and Forestry Univ, Fuzhou, Fujian, 350002, China
| | - Z- L Lin
- National Engineering Research Center for Sugarcane, Fujian Agricultural and Forestry Univ, Fuzhou, Fujian, 350002, China
| | - A Ali
- National Engineering Research Center for Sugarcane, Fujian Agricultural and Forestry Univ, Fuzhou, Fujian, 350002, China
| | - H- Y Fu
- National Engineering Research Center for Sugarcane, Fujian Agricultural and Forestry Univ, Fuzhou, Fujian, 350002, China
| | - M- T Huang
- National Engineering Research Center for Sugarcane, Fujian Agricultural and Forestry Univ, Fuzhou, Fujian, 350002, China
| | - S- J Gao
- National Engineering Research Center for Sugarcane, Fujian Agricultural and Forestry Univ, Fuzhou, Fujian, 350002, China
| | - R Wang
- College of Forestry, Fujian Agricultural and Forestry Univ, Fuzhou, Fujian, 350002, China.
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22
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Raupach MJ, Hannig K, Moriniére J, Hendrich L. A DNA barcode library for ground beetles of Germany: the genus Amara Bonelli, 1810 (Insecta, Coleoptera, Carabidae). Zookeys 2018; 759:57-80. [PMID: 29853775 PMCID: PMC5968077 DOI: 10.3897/zookeys.759.24129] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 03/27/2018] [Indexed: 01/08/2023] Open
Abstract
The genus Amara Bonelli, 1810 is a very speciose and taxonomically difficult genus of the Carabidae. The identification of many of the species is accomplished with considerable difficulty, in particular for females and immature stages. In this study the effectiveness of DNA barcoding, the most popular method for molecular species identification, was examined to discriminate various species of this genus from Central Europe. DNA barcodes from 690 individuals and 47 species were analysed, including sequences from previous studies and more than 350 newly generated DNA barcodes. Our analysis revealed unique BINs for 38 species (81%). Interspecific K2P distances below 2.2% were found for three species pairs and one species trio, including haplotype sharing between Amara alpina/Amara torrida and Amara communis/Amara convexior/Amara makolskii. This study represents another step in generating an extensive reference library of DNA barcodes for carabids, highly valuable bioindicators for characterizing disturbances in various habitats.
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Affiliation(s)
- Michael J. Raupach
- Institute for Biology and Environmental Sciences, Carl von Ossietzky University Oldenburg, Carl von Ossietzky Straße 9-11, 26111 Oldenburg, Germany
| | | | - Jérôme Moriniére
- Taxonomic coordinator – German Barcode of Life (GBOL), Bavarian State Collection of Zoology (SNSB – ZSM), Münchhausenstraße 21, 81247 München, Germany
| | - Lars Hendrich
- Sektion Insecta varia, Bavarian State Collection of Zoology (SNSB – ZSM), Münchhausenstraße 21, 81247 München, Germany
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23
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Beermann J, Westbury MV, Hofreiter M, Hilgers L, Deister F, Neumann H, Raupach MJ. Cryptic species in a well-known habitat: applying taxonomics to the amphipod genus Epimeria (Crustacea, Peracarida). Sci Rep 2018; 8:6893. [PMID: 29720606 PMCID: PMC5931980 DOI: 10.1038/s41598-018-25225-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 04/17/2018] [Indexed: 11/19/2022] Open
Abstract
Taxonomy plays a central role in biological sciences. It provides a communication system for scientists as it aims to enable correct identification of the studied organisms. As a consequence, species descriptions should seek to include as much available information as possible at species level to follow an integrative concept of 'taxonomics'. Here, we describe the cryptic species Epimeria frankei sp. nov. from the North Sea, and also redescribe its sister species, Epimeria cornigera. The morphological information obtained is substantiated by DNA barcodes and complete nuclear 18S rRNA gene sequences. In addition, we provide, for the first time, full mitochondrial genome data as part of a metazoan species description for a holotype, as well as the neotype. This study represents the first successful implementation of the recently proposed concept of taxonomics, using data from high-throughput technologies for integrative taxonomic studies, allowing the highest level of confidence for both biodiversity and ecological research.
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Affiliation(s)
- Jan Beermann
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Department of Functional Ecology, PO Box 120161, 27515, Bremerhaven, Germany.
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Biologische Anstalt Helgoland, Helgoland, Germany.
- Helmholtz Institute for Functional Marine Biodiversity, Oldenburg, Germany.
| | - Michael V Westbury
- University of Potsdam, Institute for Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany
| | - Michael Hofreiter
- University of Potsdam, Institute for Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany
| | - Leon Hilgers
- University of Potsdam, Institute for Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstr. 43, 10115, Berlin, Germany
| | - Fabian Deister
- Carl von Ossietzky University Oldenburg, Institute for Biology and Environmental Sciences, PO Box 2503, 26111, Oldenburg, Germany
| | - Hermann Neumann
- Senckenberg am Meer, Department for Marine Research, Südstrand 40, 26382, Wilhelmshaven, Germany
| | - Michael J Raupach
- Carl von Ossietzky University Oldenburg, Institute for Biology and Environmental Sciences, PO Box 2503, 26111, Oldenburg, Germany
- Senckenberg am Meer, German Center of Marine Biodiversity (DZMB), Südstrand 44, 26382, Wilhelmshaven, Germany
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24
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Havemann N, Gossner MM, Hendrich L, Morinière J, Niedringhaus R, Schäfer P, Raupach MJ. From water striders to water bugs: the molecular diversity of aquatic Heteroptera (Gerromorpha, Nepomorpha) of Germany based on DNA barcodes. PeerJ 2018; 6:e4577. [PMID: 29736329 PMCID: PMC5936072 DOI: 10.7717/peerj.4577] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 03/14/2018] [Indexed: 11/20/2022] Open
Abstract
With about 5,000 species worldwide, the Heteroptera or true bugs are the most diverse taxon among the hemimetabolous insects in aquatic and semi-aquatic ecosystems. Species may be found in almost every freshwater environment and have very specific habitat requirements, making them excellent bioindicator organisms for water quality. However, a correct determination by morphology is challenging in many species groups due to high morphological variability and polymorphisms within, but low variability between species. Furthermore, it is very difficult or even impossible to identify the immature life stages or females of some species, e.g., of the corixid genus Sigara. In this study we tested the effectiveness of a DNA barcode library to discriminate species of the Gerromorpha and Nepomorpha of Germany. We analyzed about 700 specimens of 67 species, with 63 species sampled in Germany, covering more than 90% of all recorded species. Our library included various morphological similar taxa, e.g., species within the genera Sigara and Notonecta as well as water striders of the genus Gerris. Fifty-five species (82%) were unambiguously assigned to a single Barcode Index Number (BIN) by their barcode sequences, whereas BIN sharing was observed for 10 species. Furthermore, we found monophyletic lineages for 52 analyzed species. Our data revealed interspecific K2P distances with below 2.2% for 18 species. Intraspecific distances above 2.2% were shown for 11 species. We found evidence for hybridization between various corixid species (Sigara, Callicorixa), but our molecular data also revealed exceptionally high intraspecific distances as a consequence of distinct mitochondrial lineages for Cymatia coleoptrata and the pygmy backswimmer Plea minutissima. Our study clearly demonstrates the usefulness of DNA barcodes for the identification of the aquatic Heteroptera of Germany and adjacent regions. In this context, our data set represents an essential baseline for a reference library for bioassessment studies of freshwater habitats using modern high-throughput technologies in the near future. The existing data also opens new questions regarding the causes of observed low inter- and high intraspecific genetic variation and furthermore highlight the necessity of taxonomic revisions for various taxa, combining both molecular and morphological data.
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Affiliation(s)
- Nadine Havemann
- Fakultät V, Institut für Biologie und Umweltwissenschaften (IBU), Carl von Ossietzky Universität Oldenburg, Oldenburg, Lower Saxony, Germany.,German Centre of Marine Biodiversity, Senckenberg Nature Research Society, Wilhelmshaven, Lower Saxony, Germany
| | - Martin M Gossner
- Forest Entomology, Swiss Federal Institute for Forest, Snow and Landscape Research, Birmensdorf, Switzerland
| | - Lars Hendrich
- Sektion Insecta varia, SNSB-Bavarian State Collection of Zoology, Munich, Bavaria, Germany
| | - Jèrôme Morinière
- Taxonomic coordinator-German Barcode of Life (GBOL), SNSB-Bavarian State Collection of Zoology, Munich, Bavaria, Germany
| | - Rolf Niedringhaus
- Department of Biology, Earth and Environmental Sciences, Carl von Ossietzky Universität Oldenburg, Oldenburg, Lower Saxony, Germany
| | - Peter Schäfer
- B.U.G.S. (Biologische Umwelt-Gutachten Schäfer), Telgte, North-Rhine Westphalia, Germany
| | - Michael J Raupach
- Fakultät V, Institut für Biologie und Umweltwissenschaften (IBU), Carl von Ossietzky Universität Oldenburg, Oldenburg, Lower Saxony, Germany.,German Centre of Marine Biodiversity, Senckenberg Nature Research Society, Wilhelmshaven, Lower Saxony, Germany
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25
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Zhang J, Yurchenko OV, Lutaenko KA, Kalachev AV, Nekhaev IO, Aguilar R, Zhan Z, Ogburn MB. A tale of two soft-shell clams: an integrative taxonomic analysis confirms Mya japonica as a valid species distinct from Mya arenaria (Bivalvia: Myidae). Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zlx107] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Junlong Zhang
- Department of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Olga V Yurchenko
- National Scientific Center of Marine Biology, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia
| | - Konstantin A Lutaenko
- National Scientific Center of Marine Biology, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia
| | - Alexander V Kalachev
- National Scientific Center of Marine Biology, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia
| | - Ivan O Nekhaev
- Laboratory of Macroecology and Biogeography of Invertebrates, Saint-Petersburg State University, Saint-Petersburg, Russia
| | - Robert Aguilar
- Smithsonian Environmental Research Center, Edgewater, MD, USA
| | - Zifeng Zhan
- Department of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
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26
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Wall-Palmer D, Burridge AK, Goetze E, Stokvis FR, Janssen AW, Mekkes L, Moreno-Alcántara M, Bednaršek N, Schiøtte T, Sørensen MV, Smart CW, T.C.A. Peijnenburg K. Biogeography and genetic diversity of the atlantid heteropods. PROGRESS IN OCEANOGRAPHY 2018; 160:1-25. [PMID: 29479121 PMCID: PMC5819870 DOI: 10.1016/j.pocean.2017.11.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 09/15/2017] [Accepted: 11/03/2017] [Indexed: 06/08/2023]
Abstract
The atlantid heteropods are regularly encountered, but rarely studied marine planktonic gastropods. Relying on a small (<14 mm), delicate aragonite shell and living in the upper ocean means that, in common with pteropods, atlantids are likely to be affected by imminent ocean changes. Variable shell morphology and widespread distributions indicate that the family is more diverse than the 23 currently known species. Uncovering this diversity is fundamental to determining the distribution of atlantids and to understanding their environmental tolerances. Here we present phylogenetic analyses of all described species of the family Atlantidae using 437 new and 52 previously published cytochrome c oxidase subunit 1 mitochondrial DNA (mtCO1) sequences. Specimens and published sequences were gathered from 32 Atlantic Ocean stations, 14 Indian Ocean stations and 21 Pacific Ocean stations between 35°N and 43°S. DNA barcoding and Automatic Barcode Gap Discovery (ABGD) proved to be valuable tools for the identification of described atlantid species, and also revealed ten additional distinct clades, suggesting that the diversity within this family has been underestimated. Only two of these clades displayed obvious morphological characteristics, demonstrating that much of the newly discovered diversity is hidden from morphology-based identification techniques. Investigation of six large atlantid collections demonstrated that 61% of previously described (morpho) species have a circumglobal distribution. Of the remaining 39%, two species were restricted to the Atlantic Ocean, five occurred in the Indian and Pacific oceans, one species was only found in the northeast Pacific Ocean, and one occurred only in the Southern Subtropical Convergence Zone. Molecular analysis showed that seven of the species with wide distributions were comprised of two or more clades that occupied distinct oceanographic regions. These distributions may suggest narrower environmental tolerances than the described morphospecies. Results provide an updated biogeography and mtCO1 reference dataset of the Atlantidae that may be used to identify atlantid species and provide a first step in understanding their evolutionary history and accurate distribution, encouraging the inclusion of this family in future plankton research.
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Affiliation(s)
- Deborah Wall-Palmer
- School of Geography, Earth and Environmental Sciences, University of Plymouth, Plymouth PL4 8AA, UK
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands
| | - Alice K. Burridge
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, 1090 GE Amsterdam, The Netherlands
| | - Erica Goetze
- Department of Oceanography, University of Hawai‘i at Mānoa, Honolulu, HI 96822, USA
| | - Frank R. Stokvis
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands
| | - Arie W. Janssen
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands
| | - Lisette Mekkes
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, 1090 GE Amsterdam, The Netherlands
| | - María Moreno-Alcántara
- Departamento de Plancton y Ecología Marina, Instituto Politécnico Nacional, Centro Interdisciplinario de Ciencias Marinas, La Paz C.P. 23096, Mexico
| | - Nina Bednaršek
- Southern California Coastal Waters Research Project, Harbor Blvd #110, Costa Mesa, CA 92626, USA
| | - Tom Schiøtte
- The Natural History Museum of Denmark, University of Copenhagen, 2100 Copenhagen, Denmark
| | | | - Christopher W. Smart
- School of Geography, Earth and Environmental Sciences, University of Plymouth, Plymouth PL4 8AA, UK
| | - Katja T.C.A. Peijnenburg
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, 1090 GE Amsterdam, The Netherlands
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27
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Hanisch PE, Lavinia PD, Suarez AV, Lijtmaer DA, Leponce M, Paris CI, Tubaro PL. Mind the gap! Integrating taxonomic approaches to assess ant diversity at the southern extreme of the Atlantic Forest. Ecol Evol 2017; 7:10451-10466. [PMID: 29238567 PMCID: PMC5723617 DOI: 10.1002/ece3.3549] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 09/12/2017] [Accepted: 09/14/2017] [Indexed: 01/19/2023] Open
Abstract
Understanding patterns of species diversity relies on accurate taxonomy which can only be achieved by long‐term natural history research and the use of complementary information to establish species boundaries among cryptic taxa. We used DNA barcoding to characterize the ant diversity of Iguazú National Park (INP), a protected area of the Upper Paraná Atlantic Forest ecoregion, located at the southernmost extent of this forest. We assessed ant diversity using both cytochrome c oxidase subunit 1 (COI) sequences and traditional morphological approaches, and compared the results of these two methods. We successfully obtained COI sequences for 312 specimens belonging to 124 species, providing a DNA barcode reference library for nearly 50% of the currently known ant fauna of INP. Our results support a clear barcode gap for all but two species, with a mean intraspecific divergence of 0.72%, and an average congeneric distance of 17.25%. Congruently, the library assembled here was useful for the discrimination of the ants of INP and allowed us to link unidentified males and queens to their worker castes. To detect overlooked diversity, we classified the DNA barcodes into Molecular Operational Taxonomic Units (MOTUs) using three different clustering algorithms, and compared their number and composition to that of reference species identified based on morphology. The MOTU count was always higher than that of reference species regardless of the method, suggesting that the diversity of ants at INP could be between 6% and 10% higher than currently recognized. Lastly, our survey contributed with 78 new barcode clusters to the global DNA barcode reference library, and added 36 new records of ant species for the INP, being 23 of them new citations for Argentina.
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Affiliation(s)
- Priscila Elena Hanisch
- Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" MACN-CONICET Buenos Aires Argentina
| | - Pablo D Lavinia
- Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" MACN-CONICET Buenos Aires Argentina
| | - Andrew V Suarez
- Department of Entomology and Department of Animal Biology University of Illinois Urbana USA
| | - Darío Alejandro Lijtmaer
- Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" MACN-CONICET Buenos Aires Argentina
| | - Maurice Leponce
- Aquatic and Terrestrial Ecology unit Royal Belgian Institute of Natural Sciences Brussels Belgium
| | - Carolina Ivon Paris
- Departamento Ecología Genética y Evolución Universidad de Buenos Aires Buenos Aires Argentina
| | - Pablo Luis Tubaro
- Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" MACN-CONICET Buenos Aires Argentina
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28
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Korshunova T, Martynov A, Bakken T, Evertsen J, Fletcher K, Mudianta IW, Saito H, Lundin K, Michael Schrödl, Picton B. Polyphyly of the traditional family Flabellinidae affects a major group of Nudibranchia: aeolidacean taxonomic reassessment with descriptions of several new families, genera, and species (Mollusca, Gastropoda). Zookeys 2017; 717:1-139. [PMID: 29391848 PMCID: PMC5784208 DOI: 10.3897/zookeys.717.21885] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 11/08/2017] [Indexed: 12/29/2022] Open
Abstract
The Flabellinidae, a heterogeneous assembly of supposedly plesiomorphic to very derived sea slug groups, have not yet been addressed by integrative studies. Here novel material of rarely seen Arctic taxa as well as North Atlantic, North and South Pacific, and tropical Indo-West Pacific flabellinid species is investigated morpho-anatomically and with multi-locus markers (partial COI, 16S rDNA, 28S rDNA and H3) which were generated and analysed in a comprehensive aeolid taxon sampling. It was found that the current family Flabellinidae is polyphyletic and its phylogeny and taxonomic patterns cannot be understood without considering members from all the Aeolidacean families and, based on a robust phylogenetic hypothesis, morpho-anatomical evolution of aeolids is more complex than suspected in earlier works and requires reclassification of the taxon. Morphological diversity of Flabellinidae is corroborated by molecular divergence rates and supports establishing three new families (Apataidae fam. n., Flabellinopsidae fam. n., Samlidae fam. n.), 16 new genera, 13 new species, and two new subspecies among the former Flabellinidae. Two families, namely Coryphellidae and Paracoryphellidae, are restored and traditional Flabellinidae is considerably restricted. The distinctness of the recently described family Unidentiidae is confirmed by both morphological and molecular data. Several species complexes among all ex-"Flabellinidae" lineages are recognised using both morphological and molecular data. The present study shows that Facelinidae and Aeolidiidae, together with traditional "Tergipedidae", deeply divide traditional "Flabellinidae." Diagnoses for all aeolidacean families are therefore provided and additionally two new non-flabellinid families (Abronicidae fam. n. and Murmaniidae fam. n.) within traditional tergipedids are established to accommodate molecular and morphological disparity. To address relationships and disparity, we propose a new family system for aeolids. Here the aeolidacean species are classified into at least 102 genera and 24 families. Operational rules for integration of morphological and molecular data for taxonomy are suggested.
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Affiliation(s)
- Tatiana Korshunova
- Koltzov Institute of Developmental Biology, RAS, 26 Vavilova Str., 119334 Moscow, Russia
- Zoological Museum, Moscow State University, Bolshaya Nikitskaya Str. 6, 125009 Moscow, Russia
| | - Alexander Martynov
- Zoological Museum, Moscow State University, Bolshaya Nikitskaya Str. 6, 125009 Moscow, Russia
| | - Torkild Bakken
- NTNU University Museum, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Jussi Evertsen
- NTNU University Museum, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | | | | | - Hiroshi Saito
- National Museum of Nature and Science, Amakubo 4-1-1, Tsukuba, Japan
| | - Kennet Lundin
- Gothenburg Natural History Museum, Box 7283, S-40235, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Box 461, S-40530, Gothenburg, Sweden
| | - Michael Schrödl
- Zoologische Staatssammlung München, Münchhausenstr. 21, D-81247 München, Germany
| | - Bernard Picton
- National Museums Northern Ireland, Holywood, Northern Ireland, United Kingdom
- Queen’s University, Belfast, Northern Ireland, United Kingdom
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29
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Lavinia PD, Núñez Bustos EO, Kopuchian C, Lijtmaer DA, García NC, Hebert PDN, Tubaro PL. Barcoding the butterflies of southern South America: Species delimitation efficacy, cryptic diversity and geographic patterns of divergence. PLoS One 2017; 12:e0186845. [PMID: 29049373 PMCID: PMC5648246 DOI: 10.1371/journal.pone.0186845] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 10/09/2017] [Indexed: 01/26/2023] Open
Abstract
Because the tropical regions of America harbor the highest concentration of butterfly species, its fauna has attracted considerable attention. Much less is known about the butterflies of southern South America, particularly Argentina, where over 1,200 species occur. To advance understanding of this fauna, we assembled a DNA barcode reference library for 417 butterfly species of Argentina, focusing on the Atlantic Forest, a biodiversity hotspot. We tested the efficacy of this library for specimen identification, used it to assess the frequency of cryptic species, and examined geographic patterns of genetic variation, making this study the first large-scale genetic assessment of the butterflies of southern South America. The average sequence divergence to the nearest neighbor (i.e. minimum interspecific distance) was 6.91%, ten times larger than the mean distance to the furthest conspecific (0.69%), with a clear barcode gap present in all but four of the species represented by two or more specimens. As a consequence, the DNA barcode library was extremely effective in the discrimination of these species, allowing a correct identification in more than 95% of the cases. Singletons (i.e. species represented by a single sequence) were also distinguishable in the gene trees since they all had unique DNA barcodes, divergent from those of the closest non-conspecific. The clustering algorithms implemented recognized from 416 to 444 barcode clusters, suggesting that the actual diversity of butterflies in Argentina is 3%-9% higher than currently recognized. Furthermore, our survey added three new records of butterflies for the country (Eurema agave, Mithras hannelore, Melanis hillapana). In summary, this study not only supported the utility of DNA barcoding for the identification of the butterfly species of Argentina, but also highlighted several cases of both deep intraspecific and shallow interspecific divergence that should be studied in more detail.
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Affiliation(s)
- Pablo D. Lavinia
- Museo Argentino de Ciencias Naturales ‘Bernardino Rivadavia’ (MACN-CONICET), Buenos Aires, Argentina
| | - Ezequiel O. Núñez Bustos
- Museo Argentino de Ciencias Naturales ‘Bernardino Rivadavia’ (MACN-CONICET), Buenos Aires, Argentina
| | - Cecilia Kopuchian
- Laboratorio de Biología de la Conservación, Centro de Ecología Aplicada del Litoral (CECOAL-CONICET), Corrientes, Argentina
| | - Darío A. Lijtmaer
- Museo Argentino de Ciencias Naturales ‘Bernardino Rivadavia’ (MACN-CONICET), Buenos Aires, Argentina
| | - Natalia C. García
- Museo Argentino de Ciencias Naturales ‘Bernardino Rivadavia’ (MACN-CONICET), Buenos Aires, Argentina
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Pablo L. Tubaro
- Museo Argentino de Ciencias Naturales ‘Bernardino Rivadavia’ (MACN-CONICET), Buenos Aires, Argentina
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Revision of the genus complex Gibbula: an integrative approach to delineating the Eastern Mediterranean genera Gibbula Risso, 1826, Steromphala Gray, 1847, and Phorcus Risso, 1826 using DNA-barcoding and geometric morphometrics (Vetigastropoda, Trochoidea). ORG DIVERS EVOL 2017. [DOI: 10.1007/s13127-017-0343-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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31
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Barcode index numbers expedite quarantine inspections and aid the interception of nonindigenous mealybugs (Pseudococcidae). Biol Invasions 2017. [DOI: 10.1007/s10530-017-1546-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Furfaro G, Salvi D, Mancini E, Mariottini P. A multilocus view on Mediterranean aeolid nudibranchs (Mollusca): Systematics and cryptic diversity of Flabellinidae and Piseinotecidae. Mol Phylogenet Evol 2017; 118:13-22. [PMID: 28888791 DOI: 10.1016/j.ympev.2017.09.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 06/16/2017] [Accepted: 09/04/2017] [Indexed: 01/10/2023]
Abstract
Recent molecular studies revealed high level of endemism and numerous cryptic species within opisthobranchs, with Mediterranean taxa clearly understudied. Here we used genetic data from both mitochondrial and nuclear gene fragments as well as morphological data from taxonomically relevant characters to investigate the phylogenetic relationships and systematics of Mediterranean taxa of the Flabellinidae and Piseinotecidae families. Phylogenetic analyses based on Bayesian and Maximum-Likelihood methods indicate that Flabellinidae and Pisenotecidae taxa and species within the genera Flabellina, Calmella and Piseinotecus do not form monophyletic clades. These results are supported by our morphological analyses which allowed the re-evaluation of the triseriate radula condition in Pisenotecidae and Calmella taxa and their inclusion in the genus Flabellina as Flabellina gaditanacomb. nov. (synonym of F. confusa), Flabellina gabiniereicomb. nov. and Flabellina cavolinicomb. nov. Species delimitation and barcoding gap analyses allowed uncovering cryptic species within Flabellina gracilis (Alder and Hancock, 1844), F. trophina (Bergh, 1890), F. verrucosa (M. Sars, 1829) and F. ischitana Hirano and Thompson, 1990, the latter with an Atlantic form which is under description. This study corroborates the relevance of combining molecular and morphological data from multiple populations and species in the assessment of nudibranch diversity and classification.
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Affiliation(s)
- Giulia Furfaro
- Department of Sciences, University "Roma Tre", Viale G. Marconi 446, I-00146 Rome, Italy.
| | - Daniele Salvi
- Department of Health, Life and Environmental Sciences, University of L'Aquila, 67100 Coppito, L'Aquila, Italy; CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | - Emiliano Mancini
- Department of Sciences, University "Roma Tre", Viale G. Marconi 446, I-00146 Rome, Italy
| | - Paolo Mariottini
- Department of Sciences, University "Roma Tre", Viale G. Marconi 446, I-00146 Rome, Italy
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Resolving the Taxonomic Status of Chamelea gallina and C. striatula (Veneridae, Bivalvia): A Combined Molecular Cytogenetic and Phylogenetic Approach. BIOMED RESEARCH INTERNATIONAL 2017; 2017:7638790. [PMID: 28555195 PMCID: PMC5438835 DOI: 10.1155/2017/7638790] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 03/27/2017] [Accepted: 04/03/2017] [Indexed: 12/26/2022]
Abstract
The striped venus clams Chamelea gallina and C. striatula are commercially important bivalves inhabiting European and North African coastal waters. The taxonomic status of these taxa has been the subject of debate for decades. In order to elucidate this issue, we generated 5S and 28S ribosomal RNA and H3 histone gene probes and mapped them by fluorescent in situ hybridization to the chromosomes of morphologically identified striped venus clams, collected from four geographically distant Atlantic and Mediterranean populations. The nucleotide variation at the three DNA markers, that is, the nuclear internal transcribed spacer 2 (ITS2), the mitochondrial cytochrome c oxidase subunit I (COI), and the large ribosomal subunit rRNA (16S) fragments, was also studied and the resultant phylogenetic trees were evaluated. Striking differences in both the chromosome distribution of these genes and the clustering of the samples on the phylogenetic trees observed provide clear evidence that C. gallina and C. striatula are separated species.
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Rach J, Bergmann T, Paknia O, DeSalle R, Schierwater B, Hadrys H. The marker choice: Unexpected resolving power of an unexplored CO1 region for layered DNA barcoding approaches. PLoS One 2017; 12:e0174842. [PMID: 28406914 PMCID: PMC5390999 DOI: 10.1371/journal.pone.0174842] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 03/16/2017] [Indexed: 01/13/2023] Open
Abstract
The potential of DNA barcoding approaches to identify single species and characterize species compositions strongly depends on the marker choice. The prominent “Folmer region”, a 648 basepair fragment at the 5’ end of the mitochondrial CO1 gene, has been traditionally applied as a universal DNA barcoding region for metazoans. In order to find a suitable marker for biomonitoring odonates (dragonflies and damselflies), we here explore a new region of the CO1 gene (CO1B) for DNA barcoding in 51 populations of 23 dragonfly and damselfly species. We compare the “Folmer region”, the mitochondrial ND1 gene (NADH dehydrogenase 1) and the new CO1 region with regard to (i) speed and reproducibility of sequence generation, (ii) levels of homoplasy and (iii) numbers of diagnostic characters for discriminating closely related sister taxa and populations. The performances of the gene regions regarding these criteria were quite different. Both, the amplification of CO1B and ND1 was highly reproducible and CO1B showed the highest potential for discriminating sister taxa at different taxonomic levels. In contrast, the amplification of the “Folmer region” using the universal primers was difficult and the third codon positions of this fragment have experienced nucleotide substitution saturation. Most important, exploring this new barcode region of the CO1 gene identified a higher discriminating power between closely related sister taxa. Together with the design of layered barcode approaches adapted to the specific taxonomic “environment”, this new marker will further enhance the discrimination power at the species level.
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Affiliation(s)
- Jessica Rach
- ITZ, Ecology & Evolution, TiHo Hannover, Hannover, D-30559, Germany
| | - Tjard Bergmann
- ITZ, Ecology & Evolution, TiHo Hannover, Hannover, D-30559, Germany
| | - Omid Paknia
- ITZ, Ecology & Evolution, TiHo Hannover, Hannover, D-30559, Germany
| | - Rob DeSalle
- Sackler Institute of Comparative Genomics, American Museum of Natural History, New York, NY 10024, United States of America
| | - Bernd Schierwater
- ITZ, Ecology & Evolution, TiHo Hannover, Hannover, D-30559, Germany
- Sackler Institute of Comparative Genomics, American Museum of Natural History, New York, NY 10024, United States of America
| | - Heike Hadrys
- ITZ, Ecology & Evolution, TiHo Hannover, Hannover, D-30559, Germany
- Sackler Institute of Comparative Genomics, American Museum of Natural History, New York, NY 10024, United States of America
- * E-mail:
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Sun S, Li Q, Kong L, Yu H, Zheng X, Yu R, Dai L, Sun Y, Chen J, Liu J, Ni L, Feng Y, Yu Z, Zou S, Lin J. DNA barcoding reveal patterns of species diversity among northwestern Pacific molluscs. Sci Rep 2016; 6:33367. [PMID: 27640675 PMCID: PMC5027561 DOI: 10.1038/srep33367] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 08/25/2016] [Indexed: 11/26/2022] Open
Abstract
This study represents the first comprehensive molecular assessment of northwestern Pacific molluscs. In total, 2801 DNA barcodes belonging to 569 species from China, Japan and Korea were analyzed. An overlap between intra- and interspecific genetic distances was present in 71 species. We tested the efficacy of this library by simulating a sequence-based specimen identification scenario using Best Match (BM), Best Close Match (BCM) and All Species Barcode (ASB) criteria with three threshold values. BM approach returned 89.15% true identifications (95.27% when excluding singletons). The highest success rate of congruent identifications was obtained with BCM at 0.053 threshold. The analysis of our barcode library together with public data resulted in 582 Barcode Index Numbers (BINs), 72.2% of which was found to be concordantly with morphology-based identifications. The discrepancies were divided in two groups: sequences from different species clustered in a single BIN and conspecific sequences divided in one more BINs. In Neighbour-Joining phenogram, 2,320 (83.0%) queries fromed 355 (62.4%) species-specific barcode clusters allowing their successful identification. 33 species showed paraphyletic and haplotype sharing. 62 cases are represented by deeply diverged lineages. This study suggest an increased species diversity in this region, highlighting taxonomic revision and conservation strategy for the cryptic complexes.
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Affiliation(s)
- Shao’e Sun
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Hong Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Xiaodong Zheng
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Ruihai Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Lina Dai
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Yan Sun
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Jun Chen
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Jun Liu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Lehai Ni
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Yanwei Feng
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Zhenzhen Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Shanmei Zou
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Jiping Lin
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
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Yang Y, Zhan A, Cao L, Meng F, Xu W. Selection of a marker gene to construct a reference library for wetland plants, and the application of metabarcoding to analyze the diet of wintering herbivorous waterbirds. PeerJ 2016; 4:e2345. [PMID: 27602302 PMCID: PMC4991844 DOI: 10.7717/peerj.2345] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 07/19/2016] [Indexed: 11/20/2022] Open
Abstract
Food availability and diet selection are important factors influencing the abundance and distribution of wild waterbirds. In order to better understand changes in waterbird population, it is essential to figure out what they feed on. However, analyzing their diet could be difficult and inefficient using traditional methods such as microhistologic observation. Here, we addressed this gap of knowledge by investigating the diet of greater white-fronted goose Anser albifrons and bean goose Anser fabalis, which are obligate herbivores wintering in China, mostly in the Middle and Lower Yangtze River floodplain. First, we selected a suitable and high-resolution marker gene for wetland plants that these geese would consume during the wintering period. Eight candidate genes were included: rbcL, rpoC1, rpoB, matK, trnH-psbA, trnL (UAA), atpF-atpH, and psbK-psbI. The selection was performed via analysis of representative sequences from NCBI and comparison of amplification efficiency and resolution power of plant samples collected from the wintering area. The trnL gene was chosen at last with c/h primers, and a local plant reference library was constructed with this gene. Then, utilizing DNA metabarcoding, we discovered 15 food items in total from the feces of these birds. Of the 15 unique dietary sequences, 10 could be identified at specie level. As for greater white-fronted goose, 73% of sequences belonged to Poaceae spp., and 26% belonged to Carex spp. In contrast, almost all sequences of bean goose belonged to Carex spp. (99%). Using the same samples, microhistology provided consistent food composition with metabarcoding results for greater white-fronted goose, while 13% of Poaceae was recovered for bean goose. In addition, two other taxa were discovered only through microhistologic analysis. Although most of the identified taxa matched relatively well between the two methods, DNA metabarcoding gave taxonomically more detailed information. Discrepancies were likely due to biased PCR amplification in metabarcoding, low discriminating power of current marker genes for monocots, and biases in microhistologic analysis. The diet differences between two geese species might indicate deeper ecological significance beyond the scope of this study. We concluded that DNA metabarcoding provides new perspectives for studies of herbivorous waterbird diets and inter-specific interactions, as well as new possibilities to investigate interactions between herbivores and plants. In addition, microhistologic analysis should be used together with metabarcoding methods to integrate this information.
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Affiliation(s)
- Yuzhan Yang
- School of Life Sciences, University of Science and Technology of China , Hefei , Anhui , China
| | - Aibin Zhan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing , China
| | - Lei Cao
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing , China
| | - Fanjuan Meng
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing , China
| | - Wenbin Xu
- Anhui Shengjin Lake National Nature Reserve Administration , Chizhou , Anhui , China
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37
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Raupach MJ, Hannig K, Morinière J, Hendrich L. A DNA barcode library for ground beetles (Insecta, Coleoptera, Carabidae) of Germany: The genus Bembidion Latreille, 1802 and allied taxa. Zookeys 2016; 592:121-41. [PMID: 27408547 PMCID: PMC4926639 DOI: 10.3897/zookeys.592.8316] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 04/23/2016] [Indexed: 12/23/2022] Open
Abstract
As molecular identification method, DNA barcoding based on partial cytochrome c oxidase subunit 1 (COI) sequences has been proven to be a useful tool for species determination in many insect taxa including ground beetles. In this study we tested the effectiveness of DNA barcodes to discriminate species of the ground beetle genus Bembidion and some closely related taxa of Germany. DNA barcodes were obtained from 819 individuals and 78 species, including sequences from previous studies as well as more than 300 new generated DNA barcodes. We found a 1:1 correspondence between BIN and traditionally recognized species for 69 species (89%). Low interspecific distances with maximum pairwise K2P values below 2.2% were found for three species pairs, including two species pairs with haplotype sharing (Bembidion atrocaeruleum/Bembidion varicolor and Bembidion guttula/Bembidion mannerheimii). In contrast to this, deep intraspecific sequence divergences with distinct lineages were revealed for two species (Bembidion geniculatum/Ocys harpaloides). Our study emphasizes the use of DNA barcodes for the identification of the analyzed ground beetles species and represents an important step in building-up a comprehensive barcode library for the Carabidae in Germany and Central Europe as well.
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Affiliation(s)
- Michael J. Raupach
- Molecular Taxonomy of Marine Organisms, German Centre of Marine Biodiversity Research (DZMB), Senckenberg am Meer, Südstrand 44, 26382 Wilhelmshaven, Germany
| | | | - Jérome Morinière
- Taxonomic coordinator – Barcoding Fauna Bavarica, Bavarian State Collection of Zoology (SNSB – ZSM), Münchhausenstraße 21, 81247 München, Germany
| | - Lars Hendrich
- Sektion Insecta varia, Bavarian State Collection of Zoology (SNSB – ZSM), Münchhausenstraße 21, 81247 München, Germany
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38
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Morinière J, Cancian de Araujo B, Lam AW, Hausmann A, Balke M, Schmidt S, Hendrich L, Doczkal D, Fartmann B, Arvidsson S, Haszprunar G. Species Identification in Malaise Trap Samples by DNA Barcoding Based on NGS Technologies and a Scoring Matrix. PLoS One 2016; 11:e0155497. [PMID: 27191722 PMCID: PMC4871420 DOI: 10.1371/journal.pone.0155497] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 04/30/2016] [Indexed: 11/23/2022] Open
Abstract
The German Barcoding initiatives BFB and GBOL have generated a reference library of more than 16,000 metazoan species, which is now ready for applications concerning next generation molecular biodiversity assessments. To streamline the barcoding process, we have developed a meta-barcoding pipeline: We pre-sorted a single malaise trap sample (obtained during one week in August 2014, southern Germany) into 12 arthropod orders and extracted DNA from pooled individuals of each order separately, in order to facilitate DNA extraction and avoid time consuming single specimen selection. Aliquots of each ordinal-level DNA extract were combined to roughly simulate a DNA extract from a non-sorted malaise sample. Each DNA extract was amplified using four primer sets targeting the CO1-5’ fragment. The resulting PCR products (150-400bp) were sequenced separately on an Illumina Mi-SEQ platform, resulting in 1.5 million sequences and 5,500 clusters (coverage ≥10; CD-HIT-EST, 98%). Using a total of 120,000 DNA barcodes of identified, Central European Hymenoptera, Coleoptera, Diptera, and Lepidoptera downloaded from BOLD we established a reference sequence database for a local CUSTOM BLAST. This allowed us to identify 529 Barcode Index Numbers (BINs) from our sequence clusters derived from pooled Malaise trap samples. We introduce a scoring matrix based on the sequence match percentages of each amplicon in order to gain plausibility for each detected BIN, leading to 390 high score BINs in the sorted samples; whereas 268 of these high score BINs (69%) could be identified in the combined sample. The results indicate that a time consuming presorting process will yield approximately 30% more high score BINs compared to the non-sorted sample in our case. These promising results indicate that a fast, efficient and reliable analysis of next generation data from malaise trap samples can be achieved using this pipeline.
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Affiliation(s)
- Jérôme Morinière
- SNSB, Bavarian State Collection of Zoology, Münchhausenstrasse 21, 81247, München, Germany
| | | | - Athena Wai Lam
- SNSB, Bavarian State Collection of Zoology, Münchhausenstrasse 21, 81247, München, Germany
| | - Axel Hausmann
- SNSB, Bavarian State Collection of Zoology, Münchhausenstrasse 21, 81247, München, Germany.,GeoBio-Center der LMU München, München, Germany
| | - Michael Balke
- SNSB, Bavarian State Collection of Zoology, Münchhausenstrasse 21, 81247, München, Germany.,GeoBio-Center der LMU München, München, Germany
| | - Stefan Schmidt
- SNSB, Bavarian State Collection of Zoology, Münchhausenstrasse 21, 81247, München, Germany
| | - Lars Hendrich
- SNSB, Bavarian State Collection of Zoology, Münchhausenstrasse 21, 81247, München, Germany
| | - Dieter Doczkal
- SNSB, Bavarian State Collection of Zoology, Münchhausenstrasse 21, 81247, München, Germany
| | - Berthold Fartmann
- LGC Genomics GmbH, Ostendstraße 25, TGS Haus 8, 12459, Berlin, Germany
| | - Samuel Arvidsson
- LGC Genomics GmbH, Ostendstraße 25, TGS Haus 8, 12459, Berlin, Germany
| | - Gerhard Haszprunar
- SNSB, Bavarian State Collection of Zoology, Münchhausenstrasse 21, 81247, München, Germany.,GeoBio-Center der LMU München, München, Germany
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With a little help from DNA barcoding: investigating the diversity of Gastropoda from the Portuguese coast. Sci Rep 2016; 6:20226. [PMID: 26876495 PMCID: PMC4753432 DOI: 10.1038/srep20226] [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: 08/25/2015] [Accepted: 12/30/2015] [Indexed: 01/13/2023] Open
Abstract
The Gastropoda is one of the best studied classes of marine invertebrates. Yet, most species have been delimited based on morphology only. The application of DNA barcodes has shown to be greatly useful to help delimiting species. Therefore, sequences of the cytochrome c oxidase I gene from 108 specimens of 34 morpho-species were used to investigate the molecular diversity within the gastropods from the Portuguese coast. To the above dataset, we added available COI-5P sequences of taxonomically close species, in a total of 58 morpho-species examined. There was a good match between ours and sequences from independent studies, in public repositories. We found 32 concordant (91.4%) out of the 35 Barcode Index Numbers (BINs) generated from our sequences. The application of a ranking system to the barcodes yield over 70% with top taxonomic congruence, while 14.2% of the species barcodes had insufficient data. In the majority of the cases, there was a good concordance between morphological identification and DNA barcodes. Nonetheless, the discordance between morphological and molecular data is a reminder that even the comparatively well-known European marine gastropods can benefit from being probed using the DNA barcode approach. Discordant cases should be reviewed with more integrative studies.
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