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Castillo NC, Gaitán-Espitia JD, Quintero-Galvis JF, Saldías GS, Martel SI, Lardies MA, Mesas A, Pérez-Santos IE, Gelcich S, Vargas CA. Small-scale geographic differences in multiple-driver environmental variability can modulate contrasting phenotypic plasticity despite high levels of gene flow. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 954:176772. [PMID: 39378945 DOI: 10.1016/j.scitotenv.2024.176772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Revised: 10/01/2024] [Accepted: 10/04/2024] [Indexed: 10/10/2024]
Abstract
Climate change is altering not only the mean conditions of marine environments, but also their temporal variability and predictability. As these alterations are not uniform across seascapes, their biological effects are expected to accentuate intra-specific differences in the adaptive capacity (e.g., plasticity and evolutionary potential) of natural populations. To test this theoretical framework, we assessed the phenotypic and genetic profiles of mussel from three study sites across a multi-driver heterogeneous environmental mosaic in Chilean Patagonia. Our study reveals that temporal variability, predictability, and exposure to extreme events (low pH/low salinity), collectively, can modulate the plasticity and optimal conditions of mussels. Despite these phenotypic differences, we observed low genetic differentiation, likely resulting from significant gene flow induced by aquaculture, ultimately diminishing variation among individuals from different geographic areas. Our findings underscore how variability and predictability are essential factors shaping phenotypic diversity, even at small spatial scales. Balancing these factors could enhance species resilience and ecological success, crucial for biodiversity conservation amidst climate change.
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Affiliation(s)
- Nicole C Castillo
- Coastal Ecosystems & Global Environmental Change Lab (ECCALab), Faculty of Environmental Sciences, Universidad de Concepción, Concepción, Chile; Coastal Social-Ecological Millennium Institute (SECOS), Universidad de Concepción, Concepción, Chile.
| | - Juan Diego Gaitán-Espitia
- The Swire Institute of Marine Science, School of Biological Sciences, The Hong Kong University, Hong Kong
| | - Julian F Quintero-Galvis
- Institute of Environmental and Evolutive Sciences, Universidad Austral de Chile, Valdivia, Chile; Millennium Nucleus of Patagonian Limit of Life (LiLi), Valdivia, Chile
| | - Gonzalo S Saldías
- Coastal Social-Ecological Millennium Institute (SECOS), Universidad de Concepción, Concepción, Chile; Department of Physics, Faculty of Sciences, Universidad del Bío-Bío, Concepción 4051381, Chile
| | - Sebastián I Martel
- Coastal Social-Ecological Millennium Institute (SECOS), Universidad de Concepción, Concepción, Chile; Department of Sciences, Faculty of Liberal Arts, Universidad Adolfo Ibáñez, Santiago, Chile
| | - Marco A Lardies
- Coastal Social-Ecological Millennium Institute (SECOS), Universidad de Concepción, Concepción, Chile; Department of Sciences, Faculty of Liberal Arts, Universidad Adolfo Ibáñez, Santiago, Chile
| | - Andrés Mesas
- Coastal Ecosystems & Global Environmental Change Lab (ECCALab), Faculty of Environmental Sciences, Universidad de Concepción, Concepción, Chile
| | | | - Stefan Gelcich
- Coastal Social-Ecological Millennium Institute (SECOS), Universidad de Concepción, Concepción, Chile; Center of Applied Ecology and Sustainability (CAPES), Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Cristian A Vargas
- Coastal Ecosystems & Global Environmental Change Lab (ECCALab), Faculty of Environmental Sciences, Universidad de Concepción, Concepción, Chile; Coastal Social-Ecological Millennium Institute (SECOS), Universidad de Concepción, Concepción, Chile; Millennium Institute of Oceanography (IMO), Universidad de Concepción, Concepción, Chile
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2
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Segovia NI, Coral-Santacruz D, Haye PA. Genetic homogeneity and weak signatures of local adaptation in the marine mussel Mytilus chilensis. Sci Rep 2024; 14:21081. [PMID: 39256462 PMCID: PMC11387636 DOI: 10.1038/s41598-024-71944-9] [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: 07/13/2023] [Accepted: 09/02/2024] [Indexed: 09/12/2024] Open
Abstract
The natural populations of the marine mussel Mytilus chilensis and the associated aquaculture industry forms a sensitive social-ecological system that relies on the released propagules for cultivation in the highly heterogeneous environment (temperature, productivity, and salinity) of northern Patagonia (42-44 °S). We assessed spatial genetic structure, signals of local adaptation, and population assignment of M. chilensis analyzing 5963 SNPs from 125 individuals across six natural populations sampled over two consecutive years along the southeast Pacific coast (39° 25' to 43° 07' S, ~ 430 km). Neutral and putatively adaptive loci revealed high genetic diversity and low genetic differentiation among populations. Of the whole dataset, less than 1% (50) of loci were identified as putatively adaptive through multiple approaches, with only 0.1% detected in by all of them, and only two loci of them were correlated with environmental variables. No evidence of Isolation by Environment (IBE) was found, albeit a slight differentiation in the southern sampling location (Yaldad). These results suggest that the genetic structure observed is primarily shaped by neutral processes with weak signals of local adaptation. Gene-flow appears to be the main evolutionary force influencing the species' population genetic structure. Because of the importance for the industry, the probability of correct assignment of individuals to their population of origin using allelic frequencies was evaluated. Analyses exhibited relatively low probabilities (< 50% for four out of six sites) of accurately assigning individuals to their geographic origin, with a limited success of SNP markers the for such purposes. Likely, species' high dispersal capacity, seed translocation, and the spill-over effect of mussel aquaculture prevents population genetic differentiation through high effective gene flow, hindering local genetic adaptation.
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Affiliation(s)
- Nicolás I Segovia
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo, Chile
- Instituto Milenio en Socio-Ecología Costera (SECOS), Coquimbo, Chile
| | - Diana Coral-Santacruz
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo, Chile
- Instituto Milenio en Socio-Ecología Costera (SECOS), Coquimbo, Chile
| | - Pilar A Haye
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo, Chile.
- Instituto Milenio en Socio-Ecología Costera (SECOS), Coquimbo, Chile.
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3
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Yévenes M, Gallardo-Escárate C, Gajardo G. Epigenetic variation mediated by lncRNAs accounts for adaptive genomic differentiation of the endemic blue mussel Mytiluschilensis. Heliyon 2024; 10:e23695. [PMID: 38205306 PMCID: PMC10776947 DOI: 10.1016/j.heliyon.2023.e23695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 12/09/2023] [Indexed: 01/12/2024] Open
Abstract
Epigenetic variation affects gene expression without altering the underlying DNA sequence of genes controlling ecologically relevant phenotypes through different mechanisms, one of which is long non-coding RNAs (lncRNAs). This study identified and evaluated the gene expression of lncRNAs in the gill and mantle tissues of Mytilus chilensis individuals from two ecologically different sites: Cochamó (41°S) and Yaldad (43°S), southern Chile, both impacted by climatic-related conditions and by mussel farming given their use as seedbeds. Sequences identified as lncRNAs exhibited tissue-specific differences, mapping to 3.54 % of the gill transcriptome and 1.96 % of the mantle transcriptome, representing an average of 2.76 % of the whole transcriptome. Using a high fold change value (≥|100|), we identified 43 and 47 differentially expressed lncRNAs (DE-lncRNAs) in the gill and mantle tissue of individuals sampled from Cochamó and 21 and 17 in the gill and mantle tissue of individuals sampled from Yaldad. Location-specific DE-lncRNAs were also detected in Cochamó (65) and Yaldad (94) samples. Via analysis of the differential expression of neighboring protein-coding genes, we identified enriched GO terms related to metabolic, genetic, and environmental information processing and immune system functions, reflecting how the impact of local ecological conditions may influence the M. chilensis (epi)genome expression. These DE-lncRNAs represent complementary biomarkers to DNA sequence variation for maintaining adaptive differences and phenotypic plasticity to cope with natural and human-driven perturbations.
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Affiliation(s)
- Marco Yévenes
- Laboratorio de Genética, Acuicultura y Biodiversidad, Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Osorno, Chile
| | - Cristian Gallardo-Escárate
- Centro Interdisciplinario para la Investigación en Acuicultura, Universidad de Concepción, Concepción, Chile
| | - Gonzalo Gajardo
- Laboratorio de Genética, Acuicultura y Biodiversidad, Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Osorno, Chile
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4
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Ouagajjou Y, Aghzar A, Presa P. Population Genetic Divergence among Worldwide Gene Pools of the Mediterranean Mussel Mytilus galloprovincialis. Animals (Basel) 2023; 13:3754. [PMID: 38136792 PMCID: PMC10740466 DOI: 10.3390/ani13243754] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023] Open
Abstract
The Mediterranean mussel Mytilus galloprovincialis is distributed in both hemispheres either natively or introduced. The updated population genetic distribution of this species provides a useful knowledge against which future distribution shifts could be assessed. This study, performed with seven microsatellite markers and three reference species (M. edulis, M. chilensis and M. trossulus), aimed to determine the scenario of genetic divergence between 15 samples of M. galloprovincialis from 10 localities in Europe, Africa, Asia, Australia, North America and South America. In agreement with previous data, M. trossulus was the most divergent taxon of the genus, but M. chilensis appeared as an intermediate taxon between M. edulis and M. galloprovincialis, though closer to this latter. M. galloprovincialis from the Atlantic Northeast appears as the most likely source of worldwide exotic settlements instead of the previously thought Mediterranean population. The successful worldwide establishment of M. galloprovincialis suggests it is a flexible evolutionary species (FES), i.e., a species or population whose genetic background allows it to rapidly adapt to changing environments. This natural endowed plastic adaptation makes it a candidate resilient species amidst the ongoing climatic change.
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Affiliation(s)
- Yassine Ouagajjou
- Amsa Shellfish Research Station, National Institute of Fisheries Research, Tetouan 93000, Morocco;
| | - Adil Aghzar
- Research Team of Agriculture and Aquaculture Engineering (G2A), Polydisciplinary Faculty of Larache, Abdelmalek Essaadi University, Tetouan 93000, Morocco;
| | - Pablo Presa
- Laboratory of Marine Genetic Resources (ReXenMar), CIM—Universidade de Vigo, 36310 Vigo, Spain
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Gallardo-Escárate C, Valenzuela-Muñoz V, Nuñez-Acuña G, Valenzuela-Miranda D, Tapia FJ, Yévenes M, Gajardo G, Toro JE, Oyarzún PA, Arriagada G, Novoa B, Figueras A, Roberts S, Gerdol M. Chromosome-Level Genome Assembly of the Blue Mussel Mytilus chilensis Reveals Molecular Signatures Facing the Marine Environment. Genes (Basel) 2023; 14:876. [PMID: 37107634 PMCID: PMC10137854 DOI: 10.3390/genes14040876] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 03/28/2023] [Accepted: 03/30/2023] [Indexed: 04/29/2023] Open
Abstract
The blue mussel Mytilus chilensis is an endemic and key socioeconomic species inhabiting the southern coast of Chile. This bivalve species supports a booming aquaculture industry, which entirely relies on artificially collected seeds from natural beds that are translocated to diverse physical-chemical ocean farming conditions. Furthermore, mussel production is threatened by a broad range of microorganisms, pollution, and environmental stressors that eventually impact its survival and growth. Herein, understanding the genomic basis of the local adaption is pivotal to developing sustainable shellfish aquaculture. We present a high-quality reference genome of M. chilensis, which is the first chromosome-level genome for a Mytilidae member in South America. The assembled genome size was 1.93 Gb, with a contig N50 of 134 Mb. Through Hi-C proximity ligation, 11,868 contigs were clustered, ordered, and assembled into 14 chromosomes in congruence with the karyological evidence. The M. chilensis genome comprises 34,530 genes and 4795 non-coding RNAs. A total of 57% of the genome contains repetitive sequences with predominancy of LTR-retrotransposons and unknown elements. Comparative genome analysis of M. chilensis and M. coruscus was conducted, revealing genic rearrangements distributed into the whole genome. Notably, transposable Steamer-like elements associated with horizontal transmissible cancer were explored in reference genomes, suggesting putative relationships at the chromosome level in Bivalvia. Genome expression analysis was also conducted, showing putative genomic differences between two ecologically different mussel populations. The evidence suggests that local genome adaptation and physiological plasticity can be analyzed to develop sustainable mussel production. The genome of M. chilensis provides pivotal molecular knowledge for the Mytilus complex.
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Affiliation(s)
| | | | - Gustavo Nuñez-Acuña
- Center for Aquaculture Research, University of Concepción, Concepción 4070386, Chile
| | | | - Fabian J. Tapia
- Center for Aquaculture Research, University of Concepción, Concepción 4070386, Chile
| | - Marco Yévenes
- Laboratorio de Genética, Acuicultura & Biodiversidad, Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Osorno 5310230, Chile
| | - Gonzalo Gajardo
- Laboratorio de Genética, Acuicultura & Biodiversidad, Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Osorno 5310230, Chile
| | - Jorge E. Toro
- Facultad de Ciencias, Instituto de Ciencias Marinas y Limnológicas (ICML), Universidad Austral de Chile, Valdivia 5110566, Chile
| | - Pablo A. Oyarzún
- Centro de Investigación Marina Quintay (CIMARQ), Universidad Andres Bello, Quintay 2340000, Chile
| | - Gloria Arriagada
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad Andrés Bello, Santiago 8370186, Chile
- FONDAP Center for Genome Regulation, Santiago 8370415, Chile
| | - Beatriz Novoa
- Instituto de Investigaciones Marinas (IIM), Consejo Superior de Investigaciones Científicas (CSIC), 36208 Vigo, Spain
| | - Antonio Figueras
- Instituto de Investigaciones Marinas (IIM), Consejo Superior de Investigaciones Científicas (CSIC), 36208 Vigo, Spain
| | - Steven Roberts
- School of Aquatic and Fishery Sciences (SAFS), University of Washington, Seattle, WA 98195, USA
| | - Marco Gerdol
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
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6
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Vargas-Peralta CE, Araneda C, Galindo-Sánchez CE, Larraín MA, Del Río-Portilla MA, Lafarga-De la Cruz F. Species identification in Haliotis genus from the northeastern Pacific Ocean using genome-wide RAD-SNPs. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.108979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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7
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Adaptive mitochondrial genome functioning in ecologically different farm-impacted natural seedbeds of the endemic blue mussel Mytilus chilensis. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2022; 42:100955. [PMID: 35065314 DOI: 10.1016/j.cbd.2021.100955] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 12/16/2021] [Accepted: 12/16/2021] [Indexed: 11/22/2022]
Abstract
We assessed the adaptive contribution of the mitochondrial genes involved with the respiratory chain and oxidative phosphorylation of the blue mussel Mytilus chilensis, a native and heavily exploited species in the inner sea of Chiloé Island, southern Chile. The assembled mitochondrial transcriptome of individuals from two ecologically different farm-impacted natural seedbeds, Cochamó (41°S) and Yaldad (42°S), represented about 4.5% of the whole de novo transcriptome of the species and showed location and tissue (gills, mantle) specific expression differences in 13 protein-coding mitochondrial genes. The RNA-Seq analysis detected differences in the number of up-regulated mitogenes between individuals from Cochamó (7) and Yaldad (11), some being tissue-specific (ND4L and COX2). However, the analysis did not detect transcripts-per-million (TPM = 0) of ND2 and ND5 in gills and ATP6 in mantle samples from Cochamó. Likewise, for ND6 and ATP8 in any sample. Several monomorphic location-specific mitochondrial genetic variants were detected in samples from Cochamó (78) and Yaldad (207), representing standing genetic variability to optimize mitochondrial functioning under local habitats. Overall, these mitochondrial transcriptomic differences reflect the impact of environmental conditions on the mitochondrial genome functioning and offer new markers to assess the effects on mussel fitness of habitat translocations, a routine industry practice. Likewise, these mitochondrial markers should help monitor and maintain adaptive population differences in this keystone and heavily exploited native species.
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8
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Blue mussels of the Mytilus edulis species complex from South America: The application of species delimitation models to DNA sequence variation. PLoS One 2021; 16:e0256961. [PMID: 34473778 PMCID: PMC8412288 DOI: 10.1371/journal.pone.0256961] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 08/19/2021] [Indexed: 11/30/2022] Open
Abstract
Smooth-shelled blue mussels, Mytilus spp., have a worldwide antitropical distribution and are ecologically and economically important. Mussels of the Mytilus edulis species complex have been the focus of numerous taxonomic and biogeographical studies, in particular in the Northern hemisphere, but the taxonomic classification of mussels from South America remains unclear. The present study analysed 348 mussels from 20 sites in Argentina, Chile, Uruguay and the Falkland Islands on the Atlantic and Pacific coasts of South America. We sequenced two mitochondrial locus, Cytochrome c Oxidase subunit I (625 bp) and 16S rDNA (443 bp), and one nuclear gene, ribosomal 18S rDNA (1770 bp). Mitochondrial and nuclear loci were analysed separately and in combination using maximum likelihood and Bayesian inference methods to identify the combination of the most informative dataset and model. Species delimitation using five different models (GMYC single, bGMYC, PTP, bPTP and BPP) revealed that the Mytilus edulis complex in South America is represented by three species: native M. chilensis, M. edulis, and introduced Northern Hemisphere M. galloprovincialis. However, all models failed to delimit the putative species Mytilus platensis. In contrast, however, broad spatial scale genetic structure in South America using Geneland software to analyse COI sequence variation revealed a group of native mussels (putatively M. platensis) in central Argentina and the Falkland Islands. We discuss the scope of species delimitation methods and the use of nuclear and mitochondrial genetic data to the recognition of species within the Mytilus edulis complex at regional and global scales.
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Fazzi-Gomes PF, Aguiar JDP, Marques D, Fonseca Cabral G, Moreira FC, Rodrigues MDN, Silva CS, Hamoy I, Santos S. Novel Microsatellite Markers Used for Determining Genetic Diversity and Tracing of Wild and Farmed Populations of the Amazonian Giant Fish Arapaima gigas. Genes (Basel) 2021; 12:1324. [PMID: 34573306 PMCID: PMC8467478 DOI: 10.3390/genes12091324] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/19/2021] [Accepted: 08/23/2021] [Indexed: 01/29/2023] Open
Abstract
The Amazonian symbol fish Arapaima gigas is the only living representative of the Arapamidae family. Environmental pressures and illegal fishing threaten the species' survival. To protect wild populations, a national regulation must be developed for the management of A. gigas throughout the Amazon basin. Moreover, the reproductive genetic management and recruitment of additional founders by aquaculture farms are needed to mitigate the damage caused by domestication. To contribute to the sustainable development, we investigated the genetic diversity of wild and cultivated populations of A. gigas and developed a panel composed by 12 microsatellite markers for individual and population genetic tracing. We analyzed 368 samples from three wild and four farmed populations. The results revealed low rates of genetic diversity in all populations, loss of genetic diversity and high inbreeding rates in farmed populations, and genetic structuring among wild and farmed populations. Genetic tracing using the 12 microsatellite markers was effective, and presented a better performance in identifying samples at the population level. The 12-microsatellite panel is appliable to the legal aspects of the trade of the A. gigas, such as origin discrimination, reproductive genetic management by DNA profiling, and evaluation and monitoring of genetic diversity.
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Affiliation(s)
- Paola Fabiana Fazzi-Gomes
- Laboratório de Humana e Médica, Universidade Federal do Pará, Rua Augusto Correa, 1, Belém 66075-110, Brazil; (P.F.F.-G.); (D.M.); (G.F.C.); (F.C.M.); (C.S.S.)
| | - Jonas da Paz Aguiar
- Universidade Federal do Pará, Campus Bragança, Alameda Leandro Ribeiro s/n, Bragança 68600-000, Brazil;
| | - Diego Marques
- Laboratório de Humana e Médica, Universidade Federal do Pará, Rua Augusto Correa, 1, Belém 66075-110, Brazil; (P.F.F.-G.); (D.M.); (G.F.C.); (F.C.M.); (C.S.S.)
| | - Gleyce Fonseca Cabral
- Laboratório de Humana e Médica, Universidade Federal do Pará, Rua Augusto Correa, 1, Belém 66075-110, Brazil; (P.F.F.-G.); (D.M.); (G.F.C.); (F.C.M.); (C.S.S.)
| | - Fabiano Cordeiro Moreira
- Laboratório de Humana e Médica, Universidade Federal do Pará, Rua Augusto Correa, 1, Belém 66075-110, Brazil; (P.F.F.-G.); (D.M.); (G.F.C.); (F.C.M.); (C.S.S.)
| | - Marilia Danyelle Nunes Rodrigues
- Laboratório de Genética Aplicada, Instituto de Recursos Aquáticos e Socioambientais, Universidade Federal Rural da Amazônia, Avenida Presidente Tancredo Neves, 2501, Belem 66077-830, Brazil; (M.D.N.R.); (I.H.)
| | - Caio Santos Silva
- Laboratório de Humana e Médica, Universidade Federal do Pará, Rua Augusto Correa, 1, Belém 66075-110, Brazil; (P.F.F.-G.); (D.M.); (G.F.C.); (F.C.M.); (C.S.S.)
| | - Igor Hamoy
- Laboratório de Genética Aplicada, Instituto de Recursos Aquáticos e Socioambientais, Universidade Federal Rural da Amazônia, Avenida Presidente Tancredo Neves, 2501, Belem 66077-830, Brazil; (M.D.N.R.); (I.H.)
| | - Sidney Santos
- Laboratório de Humana e Médica, Universidade Federal do Pará, Rua Augusto Correa, 1, Belém 66075-110, Brazil; (P.F.F.-G.); (D.M.); (G.F.C.); (F.C.M.); (C.S.S.)
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10
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Kotsanopoulos KV, Exadactylos A, Gkafas GA, Martsikalis PV, Parlapani FF, Boziaris IS, Arvanitoyannis IS. The use of molecular markers in the verification of fish and seafood authenticity and the detection of adulteration. Compr Rev Food Sci Food Saf 2021; 20:1584-1654. [PMID: 33586855 DOI: 10.1111/1541-4337.12719] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 12/17/2020] [Accepted: 01/10/2021] [Indexed: 12/11/2022]
Abstract
The verification of authenticity and detection of food mislabeling are elements that have been of high importance for centuries. During the last few decades there has been an increasing consumer demand for the verification of food identity and the implementation of stricter controls around these matters. Fish and seafood are among the most easily adulterated foodstuffs mainly due to the significant alterations of the species' morphological characteristics that occur during the different types of processing, which render the visual identification of the animals impossible. Even simple processes, such as filleting remove very important morphological elements and suffice to prevent the visual identification of species in marketed products. Novel techniques have therefore been developed that allow identification of species, the differentiation between species and also the differentiation of individuals that belong to the same species but grow in different populations and regions. Molecular markers have been used during the last few decades to fulfill this purpose and several improvements have been implemented rendering their use applicable to a commercial scale. The reliability, accuracy, reproducibility, and time-and cost-effectiveness of these techniques allowed them to be established as routine methods in the industry and research institutes. This review article aims at presenting the most important molecular markers used for the authentication of fish and seafood. The most important techniques are described, and the results of numerous studies are outlined and discussed, allowing interested parties to easily access and compare information about several techniques and fish/seafood species.
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Affiliation(s)
- Konstantinos V Kotsanopoulos
- Department of Ichthyology & Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
| | - Athanasios Exadactylos
- Department of Ichthyology & Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
| | - George A Gkafas
- Department of Ichthyology & Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
| | - Petros V Martsikalis
- Department of Ichthyology & Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
| | - Foteini F Parlapani
- Department of Ichthyology & Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
| | - Ioannis S Boziaris
- Department of Ichthyology & Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
| | - Ioannis S Arvanitoyannis
- Department of Ichthyology & Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
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11
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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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12
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Georges-Filteau J, Hamelin RC, Blanchette M. Mycorrhiza: genotype assignment using phylogenetic networks. Bioinformatics 2020; 36:212-220. [PMID: 31197316 DOI: 10.1093/bioinformatics/btz476] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 05/03/2019] [Accepted: 06/06/2019] [Indexed: 01/09/2023] Open
Abstract
MOTIVATION The genotype assignment problem consists of predicting, from the genotype of an individual, which of a known set of populations it originated from. The problem arises in a variety of contexts, including wildlife forensics, invasive species detection and biodiversity monitoring. Existing approaches perform well under ideal conditions but are sensitive to a variety of common violations of the assumptions they rely on. RESULTS In this article, we introduce Mycorrhiza, a machine learning approach for the genotype assignment problem. Our algorithm makes use of phylogenetic networks to engineer features that encode the evolutionary relationships among samples. Those features are then used as input to a Random Forests classifier. The classification accuracy was assessed on multiple published empirical SNP, microsatellite or consensus sequence datasets with wide ranges of size, geographical distribution and population structure and on simulated datasets. It compared favorably against widely used assessment tests or mixture analysis methods such as STRUCTURE and Admixture, and against another machine-learning based approach using principal component analysis for dimensionality reduction. Mycorrhiza yields particularly significant gains on datasets with a large average fixation index (FST) or deviation from the Hardy-Weinberg equilibrium. Moreover, the phylogenetic network approach estimates mixture proportions with good accuracy. AVAILABILITY AND IMPLEMENTATION Mycorrhiza is released as an easy to use open-source python package at github.com/jgeofil/mycorrhiza. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Richard C Hamelin
- Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, BC, Canada.,Département des sciences du bois et de la forêt, Université Laval, Québec, Canada
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13
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Yao L, Lu J, Qu M, Jiang Y, Li F, Guo Y, Wang L, Zhai Y. Methodology and application of PCR-RFLP for species identification in tuna sashimi. Food Sci Nutr 2020; 8:3138-3146. [PMID: 32724578 PMCID: PMC7382206 DOI: 10.1002/fsn3.1552] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 01/03/2020] [Accepted: 01/22/2020] [Indexed: 11/24/2022] Open
Abstract
The Thunnini, or tuna, comprise many species with very different commercial values. The principal raw tuna product on the market is sashimi, for which the species used is difficult to identify through conventional morphological analysis. The present study amplified the cytochrome b gene (Cytb) of 4 major tuna species used for preparing sashimi-yellowfin tuna (Thunnus albacares), southern bluefin tuna (Thunnus maccoyii), bigeye tuna (Thunnus obesus), and Atlantic bluefin tuna (Thunnus thynnus)-and 4 species commonly mislabeled as components of tuna sashimi-albacore tuna (Thunnus alalunga), skipjack tuna (Katsuwonus pelamis), striped marlin (Tetrapturus audax), and swordfish (Xiphias gladius). Polymerase chain reaction (PCR) amplicons were digested with 5 restriction enzymes-Eco147 I, Hinf I, Mbo I, Xag I, and Hind II-to obtain characteristic restriction maps of the above-mentioned raw tuna species and the commonly mislabeled species. An identification method using PCR restriction fragment length polymorphism (PCR-RFLP) was established and validated using 39 commercial tuna sashimi samples, which verified that this method provides results consistent with those obtained by classical sequencing. PCR-RFLP has several advantages over classical sequencing, such as simplicity, speed and accuracy. This technique could support species identification for raw tuna and sashimi.
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Affiliation(s)
- Lin Yao
- Key Laboratory of Testing and Evaluation for Aquatic Product Safety and QualityMinistry of Agriculture and Rural AffairsQingdaoChina
- Yellow Sea Fisheries Research InstituteChinese Academy of Fishery SciencesQingdaoChina
| | - Jianping Lu
- College of Food Science and EngineeringOcean University of ChinaQingdaoChina
| | - Meng Qu
- Key Laboratory of Testing and Evaluation for Aquatic Product Safety and QualityMinistry of Agriculture and Rural AffairsQingdaoChina
- Yellow Sea Fisheries Research InstituteChinese Academy of Fishery SciencesQingdaoChina
| | - Yanhua Jiang
- Key Laboratory of Testing and Evaluation for Aquatic Product Safety and QualityMinistry of Agriculture and Rural AffairsQingdaoChina
- Yellow Sea Fisheries Research InstituteChinese Academy of Fishery SciencesQingdaoChina
| | - Fengling Li
- Key Laboratory of Testing and Evaluation for Aquatic Product Safety and QualityMinistry of Agriculture and Rural AffairsQingdaoChina
- Yellow Sea Fisheries Research InstituteChinese Academy of Fishery SciencesQingdaoChina
| | - Yingying Guo
- Key Laboratory of Testing and Evaluation for Aquatic Product Safety and QualityMinistry of Agriculture and Rural AffairsQingdaoChina
- Yellow Sea Fisheries Research InstituteChinese Academy of Fishery SciencesQingdaoChina
| | - Lianzhu Wang
- Key Laboratory of Testing and Evaluation for Aquatic Product Safety and QualityMinistry of Agriculture and Rural AffairsQingdaoChina
- Yellow Sea Fisheries Research InstituteChinese Academy of Fishery SciencesQingdaoChina
| | - Yuxiu Zhai
- Key Laboratory of Testing and Evaluation for Aquatic Product Safety and QualityMinistry of Agriculture and Rural AffairsQingdaoChina
- Yellow Sea Fisheries Research InstituteChinese Academy of Fishery SciencesQingdaoChina
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14
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Conti ME, Tudino MB, Finoia MG, Simone C, Stripeikis J. Applying the monitoring breakdown structure model to trace metal content in edible biomonitors: An eight-year survey in the Beagle Channel (southern Patagonia). Food Res Int 2020; 128:108777. [DOI: 10.1016/j.foodres.2019.108777] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 10/22/2019] [Accepted: 10/26/2019] [Indexed: 01/22/2023]
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Larraín MA, González P, Pérez C, Araneda C. Comparison between single and multi-locus approaches for specimen identification in Mytilus mussels. Sci Rep 2019; 9:19714. [PMID: 31873129 PMCID: PMC6928075 DOI: 10.1038/s41598-019-55855-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 11/30/2019] [Indexed: 01/19/2023] Open
Abstract
Mytilus mussels have been the object of much research given their sentinel role in coastal ecosystems and significant value as an aquaculture resource appreciated for both, its flavour and nutritional content. Some of the most-studied Mytilus species are M. edulis, M. galloprovincialis, M. chilensis and M. trossulus. As species identification based on morphological characteristics of Mytilus specimens is difficult, molecular markers are often used. Single-locus markers can give conflicting results when used independently; not all markers differentiate among all species, and the markers target genomic regions with different evolutionary histories. We evaluated the concordance between the PCR-RFLP markers most commonly-used for species identification in mussels within the Mytilus genus (Me15-16, ITS, mac-1, 16S rRNA and COI) when used alone (mono-locus approach) or together (multi-locus approach). In this study, multi-locus strategy outperformed the mono-locus methods, clearly identifying all four species and also showed similar specimen identification performance than a 49 SNPs panel. We hope that these findings will contribute to a better understanding of DNA marker-based analysis of Mytilus taxa. These results support the use of a multi-locus approach when studying this important marine resource, including research on food quality and safety, sustainable production and conservation.
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Affiliation(s)
- María Angélica Larraín
- Food Quality Research Center, Universidad de Chile, Santiago, Chile.
- Departamento de Ciencia de los Alimentos y Tecnología Química, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile.
| | - Pía González
- Food Quality Research Center, Universidad de Chile, Santiago, Chile
- Programa de Magister en Alimentos. Mención Gestión, Calidad e Inocuidad de los Alimentos. Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Claudio Pérez
- Laboratorio de Genética y Biotecnología en Acuicultura, Departamento de Producción Animal, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago, Chile
| | - Cristián Araneda
- Food Quality Research Center, Universidad de Chile, Santiago, Chile
- Laboratorio de Genética y Biotecnología en Acuicultura, Departamento de Producción Animal, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago, Chile
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Morrison L, Bennion M, Gill S, Graham CT. Spatio-temporal trace element fingerprinting of king scallops (Pecten maximus) reveals harvesting period and location. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 697:134121. [PMID: 32380612 DOI: 10.1016/j.scitotenv.2019.134121] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 08/19/2019] [Accepted: 08/25/2019] [Indexed: 06/11/2023]
Abstract
A rapidly growing human population is increasingly relying on seafood as a source of protein and other essential nutrients. Bivalve shellfish, both from wild populations and aquaculture, will undoubtedly continue to account for a significant portion of overall seafood production, but consumption of such shellfish carries potential health risks. Biotoxins, disease causing organisms and pollution contribute to this risk, as shellfish are indiscriminate, passive filter feeders. While government bodies, industry regulators and producers are capable of managing this risk, counterfeit produce can risk public safety, in turn damaging the reputation of the entire industry. Traceability tools provide a means to uphold food safety standards and mitigate remaining risk to consumers. Here, we show how the use of trace element (TE) signatures in shells and soft tissues of king scallops combined, can predict geographic origin with 100% accuracy. Importantly, we explore the temporal stability of this method, successfully classifying 100% of individuals correctly between two dates just 42 days apart from the same harvesting location. The most important elements in the trace element signatures of the scallops, discriminating between harvesting sites and dates were barium, boron, chromium, lead, manganese, molybdenum and selenium. The traceability tool described here offers a viable method to trace produce to its source, empowering industry regulators, government authorities, aquaculture practitioners and retailers in terms of tracking shellfish throughout the supply chain, which would comply with legislation and boost consumer confidence.
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Affiliation(s)
- Liam Morrison
- Earth and Ocean Sciences, School of Natural Sciences and Ryan Institute, National University of Ireland, Galway, Ireland
| | - Matthew Bennion
- Environmental Research Institute, University of Waikato, Tauranga, New Zealand
| | - Stephen Gill
- Marine and Freshwater Research Centre, Galway-Mayo Institute of Technology, Dublin Road, Galway, Ireland
| | - Conor T Graham
- Marine and Freshwater Research Centre, Galway-Mayo Institute of Technology, Dublin Road, Galway, Ireland.
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17
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Waples RS. Null Alleles and FIS × FST Correlations. J Hered 2019; 109:457-461. [PMID: 29554281 DOI: 10.1093/jhered/esy013] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 03/14/2018] [Indexed: 11/14/2022] Open
Abstract
Three published papers in this journal have considered the proposition that, under a Wahlund effect caused by population mixture, a positive correlation is expected between single-locus values of FIS for a sample from the mixture and FST between the populations contributing to the mixture. Two of the papers assumed unbiased samples to estimate FST but did not consider possible effects of null alleles; the other paper focused on effects of nulls but used biased samples that also included Wahlund effects to estimate FST. The result is an information gap regarding scenarios that include null alleles but have unbiased estimates of FST. Simulations were used to fill this information gap, with the following results: 1) converting ~10% of alleles to nulls substantially reduced apparent heterozygosity and substantially increased FIS, with few exceptions; 2) adding null alleles also increased FST at most loci, although the effect was much more modest; 3) null alleles generally degraded correlations between FIS and FST, but the relationship remained relatively strong for FST ≥ 0.06; and 4) null alleles had only a small effect on correlations between r2, a measure of linkage disequilibrium between pairs of loci, and the product of FST values for those loci. These results argue for some caution in interpreting FIS × FST correlations under conditions where null alleles might be common and suggest that two-locus analyses might provide more robust assessments of Wahlund effects.
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18
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Zbawicka M, Gardner JPA, Wenne R. Cryptic diversity in smooth-shelled mussels on Southern Ocean islands: connectivity, hybridisation and a marine invasion. Front Zool 2019; 16:32. [PMID: 31406494 PMCID: PMC6685288 DOI: 10.1186/s12983-019-0332-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 07/24/2019] [Indexed: 01/08/2023] Open
Abstract
Background Large numbers of endemic species inhabit subantarctic continental coasts and islands that are characterised by highly variable environmental conditions. Southern hemisphere populations of taxa that are morphologically similar to northern counterparts have traditionally been considered to be extensions of such Northern hemisphere taxa, and may not exhibit differentiation amongst geographically isolated populations in the Southern Ocean. Smooth-shelled blue mussels of the genus Mytilus that exhibit an anti-tropical distribution are a model group to study phylogeography, speciation and hybridisation in the sea, and contribute to the theory and practice of marine biosecurity. Methods We used a single nucleotide polymorphism (SNPs) panel that has the ability to accurately identify reference Northern and Southern hemisphere Mytilus taxa to test for evolutionary differentiation amongst native Southern Ocean island populations. Results Native mussels from the Falkland Islands and the Kerguelen Islands exhibited greatest affinity to native M. platensis d’Orbigny 1846 from the Atlantic coast of South America. The major Southern Ocean current flow from west to east is likely to explain the spreading of M. platensis to remote offshore islands, as adults via the process of rafting or perhaps directly as larvae. SNPs variation revealed that mussels from Tasmania were native and clearly differentiated from all other blue mussel groups in the Southern and Northern hemispheres. The native mussels M. planulatus from Tasmania and from mainland New Zealand (NZ), and tentatively M. aoteanus from the two NZ Southern Ocean offshore island groups (the Auckland Islands and Campbell Island), formed a distinct M. galloprovincialis–like Southern hemisphere group with closest affinity to Northern hemisphere M. galloprovincialis from the Mediterranean Sea. In all cases, the SNPs revealed evidence of hybridisation between two or more distinct taxa. The invasive Northern hemisphere M. galloprovincialis was identified only in Tasmania, amongst native mussels of a distinct Australian M. planulatus lineage. Conclusion Overall, our results reveal that Southern hemisphere island mussels have mixed genome ancestry and are native, not introduced by human activities. The preservation of distinct evolutionary lineages of Southern hemisphere species needs to be an ongoing focus of conservation efforts, given that population sizes on some of the remote offshore oceanic islands will be small and may be more easily adversely affected by invasion and subsequent hybridisation and introgression than larger populations elsewhere. Electronic supplementary material The online version of this article (10.1186/s12983-019-0332-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Małgorzata Zbawicka
- 1Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, 81-712 Sopot, Poland
| | - Jonathan P A Gardner
- 2School of Biological Sciences, Victoria University of Wellington, P O Box 600, Wellington, 6140 New Zealand
| | - Roman Wenne
- 1Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, 81-712 Sopot, Poland
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19
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Aguiar JDP, Fazzi-Gomes PF, Hamoy IG, Dos Santos SE, Sampaio I. Tracing individuals and populations of the tambaqui, Colossoma macropomum (Cuvier, 1818), from Brazilian hatcheries using microsatellite markers. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2019; 99:2998-3004. [PMID: 30478936 DOI: 10.1002/jsfa.9513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 11/21/2018] [Accepted: 11/22/2018] [Indexed: 06/09/2023]
Abstract
BACKGROUND In recent years, tracing of alimentary produce of animal origin has become increasingly important, for economic, food safety and ecological reasons. The tambaqui, Colossoma macropomum, is the native fish most farmed in Brazil. The reliable identification of the origin of tambaquis (wild or farmed) offered for sale to the general public has become necessary to satisfy regulatory norms and uphold consumer confidence. Molecular methods based on the analysis of DNA sequences have often been used to evaluate the potential for tracing farmed fish, given their reliability and precision. RESULTS Full likelihood and Bayesian approaches proved to be the most efficient for the identification, respectively, of individuals and populations for most of the fish sampled from seven hatcheries and one wild stock. The exclusion method and genetic distances were the least effective approaches for the identification of individuals and populations. The Bayesian method identified correctly more than 99% of the fry from most stocks, except those of the Santarém hatchery and River Amazon wild stock, which presented the best results for individual identification. CONCLUSIONS The identification of populations was effective for most hatcheries, although the identification of individuals from most stocks was hampered by the reduced genetic variability. © 2018 Society of Chemical Industry.
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Affiliation(s)
- Jonas da Paz Aguiar
- Laboratory of Genetics and Molecular Biology, Institute of Coastal Studies, Federal University of Pará, Belém, Brazil
| | - Paola F Fazzi-Gomes
- Laboratory of Applied Genetics, Institute of Socio-environmental Studies and Hydrological Resources, Federal Rural University of the Amazon, Belém, Brazil
| | - Igor G Hamoy
- Laboratory of Applied Genetics, Institute of Socio-environmental Studies and Hydrological Resources, Federal Rural University of the Amazon, Belém, Brazil
| | - Sidney Eb Dos Santos
- Laboratory of Human and Medical Genetics, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
| | - Iracilda Sampaio
- Laboratory of Genetics and Molecular Biology, Institute of Coastal Studies, Federal University of Pará, Belém, Brazil
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Larraín MA, Zbawicka M, Araneda C, Gardner JPA, Wenne R. Native and invasive taxa on the Pacific coast of South America: Impacts on aquaculture, traceability and biodiversity of blue mussels (Mytilusspp.). Evol Appl 2017. [DOI: 10.1111/eva.12553] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Maria A. Larraín
- Departamento de Ciencia de los Alimentos y Tecnología Química; Facultad de Ciencias Químicas y Farmacéuticas; Universidad de Chile; Santiago Chile
| | | | - Cristian Araneda
- Departamento de Producción Animal; Facultad de Ciencias Agronómicas; Universidad de Chile; Santiago Chile
| | - Jonathan P. A. Gardner
- School of Biological Sciences; Victoria University of Wellington; Wellington New Zealand
| | - Roman Wenne
- Institute of Oceanology; Polish Academy of Sciences; Sopot Poland
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21
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Wilwet L, Jeyasekaran G, Shakila RJ, Sivaraman B, Padmavathy P. A single enzyme PCR-RFLP protocol targeting 16S rRNA/tRNA val region to authenticate four commercially important shrimp species in India. Food Chem 2017; 239:369-376. [PMID: 28873581 DOI: 10.1016/j.foodchem.2017.06.132] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 05/12/2017] [Accepted: 06/22/2017] [Indexed: 11/30/2022]
Abstract
Food authenticity is an issue of major concern for food authorities, as mislabeling represents one of the major commercial frauds. In this study, a novel PCR-RFLP protocol was developed as a tool to authenticate four shrimp products of commercial importance belonging to the family, Penaeidae, viz. Litopenaeus vannamei, Penaeus monodon, P. semisulcatus and Fenneropenaeus indicus. PCR amplification was performed targeting 16S rRNA/tRNAval region having an amplicon size of 530bp using the specific primers for shrimps, 16S-Cru4/16S-Cru3. Subsequent restriction analysis with a single restriction enzyme, Tsp5091, yielded distinct RFLP pattern for each species of shrimps having fragment sizes below 150bp. The unique RFLP patterns were also obtained in processed shrimp products without any degradation or alteration in the major fragments. The method was also validated with commercial shrimp products. Thus, the developed protocol can be performed within 8h using a single enzyme to authenticate four shrimp products of commercial significance.
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Affiliation(s)
- Lidiya Wilwet
- Department of Fish Quality Assurance and Management, Fisheries College and Research Institute, Tamil Nadu Fisheries University, Thoothukkudi 628 008, India
| | - Geevaretnam Jeyasekaran
- Department of Fish Quality Assurance and Management, Fisheries College and Research Institute, Tamil Nadu Fisheries University, Thoothukkudi 628 008, India.
| | - Robinson Jeya Shakila
- Department of Fish Quality Assurance and Management, Fisheries College and Research Institute, Tamil Nadu Fisheries University, Thoothukkudi 628 008, India
| | - Balasubramanian Sivaraman
- Department of Fish Quality Assurance and Management, Fisheries College and Research Institute, Tamil Nadu Fisheries University, Thoothukkudi 628 008, India
| | - Pandurengan Padmavathy
- Department of Fisheries Environment, Fisheries College and Research Institute, Tamil Nadu Fisheries University, Thoothukkudi 628 008, India
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Araneda C, Larraín MA, Hecht B, Narum S. Adaptive genetic variation distinguishes Chilean blue mussels ( Mytilus chilensis) from different marine environments. Ecol Evol 2016; 6:3632-3644. [PMID: 27195104 PMCID: PMC4851556 DOI: 10.1002/ece3.2110] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 02/24/2016] [Accepted: 03/03/2016] [Indexed: 01/06/2023] Open
Abstract
Chilean mussel populations have been thought to be panmictic with limited genetic structure. Genotyping-by-sequencing approaches have enabled investigation of genomewide variation that may better distinguish populations that have evolved in different environments. We investigated neutral and adaptive genetic variation in Mytilus from six locations in southern Chile with 1240 SNPs obtained with RAD-seq. Differentiation among locations with 891 neutral SNPs was low (FST = 0.005). Higher differentiation was obtained with a panel of 58 putative outlier SNPs (FST = 0.114) indicating the potential for local adaptation. This panel identified clusters of genetically related individuals and demonstrated that much of the differentiation (~92%) could be attributed to the three major regions and environments: extreme conditions in Patagonia, inner bay influenced by aquaculture (Reloncaví), and outer bay (Chiloé Island). Patagonia samples were most distinct, but additional analysis carried out excluding this collection also revealed adaptive divergence between inner and outer bay samples. The four locations within Reloncaví area were most similar with all panels of markers, likely due to similar environments, high gene flow by aquaculture practices, and low geographical distance. Our results and the SNP markers developed will be a powerful tool supporting management and programs of this harvested species.
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Affiliation(s)
- Cristián Araneda
- Departamento de Producción AnimalFacultad de Ciencias AgronómicasUniversidad de ChileAvda Santa Rosa 11315, La Pintana8820808SantiagoChile
| | - María Angélica Larraín
- Departamento de Ciencia de los Alimentos y Tecnología QuímicaFacultad de Ciencias Químicas y FarmacéuticasUniversidad de ChileSergio Livingstone 1007, Independencia8380492SantiagoChile
| | - Benjamin Hecht
- Columbia River Inter‐Tribal Fish Commission3059‐F National Fish Hatchery RoadHagermanID83332
| | - Shawn Narum
- Columbia River Inter‐Tribal Fish Commission3059‐F National Fish Hatchery RoadHagermanID83332
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Araneda C, Noriega X, Jilberto F, Ruíz J, Jara C, Lafarga F, Larraín MA. Development of genome-wide microsatellite resources in a commercially important mussel species (Mytilus chilensis). Anim Genet 2015; 47:387-8. [PMID: 26669535 DOI: 10.1111/age.12398] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/28/2015] [Indexed: 11/29/2022]
Affiliation(s)
- Cristián Araneda
- Departamento de Producción Animal, Facultad de Ciencias Agronómicas, Universidad de Chile, Avda. Santa Rosa 11315, La Pintana, Santiago, 8820808, Chile
| | - Ximena Noriega
- Departamento de Ciencias de los Alimentos y Tecnología Química, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Sergio Livingstone 1007, Independencia, 8380492, Santiago, Chile
| | - Felipe Jilberto
- Departamento de Producción Animal, Facultad de Ciencias Agronómicas, Universidad de Chile, Avda. Santa Rosa 11315, La Pintana, Santiago, 8820808, Chile
| | - Jorge Ruíz
- Departamento de Ciencias de los Alimentos y Tecnología Química, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Sergio Livingstone 1007, Independencia, 8380492, Santiago, Chile
| | - Coral Jara
- Departamento de Ciencias de los Alimentos y Tecnología Química, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Sergio Livingstone 1007, Independencia, 8380492, Santiago, Chile
| | - Fabiola Lafarga
- Departamento de Acuicultura, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Carretera Ensenada-Tijuana 3918, Zona Playitas, 22860, Ensenada, Baja California, México
| | - María Angélica Larraín
- Departamento de Ciencias de los Alimentos y Tecnología Química, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Sergio Livingstone 1007, Independencia, 8380492, Santiago, Chile
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24
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Ogden R, Linacre A. Wildlife forensic science: A review of genetic geographic origin assignment. Forensic Sci Int Genet 2015; 18:152-9. [DOI: 10.1016/j.fsigen.2015.02.008] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 02/12/2015] [Accepted: 02/24/2015] [Indexed: 10/23/2022]
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25
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Ricardo F, Génio L, Costa Leal M, Albuquerque R, Queiroga H, Rosa R, Calado R. Trace element fingerprinting of cockle (Cerastoderma edule) shells can reveal harvesting location in adjacent areas. Sci Rep 2015; 5:11932. [PMID: 26149418 PMCID: PMC5155621 DOI: 10.1038/srep11932] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 05/27/2015] [Indexed: 01/22/2023] Open
Abstract
Determining seafood geographic origin is critical for controlling its quality and safeguarding the interest of consumers. Here, we use trace element fingerprinting (TEF) of bivalve shells to discriminate the geographic origin of specimens. Barium (Ba), manganese (Mn), magnesium (Mg), strontium (Sr) and lead (Pb) were quantified in cockle shells (Cerastoderma edule) captured with two fishing methods (by hand and by hand-raking) and from five adjacent fishing locations within an estuarine system (Ria de Aveiro, Portugal). Results suggest no differences in TEF of cockle shells captured by hand or by hand-raking, thus confirming that metal rakes do not act as a potential source of metal contamination that could somehow bias TEF results. In contrast, significant differences were recorded among locations for all trace elements analysed. A Canonical Analysis of Principal Coordinates (CAP) revealed that 92% of the samples could be successfully classified according to their fishing location using TEF. We show that TEF can be an accurate, fast and reliable method to determine the geographic origin of bivalves, even among locations separated less than 1 km apart within the same estuarine system. Nonetheless, follow up studies are needed to determine if TEF can reliably discriminate between bivalves originating from different ecosystems.
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Affiliation(s)
- Fernando Ricardo
- Departamento de Biologia & CESAM, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Luciana Génio
- Departamento de Biologia & CESAM, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Miguel Costa Leal
- Departamento de Biologia & CESAM, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Rui Albuquerque
- Departamento de Biologia & CESAM, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Henrique Queiroga
- Departamento de Biologia & CESAM, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Rui Rosa
- MARE – Marine and Environmental Sciences Centre, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Ricardo Calado
- Departamento de Biologia & CESAM, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
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26
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Ricardo F, Pimentel T, Moreira ASP, Rey F, Coimbra MA, Rosário Domingues M, Domingues P, Costa Leal M, Calado R. Potential use of fatty acid profiles of the adductor muscle of cockles (Cerastoderma edule) for traceability of collection site. Sci Rep 2015; 5:11125. [PMID: 26084395 PMCID: PMC4471671 DOI: 10.1038/srep11125] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 05/05/2015] [Indexed: 01/22/2023] Open
Abstract
Geographic traceability of seafood is key for controlling its quality and safeguarding consumers’ interest. The present study assessed if the fatty acid (FA) profile of the adductor muscle (AM) of fresh cockles (Cerastoderma edule) can be used to discriminate the origin of specimens collected in different bivalve capture/production areas legally defined within a coastal lagoon. Results suggest that this biochemical approach holds the potential to trace sampling locations with a spatial resolution <10 Km, even for areas with identical classification for bivalve production. Cockles further away from the inlet, i.e. in areas exposed to a higher saline variation, exhibited lower levels of saturated fatty acids, which are key for stabilizing the bilayer structure of cell membranes, and a higher percentage of polyunsaturated fatty acids, which enhance bilayer fluidity. Results suggest that the structural nature of the lipids present in the AM provides a stable fatty acid signature and holds potential for tracing the origin of bivalves to their capture/production areas.
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Affiliation(s)
- Fernando Ricardo
- Departamento de Biologia &CESAM, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Tânia Pimentel
- Departamento de Biologia &CESAM, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Ana S P Moreira
- QOPNA, Department of Chemistry, University of Aveiro, Campus Santiago, 3810-193 Aveiro, Portugal
| | - Felisa Rey
- Departamento de Biologia &CESAM, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Manuel A Coimbra
- QOPNA, Department of Chemistry, University of Aveiro, Campus Santiago, 3810-193 Aveiro, Portugal
| | - M Rosário Domingues
- QOPNA, Department of Chemistry, University of Aveiro, Campus Santiago, 3810-193 Aveiro, Portugal
| | - Pedro Domingues
- QOPNA, Department of Chemistry, University of Aveiro, Campus Santiago, 3810-193 Aveiro, Portugal
| | - Miguel Costa Leal
- Departamento de Biologia &CESAM, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Ricardo Calado
- Departamento de Biologia &CESAM, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
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