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Single Nucleotide Polymorphism Markers with Applications in Conservation and Exploitation of Aquatic Natural Populations. Animals (Basel) 2023; 13:ani13061089. [PMID: 36978629 PMCID: PMC10044284 DOI: 10.3390/ani13061089] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/11/2023] [Accepted: 03/14/2023] [Indexed: 03/29/2023] Open
Abstract
Simple Summary In recent decades, societies, states and local authorities have become increasingly aware that for effective long-term management and protection of aquatic ecosystems and populations, it is necessary to take into account the genetic changes occurring in these populations. One type of high-resolution molecular marker suitable for studying the neutral and adaptive genetic diversity of populations is single nucleotide polymorphism (SNP). This review is an attempt to show the benefits of using SNPs to recognize natural populations of aquatic animals and detect the threats to them from accidentally or intentionally released farm animals, fishery and global climate changes. It is postulated that conservation actions should protect not only pristine natural populations that are endangered or overfished, but also protect populations of non-threatened species from unnecessarily released semi-domesticated animals. The enhancement of natural populations with farmed material usually reduces their genetic diversity. Experimental size-selective catches of artificially created populations have caused evolutionary changes in the life cycles of fishes. However, fishery-induced evolution in natural populations is difficult to observe. The negative measurable effects on populations can be expected when the number of breeding individuals is reduced below 100, which occurs very rarely in the sea and more often in fragmented freshwater streams, ponds and seasonal rivers. Abstract An increasing number of aquatic species have been studied for genetic polymorphism, which extends the knowledge on their natural populations. One type of high-resolution molecular marker suitable for studying the genetic diversity of large numbers of individuals is single nucleotide polymorphism (SNP). This review is an attempt to show the range of applications of SNPs in studies of natural populations of aquatic animals. In recent years, SNPs have been used in the genetic analysis of wild and enhanced fish and invertebrate populations in natural habitats, exploited migratory species in the oceans, migratory anadromous and freshwater fish and demersal species. SNPs have been used for the identification of species and their hybrids in natural environments, to study the genetic consequences of restocking for conservation purposes and the negative effects on natural populations of fish accidentally escaping from culture. SNPs are very useful for identifying genomic regions correlated with phenotypic variants relevant for wildlife protection, management and aquaculture. Experimental size-selective catches of populations created in tanks have caused evolutionary changes in life cycles of fishes. The research results have been discussed to clarify whether the fish populations in natural conditions can undergo changes due to selective harvesting targeting the fastest-growing fishes.
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Vaux F, Bohn S, Hyde JR, O'Malley KG. Adaptive markers distinguish North and South Pacific Albacore amid low population differentiation. Evol Appl 2021; 14:1343-1364. [PMID: 34025772 PMCID: PMC8127716 DOI: 10.1111/eva.13202] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 12/19/2022] Open
Abstract
Albacore (Thunnus alalunga) support an economically valuable global fishery, but surprisingly little is known about the population structure of this highly migratory species. Physical tagging data suggest that Albacore from the North and South Pacific Ocean are separate stocks, but results from previous genetic studies did not support this two stock hypothesis. In addition, observed biological differences among juveniles suggest that there may be population substructure in the North Pacific. We used double-digest restriction site-associated DNA sequencing to assess population structure among 308 Albacore caught in 12 sample areas across the Pacific Ocean (10 North, 2 South). Since Albacore are highly migratory and spawning areas are unknown, sample groups were not assumed to be equivalent to populations and the genetic data were analyzed iteratively. We tested for putatively adaptive differences among groups and for genetic variation associated with sex. Results indicated that Albacore in the North and South Pacific can be distinguished using 84 putatively adaptive loci, but not using the remaining 12,788 presumed neutral sites. However, two individuals likely represent F1 hybrids between the North and South Pacific populations, and 43 Albacore potentially exhibit lower degrees of mixed ancestry. In addition, four or five cross-hemisphere migrants were potentially identified. No genetic evidence was found for population substructure within the North Pacific, and no loci appeared to distinguish males from females. Potential functions for the putatively adaptive loci were identified, but an annotated Albacore genome is required for further exploration. Future research should try to locate spawning areas so that life history, demography, and genetic population structure can be linked and spatiotemporal patterns can be investigated.
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Affiliation(s)
- Felix Vaux
- State Fisheries Genomics LabCoastal Oregon Marine Experiment StationDepartment of Fisheries and WildlifeHatfield Marine Science CenterOregon State UniversityNewportORUSA
- Department of ZoologyUniversity of OtagoDunedinNew Zealand
| | - Sandra Bohn
- State Fisheries Genomics LabCoastal Oregon Marine Experiment StationDepartment of Fisheries and WildlifeHatfield Marine Science CenterOregon State UniversityNewportORUSA
| | - John R. Hyde
- Southwest Fisheries Science CenterNational Marine Fisheries ServiceLa JollaCAUSA
| | - Kathleen G. O'Malley
- State Fisheries Genomics LabCoastal Oregon Marine Experiment StationDepartment of Fisheries and WildlifeHatfield Marine Science CenterOregon State UniversityNewportORUSA
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3
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Connectivity and population structure of albacore tuna across southeast Atlantic and southwest Indian Oceans inferred from multidisciplinary methodology. Sci Rep 2020; 10:15657. [PMID: 32973260 PMCID: PMC7519111 DOI: 10.1038/s41598-020-72369-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 07/09/2020] [Indexed: 11/17/2022] Open
Abstract
Albacore tuna (Thunnus alalunga) is an important target of tuna fisheries in the Atlantic and Indian Oceans. The commercial catch of albacore is the highest globally among all temperate tuna species, contributing around 6% in weight to global tuna catches over the last decade. The accurate assessment and management of this heavily exploited resource requires a robust understanding of the species’ biology and of the pattern of connectivity among oceanic regions, yet Indian Ocean albacore population dynamics remain poorly understood and its level of connectivity with the Atlantic Ocean population is uncertain. We analysed morphometrics and genetics of albacore (n = 1,874) in the southwest Indian (SWIO) and southeast Atlantic (SEAO) Oceans to investigate the connectivity and population structure. Furthermore, we examined the species’ dispersal potential by modelling particle drift through major oceanographic features. Males appear larger than females, except in South African waters, yet the length–weight relationship only showed significant male–female difference in one region (east of Madagascar and Reunion waters). The present study produced a genetic differentiation between the southeast Atlantic and southwest Indian Oceans, supporting their demographic independence. The particle drift models suggested dispersal potential of early life stages from SWIO to SEAO and adult or sub-adult migration from SEAO to SWIO.
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Brophy D, Rodríguez-Ezpeleta N, Fraile I, Arrizabalaga H. Combining genetic markers with stable isotopes in otoliths reveals complexity in the stock structure of Atlantic bluefin tuna (Thunnus thynnus). Sci Rep 2020; 10:14675. [PMID: 32895410 PMCID: PMC7477220 DOI: 10.1038/s41598-020-71355-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 08/13/2020] [Indexed: 11/09/2022] Open
Abstract
Atlantic bluefin tuna (Thunnus thynnus) from the two main spawning populations in the Mediterranean and Gulf of Mexico occur together in the western, central and eastern Atlantic. Stock composition of catches from mixing areas is uncertain, presenting a major challenge to the sustainable management of the fisheries. This study combines genetic and chemical markers to develop an integrated method of population assignment. Stable isotope signatures (δ13C and δ18O) in the otolith core of adults from the two main spawning populations (adult baselines) showed less overlap than those of yearlings (12-18 months old) from western and eastern nursery areas suggesting that some exchange occurs towards the end of the yearling phase. The integrated model combined δ18O with four genetic markers (SNPs) to distinguish the adult baselines with greater accuracy than chemical or genetic markers alone. When used to assign individuals from the mixing areas to their population of origin, the integrated model resolved some (but not all) discrepancies between the chemistry and genetic methods. Some individuals in the mixing area had otolith δ18O values and genetic profiles which when taken together, were not representative of either population. These fish may originate from another Atlantic spawning area or may represent population contingents that move away from the main spawning areas during the first year of life. This complexity in stock structure is not captured by the current two-stock model.
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Affiliation(s)
- Deirdre Brophy
- Marine and Freshwater Research Centre, Galway Mayo Institute of Technology, Dublin road, Galway, H91 T8NW, Ireland.
| | | | - Igaratza Fraile
- Marine Research Division, AZTI, Txatxarramendi Ugartea Z/G, 48395, Sukarrieta, Bizkaia, Spain
| | - Haritz Arrizabalaga
- Marine Research Division, AZTI, Txatxarramendi Ugartea Z/G, 48395, Sukarrieta, Bizkaia, Spain
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5
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Anderson G, Hampton J, Smith N, Rico C. Indications of strong adaptive population genetic structure in albacore tuna ( Thunnus alalunga) in the southwest and central Pacific Ocean. Ecol Evol 2019; 9:10354-10364. [PMID: 31624554 PMCID: PMC6787800 DOI: 10.1002/ece3.5554] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 06/18/2019] [Accepted: 07/22/2019] [Indexed: 01/09/2023] Open
Abstract
Albacore tuna (Thunnus alalunga) has a distinctly complex life history in which juveniles and adults separate geographically but at times inhabit the same spaces sequentially. The species also migrates long distances and presumably experiences varied regimes of physical stress over a lifetime. There are, therefore, many opportunities for population structure to arise based on stochastic differences or environmental factors that promote local adaptation. However, with the extent of mobility consistently demonstrated by tagged individuals, there is also a strong argument for panmixia within an ocean basin. It is important to confirm such assumptions from a population genetics standpoint for this species in particular because albacore is one of the principal market tuna species that sustains massive global fisheries and yet is also a slow-growing temperate tuna. Consequently, we used 1,837 neutral SNP loci and 89 loci under potential selection to analyze population genetic structure among five sample groups collected from the western and central South Pacific. We found no evidence to challenge panmixia at neutral loci, but strong indications of structuring at adaptive loci. One population sample, from French Polynesia in 2004, was particularly differentiated. Unfortunately, the current study cannot infer whether the divergence is geographic or temporal, or possibly caused by sample distribution. We encourage future studies to include potentially adaptive loci and to continue fine-scale observations within an ocean basin, and not to assume genome-wide panmixia.
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Affiliation(s)
- Giulia Anderson
- School of Marine StudiesMolecular Analytics Laboratory (MOANA‐LAB)Faculty of Science Technology and EnvironmentThe University of the South PacificSuvaFiji
| | - John Hampton
- Oceanic Fisheries Programme (OFP)Pacific CommunityNouméaNew Caledonia
| | - Neville Smith
- Oceanic Fisheries Programme (OFP)Pacific CommunityNouméaNew Caledonia
| | - Ciro Rico
- School of Marine StudiesMolecular Analytics Laboratory (MOANA‐LAB)Faculty of Science Technology and EnvironmentThe University of the South PacificSuvaFiji
- Instituto de Ciencias Marinas de Andalucía (ICMAN)Consejo Superior de Investigaciones CientíficasCádizSpain
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Fairweather R, Bradbury IR, Helyar SJ, de Bruyn M, Therkildsen NO, Bentzen P, Hemmer‐Hansen J, Carvalho GR. Range-wide genomic data synthesis reveals transatlantic vicariance and secondary contact in Atlantic cod. Ecol Evol 2018; 8:12140-12152. [PMID: 30598806 PMCID: PMC6303715 DOI: 10.1002/ece3.4672] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 09/20/2018] [Accepted: 09/24/2018] [Indexed: 11/11/2022] Open
Abstract
Recent advances in genetic and genomic analysis have greatly improved our understanding of spatial population structure in marine species. However, studies addressing phylogeographic patterns at oceanic spatial scales remain rare. In Atlantic cod (Gadus morhua), existing range-wide examinations suggest significant transatlantic divergence, although the fine-scale contemporary distribution of populations and potential for secondary contact are largely unresolved. Here, we explore transatlantic phylogeography in Atlantic cod using a data-synthesis approach, integrating multiple genome-wide single-nucleotide polymorphism (SNP) datasets representative of different regions to create a single range-wide dataset containing 1,494 individuals from 54 locations and genotyped at 796 common loci. Our analysis highlights significant transatlantic divergence and supports the hypothesis of westward post-glacial colonization of Greenland from the East Atlantic. Accordingly, our analysis suggests the presence of transatlantic secondary contact off eastern North America and supports existing perspectives on the phylogeographic history of Atlantic cod with an unprecedented combination of genetic and geographic resolution. Moreover, we demonstrate the utility of integrating distinct SNP databases of high comparability.
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Affiliation(s)
- Robert Fairweather
- Department of BiologyDalhousie UniversityHalifaxNova ScotiaCanada
- School of Biological SciencesBangor UniversityBangorUK
| | - Ian R. Bradbury
- Science Branch, Department of FisheriesSt John’s, Newfoundland and LabradorCanada
| | - Sarah J. Helyar
- Institute of Global Food SecurityQueen’s University BelfastBelfastUK
| | - Mark de Bruyn
- School of Biological SciencesBangor UniversityBangorUK
- School of Life and Environmental SciencesThe University of SydneySydneyNew South WalesAustralia
| | | | - Paul Bentzen
- Department of BiologyDalhousie UniversityHalifaxNova ScotiaCanada
| | - Jakob Hemmer‐Hansen
- Section for Marine Living Resources, National Institute for Aquatic ResourcesTechnical University of DenmarkSilkeborgDenmark
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Lo E, Bonizzoni M, Hemming-Schroeder E, Ford A, Janies DA, James AA, Afrane Y, Etemesi H, Zhou G, Githeko A, Yan G. Selection and Utility of Single Nucleotide Polymorphism Markers to Reveal Fine-Scale Population Structure in Human Malaria Parasite Plasmodium falciparum. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00145] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
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8
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Development of genome-wide SNPs for population genetics and population assignment of Sebastiscus marmoratus. CONSERV GENET RESOUR 2018. [DOI: 10.1007/s12686-017-0868-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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9
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Puncher GN, Cariani A, Maes GE, Van Houdt J, Herten K, Cannas R, Rodriguez-Ezpeleta N, Albaina A, Estonba A, Lutcavage M, Hanke A, Rooker J, Franks JS, Quattro JM, Basilone G, Fraile I, Laconcha U, Goñi N, Kimoto A, Macías D, Alemany F, Deguara S, Zgozi SW, Garibaldi F, Oray IK, Karakulak FS, Abid N, Santos MN, Addis P, Arrizabalaga H, Tinti F. Spatial dynamics and mixing of bluefin tuna in the Atlantic Ocean and Mediterranean Sea revealed using next-generation sequencing. Mol Ecol Resour 2018; 18:620-638. [PMID: 29405659 DOI: 10.1111/1755-0998.12764] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 01/06/2018] [Accepted: 01/19/2018] [Indexed: 01/05/2023]
Abstract
The Atlantic bluefin tuna is a highly migratory species emblematic of the challenges associated with shared fisheries management. In an effort to resolve the species' stock dynamics, a genomewide search for spatially informative single nucleotide polymorphisms (SNPs) was undertaken, by way of sequencing reduced representation libraries. An allele frequency approach to SNP discovery was used, combining the data of 555 larvae and young-of-the-year (LYOY) into pools representing major geographical areas and mapping against a newly assembled genomic reference. From a set of 184,895 candidate loci, 384 were selected for validation using 167 LYOY. A highly discriminatory genotyping panel of 95 SNPs was ultimately developed by selecting loci with the most pronounced differences between western Atlantic and Mediterranean Sea LYOY. The panel was evaluated by genotyping a different set of LYOY (n = 326), and from these, 77.8% and 82.1% were correctly assigned to western Atlantic and Mediterranean Sea origins, respectively. The panel revealed temporally persistent differentiation among LYOY from the western Atlantic and Mediterranean Sea (FST = 0.008, p = .034). The composition of six mixed feeding aggregations in the Atlantic Ocean and Mediterranean Sea was characterized using genotypes from medium (n = 184) and large (n = 48) adults, applying population assignment and mixture analyses. The results provide evidence of persistent population structuring across broad geographic areas and extensive mixing in the Atlantic Ocean, particularly in the mid-Atlantic Bight and Gulf of St. Lawrence. The genomic reference and genotyping tools presented here constitute novel resources useful for future research and conservation efforts.
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Affiliation(s)
- Gregory N Puncher
- Department of Biological, Geological and Environmental Sciences/Laboratory of Genetics and Genomics of Marine Resources and Environment (GenoDREAM), University of Bologna, Ravenna, Italy.,Department of Biology, Marine Biology Research Group, Ghent University, Ghent, Belgium.,Department of Biology, University of New Brunswick, Saint John, NB, Canada
| | - Alessia Cariani
- Department of Biological, Geological and Environmental Sciences/Laboratory of Genetics and Genomics of Marine Resources and Environment (GenoDREAM), University of Bologna, Ravenna, Italy
| | - Gregory E Maes
- Centre for Sustainable Tropical Fisheries and Aquaculture, Comparative Genomics Centre, College of Science and Engineering, James Cook University, Townsville, Qld, Australia.,Centre for Human Genetics, Genomics Core, KU Leuven - UZ Leuven, Leuven, Belgium.,Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven (KU Leuven), Leuven, Belgium
| | - Jeroen Van Houdt
- Centre for Human Genetics, Genomics Core, KU Leuven - UZ Leuven, Leuven, Belgium
| | - Koen Herten
- Centre for Human Genetics, Genomics Core, KU Leuven - UZ Leuven, Leuven, Belgium.,Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven (KU Leuven), Leuven, Belgium
| | - Rita Cannas
- Department of Life & Environmental Sciences (DISVA), University of Cagliari, Cagliari, Italy
| | | | - Aitor Albaina
- Laboratory of Genetics Faculty of Science & Technology, Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain.,Environmental Studies Centre (CEA), Vitoria-Gasteiz City Council, Vitoria-Gasteiz, Spain
| | - Andone Estonba
- Laboratory of Genetics Faculty of Science & Technology, Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Molly Lutcavage
- School for the Environment and Large Pelagics Research Center, University of Massachusetts, Boston, Gloucester, MA, USA
| | - Alex Hanke
- Fisheries and Oceans Canada, St. Andrews Biological Station, St. Andrews, NB, Canada
| | - Jay Rooker
- Department of Marine Biology, Texas A&M University at Galveston, Galveston, TX, USA.,Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX, USA
| | - James S Franks
- Gulf Coast Research Laboratory, Center for Fisheries Research and Development, University of Southern Mississippi, Ocean Springs, MS, USA
| | - Joseph M Quattro
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA
| | - Gualtiero Basilone
- National Research Council, Institute for Marine and Coastal Environment, Detached Unit of Capo Granitola, Trapani, Italy
| | - Igaratza Fraile
- Marine Research Division, AZTI Tecnalia, Pasaia, Gipuzkoa, Spain
| | - Urtzi Laconcha
- Marine Research Division, AZTI Tecnalia, Pasaia, Gipuzkoa, Spain.,Laboratory of Genetics Faculty of Science & Technology, Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Nicolas Goñi
- Marine Research Division, AZTI Tecnalia, Pasaia, Gipuzkoa, Spain
| | - Ai Kimoto
- National Research Institute of Far Seas Fisheries, Shizuoka, Japan
| | - David Macías
- Instituto Español de Oceanografía, Centro Oceanográfico de Baleares, Palma, Spain
| | - Francisco Alemany
- Instituto Español de Oceanografía, Centro Oceanográfico de Baleares, Palma, Spain
| | - Simeon Deguara
- Federation of Maltese Aquaculture Producers (FMAP), Valletta, Malta
| | - Salem W Zgozi
- Marine Biology Research Center, Tripoli-Tajura, Libya
| | - Fulvio Garibaldi
- Department of Earth, Environmental and Life Sciences, University of Genoa, Genova, Italy
| | - Isik K Oray
- Faculty of Fisheries, Istanbul University, Laleli-Istanbul, Turkey
| | | | - Noureddine Abid
- National Institute of Fisheries Research, Regional Centre of Tangier, Tanger, Morocco
| | | | - Piero Addis
- Department of Life & Environmental Sciences (DISVA), University of Cagliari, Cagliari, Italy
| | | | - Fausto Tinti
- Department of Biological, Geological and Environmental Sciences/Laboratory of Genetics and Genomics of Marine Resources and Environment (GenoDREAM), University of Bologna, Ravenna, Italy
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10
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Montes I, Laconcha U, Iriondo M, Manzano C, Arrizabalaga H, Estonba A. Reduced Single Nucleotide Polymorphism Panels for Assigning Atlantic Albacore and Bay of Biscay Anchovy Individuals to Their Geographic Origin: Toward Sustainable Fishery Management. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:4351-4358. [PMID: 28489943 DOI: 10.1021/acs.jafc.7b00619] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
There is an increasing trend upon adding a detailed description of the origin of seafood products driven by a general interest in the implementation of sustainable fishery management plans for the conservation of marine ecosystems. North Atlantic albacore ("Bonito del Norte con Eusko Label") and Bay of Biscay anchovy ("Anchoa del Cantábrico") are two commercially important fish populations with high economical value and vulnerable to commercial fraud. This fact, together with the overexploited situation of these two populations, makes it necessary to develop a tool to identify individual origin and to detect commercial fraud. In the present study, we have developed and validated a traceability tool consisting of reduced panels of gene-associated single nucleotide polymorphisms (SNPs) suitable for assigning individuals of two species to their origin with unprecedented accuracy levels. Only 48 SNPs are necessary to assign 81.1% albacore and 93.4% anchovy individuals with 100% accuracy to their geographic origin. The total accuracy of the results demonstrates how gene-associated SNPs can revolutionize food traceability. Gene-associated SNP panels are not of mere commercial interest, but they also can result in a positive impact on sustainability of marine ecosystems through conservation of fish populations through establishing a more effective and sustainable fishery management framework and contributing to the prevention of falsified labeling.
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Affiliation(s)
- Iratxe Montes
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU) , 48940 Leioa, Spain
| | - Urtzi Laconcha
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU) , 48940 Leioa, Spain
- Marine Research Division, AZTI , 20110 Pasaia, Spain
| | - Mikel Iriondo
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU) , 48940 Leioa, Spain
| | - Carmen Manzano
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU) , 48940 Leioa, Spain
| | | | - Andone Estonba
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU) , 48940 Leioa, Spain
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11
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Barth JMI, Damerau M, Matschiner M, Jentoft S, Hanel R. Genomic Differentiation and Demographic Histories of Atlantic and Indo-Pacific Yellowfin Tuna (Thunnus albacares) Populations. Genome Biol Evol 2017; 9:1084-1098. [PMID: 28419285 PMCID: PMC5408087 DOI: 10.1093/gbe/evx067] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2017] [Indexed: 12/30/2022] Open
Abstract
Recent developments in the field of genomics have provided new and powerful insights into population structure and dynamics that are essential for the conservation of biological diversity. As a commercially highly valuable species, the yellowfin tuna (Thunnus albacares) is intensely exploited throughout its distribution in tropical oceans around the world, and is currently classified as near threatened. However, conservation efforts for this species have so far been hampered by limited knowledge of its population structure, due to incongruent results of previous investigations. Here, we use whole-genome sequencing in concert with a draft genome assembly to decipher the global population structure of the yellowfin tuna, and to investigate its demographic history. We detect significant differentiation of Atlantic and Indo-Pacific yellowfin tuna populations as well as the possibility of a third diverged yellowfin tuna group in the Arabian Sea. We further observe evidence for past population expansion as well as asymmetric gene flow from the Indo-Pacific to the Atlantic.
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Affiliation(s)
- Julia M I Barth
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Malte Damerau
- Institute of Fisheries Ecology, Johann Heinrich von Thünen Institute, Federal Research Institute for Rural Areas, Forestry and Fisheries, Hamburg, Germany
| | - Michael Matschiner
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway.,Centre for Coastal Research, Department of Natural Sciences, University of Agder, Kristiansand, Norway
| | - Reinhold Hanel
- Institute of Fisheries Ecology, Johann Heinrich von Thünen Institute, Federal Research Institute for Rural Areas, Forestry and Fisheries, Hamburg, Germany
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12
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Antoniou A, Kasapidis P, Kotoulas G, Mylonas CC, Magoulas A. Genetic diversity of Atlantic Bluefin tuna in the Mediterranean Sea: insights from genome-wide SNPs and microsatellites. ACTA ACUST UNITED AC 2017; 24:3. [PMID: 28239596 PMCID: PMC5314471 DOI: 10.1186/s40709-017-0062-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 01/28/2017] [Indexed: 11/25/2022]
Abstract
Background Elucidating the patterns of the Atlantic Bluefin tuna [ABFT, Thunnus thynnus (Linnaeus, 1758)] population structure constitutes a challenging task of great importance. Most of the unique challenges stem from its biology, as well as the attributes of the marine realm in which it disperses. Accurate information is urgently needed for stock assessment, and the identification of critical features to the persistence and adaptation of populations in order to formulate and adopt effective strategies for ABFT conservation and management. Conclusions of a great number of ABFT genetic studies on the Mediterranean Sea stock structure are rather controversial and not yet conclusive. In this study, ABFT genomic diversity was investigated in the Mediterranean Sea, which is the most important area for the species’ reproduction. Results Analyzing genome-wide SNPs and microsatellites from ABFT samples collected throughout the Mediterranean Sea did not provide strong evidence of genetic structure, pointing towards the existence of a single panmictic unit. An alternative view would recognize a failure to reject the null hypothesis of a panmictic unit as an effect of the study’s sampling design, the type of markers used, and the effectiveness/suitability of analysis methods in respect to the species biological characteristics or any combination of the above. Conclusions Unravelling the drivers of ABFT population diversity would require the consideration of important aspects of the species spawning behavior for the determination of the appropriate sampling design. Novel approaches and methods of analysis that will bring together experts in genetics/-omics, ecology and oceanography are deemed necessary. Analyzing ABFT genetic data under the discipline of seascape genetics could provide the analysis framework under which major abiotic and biotic forces controlling ABFT recruitment could be identified, elucidating the complicated population dynamics of the species, while multiple and continuous fisheries monitoring should in all cases be considered as a prerequisite in order to achieve efficient and long-term ABFT conservation.
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Affiliation(s)
- Aglaia Antoniou
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research, Gournes Pediados, P.O. Box 2214, 71003 Heraklion, Crete, Greece
| | - Panagiotis Kasapidis
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research, Gournes Pediados, P.O. Box 2214, 71003 Heraklion, Crete, Greece
| | - Georgios Kotoulas
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research, Gournes Pediados, P.O. Box 2214, 71003 Heraklion, Crete, Greece
| | - Constantinos C Mylonas
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research, Gournes Pediados, P.O. Box 2214, 71003 Heraklion, Crete, Greece
| | - Antonios Magoulas
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research, Gournes Pediados, P.O. Box 2214, 71003 Heraklion, Crete, Greece
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Nikolic N, Duthoy S, Destombes A, Bodin N, West W, Puech A, Bourjea J. Discovery of Genome-Wide Microsatellite Markers in Scombridae: A Pilot Study on Albacore Tuna. PLoS One 2015; 10:e0141830. [PMID: 26544051 PMCID: PMC4636268 DOI: 10.1371/journal.pone.0141830] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 10/13/2015] [Indexed: 11/21/2022] Open
Abstract
Recent developments in sequencing technologies and bioinformatics analysis provide a greater amount of DNA sequencing reads at a low cost. Microsatellites are the markers of choice for a variety of population genetic studies, and high quality markers can be discovered in non-model organisms, such as tuna, with these recent developments. Here, we use a high-throughput method to isolate microsatellite markers in albacore tuna, Thunnus alalunga, based on coupling multiplex enrichment and next-generation sequencing on 454 GS-FLX Titanium pyrosequencing. The crucial minimum number of polymorphic markers to infer evolutionary and ecological processes for this species has been described for the first time. We provide 1670 microsatellite design primer pairs, and technical and molecular genetics selection resulting in 43 polymorphic microsatellite markers. On this panel, we characterized 34 random and selectively neutral markers («neutral») and 9 «non-neutral» markers. The variability of «neutral» markers was screened with 136 individuals of albacore tuna from southwest Indian Ocean (42), northwest Indian Ocean (31), South Africa (31), and southeast Atlantic Ocean (32). Power analysis demonstrated that the panel of genetic markers can be applied in diversity and population genetics studies. Global genetic diversity for albacore was high with a mean number of alleles at 16.94; observed heterozygosity 66% and expected heterozygosity 77%. The number of individuals was insufficient to provide accurate results on differentiation. Of the 9 «non-neutral» markers, 3 were linked to a sequence of known function. The one is located to a sequence having an immunity function (ThuAla-Tcell-01) and the other to a sequence having energy allocation function (ThuAla-Hki-01). These two markers were genotyped on the 136 individuals and presented different diversity levels. ThuAla-Tcell-01 has a high number of alleles (20), heterozygosity (87–90%), and assignment index. ThuAla-Hki-01 has a lower number of alleles (9), low heterozygosity (24–27%), low assignment index and significant inbreeding. Finally, the 34 «neutral» and 3 «non-neutral» microsatellites markers were tested on four economically important Scombridae species—Thunnus albacares, Thunnus thynnus, Thunnus obesus, and Acanthocybium solandri.
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Affiliation(s)
- Natacha Nikolic
- IFREMER, Institut Français de Recherche pour l’Exploitation de la Mer, Délégation de La Réunion, Rue Jean Bertho, BP 60, 97 822 Le Port Cedex, La Réunion, France
- * E-mail:
| | | | | | | | - Wendy West
- Department of Agriculture Forestry and Fisheries, Private Bag X2, Roggebaai, 8012, South Africa
| | - Alexis Puech
- IFREMER, Institut Français de Recherche pour l’Exploitation de la Mer, Délégation de La Réunion, Rue Jean Bertho, BP 60, 97 822 Le Port Cedex, La Réunion, France
| | - Jérôme Bourjea
- IFREMER, Institut Français de Recherche pour l’Exploitation de la Mer, Délégation de La Réunion, Rue Jean Bertho, BP 60, 97 822 Le Port Cedex, La Réunion, France
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Laconcha U, Iriondo M, Arrizabalaga H, Manzano C, Markaide P, Montes I, Zarraonaindia I, Velado I, Bilbao E, Goñi N, Santiago J, Domingo A, Karakulak S, Oray I, Estonba A. New Nuclear SNP Markers Unravel the Genetic Structure and Effective Population Size of Albacore Tuna (Thunnus alalunga). PLoS One 2015; 10:e0128247. [PMID: 26090851 PMCID: PMC4474438 DOI: 10.1371/journal.pone.0128247] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 04/23/2015] [Indexed: 11/18/2022] Open
Abstract
In the present study we have investigated the population genetic structure of albacore (Thunnus alalunga, Bonnaterre 1788) and assessed the loss of genetic diversity, likely due to overfishing, of albacore population in the North Atlantic Ocean. For this purpose, 1,331 individuals from 26 worldwide locations were analyzed by genotyping 75 novel nuclear SNPs. Our results indicated the existence of four genetically homogeneous populations delimited within the Mediterranean Sea, the Atlantic Ocean, the Indian Ocean and the Pacific Ocean. Current definition of stocks allows the sustainable management of albacore since no stock includes more than one genetic entity. In addition, short- and long-term effective population sizes were estimated for the North Atlantic Ocean albacore population, and results showed no historical decline for this population. Therefore, the genetic diversity and, consequently, the adaptive potential of this population have not been significantly affected by overfishing.
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Affiliation(s)
- Urtzi Laconcha
- AZTI, Marine Research Division, Herrera Kaia Portualdea z/g, Pasaia (Gipuzkoa), Spain
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Sarriena auzoa z/g, Leioa (Bizkaia), Spain
| | - Mikel Iriondo
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Sarriena auzoa z/g, Leioa (Bizkaia), Spain
| | - Haritz Arrizabalaga
- AZTI, Marine Research Division, Herrera Kaia Portualdea z/g, Pasaia (Gipuzkoa), Spain
| | - Carmen Manzano
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Sarriena auzoa z/g, Leioa (Bizkaia), Spain
| | - Pablo Markaide
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Sarriena auzoa z/g, Leioa (Bizkaia), Spain
| | - Iratxe Montes
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Sarriena auzoa z/g, Leioa (Bizkaia), Spain
| | - Iratxe Zarraonaindia
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Sarriena auzoa z/g, Leioa (Bizkaia), Spain
| | - Igor Velado
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Sarriena auzoa z/g, Leioa (Bizkaia), Spain
| | - Eider Bilbao
- Cell Biology & Environmental Toxicology Research Group, Research Centre for Experimental Marine Biology & Biotechnology (PIE) & Department of Zoology & Animal Cell Biology, University of the Basque Country (UPV/EHU), Sarriena auzoa z/g, Leioa (Bizkaia), Spain
| | - Nicolas Goñi
- AZTI, Marine Research Division, Herrera Kaia Portualdea z/g, Pasaia (Gipuzkoa), Spain
| | - Josu Santiago
- AZTI, Marine Research Division, Txatxarramendi Ugartea z/g, Sukarrieta (Bizkaia), Spain
| | - Andrés Domingo
- Laboratory of Pelagic Resources, Dirección Nacional de Recursos Acuáticos (DINARA), Constituyente 1497, Montevideo, Uruguay
| | - Saadet Karakulak
- Fisheries Faculty of Istanbul University, Laleli, Istanbul, Turkey
| | - Işık Oray
- Fisheries Faculty of Istanbul University, Laleli, Istanbul, Turkey
| | - Andone Estonba
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Sarriena auzoa z/g, Leioa (Bizkaia), Spain
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