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Muhala V, Guimarães-Costa A, Macate IE, Rabelo LP, Bessa-Silva AR, Watanabe L, dos Santos GD, Sambora L, Vallinoto M, Sampaio I. DNA barcoding for the assessment of marine and coastal fish diversity from the Coast of Mozambique. PLoS One 2024; 19:e0293345. [PMID: 38319915 PMCID: PMC10846724 DOI: 10.1371/journal.pone.0293345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 10/10/2023] [Indexed: 02/08/2024] Open
Abstract
The ichthyological provinces of Mozambique are understudied hotspots of global fish diversity. In this study, we applied DNA barcoding to identify the composition of the fish fauna from the coast of Mozambique. A total of 143 species belonging to 104 genera, 59 families, and 30 orders were identified. The overall K2P distance of the COI sequences within species ranged from 0.00% to 1.51%, while interspecific distances ranged from 3.64% to 24.49%. Moreover, the study revealed 15 threatened species according to the IUCN Red List of Threatened Species, with elasmobranchs being the most represented group. Additionally, the study also uncovered four new species that were not previously recorded in this geographic area, including Boleophthalmus dussumieri, Maculabatis gerrardi, Hippocampus kelloggi, and Lethrinus miniatus. This study represents the first instance of utilizing molecular references to explore the fish fauna along the Mozambican coast. Our results indicate that DNA barcoding is a dependable technique for the identification and delineation of fish species in the waters of Mozambique. The DNA barcoding library established in this research will be an invaluable asset for advancing the understanding of fish diversity and guiding future conservation initiatives.
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Affiliation(s)
- Valdemiro Muhala
- Laboratório de Evolução, Universidade Federal do Pará, Alameda Leandro Ribeiro, Aldeia, Bragança, Pará, Brazil
- Divisão de Agricultura, Instituto Superior Politécnico de Gaza, Chókwè, Mozambique
| | - Aurycéia Guimarães-Costa
- Laboratório de Evolução, Universidade Federal do Pará, Alameda Leandro Ribeiro, Aldeia, Bragança, Pará, Brazil
| | - Isadola Eusébio Macate
- Laboratório de Evolução, Universidade Federal do Pará, Alameda Leandro Ribeiro, Aldeia, Bragança, Pará, Brazil
- Departamento de Ciências Agrárias e Ambientais, Universidade Estadual de Santa Cruz, Ilheus, BA, Brazil
| | - Luan Pinto Rabelo
- Laboratório de Evolução, Universidade Federal do Pará, Alameda Leandro Ribeiro, Aldeia, Bragança, Pará, Brazil
| | - Adam Rick Bessa-Silva
- Laboratório de Evolução, Universidade Federal do Pará, Alameda Leandro Ribeiro, Aldeia, Bragança, Pará, Brazil
| | - Luciana Watanabe
- Laboratório de Evolução, Universidade Federal do Pará, Alameda Leandro Ribeiro, Aldeia, Bragança, Pará, Brazil
| | - Gisele Damasceno dos Santos
- Laboratório de Evolução, Universidade Federal do Pará, Alameda Leandro Ribeiro, Aldeia, Bragança, Pará, Brazil
| | - Luísa Sambora
- Departamento de Produção Agrária, Escola Superior de Desenvolvimento Rural, Universidade Eduardo Mondlane, Vilankulos, Moçambique
| | - Marcelo Vallinoto
- Laboratório de Evolução, Universidade Federal do Pará, Alameda Leandro Ribeiro, Aldeia, Bragança, Pará, Brazil
| | - Iracilda Sampaio
- Laboratório de Evolução, Universidade Federal do Pará, Alameda Leandro Ribeiro, Aldeia, Bragança, Pará, Brazil
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Zeng XS, Sun CH, Huang XY, Lao YL, Huang JL, Li S, Zhang Q. DNA barcoding of Scomberomorus (Scombridae, Actinopterygii) reveals cryptic diversity and misidentifications. Zookeys 2022; 1135:157-170. [PMID: 36761794 PMCID: PMC9836712 DOI: 10.3897/zookeys.1135.93631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 11/15/2022] [Indexed: 12/16/2022] Open
Abstract
The genus Scomberomorus is economically important; however, the taxonomic status and phylogenetic relationships in this genus are not clearly resolved, making it difficult to effectively protect and exploit fish resources. To clarify the taxonomic status of Scomberomorus species, mitochondrial cytochrome c oxidase I (COI) gene sequences of 150 samples were analyzed. The average genetic distance among 14 species was approximately 11 times greater than the distances within species, in accordance with the '10× rule' of species identification. Five of the 14 species did not form monophyletic clades based on a Bayesian inference gene tree. The application of four DNA-based species delimitation methods (automatic barcode gap discovery, barcode index numbers, Poisson tree process, and the K/θ method) yielded several key results. (1) Cryptic species were detected within Scomberomoruscommerson. (2) A Scomberomorusqueenslandicus sample from Australia was misidentified as S.commerson in the Barcode of Life Data System (BOLD). (3) Specimens originally identified as Scomberomorusguttatus was differentiated into four OTUs or species, two in the Yellow, South China, and Java seas, and two in geographically distant areas, one each in the Arabian Sea and the Bay of Bengal. (4) Six specimens from South Africa originally identified as S.plurilineatus most likely do not belong to the species. (5) Specimens identified as S.maculatus and S.regalis were conspecific; however, introgression cannot be ruled out. Our findings revealed cryptic diversity and difficulties in morphological identification of species in the genus Scomberomorus. This study provides scientifically based support for the conservation of germplasm resources of the genus Scomberomorus.
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Affiliation(s)
- Xiao-Shu Zeng
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou 510632, ChinaJinan UniversityGuangzhouChina
| | - Cheng-He Sun
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou 510632, ChinaJinan UniversityGuangzhouChina
| | - Xiao-Ying Huang
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou 510632, ChinaJinan UniversityGuangzhouChina
| | - Ye-Ling Lao
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou 510632, ChinaJinan UniversityGuangzhouChina
| | - Jin-Long Huang
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou 510632, ChinaJinan UniversityGuangzhouChina
| | - Sha Li
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang 443100, Hubei, ChinaChinese Sturgeon Research Institute, China Three Gorges CorporationYichangChina,Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang 443100, Hubei, ChinaHubei Key Laboratory of Three Gorges Project for Conservation of FishesYichangChina
| | - Qun Zhang
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou 510632, ChinaJinan UniversityGuangzhouChina
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Reier S, Kruckenhauser L, Snoj A, Trontelj P, Palandačić A. The minnow Phoxinus lumaireul (Leuciscidae) shifts the Adriatic-Black Sea basin divide in the north-western Dinaric Karst region. ECOHYDROLOGY : ECOSYSTEMS, LAND AND WATER PROCESS INTERACTIONS, ECOHYDROGEOMORPHOLOGY 2022; 15:e2449. [PMID: 36245897 PMCID: PMC9539529 DOI: 10.1002/eco.2449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 05/25/2022] [Accepted: 06/26/2022] [Indexed: 06/16/2023]
Abstract
Karst landscapes are characterized by intermittent and sinking streams. The most common method used to study underground hydrological connections in karst is tracing tests. However, a more biologically oriented approach has been suggested: analysis of the genetic structure of aquatic organisms. Biological tracers can be sought among trogloxenes, that is, surface species that occasionally enter caves and groundwater. One such example is the fish genus Phoxinus, which exhibits high genetic diversity and complex phylogeography in the Balkan Peninsula. In the north-western Dinaric Karst, the complex hydrological network was digitalized in 2020. Contemporaneously, Phoxinus lumaireul populations in the Slovenian Dinaric Karst were intensively sampled and analysed for fragments of two mitochondrial genes and one nuclear gene. The derived phylogeographic structure and data on hydrological connections were compared to evaluate support for three alternative scenarios: The genetic structure (1) is a consequence of the ongoing geneflow through underground connections, (2) reflects a previous hydrological network or (3) is an outcome of anthropogenic translocations. The results suggest that the first two scenarios seem to have played a major role, while the third has not had profound effects on the genetic composition. Comparison between the genetic structure of Slovenian Dinaric Karst sampling sites and that of hydrologically isolated reference sampling sites indicated a greater genetic connectivity in the former. Moreover, the range of Adriatic (1a) and Black Sea (1c) haplotypes does not correspond to the Adriatic-Black Sea basin divide but is shifted northwards.
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Affiliation(s)
- Susanne Reier
- First Zoological DepartmentNatural History Museum ViennaViennaAustria
- Department of Evolutionary BiologyUniversity of ViennaViennaAustria
| | - Luise Kruckenhauser
- Department of Evolutionary BiologyUniversity of ViennaViennaAustria
- Central Research LaboratoriesNatural History Museum ViennaViennaAustria
| | - Aleš Snoj
- Department of Animal Science, Biotechnical FacultyUniversity of LjubljanaDomžaleSlovenia
| | - Peter Trontelj
- Department of Biology, Biotechnical FacultyUniversity of LjubljanaLjubljanaSlovenia
| | - Anja Palandačić
- First Zoological DepartmentNatural History Museum ViennaViennaAustria
- Department of Biology, Biotechnical FacultyUniversity of LjubljanaLjubljanaSlovenia
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EAGDERI SOHEIL, SECER BURAK, FREYHOF JÖRG. Cobitis indus, a new spined loach from the Dalaman River in the Eastern Aegean Sea basin (Teleostei: Cobitidae). Zootaxa 2022; 5162:410-420. [DOI: 10.11646/zootaxa.5162.4.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Indexed: 11/04/2022]
Abstract
Cobitis indus, new species, from the Dalaman River drainage, is distinguished from other Cobitis species in the eastern Aegean Sea basin by having two laminae circularis, a bifurcate suborbital spine, a narrow caudal peduncle, pigmentation zone 4 with 17–24 small blotches often fused into a stripe, pigmentation below Z4 usually absent, and one black, comma-shaped spot at the upper caudal-fin base. It is further distinguished from its closest relative, C. dorademiri, by having 13 diagnostic nucleotide substitutions in the mtDNA COI barcode region and a K2P nearest–neighbour distance of 2.3–2.7%. This is the fourth Cobitis species found in the Dalaman River drainage making this river the most species-rich in spined loaches in the Middle East.
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Zangl L, Schäffer S, Daill D, Friedrich T, Gessl W, Mladinić M, Sturmbauer C, Wanzenböck J, Weiss SJ, Koblmüller S. A comprehensive DNA barcode inventory of Austria’s fish species. PLoS One 2022; 17:e0268694. [PMID: 35679240 PMCID: PMC9182252 DOI: 10.1371/journal.pone.0268694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 05/04/2022] [Indexed: 11/19/2022] Open
Abstract
Austria is inhabited by more than 80 species of native and non-native freshwater fishes. Despite considerable knowledge about Austrian fish species, the latest Red List of threatened species dates back 15 years and a systematic genetic inventory of Austria’s fish species does not exist. To fulfill this deficit, we employed DNA barcoding to generate an up-to-date and comprehensive genetic reference database for Austrian fish species. In total, 639 newly generated cytochrome c oxidase subunit 1 (COI) sequences were added to the 377 existing records from the BOLD data base, to compile a near complete reference dataset. Standard sequence similarity analyses resulted in 83 distinct clusters almost perfectly reflecting the expected number of species in Austria. Mean intraspecific distances of 0.22% were significantly lower than distances to closest relatives, resulting in a pronounced barcoding gap and unique Barcode Index Numbers (BINs) for most of the species. Four cases of BIN sharing were detected, pointing to hybridization and/or recent divergence, whereas in Phoxinus spp., Gobio spp. and Barbatula barbatula intraspecific splits, multiple BINs and consequently cryptic diversity were observed. The overall high identification success and clear genetic separation of most of the species confirms the applicability and accuracy of genetic methods for bio-surveillance. Furthermore, the new DNA barcoding data pinpoints cases of taxonomic uncertainty, which need to be addressed in further detail, to more precisely assort genetic lineages and their local distribution ranges in a new National Red-List.
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Affiliation(s)
- Lukas Zangl
- Institute of Biology, University of Graz, Graz, Austria
- Universalmuseum Joanneum, Studienzentrum Naturkunde, Graz, Austria
- * E-mail:
| | | | - Daniel Daill
- Institute of Biology, University of Graz, Graz, Austria
- Consultants in Aquatic Ecology and Engineering—blattfisch e.U., Wels, Austria
| | - Thomas Friedrich
- Institute of Hydrobiology and Aquatic Ecosystem Management, University of Natural Resources and Life Sciences, Vienna, Austria
| | | | - Marija Mladinić
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | | | - Josef Wanzenböck
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
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Molecular analysis reveals multiple native and alien Phoxinus species (Leusciscidae) in the Netherlands and Belgium. Biol Invasions 2022. [DOI: 10.1007/s10530-022-02784-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
AbstractFresh waters are among the most endangered ecosystems, one of the problems being the lack of data on biodiversity. In the center of the missing knowledge are cryptic species, two (or more) species classified as a single one due to their (seemingly) indistinguishable morphology. Lack of research and stabilizing selection are reflected in the cryptic diversity of the genus Phoxinus (Leusciscidae), the studies of which have intensified over the last two decades and reveal undetected taxonomic complexity. Moreover, some of the Phoxinus lineages act as invasive species, while others are endangered by their alien counterparts. Minnows have been intentionally (as food for predatory fish species) or unintentionally (with other fries) stocked causing hybridisation zones in Norway, Portugal, Spain, France, Italy, Germany and Austria. Given that genetic identity and lineage assignment of Phoxinus from Belgium and the Netherlands have not been researched, the goal of the study was to examine available samples from known localities in the area in order to infer- whether they are native or not. For this purpose, the barcoding region cytochrome oxidase I, another mitochondrial gene cytochrome b, a nuclear recombination activating gene 1 and a combination of these markers from a wider neighboring region were analyzed. The study found four different Phoxinus species/lineages occurring in Belgium and the Netherlands: P. phoxinus, P. csikii, P. septimaniae and genetic lineage 11 (possibly P.cf. morella). While the first seem to be native, the other three were probably introduced.
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Tsoupas A, Papavasileiou S, Minoudi S, Gkagkavouzis K, Petriki O, Bobori D, Sapounidis A, Koutrakis E, Leonardos I, Karaiskou N, Triantafyllidis A. DNA barcoding identification of Greek freshwater fishes. PLoS One 2022; 17:e0263118. [PMID: 35081163 PMCID: PMC8791500 DOI: 10.1371/journal.pone.0263118] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 01/12/2022] [Indexed: 11/18/2022] Open
Abstract
Biodiversity is a key factor for the functioning and efficiency of an ecosystem. Greece, though covering a relatively small surface area, hosts a great deal of species diversity. This is especially true for freshwater fishes. In recent years, the traditional methods of species identification have been supplemented by the use of molecular markers. The present study therefore aims to extensively produce DNA barcodes for Greek freshwater fish species and investigate thoroughly if the presently accepted species classification is in agreement with molecular data. A 624-bases long fragment of the COI gene was sequenced, from 406 freshwater fish specimens belonging to 24 genera and originating from 18 lake and river sites. These sequences were used along with 596 sequences from the same genera, recovered from BOLD, for the construction of phylogenetic trees and the estimation of genetic distances between individuals. In total, 1002 sequences belonging to 72 species were analyzed. The method was found to be effective for 55 of 72 studied species. 17 closely related species with low interspecific genetic distances were observed, for which further study is proposed. It should also be noted that, in four cases, cryptic diversity was observed, where groups originally identified as one species exhibited genetic distance great enough to be separated into discrete species. Region specific haplotypes were also detected within populations of 14 species, giving the possibility to identify even the geographic origin of a species. Our findings are discussed in the light of the rich history of the Balkan peninsula and provide a significant steppingstone for the further study of Greek and European freshwater fish biodiversity.
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Affiliation(s)
- Alexandros Tsoupas
- Faculty of Sciences, Department of Genetics, Development and Molecular Biology, Laboratory of Animal Population Genetics, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Sofia Papavasileiou
- Faculty of Sciences, Department of Genetics, Development and Molecular Biology, Laboratory of Animal Population Genetics, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Styliani Minoudi
- Faculty of Sciences, Department of Genetics, Development and Molecular Biology, Laboratory of Animal Population Genetics, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Bioanalysis and Omics (BIOMIC), Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, Thessaloniki, Greece
| | - Konstantinos Gkagkavouzis
- Faculty of Sciences, Department of Genetics, Development and Molecular Biology, Laboratory of Animal Population Genetics, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Bioanalysis and Omics (BIOMIC), Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, Thessaloniki, Greece
| | - Olga Petriki
- Faculty of Sciences, Department of Zoology, Laboratory of Ichthyology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Dimitra Bobori
- Faculty of Sciences, Department of Zoology, Laboratory of Ichthyology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
- * E-mail: (DB); (AT)
| | - Argyrios Sapounidis
- Department of Inland Waters and Lagoons, Fisheries Research Institute, Hellenic Agricultural Organization “DEMETER”, Nea Peramos, Kavala, Greece
| | - Emmanouil Koutrakis
- Department of Inland Waters and Lagoons, Fisheries Research Institute, Hellenic Agricultural Organization “DEMETER”, Nea Peramos, Kavala, Greece
| | - Ioannis Leonardos
- Department of Biological Applications and Technologies, Laboratory of Zoology, School of Health Sciences, University of Ioannina, Ioannina, Greece
| | - Nikoleta Karaiskou
- Faculty of Sciences, Department of Genetics, Development and Molecular Biology, Laboratory of Animal Population Genetics, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Bioanalysis and Omics (BIOMIC), Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, Thessaloniki, Greece
| | - Alexandros Triantafyllidis
- Faculty of Sciences, Department of Genetics, Development and Molecular Biology, Laboratory of Animal Population Genetics, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Bioanalysis and Omics (BIOMIC), Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center, Thessaloniki, Greece
- * E-mail: (DB); (AT)
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Tarkan AS, Emiroğlu Ö, Aksu S, Başkurt S, Aksu İ, Vilizzi L, Yoğurtçuoğlu B. Coupling molecular and risk analysis to investigate the origin, distribution and potential impact of non-native species: an application to ruffe Gymnocephalus cernua in Turkey. THE EUROPEAN ZOOLOGICAL JOURNAL 2022. [DOI: 10.1080/24750263.2021.2022222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
- A. S. Tarkan
- Faculty of Fisheries, Muğla Sıtkı Koçman University, Muğla, Turkey
- Department of Ecology and Vertebrate Zoology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Ö. Emiroğlu
- Department of Biology, Faculty of Science, Eskişehir Osmangazi University, Eskişehir, Turkey
| | - S. Aksu
- Vocational School of Health Services, Eskişehir Osmangazi University, Eskişehir, Turkey
| | - S. Başkurt
- Department of Biology, Faculty of Science, Eskişehir Osmangazi University, Eskişehir, Turkey
| | - İ. Aksu
- Department of Basic Sciences, Faculty of Fisheries, Recep Tayyip Erdogan University, Rize, Turkey
| | - L. Vilizzi
- Department of Ecology and Vertebrate Zoology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - B. Yoğurtçuoğlu
- Department of Biology, Faculty of Science, Hacettepe University, Ankara, Turkey
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Pawlowski J, Bonin A, Boyer F, Cordier T, Taberlet P. Environmental DNA for biomonitoring. Mol Ecol 2021; 30:2931-2936. [PMID: 34176165 PMCID: PMC8451586 DOI: 10.1111/mec.16023] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 06/10/2021] [Indexed: 12/17/2022]
Affiliation(s)
- Jan Pawlowski
- Department of Genetics and EvolutionUniversity of GenevaGenevaSwitzerland
- Institute of OceanologyPolish Academy of SciencesSopotPoland
- ID‐Gene EcodiagnosticsGenevaSwitzerland
| | - Aurélie Bonin
- Department of Environmental Science and PolicyUniversità degli Studi di MilanoMilanItaly
| | - Frédéric Boyer
- Laboratoire d'Ecologie Alpine (LECA)CNRSUniversité Grenoble AlpesGrenobleFrance
| | - Tristan Cordier
- Department of Genetics and EvolutionUniversity of GenevaGenevaSwitzerland
- NORCE ClimateNORCE Norwegian Research Centre ASBjerknes Centre for Climate ResearchBergenNorway
| | - Pierre Taberlet
- Laboratoire d'Ecologie Alpine (LECA)CNRSUniversité Grenoble AlpesGrenobleFrance
- Tromsø MuseumUiT – The Arctic University of NorwayTromsøNorway
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De Santis V, Delmastro GB, Vanetti I, Britton JR, Zaccara S. Species composition of introduced and natural minnow populations of the Phoxinus cryptic complex in the westernmost part of the Po River Basin (north Italy). Biol Invasions 2020. [DOI: 10.1007/s10530-020-02406-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AbstractInvasive alien species are a major driver of biodiversity loss, with their impacts potentially more intense when complexes of cryptic species are involved. In freshwaters, the anthropogenic manipulation of fish communities has resulted in altered fish communities, and in Europe has increased the complexity of Phoxinus species assemblages. Here, we investigated the Phoxinus communities of the westernmost part of the Po river basin, where adjacent freshwater ecosystems (Alpine high-altitude lakes and lowland streams) are representative of different management strategies (i.e. manipulated fish communities via stocking in Alpine lakes vs. natural populations in streams). We tested the genetic composition of the cryptic Phoxinus populations inhabiting these waters, as the species are morphologically indistinct. Sequences of the mitochondrial cytochrome oxidase I (COI) were obtained from 239 specimens, with the results indicating that 17 Alpine high-altitude lakes are now populated by a complex of Phoxinus species, comprising P. septimaniae (native to the Mediterranean area of France), P. csikii (native to the Central Balkans) and P. lumaireul (native to the North Adriatic Sea basins). Their introduction resulted from their use as angling live baits. Minnow populations in lowland streams were primarily comprised of native P. lumaireul, with only a single P. csikii specimen detected. While nuclear sequences of the recombination activating gene 1 (RAG1) marker were not useful for tracking the presence of alien alleles in these stream populations, the COI data emphasised the importance of using molecular tools to investigate cryptic species complexes that have been modified by anthropogenic activities.
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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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12
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Limmon G, Delrieu-Trottin E, Patikawa J, Rijoly F, Dahruddin H, Busson F, Steinke D, Hubert N. Assessing species diversity of Coral Triangle artisanal fisheries: A DNA barcode reference library for the shore fishes retailed at Ambon harbor (Indonesia). Ecol Evol 2020; 10:3356-3366. [PMID: 32273993 PMCID: PMC7141007 DOI: 10.1002/ece3.6128] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 01/30/2020] [Accepted: 02/03/2020] [Indexed: 01/01/2023] Open
Abstract
The Coral Triangle (CT), a region spanning across Indonesia and Philippines, is home to about 4,350 marine fish species and is among the world's most emblematic regions in terms of conservation. Threatened by overfishing and oceans warming, the CT fisheries have faced drastic declines over the last decades. Usually monitored through a biomass-based approach, fisheries trends have rarely been characterized at the species level due to the high number of taxa involved and the difficulty to accurately and routinely identify individuals to the species level. Biomass, however, is a poor proxy of species richness, and automated methods of species identification are required to move beyond biomass-based approaches. Recent meta-analyses have demonstrated that species richness peaks at intermediary levels of biomass. Consequently, preserving biomass is not equal to preserving biodiversity. We present the results of a survey to estimate the shore fish diversity retailed at the harbor of Ambon Island, an island located at the center of the CT that display exceptionally high biomass despite high levels of threat, while building a DNA barcode reference library of CT shore fishes targeted by artisanal fisheries. We sampled 1,187 specimens and successfully barcoded 696 of the 760 selected specimens that represent 202 species. Our results show that DNA barcodes were effective in capturing species boundaries for 96% of the species examined, which opens new perspectives for the routine monitoring of the CT fisheries.
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Affiliation(s)
- Gino Limmon
- Pusat Kemaritiman dan Kelautan Universitas Pattimura (Maritime and Marine Science Center of Excellence) Ambon Indonesia
| | - Erwan Delrieu-Trottin
- Institut de Recherche pour le Développement UMR 226 ISEM (UM-CNRS-IRD-EPHE) Montpellier France
- Museum für Naturkunde Leibniz-Institut für Evolutions-und Biodiversitätsforschung an der Humboldt-Universität zu Berlin Berlin Germany
| | - Jesaya Patikawa
- Pusat Kemaritiman dan Kelautan Universitas Pattimura (Maritime and Marine Science Center of Excellence) Ambon Indonesia
| | - Frederik Rijoly
- Pusat Kemaritiman dan Kelautan Universitas Pattimura (Maritime and Marine Science Center of Excellence) Ambon Indonesia
| | - Hadi Dahruddin
- Division of Zoology Research Center for Biology Indonesian Institute of Sciences (LIPI) Cibinong Indonesia
| | - Frédéric Busson
- Institut de Recherche pour le Développement UMR 226 ISEM (UM-CNRS-IRD-EPHE) Montpellier France
- UMR 7208 BOREA (MNHN-CNRS-UPMC-IRD-UCBN) Muséum National d'Histoire Naturelle Paris France
| | - Dirk Steinke
- Department of Integrative Biology Centre for Biodiversity Genomics University of Guelph Guelph ON Canada
| | - Nicolas Hubert
- Institut de Recherche pour le Développement UMR 226 ISEM (UM-CNRS-IRD-EPHE) Montpellier France
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13
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Detection of lamprey in Southernmost South America by environmental DNA (eDNA) and molecular evidence for a new species. Polar Biol 2020. [DOI: 10.1007/s00300-020-02640-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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14
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Palandačić A, Kruckenhauser L, Ahnelt H, Mikschi E. European minnows through time: museum collections aid genetic assessment of species introductions in freshwater fishes (Cyprinidae: Phoxinus species complex). Heredity (Edinb) 2020; 124:410-422. [PMID: 31896822 DOI: 10.1038/s41437-019-0292-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 12/18/2019] [Accepted: 12/18/2019] [Indexed: 11/09/2022] Open
Abstract
Massive fish introductions have taken place throughout much of the world, mostly over the last 70 years, and present a major threat to the genetic diversity of native fishes. Introductions have been reported for European Phoxinus, a ubiquitous small cyprinid that populates a wide variety of habitats. Species delineation in European Phoxinus has proven difficult with one reason being ranges of distribution that often traverse drainage boundaries. The present study combines recent samples with museum samples to better understand the current distribution of Phoxinus species and their distributions prior to the massive introductions of fishes in Europe, and to evaluate the use of museum specimens for species distribution studies. For these purposes, genetic lineages from sites collected prior to 1900 (n = 14), and between 1900 and 1950 (n = 8), were analysed using two mitochondrial and nuclear markers. Although possible fish introductions were detected, our results show that the distribution of genetic lineages of museum samples is comparable to that of the extant lineages of European Phoxinus present in those areas. These observations suggest that in the studied ranges the distribution of Phoxinus lineages has been driven by natural processes.
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Affiliation(s)
- Anja Palandačić
- First Zoological Department, Vienna Museum of Natural History, Burgring 7, 1010, Vienna, Austria.
| | - Luise Kruckenhauser
- Laboratory of Molecular Systematics, Vienna Museum of Natural History, Burgring 7, 1010, Vienna, Austria
| | - Harald Ahnelt
- First Zoological Department, Vienna Museum of Natural History, Burgring 7, 1010, Vienna, Austria.,Department of Theoretical Biology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Ernst Mikschi
- First Zoological Department, Vienna Museum of Natural History, Burgring 7, 1010, Vienna, Austria
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15
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Sampieri BR, Steiner TM, Baroni PC, Silva CFD, Teixeira MAL, Vieira PE, Costa FO, Amaral ACZ. How oogenesis analysis combined with DNA barcode can help to elucidate taxonomic ambiguities: a polychaete study-based approach. BIOTA NEOTROPICA 2020. [DOI: 10.1590/1676-0611-bn-2020-0959] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Abstract: Polychaetes are common in coastal and estuarine environments worldwide and constitute one of the most complex groups of marine invertebrates. The morpho-physiology of the female reproductive system (FRS) can be understood by using histological tools to describe reproductive cycle and gametogenesis paths and, among other purposes, aiming to identify and differentiate polychaete species. However, this histology-based approach is rarely combined with molecular tools, which is known to accurately delimitate species. In the same way, the description and understanding of oogenesis and vitellogenesis paths within polychaetes are lacking for most families, narrowing the range of its utility. Therefore, the present study aims to describe the oogenesis in three polychaete species common and abundant on the South American Atlantic coast (Laeonereis culveri, Scolelepis goodbodyi and Capitella biota) and investigate the utility of reproductive features and gametogenesis as a relevant associate knowledge to discriminate species, particularly useful for putative cryptic species, integrated with morphological and molecular data. In a first attempt, the results obtained herein allow the authors to describe two new subtypes of oogenesis, dividing it in extraovarian oogenesis type I and II and intraovarian type I and II. The results also demonstrate that the following histological characters of the FRS can be relevant for the separation of related species: a) oogenesis type, b) occurrence or absence of a true ovary, c) ovary tissue organization, d) type of accessory cells present, and e) oocyte morphology. Additionally, these histological features of FRS, when compared with correlated species studied under this scope, converge with the genetic data. The analysis of cytochrome oxidase I (COI) barcode sequences differentiates between North and South American Atlantic populations of L. culveri (16.78% genetic distance), while in S. goodbodyi and C. biota it discriminates them from their congeneric species. These results highlight the importance of multi-tool approach and shows that both FRS histology and histo-physiology, and DNA barcoding can be used to identify and discriminate cryptic species, which is usually not possible when using morphological characters. Besides, these characters may also be useful in differentiating related species, and/or geographically distinct populations among polychaetes.
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Affiliation(s)
- Bruno R. Sampieri
- Universidade Estadual de Campinas, Brasil; Universidade do Minho, Portugal; Universidade do Minho, Portugal
| | | | | | | | | | - Pedro E. Vieira
- Universidade do Minho, Portugal; Universidade do Minho, Portugal
| | - Filipe O. Costa
- Universidade do Minho, Portugal; Universidade do Minho, Portugal
| | - Antônia C. Z. Amaral
- Universidade Estadual de Campinas, Brasil; Universidade Estadual de Campinas, Brasil
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16
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Zangl L, Daill D, Gessl W, Friedrich T, Koblmüller S. Austrian gudgeons of the genusGobio(Teleostei: Gobionidae): A mixture of divergent lineages. J ZOOL SYST EVOL RES 2019. [DOI: 10.1111/jzs.12340] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Lukas Zangl
- Institute of Biology University of Graz Graz Austria
| | - Daniel Daill
- Institute of Biology University of Graz Graz Austria
- Consultants in Aquatic Ecology and Engineering –blattfisch e.U. Wels Austria
| | | | - Thomas Friedrich
- Institute of Hydrobiology and Aquatic Ecosystem Management University of Natural Resources and Life Sciences Vienna Vienna Austria
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17
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Corral‐Lou A, Perea S, Aparicio E, Doadrio I. Phylogeography and species delineation of the genusPhoxinusRafinesque, 1820 (Actinopterygii: Leuciscidae) in the Iberian Peninsula. J ZOOL SYST EVOL RES 2019. [DOI: 10.1111/jzs.12320] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Andrea Corral‐Lou
- Biodiversity and Evolutionary Biology Department Museo Nacional de Ciencias Naturales, CSIC Madrid Spain
| | - Silvia Perea
- Biodiversity and Evolutionary Biology Department Museo Nacional de Ciencias Naturales, CSIC Madrid Spain
| | - Enric Aparicio
- Institute of Aquatic Ecology University of Girona Girona Spain
| | - Ignacio Doadrio
- Biodiversity and Evolutionary Biology Department Museo Nacional de Ciencias Naturales, CSIC Madrid Spain
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18
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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: 157] [Impact Index Per Article: 31.4] [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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Shen Y, Hubert N, Huang Y, Wang X, Gan X, Peng Z, He S. DNA barcoding the ichthyofauna of the Yangtze River: Insights from the molecular inventory of a mega‐diverse temperate fauna. Mol Ecol Resour 2019; 19:1278-1291. [DOI: 10.1111/1755-0998.12961] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 09/07/2018] [Accepted: 09/24/2018] [Indexed: 01/04/2023]
Affiliation(s)
- Yanjun Shen
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology Chinese Academy of Sciences Wuhan China
- University of Chinese Academy of Sciences Beijing China
| | - Nicolas Hubert
- Institut de Recherche pour le Développement UMR 226 ISEM (UM2‐CNRS‐IRD) Montpellier cedex 05 France
| | - Yan Huang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education) Southwest University School of Life Sciences Chongqing China
| | - Xuzheng Wang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology Chinese Academy of Sciences Wuhan China
| | - Xiaoni Gan
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology Chinese Academy of Sciences Wuhan China
| | - Zuogang Peng
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education) Southwest University School of Life Sciences Chongqing China
| | - Shunping He
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology Chinese Academy of Sciences Wuhan China
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20
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Turanov SV, Kartavtsev YP, Shapovalov ME. The First Attempt at Studying the Species Diversity of Fish in Lake Khanka Using DNA Barcoding Techniques. RUSS J GENET+ 2019. [DOI: 10.1134/s102279541904015x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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21
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Revisiting species boundaries and distribution ranges of Nemacheilus spp. (Cypriniformes: Nemacheilidae) and Rasbora spp. (Cypriniformes: Cyprinidae) in Java, Bali and Lombok through DNA barcodes: implications for conservation in a biodiversity hotspot. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01152-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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22
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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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Hou G, Chen WT, Lu HS, Cheng F, Xie SG. Developing a DNA barcode library for perciform fishes in the South China Sea: Species identification, accuracy and cryptic diversity. Mol Ecol Resour 2017; 18:137-146. [DOI: 10.1111/1755-0998.12718] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 06/14/2017] [Accepted: 08/14/2017] [Indexed: 11/26/2022]
Affiliation(s)
- Gang Hou
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences; Institute of Hydrobiology; Chinese Academy of Sciences; Wuhan China
- University of Chinese Academy of Sciences; Beijing China
- Guangdong Ocean University; Zhanjiang China
| | - Wei-Tao Chen
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences; Institute of Hydrobiology; Chinese Academy of Sciences; Wuhan China
- University of Chinese Academy of Sciences; Beijing China
| | | | - Fei Cheng
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences; Institute of Hydrobiology; Chinese Academy of Sciences; Wuhan China
| | - Song-Guang Xie
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences; Institute of Hydrobiology; Chinese Academy of Sciences; Wuhan China
- Huai'an Research Center; Institute of Hydrobiology; Chinese Academy of Sciences; Huai'an China
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Palandačić A, Naseka A, Ramler D, Ahnelt H. Contrasting morphology with molecular data: an approach to revision of species complexes based on the example of European Phoxinus (Cyprinidae). BMC Evol Biol 2017; 17:184. [PMID: 28793855 PMCID: PMC5549366 DOI: 10.1186/s12862-017-1032-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 08/02/2017] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Molecular taxonomy studies and barcoding projects can provide rapid means of detecting cryptic diversity. Nevertheless, the use of molecular data for species delimitation should be undertaken with caution. Especially the single-gene approaches are linked with certain pitfalls for taxonomical inference. In the present study, recent and historical species descriptions based upon morphology were used as primary species hypotheses, which were then evaluated with molecular data (including in type and historical museum material) to form secondary species hypotheses. As an example of cryptic diversity and taxonomic controversy, the European Phoxinus phoxinus species complex was used. RESULTS The results of the revision showed that of the fourteen primary species hypotheses, three were rejected, namely P. ketmaieri, P. likai, and P. apollonicus. For three species (P. strandjae, P. strymonicus, P. morella), further investigation with increased data sampling was suggested, while two primary hypotheses, P. bigerri and P. colchicus, were supported as secondary species hypotheses. Finally, six of the primary species hypotheses (P. phoxinus, P. lumaireul, P. karsticus, P. septimanae, P. marsilii and P. csikii) were well supported by mitochondrial but only limitedly corroborated by nuclear data analysis. CONCLUSION The approach has proven useful for revision of species complexes, and the study can serve as an overview of the Phoxinus genus in Europe, as well as a solid basis for further work.
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Affiliation(s)
- Anja Palandačić
- First Zoological Department, Vienna Museum of Natural History, Burgring 7, 1010, Vienna, Austria.
| | - Alexander Naseka
- First Zoological Department, Vienna Museum of Natural History, Burgring 7, 1010, Vienna, Austria
- Department of Ichthyology and Hydrobiology, Faculty for Biology and Soil, Saint Petersburg State University, 7/9 Universitetskaya nab, St. Petersburg, 199034, Russia
| | - David Ramler
- Department of Limnology and Bio-Oceanography, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Harald Ahnelt
- First Zoological Department, Vienna Museum of Natural History, Burgring 7, 1010, Vienna, Austria
- Department of Theoretical Biology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
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25
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Borovikova EA. Special traits of the genetic structure and origin of the population of vendace Coregonus albula of Pleshcheyevo Lake. BIOL BULL+ 2017. [DOI: 10.1134/s1062359017030037] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Ramler D, Palandačić A, Delmastro GB, Wanzenböck J, Ahnelt H. Morphological divergence of lake and stream Phoxinus of Northern Italy and the Danube basin based on geometric morphometric analysis. Ecol Evol 2017; 7:572-584. [PMID: 28116054 PMCID: PMC5243779 DOI: 10.1002/ece3.2648] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 11/01/2016] [Accepted: 11/05/2016] [Indexed: 01/31/2023] Open
Abstract
Minnows of the genus Phoxinus are promising candidates to investigate adaptive divergence, as they inhabit both still and running waters of a variety of altitudes and climatic zones in Europe. We used landmark-based geometric morphometric methods to quantify the level of morphological variability in Phoxinus populations from streams and lakes of Northern Italy and the Danube basin. We analyzed body shape differences of populations in the dorsal, lateral, and ventral planes, using a large array of landmarks and semilandmarks. As the species identification of Phoxinus on morphological characters is ambiguous, we used two mitochondrial genes to determine the genetic background of the samples and to ensure we are comparing homogenous groups. We have found significant body shape differences between habitats: Minnow populations inhabiting streams had a deeper body and caudal peduncle and more laterally inserted pectoral fins than minnows inhabiting lakes. We have also found significant body shape differences between genetic groups: Italian minnows had deeper bodies, deeper and shorter caudal peduncles, and a shorter and wider gape than both groups from the Danube. Our results show that the morphology of Phoxinus is highly influenced by habitat and that body shape variation between habitats was within the same range as between genetic groups. These morphological differences are possibly linked to different modes of swimming and foraging in the respective habitats and are likely results of phenotypic plasticity. However, differences in shape and interlandmark distances between the groups suggest that some (though few) morphometric characters might be useful for separating Phoxinus species.
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Affiliation(s)
- David Ramler
- First Zoological DepartmentMuseum of Natural History ViennaViennaAustria
- Department of Limnology and Bio‐OceanographyUniversity of ViennaViennaAustria
| | - Anja Palandačić
- First Zoological DepartmentMuseum of Natural History ViennaViennaAustria
| | | | - Josef Wanzenböck
- Research Institute for Limnology MondseeUniversity of InnsbruckMondseeAustria
| | - Harald Ahnelt
- First Zoological DepartmentMuseum of Natural History ViennaViennaAustria
- Department of Theoretical BiologyUniversity of ViennaViennaAustria
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Kirtiklis L, Palińska-Żarska K, Krejszeff S, Kupren K, Żarski D, Fopp-Bayat D, Szabelska A. Comparison of molecular and morphometric analysis in species discrimination of larvae among five cyprinids from the subfamily Leuciscinae: A tool for sustainable conservation of riverine ichthyofauna. Biologia (Bratisl) 2016. [DOI: 10.1515/biolog-2016-0139] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Li J, Wang Y, Jin H, Li W, Yan C, Yan P, Zhang X, He S, Song Z. Identification of Triplophysa species from the Qinghai-Tibetan Plateau (QTP) and its adjacent regions through DNA barcodes. Gene 2016; 605:12-19. [PMID: 28104086 DOI: 10.1016/j.gene.2016.11.045] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 10/21/2016] [Accepted: 11/30/2016] [Indexed: 11/16/2022]
Abstract
The genus Triplophysa is the largest and most difficult to identity morphologically fish group of superfamily Cobitoidea with 140 currently valid species, and is mainly distributed in the Qinghai-Tibetan Plateau (QTP) and adjacent regions. Most species within this genus possess highly similar morphological characteristics for adaption to the highland environment and are very difficult to be identified only based on morphology. The traditional species identification, mainly based on external morphological diagnostic characters, leads to inconsistent results in many cases. Herein, we provided a molecular method based on mitochondrial cytochrome c subunit I (COI) for the identification of Triplophysa fishes. Thirty-three Triplophysa species, 244 individuals, were used to determine whether barcoding was effective in discriminating species for this genus. The mean intraspecific and interspecific K2P distances ranged from 0 to 14.9% (mean, 2.9%) and 0 to 23.4% (mean, 9.7%), respectively. The tree-based analysis displayed most of species formed discrete clusters with strong bootstrap support values (>90%). The results showed that most of Triplophysa species could be identified by DNA barcode and indicated DNA barcode could be used as a molecular marker for these species.
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Affiliation(s)
- Jiuxuan Li
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610065, PR China
| | - Ying Wang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610065, PR China; Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China; School of Life Sciences, Jianghan University, Wuhan 430056, PR China
| | - Huifang Jin
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610065, PR China
| | - Wujiao Li
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610065, PR China
| | - Chaochao Yan
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610065, PR China
| | - Pengfei Yan
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610065, PR China
| | - Xiuyue Zhang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610065, PR China
| | - Shunping He
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
| | - Zhaobin Song
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610065, PR China; Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, PR China.
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30
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Geiger MF, Moriniere J, Hausmann A, Haszprunar G, Wägele W, Hebert PDN, Rulik B. Testing the Global Malaise Trap Program - How well does the current barcode reference library identify flying insects in Germany? Biodivers Data J 2016:e10671. [PMID: 27932930 PMCID: PMC5136679 DOI: 10.3897/bdj.4.e10671] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 11/29/2016] [Indexed: 11/25/2022] Open
Abstract
Background Biodiversity patterns are inherently complex and difficult to comprehensively assess. Yet, deciphering shifts in species composition through time and space are crucial for efficient and successful management of ecosystem services, as well as for predicting change. To better understand species diversity patterns, Germany participated in the Global Malaise Trap Program, a world-wide collection program for arthropods using this sampling method followed by their DNA barcode analysis. Traps were deployed at two localities: “Nationalpark Bayerischer Wald” in Bavaria, the largest terrestrial Natura 2000 area in Germany, and the nature conservation area Landskrone, an EU habitats directive site in the Rhine Valley. Arthropods were collected from May to September to track shifts in the taxonomic composition and temporal succession at these locations. New information In total, 37,274 specimens were sorted and DNA barcoded, resulting in 5,301 different genetic clusters (BINs, Barcode Index Numbers, proxy for species) with just 7.6% of their BINs shared. Accumulation curves for the BIN count versus the number of specimens analyzed suggest that about 63% of the potential diversity at these sites was recovered with this single season of sampling. Diversity at both sites rose from May (496 & 565 BINs) to July (1,236 & 1,522 BINs) before decreasing in September (572 & 504 BINs). Unambiguous species names were assigned to 35% of the BINs (1,868) which represented 12,640 specimens. Another 7% of the BINs (386) with 1,988 specimens were assigned to genus, while 26% (1,390) with 12,092 specimens were only placed to a family. These results illustrate how a comprehensive DNA barcode reference library can identify unknown specimens, but also reveal how this potential is constrained by gaps in the quantity and quality of records in BOLD, especially for Hymenoptera and Diptera. As voucher specimens are available for morphological study, we invite taxonomic experts to assist in the identification of unnamed BINs.
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Affiliation(s)
| | | | | | | | - Wolfgang Wägele
- Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Canada
| | - Björn Rulik
- Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
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31
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Chang CH, Shao KT, Lin HY, Chiu YC, Lee MY, Liu SH, Lin PL. DNA barcodes of the native ray-finned fishes in Taiwan. Mol Ecol Resour 2016; 17:796-805. [DOI: 10.1111/1755-0998.12601] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 09/19/2016] [Accepted: 09/21/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Chia-Hao Chang
- Biodiversity Research Center; Academia Sinica; 128 Academia Road Sec. 2 Nankang Taipei 115 Taiwan
| | - Kwang-Tsao Shao
- Biodiversity Research Center; Academia Sinica; 128 Academia Road Sec. 2 Nankang Taipei 115 Taiwan
| | - Han-Yang Lin
- Biodiversity Research Center; Academia Sinica; 128 Academia Road Sec. 2 Nankang Taipei 115 Taiwan
| | - Yung-Chieh Chiu
- Department of Aquaculture; National Taiwan Ocean University; Keelung Taiwan
| | - Mao-Ying Lee
- Biodiversity Research Center; Academia Sinica; 128 Academia Road Sec. 2 Nankang Taipei 115 Taiwan
| | - Shih-Hui Liu
- Department of Biology; Saint Louis University; 3507 Laclede Avenue, Macelwane Hall St. Louis MO 63103 USA
| | - Pai-Lei Lin
- Biodiversity Research Center; Academia Sinica; 128 Academia Road Sec. 2 Nankang Taipei 115 Taiwan
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32
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Yang T, Meng W, Zhang R, Gao T, Cai L, Hai S, Zhou Q. DNA barcoding of fishes in Irtysh River China. RUSS J GENET+ 2016. [DOI: 10.1134/s1022795416090167] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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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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34
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Thiel R, Knebelsberger T. How reliably can northeast Atlantic sand lances of the genera Ammodytes and Hyperoplus be distinguished? A comparative application of morphological and molecular methods. Zookeys 2016:139-64. [PMID: 27667958 PMCID: PMC5027774 DOI: 10.3897/zookeys.617.8866] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 08/06/2016] [Indexed: 11/21/2022] Open
Abstract
Accurate stock assessments for each of the dominant species of sand lances in the northeast Atlantic Ocean and adjacent areas are not available due to the lack of a reliable identification procedure; therefore, appropriate measures of fisheries management or conservation of sand lances cannot be implemented. In this study, detailed morphological and molecular features are assessed to discriminate between four species of sand lances belonging to the genera Ammodytes and Hyperoplus. Morphological characters described by earlier authors as useful for identification of the genera are confirmed, and two additional distinguishing characters are added. A combination of the following morphological characters is recommended to distinguish between the genera Hyperoplus and Ammodytes: the protrusibility of the premaxillae, the presence of hooked ends of the prevomer, the number of dermal plicae, and the pectoral-fin length as a percentage of the standard length. The discriminant function analysis revealed that morphometric data are not very useful to distinguish the species of each of the two genera. The following meristic characters improve the separation of Hyperopluslanceolatus from Hyperoplusimmaculatus: the number of lower arch gill rakers, total number of gill rakers, numbers of caudal vertebrae and total vertebrae, and numbers of dorsal-fin and anal-fin rays. It is confirmed that Ammodytestobianus differs from Ammodytesmarinus by its belly scales that are organised in tight chevrons, scales which are present over the musculature at the base of the caudal fin, as well as by the lower numbers of dermal plicae, dorsal-fin rays, and total vertebrae. In contrast to the morphological data, mitochondrial COI sequences (DNA barcodes) failed to separate unambiguously the four investigated species. Ammodytestobianus and Hyperopluslanceolatus showed an overlap between intraspecific and interspecific K2P genetic distances and cannot be reliably distinguished using the common DNA barcoding approach. Ammodytesmarinus and Hyperoplusimmaculatus exhibited gaps between intraspecific and interspecific K2P distances of 2.73 and 3.34% respectively, indicating that their DNA barcodes can be used for species identification. As an alternative, short nuclear Rhodopsin sequences were analysed and one diagnostic character was found for each of the species Ammodytesmarinus, Hyperopluslanceolatus, and Hyperoplusimmaculatus. Ammodytestobianus can be characterised by the lack of species-specific mutations when compared to the other three species. In contrast to COI, the short nuclear sequences represent a useful alternative for rapid species identification whenever an examination of morphological characters is not available.
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Affiliation(s)
- Ralf Thiel
- University of Hamburg, Center of Natural History, Zoological Museum, 20146 Hamburg, Germany
| | - Thomas Knebelsberger
- Senckenberg am Meer, German Centre for Marine Biodiversity Research (DZMB), 26382 Wilhelmshaven, Germany
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35
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Geiger MF, Astrin JJ, Borsch T, Burkhardt U, Grobe P, Hand R, Hausmann A, Hohberg K, Krogmann L, Lutz M, Monje C, Misof B, Morinière J, Müller K, Pietsch S, Quandt D, Rulik B, Scholler M, Traunspurger W, Haszprunar G, Wägele W. How to tackle the molecular species inventory for an industrialized nation-lessons from the first phase of the German Barcode of Life initiative GBOL (2012-2015). Genome 2016; 59:661-70. [PMID: 27314158 DOI: 10.1139/gen-2015-0185] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Biodiversity loss is mainly driven by human activity. While concern grows over the fate of hot spots of biodiversity, contemporary species losses still prevail in industrialized nations. Therefore, strategies were formulated to halt or reverse the loss, driven by evidence for its value for ecosystem services. Maintenance of the latter through conservation depends on correctly identified species. To this aim, the German Federal Ministry of Education and Research is funding the GBOL project, a consortium of natural history collections, botanic gardens, and universities working on a barcode reference database for the country's fauna and flora. Several noticeable findings could be useful for future campaigns: (i) validating taxon lists to serve as a taxonomic backbone is time-consuming, but without alternative; (ii) offering financial incentives to taxonomic experts, often citizen scientists, is indispensable; (iii) completion of the libraries for widespread species enables analyses of environmental samples, but the process may not hold pace with technological advancements; (iv) discoveries of new species are among the best stories for the media; (v) a commitment to common data standards and repositories is needed, as well as transboundary cooperation between nations; (vi) after validation, all data should be published online via the BOLD to make them searchable for external users and to allow cross-checking with data from other countries.
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Affiliation(s)
- M F Geiger
- a Stiftung Zoologisches Forschungsmuseum Alexander Koenig, Leibniz Institut für Biodiversität der Tiere, Adenauerallee 160, 53113 Bonn, Germany
| | - J J Astrin
- a Stiftung Zoologisches Forschungsmuseum Alexander Koenig, Leibniz Institut für Biodiversität der Tiere, Adenauerallee 160, 53113 Bonn, Germany
| | - T Borsch
- b Botanischer Garten und Botanisches Museum Berlin-Dahlem, Freie Universität Berlin, Königin-Luise-Straße 6-8, 14195 Berlin, Germany
| | - U Burkhardt
- d Senckenberg Museum für Naturkunde Görlitz, Am Museum 1, 02826 Görlitz, Germany
| | - P Grobe
- a Stiftung Zoologisches Forschungsmuseum Alexander Koenig, Leibniz Institut für Biodiversität der Tiere, Adenauerallee 160, 53113 Bonn, Germany
| | - R Hand
- b Botanischer Garten und Botanisches Museum Berlin-Dahlem, Freie Universität Berlin, Königin-Luise-Straße 6-8, 14195 Berlin, Germany
| | - A Hausmann
- c SNSB-Zoologische Staatssammlung München, Münchhausenstraße 21, 81247 München, Germany
| | - K Hohberg
- d Senckenberg Museum für Naturkunde Görlitz, Am Museum 1, 02826 Görlitz, Germany
| | - L Krogmann
- e Staatliches Museum für Naturkunde Stuttgart, Rosenstein 1, 70191 Stuttgart, Germany
| | - M Lutz
- j Plant Evolutionary Ecology, Institute of Evolution and Ecology, University of Tübingen, Auf der Morgenstelle 5, 72076 Tübingen, Germany
| | - C Monje
- e Staatliches Museum für Naturkunde Stuttgart, Rosenstein 1, 70191 Stuttgart, Germany
| | - B Misof
- a Stiftung Zoologisches Forschungsmuseum Alexander Koenig, Leibniz Institut für Biodiversität der Tiere, Adenauerallee 160, 53113 Bonn, Germany
| | - J Morinière
- c SNSB-Zoologische Staatssammlung München, Münchhausenstraße 21, 81247 München, Germany
| | - K Müller
- f Institute for Evolution and Biodiversity, Westfälische Wilhelms-Universität, Hüfferstrasse 1, 48149 Münster, Germany
| | - S Pietsch
- a Stiftung Zoologisches Forschungsmuseum Alexander Koenig, Leibniz Institut für Biodiversität der Tiere, Adenauerallee 160, 53113 Bonn, Germany
| | - D Quandt
- g Nees-Institut für Biodiversität der Pflanzen, Meckenheimer Allee 170, 53115 Bonn, Germany
| | - B Rulik
- a Stiftung Zoologisches Forschungsmuseum Alexander Koenig, Leibniz Institut für Biodiversität der Tiere, Adenauerallee 160, 53113 Bonn, Germany
| | - M Scholler
- h Staatliches Museum für Naturkunde Karlsruhe, Erbprinzenstr. 13, 76133 Karlsruhe, Germany
| | - W Traunspurger
- i Universität Bielefeld, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - G Haszprunar
- c SNSB-Zoologische Staatssammlung München, Münchhausenstraße 21, 81247 München, Germany
| | - W Wägele
- a Stiftung Zoologisches Forschungsmuseum Alexander Koenig, Leibniz Institut für Biodiversität der Tiere, Adenauerallee 160, 53113 Bonn, Germany
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37
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Chen W, Ma X, Shen Y, Mao Y, He S. The fish diversity in the upper reaches of the Salween River, Nujiang River, revealed by DNA barcoding. Sci Rep 2015; 5:17437. [PMID: 26616046 PMCID: PMC4663501 DOI: 10.1038/srep17437] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 10/29/2015] [Indexed: 11/09/2022] Open
Abstract
Nujiang River (NR), an essential component of the biodiversity hotspot of the
Mountains of Southwest China, possesses a characteristic fish fauna and contains
endemic species. Although previous studies on fish diversity in the NR have
primarily consisted of listings of the fish species observed during field
collections, in our study, we DNA-barcoded 1139 specimens belonging to 46
morphologically distinct fish species distributed throughout the NR basin by
employing multiple analytical approaches. According to our analyses, DNA barcoding
is an efficient method for the identification of fish by the presence of barcode
gaps. However, three invasive species are characterized by deep conspecific
divergences, generating multiple lineages and Operational Taxonomic Units (OTUs),
implying the possibility of cryptic species. At the other end of the spectrum, ten
species (from three genera) that are characterized by an overlap between their
intra- and interspecific genetic distances form a single genetic cluster and share
haplotypes. The neighbor-joining phenogram, Barcode Index Numbers (BINs) and
Automatic Barcode Gap Discovery (ABGD) identified 43 putative species, while the
General Mixed Yule-coalescence (GMYC) identified five more OTUs. Thus, our study
established a reliable DNA barcode reference library for the fish in the NR and
sheds new light on the local fish diversity.
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Affiliation(s)
- Weitao Chen
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China.,Graduate school of Chinese Academy of Sciences, Beijing, 10001, China
| | - Xiuhui Ma
- School of life science, Southwest University, Beibei, Chongqing, 400715, China
| | - Yanjun Shen
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China.,Graduate school of Chinese Academy of Sciences, Beijing, 10001, China
| | - Yuntao Mao
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China.,Graduate school of Chinese Academy of Sciences, Beijing, 10001, China
| | - Shunping He
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China
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38
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Rougemont Q, Gaigher A, Lasne E, Côte J, Coke M, Besnard AL, Launey S, Evanno G. Low reproductive isolation and highly variable levels of gene flow reveal limited progress towards speciation between European river and brook lampreys. J Evol Biol 2015; 28:2248-63. [PMID: 26348652 DOI: 10.1111/jeb.12750] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 09/02/2015] [Accepted: 09/02/2015] [Indexed: 01/10/2023]
Abstract
Ecologically based divergent selection is a factor that could drive reproductive isolation even in the presence of gene flow. Population pairs arrayed along a continuum of divergence provide a good opportunity to address this issue. Here, we used a combination of mating trials, experimental crosses and population genetic analyses to investigate the evolution of reproductive isolation between two closely related species of lampreys with distinct life histories. We used microsatellite markers to genotype over 1000 individuals of the migratory parasitic river lamprey (Lampetra fluviatilis) and freshwater-resident nonparasitic brook lamprey (Lampetra planeri) distributed in 10 sympatric and parapatric population pairs in France. Mating trials, parentage analyses and artificial fertilizations demonstrated a low level of reproductive isolation between species even though size-assortative mating may contribute to isolation. Most parapatric population pairs were strongly differentiated due to the joint effects of geographic distance and barriers to migration. In contrast, we found variable levels of gene flow between sympatric populations ranging from panmixia to moderate differentiation, which indicates a gradient of divergence with some population pairs that may correspond to alternative morphs or ecotypes of a single species and others that remain partially isolated. Ecologically based divergent selection may explain these variable levels of divergence among sympatric population pairs, but incomplete genome swamping following secondary contact could have also played a role. Overall, this study illustrates how highly differentiated phenotypes can be maintained despite high levels of gene flow that limit the progress towards speciation.
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Affiliation(s)
- Q Rougemont
- UMR 985 Ecologie et Santé des Ecosystèmes, INRA, Rennes, France.,UMR ESE, Agrocampus Ouest, Rennes, France
| | - A Gaigher
- UMR 985 Ecologie et Santé des Ecosystèmes, INRA, Rennes, France.,UMR ESE, Agrocampus Ouest, Rennes, France.,Laboratory for Conservation Biology, Department of Ecology and Evolution, University of Lausanne, Biophore, Switzerland
| | - E Lasne
- Muséum National d'Histoire Naturelle, CRESCO, Dinard, France.,UMR CARRTEL, INRA, Thonon-les-Bains, France
| | - J Côte
- UMR 985 Ecologie et Santé des Ecosystèmes, INRA, Rennes, France.,UMR ESE, Agrocampus Ouest, Rennes, France
| | - M Coke
- Unité Expérimentale d'Ecologie et d'Ecotoxicologie Aquatique, INRA, Rennes, France
| | - A-L Besnard
- UMR 985 Ecologie et Santé des Ecosystèmes, INRA, Rennes, France.,UMR ESE, Agrocampus Ouest, Rennes, France
| | - S Launey
- UMR 985 Ecologie et Santé des Ecosystèmes, INRA, Rennes, France.,UMR ESE, Agrocampus Ouest, Rennes, France
| | - G Evanno
- UMR 985 Ecologie et Santé des Ecosystèmes, INRA, Rennes, France.,UMR ESE, Agrocampus Ouest, Rennes, France
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