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Najafikhah A, Zeinalabedini M, Arefnezhad B, Mardi M, Nafari M, Nasrolahpourmoghadam M, Jafari O. Genome-wide data suggest a revision in management of the Caspian Sea trout Salmo caspius. PLoS One 2023; 18:e0287777. [PMID: 37471390 PMCID: PMC10358921 DOI: 10.1371/journal.pone.0287777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 06/13/2023] [Indexed: 07/22/2023] Open
Abstract
Salmo caspius Kessler, 1877 is one of the most commercially important species of Salmonidae in the southern basin of the Caspian Sea. The occurrence of its wild populations has undergone sever reduction during the last years. In spite of the yearly restocking activity, still no progress on the recovery of its wild population has been observed. Hence, the present study was done in order to assess the efficiency of the current restocking activity in the southern Caspian basin in term of genetic diversity. DNA extracts of 32 S. caspius from four different groups were screened using 62621 genome-wide single nucleotide polymorphisms (SNP). The overal genetic diversity and Fst values were 0.18 and 0.08, respectively. Considering the observed admixture pattern and the positive values for inbreeding coeficient it seems that S. caspius suffers from its small effective population size. In order to obtain the maximum performance, alonside with expanding the size of brood stocks, rehabilitation of the habitats and spawning rivers of this nationally endangered species is of great importance.
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Affiliation(s)
- Arezo Najafikhah
- Department of Biotechnology, Payame Noor University, Tehran, Iran
| | - Mehrshad Zeinalabedini
- Department of Genomics, Agricultural Biotechnology Research Institute of Iran (ABRII), Karaj, Iran
| | | | - Mohsen Mardi
- Seed and Plant Certification and Registration Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | | | | | - Omid Jafari
- International Sturgeon Research Institute, Iranian Fisheries Science Research Institute, Agricultural Research, Education and Extension Organization, Rasht, Iran
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Halasan LC, Lin HC. Integrated morphometrics reveals conservatism in the cryptic yellowstripe scad (Perciformes: Carangidae) lineages from the Tropical Western Pacific. ZOOL ANZ 2022. [DOI: 10.1016/j.jcz.2022.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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Hashemzadeh Segherloo I, Freyhof J, Berrebi P, Ferchaud AL, Geiger M, Laroche J, Levin BA, Normandeau E, Bernatchez L. A genomic perspective on an old question: Salmo trouts or Salmo trutta (Teleostei: Salmonidae)? Mol Phylogenet Evol 2021; 162:107204. [PMID: 34015446 DOI: 10.1016/j.ympev.2021.107204] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 04/29/2021] [Accepted: 05/06/2021] [Indexed: 10/21/2022]
Abstract
There are particular challenges in defining the taxonomic status of recently radiated groups due to the low level of phylogenetic signal. Members of the Salmo trutta species-complex, which mostly evolved during and following the Pleistocene, show high morphological and ecological diversity that, along with their very wide geographic distribution, have led to morphological description of 47 extant nominal species. However, many of these species have not been supported by previous phylogenetic studies, which could be partly due to lack of significant genetic differences among them, the limited resolution offered by molecular methods previously used, as well as the often local scale of these studies. The development of next-generation sequencing (NGS) and related analytical tools have enhanced our ability to address such challenging questions. In this study, Genotyping-by-Sequencing (GBS) of 15,169 filtered SNPs and mitochondrial DNA (mtDNA) D-loop sequences were combined to assess the phylogenetic relationships among 166 brown trouts representing 21 described species and three undescribed groups collected from 84 localities throughout their natural distribution in Europe, west Asia, and North Africa. The data were analysed using different clustering algorithms (admixture analysis and discriminant analysis of principal components-DAPC), a Bayes Factor Delimitation (BFD) test, species tree reconstruction, gene flow tests (three- and four-population tests), and Rogue taxa identification tests. Genomic contributions of the Atlantic lineage brown trout were found in all major sea basins excluding the North African and Aral Sea basins, suggesting introgressive hybridization of native brown trouts driven by stocking using strains of the Atlantic lineage. After removing the phylogenetic noise caused by the Atlantic brown trout, admixture clusters and DAPC clustering based on GBS data, respectively, resolved 11 and 13 clusters among the previously described brown trout species, which were also supported by BFD test results. Our results suggest that natural hybridization between different brown trout lineages has probably played an important role in the origin of several of the putative species, including S. marmoratus, S. carpio, S. farioides, S. pellegrini, S. caspius (in the Kura River drainage) and Salmo sp. in the Danube River basin. Overall, our results support a multi-species taxonomy for brown trouts. They also resolve some species in the Adriatic-Mediterranean and Black Sea drainages as members of very closely related genomic clusters that may need taxonomic revision. However, any final conclusions pertaining to the taxonomy of the brown trout complex should be based on an integrative approach combining genomic, morphological, and ecological data. To avoid challenges in taxonomy and conservation of species complexes like brown trouts, it is suggested to describe species based on genomic clusters of populations instead of describing species based only on morphologically differentiated single type populations.
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Affiliation(s)
- Iraj Hashemzadeh Segherloo
- Department of Fisheries and Environmental Sciences, Faculty of Natural Resources and Earth Sciences, Shahr-e-Kord University, Shahr-e-Kord, Iran; Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada.
| | - Jörg Freyhof
- Museum für Naturkunde Leibniz Institute for Research on Evolution and Biodiversity at the Humboldt University Berlin, 10115 Berlin, Germany
| | - Patrick Berrebi
- Genome - Research & Diagnostic, 697 avenue de Lunel, 34400 Saint-Just, France
| | - Anne-Laure Ferchaud
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada
| | - Matthias Geiger
- Zoologisches Forschungsmuseum Museum Alexander Koenig, Leibniz Institute for Animal Biodiversity, 53133 Bonn, Germany
| | - Jérôme Laroche
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada
| | - Boris A Levin
- Papanin Institute of Biology of Inland Waters, Russian Academy of Sciences, Borok, Yaroslavl Region, Russia & Cherepovets State University, Cherepovets, Vologda Region, Russia
| | - Eric Normandeau
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada
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Saint-Pé K, Leitwein M, Tissot L, Poulet N, Guinand B, Berrebi P, Marselli G, Lascaux JM, Gagnaire PA, Blanchet S. Development of a large SNPs resource and a low-density SNP array for brown trout (Salmo trutta) population genetics. BMC Genomics 2019; 20:582. [PMID: 31307373 PMCID: PMC6631668 DOI: 10.1186/s12864-019-5958-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 07/04/2019] [Indexed: 01/04/2023] Open
Abstract
Background The brown trout (Salmo trutta) is an economically and ecologically important species for which population genetic monitoring is frequently performed. The most commonly used genetic markers for this species are microsatellites and mitochondrial markers that lack replicability among laboratories, and a large genome coverage. An alternative that may be particularly efficient and universal is the development of small to large panels of Single Nucleotide Polymorphism markers (SNPs). Here, we used Restriction site Associated DNA sequences (RADs) markers to identify a set of 12,204 informative SNPs positioned on the brown trout linkage map and suitable for population genetics studies. Then, we used this novel resource to develop a cost-effective array of 192 SNPs (96 × 2) evenly spread on this map. This array was tested for genotyping success in five independent rivers occupied by two main brown trout evolutionary lineages (Atlantic -AT- and Mediterranean -ME-) on a total of 1862 individuals. Moreover, inference of admixture rate with domestic strains and population differentiation were assessed for a small river system (the Taurion River, 190 individuals) and results were compared to a panel of 13 microsatellites. Results A high genotyping success was observed for all rivers (< 1% of non-genotyped loci per individual), although some initially used SNP failed to be amplified, probably because of mutations in primers, and were replaced. These SNPs permitted to identify patterns of isolation-by-distance for some rivers. Finally, we found that microsatellite and SNP markers yielded very similar patterns for population differentiation and admixture assessments, with SNPs having better ability to detect introgression and differentiation. Conclusions The novel resources provided here opens new perspectives for universality and genome-wide studies in brown trout populations. Electronic supplementary material The online version of this article (10.1186/s12864-019-5958-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Keoni Saint-Pé
- Centre National de la Recherche Scientifique (CNRS), Université Paul Sabatier (UPS), Station d'Ecologie Théorique et Expérimentale, SETE, UMR 5321, 2 route du CNRS, 09200, Moulis, France.
| | - Maeva Leitwein
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada.,ISEM, CNRS, Univ. Montpellier, IRD, EPHE, Montpellier, France
| | - Laurence Tissot
- EDF R and D LNHE - Laboratoire National d'Hydraulique et Environnement, 6 quai Watier, 78401, Chatou Cedex, France
| | - Nicolas Poulet
- Pôle écohydraulique AFB-IMT, allée du Pr Camille Soula, 31400, Toulouse, France
| | - Bruno Guinand
- ISEM, CNRS, Univ. Montpellier, IRD, EPHE, Montpellier, France
| | - Patrick Berrebi
- ISEM, CNRS, Univ. Montpellier, IRD, EPHE, Montpellier, France.,Present address: Genome - Research and Diagnostic, 697 avenue de Lunel, 34400, Saint-Just, France
| | - Geoffrey Marselli
- Centre National de la Recherche Scientifique (CNRS), Université Paul Sabatier (UPS), Station d'Ecologie Théorique et Expérimentale, SETE, UMR 5321, 2 route du CNRS, 09200, Moulis, France
| | | | | | - Simon Blanchet
- Centre National de la Recherche Scientifique (CNRS), Université Paul Sabatier (UPS), Station d'Ecologie Théorique et Expérimentale, SETE, UMR 5321, 2 route du CNRS, 09200, Moulis, France.,Université de Toulouse, UPS, UMR 5174 (EDB), 118 route de Narbonne, F-31062, Toulouse cedex 4, France
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Tougard C, Justy F, Guinand B, Douzery EJP, Berrebi P. Salmo macrostigma (Teleostei, Salmonidae): Nothing more than a brown trout (S. trutta) lineage? J Fish Biol 2018; 93:302-310. [PMID: 29992566 DOI: 10.1111/jfb.13751] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 03/07/2018] [Indexed: 06/08/2023]
Abstract
We examined specimens of the macrostigma trout Salmo macrostigma, which refers to big black spots on the flanks, to assess whether it is an example of taxonomic inflation within the brown trout Salmo trutta complex. Using new specimens, publicly available data and a mitogenomic protocol to amplify the control and cytochrome b regions of the mitochondrial genome from degraded museum samples, including one syntype specimen, the present study shows that the macrostigma trout is not a valid species. Our results suggest the occurrence of a distinct evolutionary lineage of S. trutta in North Africa and Sicily. The name of the North African lineage is proposed for this lineage, which was found to be sister to the Atlantic lineage of brown trout, S. trutta.
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Affiliation(s)
| | - Fabienne Justy
- ISEM, CNRS, Université de Montpellier, IRD, EPHE, Montpellier, France
| | - Bruno Guinand
- ISEM, CNRS, Université de Montpellier, IRD, EPHE, Montpellier, France
| | | | - Patrick Berrebi
- ISEM, CNRS, Université de Montpellier, IRD, EPHE, Montpellier, France
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Ninua L, Tarkhnishvili D, Gvazava E. Phylogeography and taxonomic status of trout and salmon from the Ponto-Caspian drainages, with inferences on European Brown Trout evolution and taxonomy. Ecol Evol 2018; 8:2645-2658. [PMID: 29531683 PMCID: PMC5838059 DOI: 10.1002/ece3.3884] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 12/07/2017] [Accepted: 01/02/2018] [Indexed: 01/19/2023] Open
Abstract
Current taxonomy of western Eurasian trout leaves a number of questions open; it is not clear to what extent some species are distinct genetically and morphologically. The purpose of this paper was to explore phylogeography and species boundaries in freshwater and anadromous trout from the drainages of the Black and the Caspian Seas (Ponto-Caspian). We studied morphology and mitochondrial phylogeny, combining samples from the western Caucasus within the potential range of five nominal species of trout that are thought to inhabit this region, and using the sequences available from GenBank. Our results suggest that the genetic diversity of trout in the Ponto-Caspian region is best explained with the fragmentation of catchments. (1) All trout species from Ponto-Caspian belong to the same mitochondrial clade, separated from the other trout since the Pleistocene; (2) the southeastern Black Sea area is the most likely place of diversification of this clade, which is closely related to the clades from Anatolia; (3) The species from the Black Sea and the Caspian Sea drainages are monophyletic; (4) except for the basal lineage of the Ponto-Caspian clade, Salmo rizeensis, all the lineages produce anadromous forms; (5) genetic diversification within the Ponto-Caspian clade is related to Pleistocene glacial waves; (6) the described morphological differences between the species are not fully diagnostic, and some earlier described differences depend on body size; the differences between freshwater and marine forms exceed those between the different lineages. We suggest a conservative taxonomic approach, using the names S. rizeensis and Salmo labrax for trout from the Black Sea basin and Salmo caspius and Salmo ciscaucasicus for the fish from the Caspian basin.
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Affiliation(s)
- Levan Ninua
- Institute of EcologyIlia State UniversityTbilisiGeorgia
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Leitwein M, Gagnaire PA, Desmarais E, Guendouz S, Rohmer M, Berrebi P, Guinand B. Genome-wide nucleotide diversity of hatchery-reared Atlantic and Mediterranean strains of brown trout Salmo trutta compared to wild Mediterranean populations. J Fish Biol 2016; 89:2717-2734. [PMID: 27666575 DOI: 10.1111/jfb.13131] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 08/01/2016] [Indexed: 06/06/2023]
Abstract
A genome-wide assessment of diversity is provided for wild Mediterranean brown trout Salmo trutta populations from headwater tributaries of the Orb River and from Atlantic and Mediterranean hatchery-reared strains that have been used for stocking. Double-digest restriction-site-associated DNA sequencing (dd-RADseq) was performed and the efficiency of de novo and reference-mapping approaches to obtain individual genotypes was compared. Large numbers of single nucleotide polymorphism (SNP) markers with similar genome-wide distributions were discovered using both approaches (196 639 v. 121 016 SNPs, respectively), with c. 80% of the loci detected de novo being also found with reference mapping, using the Atlantic salmon Salmo salar genome as a reference. Lower mapping density but larger nucleotide diversity (π) was generally observed near extremities of linkage groups, consistent with regions of residual tetrasomic inheritance observed in salmonids. Genome-wide diversity estimates revealed reduced polymorphism in hatchery strains (π = 0·0040 and π = 0·0029 in Atlantic and Mediterranean strains, respectively) compared to wild populations (π = 0·0049), a pattern that was congruent with allelic richness estimated from microsatellite markers. Finally, pronounced heterozygote deficiency was found in hatchery strains (Atlantic FIS = 0·18; Mediterranean FIS = 0·42), indicating that stocking practices may affect the genetic diversity in wild populations. These new genomic resources will provide important tools to define better conservation strategies in S. trutta.
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Affiliation(s)
- M Leitwein
- UMR ISEM, Institut des Sciences de l'Evolution de Montpellier, Université de Montpellier, Place E. Bataillon - cc65, 34095, Montpellier Cedex 5, France
| | - P-A Gagnaire
- UMR ISEM, Institut des Sciences de l'Evolution de Montpellier, Université de Montpellier, Place E. Bataillon - cc65, 34095, Montpellier Cedex 5, France
- Station Biologique Marine, 2 Avenue des Chantiers, 34200, Sète, France
| | - E Desmarais
- UMR ISEM, Institut des Sciences de l'Evolution de Montpellier, Université de Montpellier, Place E. Bataillon - cc65, 34095, Montpellier Cedex 5, France
| | - S Guendouz
- MGX-Montpellier GenomiX, Institut de Génomique Fonctionnelle, 141 rue de Cardonille, 34094, Montpellier Cedex 5, France
| | - M Rohmer
- MGX-Montpellier GenomiX, Institut de Génomique Fonctionnelle, 141 rue de Cardonille, 34094, Montpellier Cedex 5, France
| | - P Berrebi
- UMR ISEM, Institut des Sciences de l'Evolution de Montpellier, Université de Montpellier, Place E. Bataillon - cc65, 34095, Montpellier Cedex 5, France
| | - B Guinand
- UMR ISEM, Institut des Sciences de l'Evolution de Montpellier, Université de Montpellier, Place E. Bataillon - cc65, 34095, Montpellier Cedex 5, France
- Département Biologie-Ecologie, Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier Cedex 5, France
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Mostafavi H, Pletterbauer F, Coad BW, Mahini AS, Schinegger R, Unfer G, Trautwein C, Schmutz S. Predicting presence and absence of trout ( Salmo trutta) in Iran. Limnologica 2014; 46:1-8. [PMID: 24707064 PMCID: PMC3974070 DOI: 10.1016/j.limno.2013.12.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Revised: 12/04/2013] [Accepted: 12/04/2013] [Indexed: 06/01/2023]
Abstract
Species distribution modelling, as a central issue in freshwater ecology, is an important tool for conservation and management of aquatic ecosystems. The brown trout (Salmo trutta) is a sensitive species which reacts to habitat changes induced by human impacts. Therefore, the identification of suitable habitats is essential. This study explores the potential distribution of brown trout by a species distribution modelling approach for Iran. Furthermore, modelling results are compared to the distribution described in the literature. Areas outside the currently known distribution which may offer potential habitats for brown trout are identified. The species distribution modelling was based on five different modelling techniques: Generalised Linear Model, Generalised Additive Model, Generalised Boosting Model, Classification Tree Analysis and Random Forests, which are finally summarised in an ensemble forecasting approach. We considered four environmental descriptors at the local scale (slope, bankfull width, wetted width, and elevation) and three climatic parameters (mean air temperature, range of air temperature and annual precipitation) which were extracted on three different spatial extents (1/5/10 km). The performance of all models was excellent (≥0.8) according to the TSS (True Skill Statistic) criterion. Slope, mean and range of air temperature were the most important variables in predicting brown trout occurrence. Presented results deepen the knowledge about distribution patterns of brown trout in Iran. Moreover, this study gives a basic background for the future development of assessment methods for riverine ecosystems in Iran.
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Affiliation(s)
- Hossein Mostafavi
- Department of Water, Atmosphere and Environment, Institute of Hydrobiology and Aquatic Ecosystem Management, BOKU University of Natural Resources and Life Sciences, Vienna, Austria
- Department of Bio-diversity and Ecosystem Management, Environmental Sciences Research Institute, Shahid Beheshti University, Tehran, Iran
| | - Florian Pletterbauer
- Department of Water, Atmosphere and Environment, Institute of Hydrobiology and Aquatic Ecosystem Management, BOKU University of Natural Resources and Life Sciences, Vienna, Austria
| | | | - Abdolrassoul Salman Mahini
- Faculty of Fishery and Environment, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran
| | - Rafaela Schinegger
- Department of Water, Atmosphere and Environment, Institute of Hydrobiology and Aquatic Ecosystem Management, BOKU University of Natural Resources and Life Sciences, Vienna, Austria
| | - Günther Unfer
- Department of Water, Atmosphere and Environment, Institute of Hydrobiology and Aquatic Ecosystem Management, BOKU University of Natural Resources and Life Sciences, Vienna, Austria
| | - Clemens Trautwein
- Department of Water, Atmosphere and Environment, Institute of Hydrobiology and Aquatic Ecosystem Management, BOKU University of Natural Resources and Life Sciences, Vienna, Austria
| | - Stefan Schmutz
- Department of Water, Atmosphere and Environment, Institute of Hydrobiology and Aquatic Ecosystem Management, BOKU University of Natural Resources and Life Sciences, Vienna, Austria
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Kohout J, Šedivá A, Apostolou A, Stefanov T, Marić S, Gaffaroğlu M, Šlechta V. Genetic diversity and phylogenetic origin of brown trout Salmo trutta populations in eastern Balkans. Biologia (Bratisl) 2013; 68:1229-37. [DOI: 10.2478/s11756-013-0271-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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