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Kotsanopoulos K, Martsikalis PV, Gkafas GA, Exadactylos A. The use of various statistical methods for authenticity and detection of adulteration in fish and seafood. Crit Rev Food Sci Nutr 2022; 64:1553-1571. [PMID: 36052815 DOI: 10.1080/10408398.2022.2117786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Various methodologies including genetic analyses, morphometrics, proteomics, lipidomics, metabolomics, etc. are now used or being developed to authenticate fish and seafood. Such techniques usually lead to the generation of enormous amounts of data. The analysis and interpretation of this information can be particularly challenging. Statistical techniques are therefore commonly used to assist in analyzing these data, visualizing trends and differences and extracting conclusions. This review article aims at presenting and discussing statistical methods used in studies on fish and seafood authenticity and adulteration, allowing researchers to consider their options based on previous successes/failures but also offering some recommendations about the future of such techniques. Techniques such as PCA, AMOVA and FST statistics, that allow the differentiation of genetic groups, or techniques such as MANOVA that allow large data sets of morphometric characteristics or elemental differences to be analyzed are discussed. Furthermore, methods such as cluster analysis, DFA, CVA, CDA and heatmaps/Circos plots that allow samples to be differentiated based on their geographical origin are also reviewed and their advantages and disadvantages as found in past studies are given. Finally, mathematical simulations and modeling are presented in a detailed review of studies using them, together with their advantages and limitations.
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Affiliation(s)
- Konstantinos Kotsanopoulos
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
| | - Petros V Martsikalis
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
| | - George A Gkafas
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
| | - Athanasios Exadactylos
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
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Lebedeva D, Muñoz G, Lumme J. New Salinity Tolerant Species of Gyrodactylus (Platyhelminthes, Monogenea) on Intertidal and Supratidal Fish Species from the Chilean Coast. Acta Parasitol 2021; 66:1021-1030. [PMID: 33792830 DOI: 10.1007/s11686-021-00347-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 02/05/2021] [Indexed: 11/28/2022]
Abstract
PURPOSE The intertidal and supratidal coastal zone challenges the osmoregulatory capacity of aquatic inhabitants. Four new species of Gyrodactylus ectoparasites on two intertidal fishes from Chile are described based on molecular and morphological analyses. METHODS Monogeneans were found from two fish species, the clingfish Sicyases sanguineus Müller & Troschel, 1843 and the combtooth blenny Scartichthys viridis Valenciennes, 1836. The morphology was described by drawings, and minimal measurements. The parasites were barcoded via the sequencing of the ribosomal DNA over ITS1-5.8S-ITS2. RESULTS The air-breathing clingfish S. sanguineus carried Gyrodactylus amphibius sp. nov., hiding in the ventral sucker formed by the modified pectoral fins of the fish. The intertidal combtooth blenny S. viridis carried three other new species: Gyrodactylus scartichthi sp. nov., Gyrodactylus viridae sp. nov., and Gyrodactylus zietarae sp. nov. CONCLUSION The four new species were all phylogenetically related with the previously described G. chileani Ziętara et al. 2012 on triplefin Helcogrammoides chilensis Cancino, 1960 in the same habitat. Thus, the five Chilean Pacific Gyrodactylus species formed a statistically well-supported (100%) monophyletic clade together with three geographically distant species recorded in Europe. The Chilean Pacific parasites are not related to G. salinae and G. magadiensis, parasites described in extreme osmotic stress environments earlier.
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Affiliation(s)
- Daria Lebedeva
- Institute of Biology, Karelian Research Centre, RAS Petrozavodsk, Pushkinskaya 11, Republic of Karelia, Russia.
| | - Gabriela Muñoz
- Facultad de Ciencias del Mar y de Recursos Naturales, Universidad de Valparaíso, Avenida Borgoño 16344, Viña del Mar, Chile
| | - Jaakko Lumme
- Ecology and Genetics, University of Oulu, POB 3000, 90014, Oulu, Finland
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Complementarity and discriminatory power of genotype and otolith shape in describing the fine-scale population structure of an exploited fish, the common sole of the Eastern English Channel. PLoS One 2020; 15:e0241429. [PMID: 33151981 PMCID: PMC7643961 DOI: 10.1371/journal.pone.0241429] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 10/15/2020] [Indexed: 12/13/2022] Open
Abstract
Marine organisms show population structure at a relatively fine spatial scale, even in open habitats. The tools commonly used to assess subtle patterns of connectivity have diverse levels of resolution and can complement each other to inform on population structure. We assessed and compared the discriminatory power of genetic markers and otolith shape to reveal the population structure on evolutionary and ecological time scales of the common sole (Solea solea), living in the Eastern English Channel (EEC) stock off France and the UK. First, we genotyped fish with Single Nucleotide Polymorphisms to assess population structure at an evolutionary scale. Then, we tested for spatial segregation of the subunits using otolith shape as an integrative tracer of life history. Finally, a supervised machine learning framework was applied to genotypes and otolith phenotypes to probabilistically assign adults to subunits and assess the discriminatory power of each approach. Low but significant genetic differentiation was found among subunits. Moreover, otolith shape appeared to vary spatially, suggesting spatial population structure at fine spatial scale. However, results of the supervised discriminant analyses failed to discriminate among subunits, especially for otolith shape. We suggest that the degree of population segregation may not be strong enough to allow for robust fish assignments. Finally, this study revealed a weak yet existing metapopulation structure of common sole at the fine spatial scale of the EEC based on genotypes and otolith shape, with one subunit being more isolated. Our study argues for the use of complementary tracers to investigate marine population structure.
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Lazic T, Pierri C, Cardone F, Cariani A, Colangelo P, Corriero G, Ferrari A, Marzano M, Messinetti S, Pesole G, Senczuk G, Santamaria M, Tinti F, Gristina M. Genetic structure of the long-snouted seahorse, Hippocampus guttulatus, in the Central–Western Mediterranean Sea. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa074] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
AbstractThe seahorse Hippocampus guttulatus reaches its highest abundance in confined environments, where it has unique biological and ecological traits that suggest significant genetic differentiation among populations. In the present study, we aimed to reveal the genetic structure of this species by analysing eight microsatellite loci and a mitochondrial DNA region (cytochrome b) of eight populations from the Central–Western Mediterranean Sea, including lagoon sites. Levels of genetic diversity, as measured by the total number of alleles, number of private alleles, allelic richness and heterozygosity, ranged from low to moderate. The overall value of inbreeding was high, indicating a deficiency in heterozygotes. The haplotype network had a star-like construction, with the most common haplotype present in all populations. Data from the two molecular markers congruently displayed a similar pattern and revealed low genetic differentiation, notwithstanding predictions based on species traits. The observed genetic structure is probably the result of both historical population demographic events and current gene flow. The investigated lagoons, however, revealed a unique genetic profile, which is especially highlighted by the Taranto population. At this site, the results also showed altered values of observed/expected heterozygosity and allelic richness, a characteristic of marginal populations. Our study suggests that lagoon populations should be managed as distinct genetic units.
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Affiliation(s)
- Tamara Lazic
- Department of Biology, University of Bari, Bari, Italy
| | | | - Frine Cardone
- Department of Biology, University of Bari, Bari, Italy
| | - Alessia Cariani
- Laboratory of Genetics & Genomics of Marine Resources and Environment (GenoDREAM), Department of Biological, Geological and Environmental Sciences (BiGeA), Alma Mater Studiorum – University of Bologna, Ravenna, Italy
| | - Paolo Colangelo
- National Council of Research (CNR), Research Institute on Terrestrial Ecosystems (IRET), Montelibretti (Rome), Italy
| | | | - Alice Ferrari
- Laboratory of Genetics & Genomics of Marine Resources and Environment (GenoDREAM), Department of Biological, Geological and Environmental Sciences (BiGeA), Alma Mater Studiorum – University of Bologna, Ravenna, Italy
| | - Marinella Marzano
- National Council of Research (CNR), Institute of Biomembrane, Bioenergetics and Molecular Biotechnology (IBIOM), Bari, Italy
| | - Silvia Messinetti
- Laboratory of Genetics & Genomics of Marine Resources and Environment (GenoDREAM), Department of Biological, Geological and Environmental Sciences (BiGeA), Alma Mater Studiorum – University of Bologna, Ravenna, Italy
| | - Graziano Pesole
- National Council of Research (CNR), Institute of Biomembrane, Bioenergetics and Molecular Biotechnology (IBIOM), Bari, Italy
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, Bari, Italy
| | - Gabriele Senczuk
- Department of Agricultural, Environmental and Food Sciences, University of Molise, Campobasso, Italy
| | - Monica Santamaria
- National Council of Research (CNR), Institute of Biomembrane, Bioenergetics and Molecular Biotechnology (IBIOM), Bari, Italy
| | - Fausto Tinti
- Laboratory of Genetics & Genomics of Marine Resources and Environment (GenoDREAM), Department of Biological, Geological and Environmental Sciences (BiGeA), Alma Mater Studiorum – University of Bologna, Ravenna, Italy
| | - Michele Gristina
- National Council of Research (CNR), Institute of Anthropic Impacts and Sustainability in Marine Environment (IAS), Palermo, Italy
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Brandl SJ, Tornabene L, Goatley CHR, Casey JM, Morais RA, Côté IM, Baldwin CC, Parravicini V, Schiettekatte NMD, Bellwood DR. Demographic dynamics of the smallest marine vertebrates fuel coral reef ecosystem functioning. Science 2019; 364:1189-1192. [DOI: 10.1126/science.aav3384] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 05/07/2019] [Indexed: 01/06/2023]
Abstract
How coral reefs survive as oases of life in low-productivity oceans has puzzled scientists for centuries. The answer may lie in internal nutrient cycling and/or input from the pelagic zone. Integrating meta-analysis, field data, and population modeling, we show that the ocean’s smallest vertebrates, cryptobenthic reef fishes, promote internal reef fish biomass production through extensive larval supply from the pelagic environment. Specifically, cryptobenthics account for two-thirds of reef fish larvae in the near-reef pelagic zone despite limited adult reproductive outputs. This overwhelming abundance of cryptobenthic larvae fuels reef trophodynamics via rapid growth and extreme mortality, producing almost 60% of consumed reef fish biomass. Although cryptobenthics are often overlooked, their distinctive demographic dynamics may make them a cornerstone of ecosystem functioning on modern coral reefs.
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Medina I, Cooke GM, Ord TJ. Walk, swim or fly? Locomotor mode predicts genetic differentiation in vertebrates. Ecol Lett 2018. [DOI: 10.1111/ele.12930] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Iliana Medina
- Division of Ecology and Evolution Australian National University Building 44 Act on 2601 ACT Australia
- School of BioSciences The University of Melbourne Parkville Vic. Australia
| | - Georgina M. Cooke
- Evolution and Ecology Research Centre School of Biological, Earth and Environmental Sciences University of New South Wales Kensington2052 NSWAustralia
- Australian Museum Research Institute IchthyologyAustralian Museum, 6 College St Sydney NSW2010 Australia
| | - Terry J. Ord
- Evolution and Ecology Research Centre School of Biological, Earth and Environmental Sciences University of New South Wales Kensington2052 NSWAustralia
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Sherwin WB, Chao A, Jost L, Smouse PE. Information Theory Broadens the Spectrum of Molecular Ecology and Evolution. Trends Ecol Evol 2017; 32:948-963. [PMID: 29126564 DOI: 10.1016/j.tree.2017.09.012] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 09/22/2017] [Accepted: 09/26/2017] [Indexed: 01/18/2023]
Abstract
Information or entropy analysis of diversity is used extensively in community ecology, and has recently been exploited for prediction and analysis in molecular ecology and evolution. Information measures belong to a spectrum (or q profile) of measures whose contrasting properties provide a rich summary of diversity, including allelic richness (q=0), Shannon information (q=1), and heterozygosity (q=2). We present the merits of information measures for describing and forecasting molecular variation within and among groups, comparing forecasts with data, and evaluating underlying processes such as dispersal. Importantly, information measures directly link causal processes and divergence outcomes, have straightforward relationship to allele frequency differences (including monotonicity that q=2 lacks), and show additivity across hierarchical layers such as ecology, behaviour, cellular processes, and nongenetic inheritance.
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Affiliation(s)
- W B Sherwin
- Evolution and Ecology Research Centre, School of Biological Earth and Environmental Science, University of New South Wales, Sydney, NSW 2052, Australia; Murdoch University Cetacean Research Unit, Murdoch University, South Road, Murdoch, WA 6150, Australia.
| | - A Chao
- Institute of Statistics, National Tsing Hua University, Hsin-Chu 30043, Taiwan
| | - L Jost
- EcoMinga Foundation, Via a Runtun, Baños, Tungurahua, Ecuador
| | - P E Smouse
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ 08901-8551, USA
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Ord TJ, Summers TC, Noble MM, Fulton CJ. Ecological Release from Aquatic Predation Is Associated with the Emergence of Marine Blenny Fishes onto Land. Am Nat 2017; 189:570-579. [PMID: 28410030 DOI: 10.1086/691155] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
An ecological release from competition or predation is a frequent adaptive explanation for the colonization of novel environments, but empirical data are limited. On the island of Rarotonga, several blenny fish species appear to be in the process of colonizing land. Anecdotal observations have implied that aquatic predation is an important factor in prompting such amphibious fish behavior. We provide evidence supporting this hypothesis by demonstrating that amphibious blennies shift their abundance up and down the shoreline to remain above predatory fishes that periodically move into intertidal areas during high tide. A predation experiment using blenny mimics confirmed a high risk of aquatic predation for blennies, significantly higher than predation experienced on land. These data suggest that predation has played an active role in promoting terrestrial activity in amphibious blennies and provide a rare example of how ecological release from predation could drive the colonization of a novel environment.
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D’Aloia CC, Bogdanowicz SM, Harrison RG, Buston PM. Cryptic genetic diversity and spatial patterns of admixture within Belizean marine reserves. CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0895-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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