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Benavente JN, Véliz D, Quezada-Romegialli C, Gomez-Uchida D. Uniparental and biparental markers unravel invasion pathways, population admixture, and genetic structure in naturalized rainbow trout (Oncorhynchus mykiss). JOURNAL OF FISH BIOLOGY 2023; 103:1277-1288. [PMID: 37535430 DOI: 10.1111/jfb.15520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 06/27/2023] [Accepted: 08/02/2023] [Indexed: 08/05/2023]
Abstract
The present study combined uniparental mtDNA and biparental SNPs to illuminate the invasion and colonization pathways of rainbow trout, Oncorhynchus mykiss, one of the world's most widespread invasive fishes, that has been intensively propagated in Chile, South America. The specific aims of the study were (i) to evaluate potential donor populations, which could be either from the species' native range in North America or from introduced populations in Europe, by comparing mtDNA D-loop/control region haplotypes; and (ii) to assess the factors that have shaped genetic diversity and contemporary genetic structure of rainbow trout populations introduced to Chile through SNP genotyping. The authors comprehensively sampled 24 sites in 12 basins ranging from the High Andean Plateau (Altiplano, 18° S) to northern Patagonia (41° S). Results of the mtDNA data of naturalized trout populations from rivers in the Altiplano (northern Chile) differed from those collected in central and southern Chile, suggesting an origin from North American hatcheries. Naturalized trout populations in central and southern Chile, on the contrary, shared haplotypes with specimens found in European hatcheries. The southern and central Chile populations also contained rare haplotypes, possibly indicating potential spread through aquaculture escapes. Results of the SNP analysis revealed higher allelic richness for trout sampled in sites influenced by commercial aquaculture than sites without commercial aquaculture, likely due to increased admixture between aquaculture broodstock and naturalized trout. The analysis further uncovered some complex patterns of divergent trout populations with low genetic diversity as well as increased relatedness between individuals from isolated sites, suggesting possible local populations. A comprehensive characterization of genetic diversity and structure of rainbow trout should help identify management areas that may augment socioeconomic benefits while preventing the spread and further impacts on biodiversity.
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Affiliation(s)
- Javiera N Benavente
- Departmento de Ciencias Ecológicas, Universidad de Chile, Santiago, Chile
- Genomics in Ecology, Evolution and Conservation Lab, Departmento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
| | - David Véliz
- Departmento de Ciencias Ecológicas, Universidad de Chile, Santiago, Chile
- Centro de Ecología y Manejo de Islas Oceánicas (ESMOI), Coquimbo, Chile
| | - Claudio Quezada-Romegialli
- Plataforma de Monitoreo Genómico y Ambiental (PGMA), Departamento de Química, Facultad de Ciencias, Universidad de Tarapacá, Tarapacá, Chile
| | - Daniel Gomez-Uchida
- Genomics in Ecology, Evolution and Conservation Lab, Departmento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
- Núcleo Milenio INVASAL, Concepción, Chile
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Prida V, Sepúlveda M, Quezada-Romegialli C, Harrod C, Gomez-Uchida D, Cid B, Canales-Aguirre CB. Chilean Salmon Sushi: Genetics Reveals Product Mislabeling and a Lack of Reliable Information at the Point of Sale. Foods 2020; 9:E1699. [PMID: 33228244 PMCID: PMC7699462 DOI: 10.3390/foods9111699] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/14/2020] [Accepted: 11/16/2020] [Indexed: 11/16/2022] Open
Abstract
Species diagnosis is essential to assess the level of mislabeling or misnamed seafood products such as sushi. In Chile, sushi typically includes salmon as the main ingredient, but species used are rarely declared on the menu. In order to identify which species are included in the Chilean sushi market, we analyzed 84 individual sushi rolls sold as "salmon" from sushi outlets in ten cities across Chile. Using a polymerase chain reaction-restriction fragment length polymorphism protocol (PCR-RFLP), we identified mislabeled and misnamed products. Atlantic salmon was the most common salmonid fish used in sushi, followed by coho salmon, rainbow trout, and Chinook salmon. We found a total of 23% and 18% of the products were mislabeled and misnamed, respectively. In 64% of cases, the salesperson selling the product could not identify the species. We also identified the use of wild-captured Chinook salmon samples from a naturalized population. Our results provide a first indication regarding species composition in Chilean sushi, a quantification of mislabeling and the level of misinformation declared by sales people to consumers. Finally, considering that Chinook salmon likely originates from a non-licensed origin and that sushi is an uncooked product, proper identification in the food production chain may have important consequences for the health of consumers.
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Affiliation(s)
- Valentina Prida
- Centro i~mar, Universidad de Los Lagos, Puerto Montt 5480000, Chile;
- Núcleo Milenio de Salmónidos Invasores (INVASAL), Concepción 4030000, Chile; (M.S.); (C.Q.-R.); (C.H.); (D.G.-U.); (B.C.)
| | - Maritza Sepúlveda
- Núcleo Milenio de Salmónidos Invasores (INVASAL), Concepción 4030000, Chile; (M.S.); (C.Q.-R.); (C.H.); (D.G.-U.); (B.C.)
- Centro de Investigación y Gestión de Recursos Naturales (CIGREN), Instituto de Biología, Facultad de Ciencias, Universidad de Valparaíso, Playa Ancha, Valparaíso 2340000, Chile
| | - Claudio Quezada-Romegialli
- Núcleo Milenio de Salmónidos Invasores (INVASAL), Concepción 4030000, Chile; (M.S.); (C.Q.-R.); (C.H.); (D.G.-U.); (B.C.)
- Departamento de Biología, Facultad de Ciencias Naturales y Exactas, Universidad de Valparaíso, Playa Ancha, Valparaíso 2340000, Chile
| | - Chris Harrod
- Núcleo Milenio de Salmónidos Invasores (INVASAL), Concepción 4030000, Chile; (M.S.); (C.Q.-R.); (C.H.); (D.G.-U.); (B.C.)
- Instituto de Ciencias Naturales Alexander von Humboldt, Universidad de Antofagasta, Antofagasta 1271155, Chile
| | - Daniel Gomez-Uchida
- Núcleo Milenio de Salmónidos Invasores (INVASAL), Concepción 4030000, Chile; (M.S.); (C.Q.-R.); (C.H.); (D.G.-U.); (B.C.)
- Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción 4070032, Chile
| | - Beatriz Cid
- Núcleo Milenio de Salmónidos Invasores (INVASAL), Concepción 4030000, Chile; (M.S.); (C.Q.-R.); (C.H.); (D.G.-U.); (B.C.)
- Departamento de Sociología, Facultad de Ciencias Sociales, Universidad de Concepción, Concepción 4070032, Chile
| | - Cristian B. Canales-Aguirre
- Centro i~mar, Universidad de Los Lagos, Puerto Montt 5480000, Chile;
- Núcleo Milenio de Salmónidos Invasores (INVASAL), Concepción 4030000, Chile; (M.S.); (C.Q.-R.); (C.H.); (D.G.-U.); (B.C.)
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3
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Colihueque N, Estay FJ, Crespo JE, Arriagada A, Baessolo L, Canales-Aguirre CB, Marín J, Carrasco R. Genetic Differentiation and Origin of Naturalized Rainbow Trout Populations From Southern Chile, Revealed by the mtDNA Control Region Marker. Front Genet 2019; 10:1212. [PMID: 31921284 PMCID: PMC6933019 DOI: 10.3389/fgene.2019.01212] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 11/04/2019] [Indexed: 12/03/2022] Open
Abstract
Numerous self-sustaining naturalized or introduced populations of rainbow trout (Oncorhynchus mykiss) are widely distributed throughout the freshwaters of southern Chile. In this study, analysis of the mitochondrial DNA control region (CR) marker was conducted to investigate the level of genetic divergence among populations and their phylogenetic relationships with respect to native lineages. This information provided a framework to interpret the genetic structure and origin that was shaped during historical trout introduction efforts. To this end, we analyzed eleven naturalized populations of lakes and rivers from five basins. The CR marker revealed five haplotypes. The overall haplotype (H) and nucleotide (Π) diversities were 0.684 ± 0.030 and 0.00460 ± 0.00012, respectively. Global FST was 0.169, with several pairwise FST estimates showing significant differences (P < 0.05). The exact test of population differentiation corroborated this result (P < 0.001). Significant geographic structure was found (P < 0.05), with variations explained primarily by differences within populations (61.65%) and among group basins (20.82%). Maximum likelihood phylogenetic analysis resolved two distinct clades with medium bootstrap support when naturalized populations were aligned in conjunction with reference native lineages. The haplotype network revealed a close association between naturalized populations and four main haplotypes representative of three native ecotypes or lineages from western North America (rainbow trout, steelhead trout and redband trout). These results indicate a genetic population structuring for naturalized rainbow trout from southern Chile and an origin probably represented by multiple lineages sources. Thus, mitochondrial DNA data strongly suggest that stocking of rainbow trout from different origins may have occurred during or after the initial introduction efforts.
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Affiliation(s)
- Nelson Colihueque
- Laboratorio de Biología Molecular y Citogenética, Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Osorno, Chile
| | - Francisco J Estay
- Gerencia de Investigación y Desarrollo, Piscícola Huililco Ltda., Pucón, Chile
| | - Julio E Crespo
- Laboratorio de Ciencias Naturales y Sostenibilidad-Programa IBAM, Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Osorno, Chile
| | - Aldo Arriagada
- Laboratorio de Biología Molecular y Citogenética, Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Osorno, Chile
| | | | - Cristian B Canales-Aguirre
- Centro i∼mar, Universidad de Los Lagos, Puerto Montt, Chile.,Núcleo Milenio de Salmónidos Invasores (INVASAL), Concepción, Chile
| | - Javier Marín
- Programa de Pesca Recreativa, Departamento de Acuicultura y Recursos Agroalimentarios, Universidad de Los Lagos, Osorno, Chile
| | - René Carrasco
- Programa de Pesca Recreativa, Departamento de Acuicultura y Recursos Agroalimentarios, Universidad de Los Lagos, Osorno, Chile
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Vera-Escalona I, Habit E, Ruzzante DE. Invasive species and postglacial colonization: their effects on the genetic diversity of a Patagonian fish. Proc Biol Sci 2019; 286:20182567. [PMID: 30963839 PMCID: PMC6408905 DOI: 10.1098/rspb.2018.2567] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 02/01/2019] [Indexed: 01/18/2023] Open
Abstract
The present distribution of Patagonian species is the result of a complex history involving Quaternary refugial populations, Holocene range expansions and demographic changes occurring during the Anthropocene. Invasive salmonids were introduced in Patagonia during the last century, occupying most rivers and lakes, preying on and competing with native species, including the fish Galaxias platei. Here, we used G. platei as a case study to understand how long-term (i.e. population differentiation during the Holocene) and short-term historical processes (salmonid introductions) affect genetic diversity. Using a suite of microsatellite markers, we found that the number of alleles is negatively correlated with the presence of salmonids (short-term processes), with G. platei populations from lakes with salmonids exhibiting significantly lower genetic diversity than populations from lakes without salmonids. Simulations (100 years backwards) showed that this difference in genetic diversity can be explained by a 99% reduction in population size. Allelic richness and observed heterozygosities were also negatively correlated with the presence of salmonids, but also positively correlated with long-term processes linked to Quaternary glaciations. Our results show how different genetic parameters can help identify processes taking place at different scales and their importance in terms of conservation.
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Affiliation(s)
- Iván Vera-Escalona
- Department of Biology, Dalhousie University, 1355 Oxford Street, Halifax, Nova Scotia, Canada B3H 4R2
- Centro de Investigación en Biodiversidad y Ambientes Sustentables (CIBAS), Universidad Católica de la Santísima Concepción, Alonso de Ribera 2850, Concepción, Chile
| | - Evelyn Habit
- Departamento de Sistemas Acuáticos, Facultad de Ciencias Ambientales y Centro EULA-Chile, Universidad de Concepción, Barrio Universitario s/n. Concepción, Casilla 160-C, Chile
| | - Daniel E. Ruzzante
- Department of Biology, Dalhousie University, 1355 Oxford Street, Halifax, Nova Scotia, Canada B3H 4R2
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Gomez‐Uchida D, Cañas‐Rojas D, Riva‐Rossi CM, Ciancio JE, Pascual MA, Ernst B, Aedo E, Musleh SS, Valenzuela‐Aguayo F, Quinn TP, Seeb JE, Seeb LW. Genetic signals of artificial and natural dispersal linked to colonization of South America by non-native Chinook salmon ( Oncorhynchus tshawytscha). Ecol Evol 2018; 8:6192-6209. [PMID: 29988411 PMCID: PMC6024130 DOI: 10.1002/ece3.4036] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 01/31/2018] [Accepted: 03/13/2018] [Indexed: 12/12/2022] Open
Abstract
Genetics data have provided unprecedented insights into evolutionary aspects of colonization by non-native populations. Yet, our understanding of how artificial (human-mediated) and natural dispersal pathways of non-native individuals influence genetic metrics, evolution of genetic structure, and admixture remains elusive. We capitalize on the widespread colonization of Chinook salmon Oncorhynchus tshawytscha in South America, mediated by both dispersal pathways, to address these issues using data from a panel of polymorphic SNPs. First, genetic diversity and the number of effective breeders (Nb) were higher among artificial than natural populations. Contemporary gene flow was common between adjacent artificial and natural and adjacent natural populations, but uncommon between geographically distant populations. Second, genetic structure revealed four distinct clusters throughout the Chinook salmon distributional range with varying levels of genetic connectivity. Isolation by distance resulted from weak differentiation between adjacent artificial and natural and between natural populations, with strong differentiation between distant Pacific Ocean and Atlantic Ocean populations, which experienced strong genetic drift. Third, genetic mixture analyses revealed the presence of at least six donor geographic regions from North America, some of which likely hybridized as a result of multiple introductions. Relative propagule pressure or the proportion of Chinook salmon propagules introduced from various geographic regions according to government records significantly influenced genetic mixtures for two of three artificial populations. Our findings support a model of colonization in which high-diversity artificial populations established first; some of these populations exhibited significant admixture resulting from propagule pressure. Low-diversity natural populations were likely subsequently founded from a reduced number of individuals.
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Affiliation(s)
- Daniel Gomez‐Uchida
- Genomics in Ecology, Evolution and Conservation Lab (GEECLAB)Department of ZoologyFacultad de Ciencias Naturales y OceanográficasUniversidad de ConcepciónConcepciónChile
- Núcleo Milenio INVASALConcepciónChile
| | - Diego Cañas‐Rojas
- Genomics in Ecology, Evolution and Conservation Lab (GEECLAB)Department of ZoologyFacultad de Ciencias Naturales y OceanográficasUniversidad de ConcepciónConcepciónChile
- Núcleo Milenio INVASALConcepciónChile
| | - Carla M. Riva‐Rossi
- Instituto de Diversidad y Evolución AustralIDEAUS‐CONICETCentro Nacional PatagónicoPuerto MadrynArgentina
| | - Javier E. Ciancio
- Centro para el estudio de Sistemas MarinosCESIMAR‐CONICETCentro Nacional PatagónicoPuerto MadrynArgentina
| | - Miguel A. Pascual
- Instituto Patagónico para el estudio de Ecosistemas ContinentalesIPEEC‐CONICETCentro Nacional PatagónicoPuerto MadrynArgentina
| | - Billy Ernst
- Núcleo Milenio INVASALConcepciónChile
- Department of OceanographyUniversidad de ConcepciónConcepciónChile
- Facultad de Ciencias Naturales y OceanográficasUniversidad de ConcepciónConcepciónChile
| | - Eduardo Aedo
- Centro TrapanandaUniversidad Austral de ChileCoyhaiqueChile
| | - Selim S. Musleh
- Genomics in Ecology, Evolution and Conservation Lab (GEECLAB)Department of ZoologyFacultad de Ciencias Naturales y OceanográficasUniversidad de ConcepciónConcepciónChile
- Núcleo Milenio INVASALConcepciónChile
| | - Francisca Valenzuela‐Aguayo
- Genomics in Ecology, Evolution and Conservation Lab (GEECLAB)Department of ZoologyFacultad de Ciencias Naturales y OceanográficasUniversidad de ConcepciónConcepciónChile
- Present address:
Department of Aquatic SystemsFaculty of Environmental Sciences and EULA‐CentreUniversidad de ConcepciónConcepciónChile
| | - Thomas P. Quinn
- Núcleo Milenio INVASALConcepciónChile
- School of Aquatic and Fishery SciencesUniversity of WashingtonSeattleWAUSA
| | - James E. Seeb
- Núcleo Milenio INVASALConcepciónChile
- School of Aquatic and Fishery SciencesUniversity of WashingtonSeattleWAUSA
| | - Lisa W. Seeb
- Núcleo Milenio INVASALConcepciónChile
- School of Aquatic and Fishery SciencesUniversity of WashingtonSeattleWAUSA
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Canales-Aguirre CB, Seeb LW, Seeb JE, Cádiz MI, Musleh SS, Arismendi I, Gajardo G, Galleguillos R, Gomez-Uchida D. Contrasting genetic metrics and patterns among naturalized rainbow trout ( Oncorhynchus mykiss) in two Patagonian lakes differentially impacted by trout aquaculture. Ecol Evol 2017; 8:273-285. [PMID: 29321870 PMCID: PMC5756871 DOI: 10.1002/ece3.3574] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 10/01/2017] [Accepted: 10/04/2017] [Indexed: 11/29/2022] Open
Abstract
Different pathways of propagation and dispersal of non‐native species into new environments may have contrasting demographic and genetic impacts on established populations. Repeated introductions of rainbow trout (Oncorhynchus mykiss) to Chile in South America, initially through stocking and later through aquaculture escapes, provide a unique setting to contrast these two pathways. Using a panel of single nucleotide polymorphisms, we found contrasting genetic metrics and patterns among naturalized trout in Lake Llanquihue, Chile's largest producer of salmonid smolts for nearly 50 years, and Lake Todos Los Santos (TLS), a reference lake where aquaculture has been prohibited by law. Trout from Lake Llanquihue showed higher genetic diversity, weaker genetic structure, and larger estimates for the effective number of breeders (Nb) than trout from Lake TLS. Trout from Lake TLS were divergent from Lake Llanquihue and showed marked genetic structure and a significant isolation‐by‐distance pattern consistent with secondary contact between documented and undocumented stocking events in opposite shores of the lake. Multiple factors, including differences in propagule pressure, origin of donor populations, lake geomorphology, habitat quality or quantity, and life history, may help explain contrasting genetic metrics and patterns for trout between lakes. We contend that high propagule pressure from aquaculture may not only increase genetic diversity and Nb via demographic effects and admixture, but also may impact the evolution of genetic structure and increase gene flow, consistent with findings from artificially propagated salmonid populations in their native and naturalized ranges.
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Affiliation(s)
- Cristian B Canales-Aguirre
- Genomics in Ecology, Evolution and Conservation Lab (GEECLAB) Departamento de Zoología Universidad de Concepción Concepción Chile.,Laboratorio de Genética y Acuicultura Departamento de Oceanografía Facultad de Ciencias Naturales y Oceanográficas Universidad de Concepción Concepción Chile.,Nucleo Milenio INVASAL Concepción Chile.,Centro i-mar Universidad de Los Lagos Camino Chinquihue 6 km Puerto Montt Chile
| | - Lisa W Seeb
- Nucleo Milenio INVASAL Concepción Chile.,School of Aquatic and Fishery Sciences University of Washington Seattle WA USA
| | - James E Seeb
- Nucleo Milenio INVASAL Concepción Chile.,School of Aquatic and Fishery Sciences University of Washington Seattle WA USA
| | - María I Cádiz
- Genomics in Ecology, Evolution and Conservation Lab (GEECLAB) Departamento de Zoología Universidad de Concepción Concepción Chile
| | - Selim S Musleh
- Genomics in Ecology, Evolution and Conservation Lab (GEECLAB) Departamento de Zoología Universidad de Concepción Concepción Chile.,Nucleo Milenio INVASAL Concepción Chile
| | - Ivan Arismendi
- Department of Fisheries and Wildlife Oregon State University Corvallis OR USA
| | - Gonzalo Gajardo
- Laboratorio de Genética, Acuicultura & Biodiversidad Universidad de Los Lagos Osorno Chile
| | - Ricardo Galleguillos
- Laboratorio de Genética y Acuicultura Departamento de Oceanografía Facultad de Ciencias Naturales y Oceanográficas Universidad de Concepción Concepción Chile
| | - Daniel Gomez-Uchida
- Genomics in Ecology, Evolution and Conservation Lab (GEECLAB) Departamento de Zoología Universidad de Concepción Concepción Chile.,Nucleo Milenio INVASAL Concepción Chile.,Centro i-mar Universidad de Los Lagos Camino Chinquihue 6 km Puerto Montt Chile
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