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da Fonseca RR, Campos PF, Rey-Iglesia A, Barroso GV, Bergeron LA, Nande M, Tuya F, Abidli S, Pérez M, Riveiro I, Carrera P, Jurado-Ruzafa A, G. Santamaría MT, Faria R, Machado AM, Fonseca MM, Froufe E, C. Castro LF. Population Genomics Reveals the Underlying Structure of the Small Pelagic European Sardine and Suggests Low Connectivity within Macaronesia. Genes (Basel) 2024; 15:170. [PMID: 38397160 PMCID: PMC10888339 DOI: 10.3390/genes15020170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/08/2024] [Accepted: 01/23/2024] [Indexed: 02/25/2024] Open
Abstract
The European sardine (Sardina pilchardus, Walbaum 1792) is indisputably a commercially important species. Previous studies using uneven sampling or a limited number of makers have presented sometimes conflicting evidence of the genetic structure of S. pilchardus populations. Here, we show that whole genome data from 108 individuals from 16 sampling areas across 5000 km of the species' distribution range (from the Eastern Mediterranean to the archipelago of Azores) support at least three genetic clusters. One includes individuals from Azores and Madeira, with evidence of substructure separating these two archipelagos in the Atlantic. Another cluster broadly corresponds to the center of the distribution, including the sampling sites around Iberia, separated by the Almeria-Oran front from the third cluster that includes all of the Mediterranean samples, except those from the Alboran Sea. Individuals from the Canary Islands appear to belong to the Mediterranean cluster. This suggests at least two important geographical barriers to gene flow, even though these do not seem complete, with many individuals from around Iberia and the Mediterranean showing some patterns compatible with admixture with other genetic clusters. Genomic regions corresponding to the top outliers of genetic differentiation are located in areas of low recombination indicative that genetic architecture also has a role in shaping population structure. These regions include genes related to otolith formation, a calcium carbonate structure in the inner ear previously used to distinguish S. pilchardus populations. Our results provide a baseline for further characterization of physical and genetic barriers that divide European sardine populations, and information for transnational stock management of this highly exploited species towards sustainable fisheries.
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Affiliation(s)
- Rute R. da Fonseca
- Center for Global Mountain Biodiversity, GLOBE Institute, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark;
| | - Paula F. Campos
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark;
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4050-123 Porto, Portugal; (M.N.); (R.F.); (A.M.M.); (M.M.F.); (E.F.)
| | - Alba Rey-Iglesia
- Centre for GeoGenetics, Natural History Museum Denmark, University of Copenhagen, Østervoldgade 5-7, 1350 Copenhagen, Denmark;
| | - Gustavo V. Barroso
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA;
| | - Lucie A. Bergeron
- Section for Ecology and Evolution, University of Copenhagen, 2100 Copenhagen, Denmark;
| | - Manuel Nande
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4050-123 Porto, Portugal; (M.N.); (R.F.); (A.M.M.); (M.M.F.); (E.F.)
| | - Fernando Tuya
- Grupo en Biodiversidad y Conservación, IU-ECOAQUA, Universidad de Las Palmas de Gran Canaria, 35017 Las Palmas, Spain;
| | - Sami Abidli
- Laboratory of Environment Bio-Monitoring, Faculty of Sciences of Bizerte, University of Carthage, Bizerte 7021, Tunisia;
| | - Montse Pérez
- Centro Oceanográfico de Vigo, Instituto Español de Oceanografía, IEO-CSIC, 36390 Vigo, Spain; (M.P.); (I.R.); (P.C.)
| | - Isabel Riveiro
- Centro Oceanográfico de Vigo, Instituto Español de Oceanografía, IEO-CSIC, 36390 Vigo, Spain; (M.P.); (I.R.); (P.C.)
| | - Pablo Carrera
- Centro Oceanográfico de Vigo, Instituto Español de Oceanografía, IEO-CSIC, 36390 Vigo, Spain; (M.P.); (I.R.); (P.C.)
| | - Alba Jurado-Ruzafa
- Centro Oceanográfico de Canarias, Instituto Español de Oceanografía, IEO-CSIC, 38180 Santa Cruz de Tenerife, Spain; (A.J.-R.); (M.T.G.S.)
| | - M. Teresa G. Santamaría
- Centro Oceanográfico de Canarias, Instituto Español de Oceanografía, IEO-CSIC, 38180 Santa Cruz de Tenerife, Spain; (A.J.-R.); (M.T.G.S.)
| | - Rui Faria
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4050-123 Porto, Portugal; (M.N.); (R.F.); (A.M.M.); (M.M.F.); (E.F.)
| | - André M. Machado
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4050-123 Porto, Portugal; (M.N.); (R.F.); (A.M.M.); (M.M.F.); (E.F.)
| | - Miguel M. Fonseca
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4050-123 Porto, Portugal; (M.N.); (R.F.); (A.M.M.); (M.M.F.); (E.F.)
| | - Elsa Froufe
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4050-123 Porto, Portugal; (M.N.); (R.F.); (A.M.M.); (M.M.F.); (E.F.)
| | - L. Filipe C. Castro
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4050-123 Porto, Portugal; (M.N.); (R.F.); (A.M.M.); (M.M.F.); (E.F.)
- Department of Biology, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
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Valente S, Moro S, Di Lorenzo M, Milisenda G, Maiorano L, Colloca F. Mediterranean fish communities are struggling to adapt to global warming. Evidence from the western coast of Italy. MARINE ENVIRONMENTAL RESEARCH 2023; 191:106176. [PMID: 37716279 DOI: 10.1016/j.marenvres.2023.106176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/08/2023] [Accepted: 09/11/2023] [Indexed: 09/18/2023]
Abstract
Climate change has significant impacts on marine ecosystems, resulting in disruptions in biological interactions, shifts in community composition, and changes in the physiology of fish and other marine organisms. In this study conducted in the central Mediterranean Sea, the mean temperature of the catch (MTC) was employed as an indicator to investigate the climatological factors influencing the fish community. The MTC, which utilizes species-preferred temperatures, was calculated using bottom temperature (BT) data weighted against scientific catches. The estimated MTC increasing rates were 0.01 °C year-1 for the entire community, 0.017 °C year-1 for the shelf break, and 0.004 °C year-1 for the continental slope assemblage. We found that MTC is increasing at a lower rate compared to BT, suggesting a progressive under-adaptation of the fish community that seems not fully able to keep up with the ongoing pace of warming. The study identified sea surface temperature and bottom temperature as key drivers of changes in fish community composition. Notably, the fish community composition exhibited drastic changes over the studied period, and we suggest that the MTC can be a useful index to monitor such changes within the context of the EU's climate change adaptation strategy.
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Affiliation(s)
- Salvatore Valente
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, via Po' 25c, 00189, Rome, Italy; Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, Rome, Italy.
| | - Stefano Moro
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, via Po' 25c, 00189, Rome, Italy
| | - Manfredi Di Lorenzo
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Lungomare Cristoforo Colombo, I-90149, Palermo, Italy
| | - Giacomo Milisenda
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Lungomare Cristoforo Colombo, I-90149, Palermo, Italy
| | - Luigi Maiorano
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, Rome, Italy
| | - Francesco Colloca
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, via Po' 25c, 00189, Rome, Italy
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3
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Çetin C, Furman A, Kalkan E, Bilgin R. Mitonuclear genetic patterns of divergence in the marbled crab, Pachygrapsus marmoratus (Fabricius, 1787) along the Turkish seas. PLoS One 2022; 17:e0266506. [PMID: 35381029 PMCID: PMC8982882 DOI: 10.1371/journal.pone.0266506] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 03/22/2022] [Indexed: 12/03/2022] Open
Abstract
Biogeographical transition zones present good opportunities for studying the effect of the past ice ages on genetic structure of species because secondary contact zones of post-glacial lineages can be formed. In this study, we investigated the population genetic structure of the marbled rock crab, Pachygrapsus marmoratus along the coasts of Turkey. We genotyped 334 individuals from the Black Sea, the Turkish Straits System (TSS), the Aegean, and the Eastern Mediterranean basins. In order to reveal its evolutionary history and its population connectivity, we used mitochondrial CO1 region and five microsatellite loci. CO1 analyzes also included 610 additional samples from Genbank, which covered most of its distribution range. Both microsatellites and mtDNA showed decreased diversity in sampling sites of the TSS and the Black Sea as compared to those along the Aegean and the Levantine coasts. There is an especially strong geographical pattern in distributions of haplotypes in mtDNA, most probably as a result of genetic drift in the Black Sea and the Sea of Marmara (SoM). Microsatellite data analyses revealed two genetically distinct clusters of P. marmoratus (clusters C and M). While individuals belonging to cluster C are present in all the sampling locations, those belonging to cluster M are only detected along the Mediterranean coasts including the Aegean and the Levantine basins. These clusters shared similar haplotypes in the Mediterranean. Haplotypes of two sympatric clusters could be similar due to incomplete lineage sorting of ancestral polymorphisms. In order to retrieve the complex demographic history and to investigate evolutionary processes resulting in sympatric clusters in the Aegean Sea and the Levantine basin, mitochondrial markers with faster mutation rates than CO1 and/or SNP data will be useful.
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Affiliation(s)
- Cansu Çetin
- Institute of Environmental Sciences, Boğaziçi University, Bebek, Istanbul, Turkey
- Institute of Integrative Biology (IBZ), ETH Zürich, Zürich, Switzerland
- Department of Aquatic Ecology, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- * E-mail:
| | - Andrzej Furman
- Institute of Environmental Sciences, Boğaziçi University, Bebek, Istanbul, Turkey
| | - Evrim Kalkan
- Institute of Marine Sciences, Middle East Technical University, Erdemli-Mersin, Turkey
| | - Raşit Bilgin
- Institute of Environmental Sciences, Boğaziçi University, Bebek, Istanbul, Turkey
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Francisco SM, Castilho R, Lima CS, Almada F, Rodrigues F, Šanda R, Vukić J, Pappalardo AM, Ferrito V, Robalo JI. Genetic hypervariability of a Northeastern Atlantic venomous rockfish. PeerJ 2021; 9:e11730. [PMID: 34306828 PMCID: PMC8280884 DOI: 10.7717/peerj.11730] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 06/15/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Understanding the interplay between climate and current and historical factors shaping genetic diversity is pivotal to infer changes in marine species range and communities' composition. A phylogeographical break between the Atlantic and the Mediterranean has been documented for several marine organisms, translating into limited dispersal between the two basins. METHODS In this study, we screened the intraspecific diversity of 150 individuals of the Madeira rockfish (Scorpaena maderensis) across its distributional range (seven sampling locations in the Atlantic and Mediterranean basins) using the mitochondrial control region and the nuclear S7 first intron. RESULTS The present work is the most comprehensive study done for this species, yielding no genetic structure across sampled locations and no detectable Atlantic-Mediterranean break in connectivity. Our results reveal deep and hyper-diverse bush-like genealogies with large numbers of singletons and very few shared haplotypes. The genetic hyper-diversity found for the Madeira rockfish is relatively uncommon in rocky coastal species, whose dispersal capability is limited by local oceanographic patterns. The effect of climate warming on the distribution of the species is discussed.
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Affiliation(s)
- Sara M. Francisco
- MARE—Marine and Environmental Sciences Centre, ISPA Instituto Universitário de Ciências Psicológicas, Sociais e da Vida, Lisbon, Portugal
| | - Rita Castilho
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, Faro, Portugal
| | - Cristina S. Lima
- MARE—Marine and Environmental Sciences Centre, ISPA Instituto Universitário de Ciências Psicológicas, Sociais e da Vida, Lisbon, Portugal
| | - Frederico Almada
- MARE—Marine and Environmental Sciences Centre, ISPA Instituto Universitário de Ciências Psicológicas, Sociais e da Vida, Lisbon, Portugal
| | - Francisca Rodrigues
- MARE—Marine and Environmental Sciences Centre, ISPA Instituto Universitário de Ciências Psicológicas, Sociais e da Vida, Lisbon, Portugal
| | - Radek Šanda
- Department of Zoology, National Museum, Prague, Czeck Republic
| | - Jasna Vukić
- Faculty of Science, Department of Ecology, Charles University, Prague, Czech Republic
| | - Anna Maria Pappalardo
- Department of Biological, Geological and Environmental Sciences, Section of Animal Biology Biology ‘‘Marcello La Greca’’, University of Catania, Catania, Italy
| | - Venera Ferrito
- Department of Biological, Geological and Environmental Sciences, Section of Animal Biology Biology ‘‘Marcello La Greca’’, University of Catania, Catania, Italy
| | - Joana I. Robalo
- MARE—Marine and Environmental Sciences Centre, ISPA Instituto Universitário de Ciências Psicológicas, Sociais e da Vida, Lisbon, Portugal
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Torri M, Pappalardo AM, Ferrito V, Giannì S, Armeri GM, Patti C, Mangiaracina F, Biondo G, Di Natale M, Musco M, Masullo T, Bennici C, Russo S, Nicosia A, Tagliavia M, Mazzola A, Patti B, Cuttitta A. Signals from the deep-sea: Genetic structure, morphometric analysis, and ecological implications of Cyclothone braueri (Pisces, Gonostomatidae) early life stages in the Central Mediterranean Sea. MARINE ENVIRONMENTAL RESEARCH 2021; 169:105379. [PMID: 34119918 DOI: 10.1016/j.marenvres.2021.105379] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 04/30/2021] [Accepted: 05/21/2021] [Indexed: 06/12/2023]
Abstract
Cyclothone braueri (Stomiiformes, Gonostomatidae) is a widely distributed fish inhabiting the mesopelagic zone of marine tropical and temperate waters. Constituting one of the largest biomasses of the ocean, C. braueri is a key element in most of the ecological processes occurring in the twilight layer. We focused on the ecological processes linked to early life stages in relation to marine pelagic environmental drivers (temperature, salinity, food availability and geostrophic currents) considering different regions of the Central Mediterranean Sea. A multivariate morphometric analysis was carried out using six parameters with the aim of discerning different larval morphotypes, while a fragment of 367 bp representing the 12S ribosomal RNA gene was used to perform molecular analyses aimed at determining the intraspecific genetic variability. Analysis highlighted two geographically distinct morphotypes not genetically discernible and related to the different nutritional conditions due to spatial heterogeneities in terms of temperature and food availability. The body depth (BD) emerged as an appropriate morphometric parameter to detect the larval condition in this species. Molecular analysis highlighted a moderate genetic divergence in the fish population, showing the recurrence of two phylogroups not geographically separated.
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Affiliation(s)
- Marco Torri
- National Research Council of Italy, Institute for the Anthropic Impacts and Sustainability in Marine Environment (IAS-CNR), Detached Unit of Capo Granitola, via del mare, 3 Campobello di Mazara, loc. Torretta Granitola, 91021, Trapani, Italy
| | - Anna Maria Pappalardo
- University of Catania, Department of Biological, Geological and Environmental Sciences, via Androne 81, 95124, Catania (CT), Italy.
| | - Venera Ferrito
- University of Catania, Department of Biological, Geological and Environmental Sciences, via Androne 81, 95124, Catania (CT), Italy
| | - Salvatore Giannì
- National Research Council of Italy, Institute for the Anthropic Impacts and Sustainability in Marine Environment (IAS-CNR), Detached Unit of Capo Granitola, via del mare, 3 Campobello di Mazara, loc. Torretta Granitola, 91021, Trapani, Italy; University of Palermo, Department of Earth and Marine Sciences, via Archirafi 22, 90123, Palermo (PA), Italy
| | - Grazia Maria Armeri
- National Research Council of Italy, Institute for the Anthropic Impacts and Sustainability in Marine Environment (IAS-CNR), Detached Unit of Capo Granitola, via del mare, 3 Campobello di Mazara, loc. Torretta Granitola, 91021, Trapani, Italy
| | - Carlo Patti
- National Research Council of Italy, Institute for the Anthropic Impacts and Sustainability in Marine Environment (IAS-CNR), Detached Unit of Palermo, c/o Complesso monumentale ex-Roosevelt, Lungomare Cristoforo Colombo 4521, Località Addaura, 90149, Palermo, Italy
| | - Francesca Mangiaracina
- National Research Council of Italy, Institute for the Anthropic Impacts and Sustainability in Marine Environment (IAS-CNR), Detached Unit of Capo Granitola, via del mare, 3 Campobello di Mazara, loc. Torretta Granitola, 91021, Trapani, Italy
| | - Girolama Biondo
- National Research Council of Italy, Institute for the Anthropic Impacts and Sustainability in Marine Environment (IAS-CNR), Detached Unit of Capo Granitola, via del mare, 3 Campobello di Mazara, loc. Torretta Granitola, 91021, Trapani, Italy
| | - Marilena Di Natale
- University of Palermo, Department of Earth and Marine Sciences, via Archirafi 22, 90123, Palermo (PA), Italy; National Research Council of Italy, Institute for Studies on the Mediterranean (ISMed-CNR), Detached Unit of Palermo, via Filippo Parlatore 95, 90145, Palermo, Italy
| | - Marianna Musco
- National Research Council of Italy, Institute for Studies on the Mediterranean (ISMed-CNR), Detached Unit of Palermo, via Filippo Parlatore 95, 90145, Palermo, Italy
| | - Tiziana Masullo
- National Research Council of Italy, Institute for Studies on the Mediterranean (ISMed-CNR), Detached Unit of Palermo, via Filippo Parlatore 95, 90145, Palermo, Italy
| | - Carmelo Bennici
- National Research Council of Italy, Institute for Studies on the Mediterranean (ISMed-CNR), Detached Unit of Palermo, via Filippo Parlatore 95, 90145, Palermo, Italy
| | - Stefania Russo
- University of Palermo, Department of Earth and Marine Sciences, via Archirafi 22, 90123, Palermo (PA), Italy; National Research Council of Italy, Institute for Studies on the Mediterranean (ISMed-CNR), Detached Unit of Palermo, via Filippo Parlatore 95, 90145, Palermo, Italy
| | - Aldo Nicosia
- National Research Council of Italy, Institute for Biomedical Research and Innovation (IRIB-CNR), Via Ugo La Malfa, 153, 90146, Palermo, Italy
| | - Marcello Tagliavia
- National Research Council of Italy, Institute for Biomedical Research and Innovation (IRIB-CNR), Via Ugo La Malfa, 153, 90146, Palermo, Italy
| | - Antonio Mazzola
- University of Palermo, Department of Earth and Marine Sciences, via Archirafi 22, 90123, Palermo (PA), Italy
| | - Bernardo Patti
- National Research Council of Italy, Institute for the Anthropic Impacts and Sustainability in Marine Environment (IAS-CNR), Detached Unit of Palermo, c/o Complesso monumentale ex-Roosevelt, Lungomare Cristoforo Colombo 4521, Località Addaura, 90149, Palermo, Italy
| | - Angela Cuttitta
- National Research Council of Italy, Institute for Studies on the Mediterranean (ISMed-CNR), Detached Unit of Palermo, via Filippo Parlatore 95, 90145, Palermo, Italy
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Boissin E, Neglia V, Baksay S, Micu D, Bat L, Topaloglu B, Todorova V, Panayotova M, Kruschel C, Milchakova N, Voutsinas E, Beqiraj S, Nasto I, Aglieri G, Taviani M, Zane L, Planes S. Chaotic genetic structure and past demographic expansion of the invasive gastropod Tritia neritea in its native range, the Mediterranean Sea. Sci Rep 2020; 10:21624. [PMID: 33303767 PMCID: PMC7730386 DOI: 10.1038/s41598-020-77742-3] [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: 04/11/2019] [Accepted: 11/16/2020] [Indexed: 11/21/2022] Open
Abstract
To better predict population evolution of invasive species in introduced areas it is critical to identify and understand the mechanisms driving genetic diversity and structure in their native range. Here, we combined analyses of the mitochondrial COI gene and 11 microsatellite markers to investigate both past demographic history and contemporaneous genetic structure in the native area of the gastropod Tritia neritea, using Bayesian skyline plots (BSP), multivariate analyses and Bayesian clustering. The BSP framework revealed population expansions, dated after the last glacial maximum. The haplotype network revealed a strong geographic clustering. Multivariate analyses and Bayesian clustering highlighted the strong genetic structure at all scales, between the Black Sea and the Adriatic Sea, but also within basins. Within basins, a random pattern of genetic patchiness was observed, suggesting a superimposition of processes involving natural biological effects (no larval phase and thus limited larval dispersal) and putative anthropogenic transport of specimens. Contrary to the introduced area, no isolation-by-distance patterns were recovered in the Mediterranean or the Black Seas, highlighting different mechanisms at play on both native and introduced areas, triggering unknown consequences for species’ evolutionary trajectories. These results of Tritia neritea populations on its native range highlight a mixture of ancient and recent processes, with the effects of paleoclimates and life history traits likely tangled with the effects of human-mediated dispersal.
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Affiliation(s)
- Emilie Boissin
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence « CORAIL », Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France.
| | - Valentina Neglia
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence « CORAIL », Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France
| | - Sandra Baksay
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence « CORAIL », Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France.,Laboratoire Evolution & Diversite Biologique, University TOULOUSE III - Paul Sabatier, 118 route de Narbonne, 31062, Toulouse Cedex 09, France
| | - Dragos Micu
- Romanian Waters National Authority, 127 Mircea cel Batran Blvd., 900592, Constanţa, Romania
| | - Levent Bat
- Department of Hydrobiology, Sinop University Faculty of Fisheries, 57000, Sinop, Turkey
| | - Bulent Topaloglu
- Faculty of Aquatic Sciences, Istanbul University, Ordu St No: 8, 34134, Istanbul, Turkey
| | - Valentina Todorova
- Institute of Oceanology-BAS (IO-BAS), P.O. Box 152, 9000, Varna, Bulgaria
| | - Marina Panayotova
- Institute of Oceanology-BAS (IO-BAS), P.O. Box 152, 9000, Varna, Bulgaria
| | - Claudia Kruschel
- University of Zadar, Ul. Mihovila Pavlinovića, 23000, Zadar, Croatia
| | - Nataliya Milchakova
- Institute of Biology of the Southern Seas, 2 Nakhimov Ave., Sevastopol, Russia, 299011
| | - Emanuela Voutsinas
- Institute of Oceanography, Hellenic Centre for Marine Research, P.O. Box 712, 19013, Anavyssos, Greece
| | - Sajmir Beqiraj
- Faculty of Natural Sciences, Department of Biology, University of Tirana, Bulevardi "Zogu I Parë", 25/1, 1001, Tiranë, Albania
| | - Ina Nasto
- Department of Biology, Faculty of Technical Sciences, Vlora University, 9401, Vlora, Albania
| | - Giorgio Aglieri
- Department of Earth and Marine Sciences (DiSTeM), University of Palermo, via Archirafi 28, 90123, Palermo, Italy.,Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa), Piazzale Flaminio 9, 00196, Rome, Italy
| | - Marco Taviani
- Institute of Marine Sciences (ISMAR), CNR, via Gobetti 101, 40129, Bologna, Italy.,Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy.,Department of Biology, Woods Hole Oceanographic Institution, 266 Woods Hole Road, Woods Hole, MA, 02543, USA
| | - Lorenzo Zane
- Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa), Piazzale Flaminio 9, 00196, Rome, Italy.,Dipartimento di Biologia, Università di Padova, via U. Bassi/58B, 35121, Padua, Italy
| | - Serge Planes
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence « CORAIL », Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France
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Population Genetic Diversity of Two Marine Gobies (Gobiiformes: Gobiidae) from the North-Eastern Atlantic and the Mediterranean Sea. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2020. [DOI: 10.3390/jmse8100792] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Gobies (Gobiiformes: Gobiidae) are the most species-rich family of fishes in general, and the most abundant fish group in the European seas. Nonetheless, our knowledge on many aspects of their biology, including the population genetic diversity, is poor. Although barriers to gene flow are less apparent in the marine environment, the ocean is not a continuous habitat, as has been shown by studies on population genetics of various marine biota. For the first time, European marine goby species which cannot be collected by common fishery techniques were studied. The population genetic structure of two epibenthic species, Gobius geniporus and Gobius cruentatus, from seven localities across their distribution ranges was assessed, using one mitochondrial (cytochrome b) and one nuclear gene (first intron of ribosomal protein gene S7). Our results showed that there is a great diversity of haplotypes of mitochondrial gene cytochrome b in both species at all localities. Global fixation indices (FST) indicated a great differentiation of populations in both studied gobies. Our results did not show a geographic subdivision to individual populations. Instead, the data correspond with the model of migration which allow divergence and recurrent migration from the ancestral population. The estimated migration routes coincide with the main currents in the studied area. This matches well the biology of the studied species, with adults exhibiting only short-distance movements and planktonic larval stages.
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8
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Giusti A, Tinacci L, Sotelo CG, Acutis PL, Ielasi N, Armani A. Authentication of ready-to-eat anchovy products sold on the Italian market by BLAST analysis of a highly informative cytochrome b gene fragment. Food Control 2019. [DOI: 10.1016/j.foodcont.2018.10.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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9
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Ferrari A, Tinti F, Bertucci Maresca V, Velonà A, Cannas R, Thasitis I, Costa FO, Follesa MC, Golani D, Hemida F, Helyar SJ, Mancusi C, Mulas A, Serena F, Sion L, Stagioni M, Cariani A. Natural history and molecular evolution of demersal Mediterranean sharks and skates inferred by comparative phylogeographic and demographic analyses. PeerJ 2018; 6:e5560. [PMID: 30245927 PMCID: PMC6149499 DOI: 10.7717/peerj.5560] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 08/09/2018] [Indexed: 11/22/2022] Open
Abstract
Background The unique and complex paleoclimatic and paleogeographic events which affected the Mediterranean Sea since late Miocene deeply influenced the distribution and evolution of marine organisms and shaped their genetic structure. Following the Messinian salinity crisis and the sea-level fluctuations during the Pleistocene, several Mediterranean marine species developed deep genetic differentiation, and some underwent rapid radiation. Here, we consider two of the most prioritized groups for conservation in the light of their evolutionary history: sharks and rays (elasmobranchs). This paper deals with a comparative multispecies analysis of phylogeographic structure and historical demography in two pairs of sympatric, phylogenetically- and ecologically-related elasmobranchs, two scyliorhinid catsharks (Galeus melastomus, Scyliorhinus canicula) and two rajid skates (Raja clavata, Raja miraletus). Sampling and experimental analyses were designed to primarily test if the Sicilian Channel can be considered as effective eco-physiological barrier for Mediterranean demersal sympatric elasmobranchs. Methods The phylogeography and the historical demography of target species were inferred by analysing the nucleotide variation of three mitochondrial DNA markers (i.e., partial sequence of COI, NADH2 and CR) obtained from a total of 248 individuals sampled in the Western and Eastern Mediterranean Sea as well as in the adjacent northeastern Atlantic Ocean. Phylogeographic analysis was performed by haplotype networking and testing spatial genetic differentiation of samples (i.e., analysis of molecular variance and of principal components). Demographic history of Mediterranean populations was reconstructed using mismatch distribution and Bayesian Skyline Plot analyses. Results No spatial genetic differentiation was identified in either catshark species, while phylogeographic structure of lineages was identified in both skates, with R. miraletus more structured than R. clavata. However, such structuring of skate lineages was not consistent with the separation between Western and Eastern Mediterranean. Sudden demographic expansions occurred synchronously during the upper Pleistocene (40,000–60,000 years ago) in both skates and G. melastomus, likely related to optimal environmental conditions. In contrast, S. canicula experienced a slow and constant increase in population size over the last 350,000 years. Discussion The comparative analysis of phylogeographic and historical demographic patterns for the Mediterranean populations of these elasmobranchs reveals that historical phylogeographic breaks have not had a large impact on their microevolution. We hypothesize that interactions between environmental and ecological/physiological traits may have been the driving force in the microevolution of these demersal elasmobranch species in the Mediterranean rather than oceanographic barriers.
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Affiliation(s)
- Alice Ferrari
- Department of Biological, Geological & Environmental Sciences (BiGeA), University of Bologna, Bologna, Italy
| | - Fausto Tinti
- Department of Biological, Geological & Environmental Sciences (BiGeA), University of Bologna, Bologna, Italy
| | - Victoria Bertucci Maresca
- Department of Biological, Geological & Environmental Sciences (BiGeA), University of Bologna, Bologna, Italy.,Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Alessandro Velonà
- Department of Biological, Geological & Environmental Sciences (BiGeA), University of Bologna, Bologna, Italy
| | - Rita Cannas
- Department of Life Sciences and Environment, University of Cagliari, Cagliari, Italy
| | - Ioannis Thasitis
- Department of Fisheries and Marine Research, Ministry of Agriculture, Natural Resources and Environment, Nicosia, Cyprus
| | - Filipe Oliveira Costa
- Centre of Molecular and Environmental Biology (CBMA), University of Minho, Braga, Portugal
| | | | - Daniel Golani
- Department of Evolution, Systematics and Ecology, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Farid Hemida
- Ecole Nationale Supérieure des Sciences de la Mer et de Aménagement du Littoral (ENSSMAL), Algiers, Algeria
| | - Sarah J Helyar
- School of Biological Sciences, Institute for Global Food Security, The Queen's University Belfast, Belfast, United Kingdom
| | - Cecilia Mancusi
- Regional Agency for Environmental Protection-Toscana (ARPAT), Livorno, Italy
| | - Antonello Mulas
- Department of Life Sciences and Environment, University of Cagliari, Cagliari, Italy
| | - Fabrizio Serena
- Institute Coastal Marine Environment, Italian National Research Council (CNR-IAMC), Mazara del Vallo, Italy
| | - Letizia Sion
- Department of Biology, University of Bari, Bari, Italy
| | - Marco Stagioni
- Department of Biological, Geological & Environmental Sciences (BiGeA), University of Bologna, Bologna, Italy
| | - Alessia Cariani
- Department of Biological, Geological & Environmental Sciences (BiGeA), University of Bologna, Bologna, Italy
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10
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Maisnam M, Gupta A, Lal KK, Singh RK, Mohindra V. Genetic divergence in natural and farm populations of Pengba fish, Osteobrama belangeri (Valenciennes, 1844), an endemic fish of North-East India derived from mtDNA ATPase 6/8 gene. Mitochondrial DNA B Resour 2017; 2:658-661. [PMID: 33473937 PMCID: PMC7799695 DOI: 10.1080/23802359.2017.1372700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Pengba fish, Osteobrama belangeri is a freshwater inhabitant, highly endemic, threatened and economically important minor carp for its food value. In the present investigation, population structure of O. belangeri was examined using mitochondrial ATPase 6/8 gene from geographically distinct locations along the Indo-Burma biodiversity hotspot. A total of 80 individuals were collected belonging to natural and farm populations. The hierarchical analysis of molecular variance and conventional Fst values (0.825 in ATPase 6/8, p < .05) indicated significant genetic structure among populations. The result showed that ATPase 6/8 genes are potential marker in determining the genetic divergence between natural and farm populations of O. belangeri from North-East India.
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Affiliation(s)
| | - Arti Gupta
- ICAR-National Bureau of Fish Genetic Resources, Lucknow, India
| | - Kuldeep K. Lal
- ICAR-National Bureau of Fish Genetic Resources, Lucknow, India
| | - Rajeev K. Singh
- ICAR-National Bureau of Fish Genetic Resources, Lucknow, India
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11
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Nakazawa T, Liu SYV, Sakai Y, Araki KS, Tsai CH, Okuda N. Spatial genetic structure and body size divergence in endangered Gymnogobius isaza in ancient Lake Biwa. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:756-764. [PMID: 28745537 DOI: 10.1080/24701394.2017.1357708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Gymnogobius isaza is a freshwater goby endemic to ancient Lake Biwa, the largest lake in Japan. The species is now listed as 'Critically Endangered' in the Red Data Book of Japan. Nevertheless, it remains subject to fishing without any specific management strategies. Previous studies using mitochondrial DNA markers showed that this fish species has two cryptic lineages. However, little is known about spatial genetic structure and ecological differences across the broad lakescape. In this study, we collected fish samples at nine locations along the lakeshore during the breeding season and tested for the presence of spatial heterogeneity in the lineage's composition while measuring body size as the most fundamental biological trait. The results showed that the major lineage dominated all the sampling locations whereas the minor lineage consisted of only 11% (16/143) of samples. Furthermore, although their spatial distributions overlapped (i.e. the two lineages may be well mixed), we found it possible that the minor lineage may have a potentially narrower distribution than the major lineage. In addition, we found that the two lineages differ in body size; specifically, the minor lineage is smaller in size. From the viewpoint of genetic diversity conservation and sustainable resource use, this fish should be managed as two genetic stocks and spatial and/or body size-based fishery management is desirable, with particular attention to the minor (smaller sized) lineage.
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Affiliation(s)
- Takefumi Nakazawa
- a Department of Life Sciences , National Cheng Kung University , Tainan , Taiwan
| | - Shang-Yin Vanson Liu
- b Department of Marine Biotechnology and Resources , National Sun Yat-Sen University , Kaohsiung , Taiwan
| | - Yoichiro Sakai
- c Lake Biwa Environmental Research Institute , Shiga , Japan
| | - Kiwako S Araki
- d Faculty of Life Sciences , Ristumeikan University , Shiga , Japan
| | - Cheng-Han Tsai
- e Australian Institute of Marine Science, School of Marine and Tropical Biology , James Cook University , Australia
| | - Noboru Okuda
- f Research Institute for Humanity and Nature , Kyoto , Japan
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12
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Catanese G, Watteaux R, Montes I, Barra M, Rumolo P, Borme D, Buongiorno Nardelli B, Botte V, Mazzocchi MG, Genovese S, Di Capua I, Iriondo M, Estonba A, Ruggeri P, Tirelli V, Caputo-Barucchi V, Basilone G, Bonanno A, Iudicone D, Procaccini G. Insights on the drivers of genetic divergence in the European anchovy. Sci Rep 2017. [PMID: 28646131 PMCID: PMC5482869 DOI: 10.1038/s41598-017-03926-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Anchovies represent the largest world's marine fish catches and the current threats on their populations impose a sustainable exploitment based on sound scientific information. In the European anchovy (Engraulis encrasicolus), the existence of several populations has been proposed but a global view is missing. Using a multidisciplinary approach, here we assessed the divergence among different ecotypes and its possible causes. SNPs have revealed two functionally distinct ecotypes overlapping in the Central Mediterranean, with one ecotype confined near the river estuaries. The same SNPs outliers also segregated two distinct populations in the near Atlantic, despite their large spatial distance. In addition, while most studies suggested that adaptation to low salinity is key to divergence, here we show that the offshore ecotype has higher environmental tolerance and an opportunistic feeding behaviour, as assessed by the study of environmental conditions, anchovy diet and trophic levels, and passive egg dispersal. These results provide insights into the anchovy evolutionary history, stressing the importance of behaviour in shaping ecotypes.
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Affiliation(s)
- Gaetano Catanese
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy.,Laboratorio de Investigaciones Marinas y Acuicultura (LIMIA) Govern de les Illes Balears, Av. Gabriel Roca 69, 07158, Port d'Andratx - Mallorca, Spain
| | - Romain Watteaux
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy
| | - Iratxe Montes
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Sarriena auzoa z/g, Leioa - Bizkaia, Spain
| | - Marco Barra
- Institute for Coastal and Marine Environment (IAMC), Consiglio Nazionale delle Ricerche (CNR), Detached Units of Capo Granitola (TP) and Naples, Napoli, Italy
| | - Paola Rumolo
- Institute for Coastal and Marine Environment (IAMC), Consiglio Nazionale delle Ricerche (CNR), Detached Units of Capo Granitola (TP) and Naples, Napoli, Italy
| | - Diego Borme
- Department of Oceanography, Istituto Nazionale di Oceanografia e di Geofisica Sperimentale (OGS), Via A. Piccard 54, 34151, Trieste, Italy
| | - Bruno Buongiorno Nardelli
- Institute for Coastal and Marine Environment (IAMC), Consiglio Nazionale delle Ricerche (CNR), Detached Units of Capo Granitola (TP) and Naples, Napoli, Italy
| | - Vincenzo Botte
- Institute for Coastal and Marine Environment (IAMC), Consiglio Nazionale delle Ricerche (CNR), Detached Units of Capo Granitola (TP) and Naples, Napoli, Italy
| | - Maria Grazia Mazzocchi
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy
| | - Simona Genovese
- Institute for Coastal and Marine Environment (IAMC), Consiglio Nazionale delle Ricerche (CNR), Detached Units of Capo Granitola (TP) and Naples, Napoli, Italy
| | - Iole Di Capua
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy
| | - Mikel Iriondo
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Sarriena auzoa z/g, Leioa - Bizkaia, Spain
| | - Andone Estonba
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Sarriena auzoa z/g, Leioa - Bizkaia, Spain
| | - Paolo Ruggeri
- Dipartimento di Scienze della Vita e dell'Ambiente (DiSVA), Università Politecnica delle Marche, via Brecce Bianche, 60131, Ancona, Italy.,University of Miami, RSMAS, 4600 Rickenbacker Causeway, 33149, Miami, Florida, USA
| | - Valentina Tirelli
- Department of Oceanography, Istituto Nazionale di Oceanografia e di Geofisica Sperimentale (OGS), Via A. Piccard 54, 34151, Trieste, Italy
| | - Vincenzo Caputo-Barucchi
- Dipartimento di Scienze della Vita e dell'Ambiente (DiSVA), Università Politecnica delle Marche, via Brecce Bianche, 60131, Ancona, Italy
| | - Gualtiero Basilone
- Institute for Coastal and Marine Environment (IAMC), Consiglio Nazionale delle Ricerche (CNR), Detached Units of Capo Granitola (TP) and Naples, Napoli, Italy
| | - Angelo Bonanno
- Institute for Coastal and Marine Environment (IAMC), Consiglio Nazionale delle Ricerche (CNR), Detached Units of Capo Granitola (TP) and Naples, Napoli, Italy.
| | - Daniele Iudicone
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy.
| | - Gabriele Procaccini
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy.
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13
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Silva G, Cunha RL, Ramos A, Castilho R. Wandering behaviour prevents inter and intra oceanic speciation in a coastal pelagic fish. Sci Rep 2017; 7:2893. [PMID: 28588244 PMCID: PMC5460251 DOI: 10.1038/s41598-017-02945-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 04/26/2017] [Indexed: 11/25/2022] Open
Abstract
Small pelagic fishes have the ability to disperse over long distances and may present complex evolutionary histories. Here, Old World Anchovies (OWA) were used as a model system to understand genetic patterns and connectivity of fish between the Atlantic and Pacific basins. We surveyed 16 locations worldwide using mtDNA and 8 microsatellite loci for genetic parameters, and mtDNA (cyt b; 16S) and nuclear (RAG1; RAG2) regions for dating major lineage-splitting events within Engraulidae family. The OWA genetic divergences (0-0.4%) are compatible with intra-specific divergence, showing evidence of both ancient and contemporary admixture between the Pacific and Atlantic populations, enhanced by high asymmetrical migration from the Pacific to the Atlantic. The estimated divergence between Atlantic and Pacific anchovies (0.67 [0.53-0.80] Ma) matches a severe drop of sea temperature during the Günz glacial stage of the Pleistocene. Our results support an alternative evolutionary scenario for the OWA, suggesting a coastal migration along south Asia, Middle East and eastern Africa continental platforms, followed by the colonization of the Atlantic via the Cape of the Good Hope.
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Affiliation(s)
- Gonçalo Silva
- Centre of Marine Sciences, CCMAR, University of Algarve, Gambelas, 8005-139, Faro, Portugal.
- MARE - Marine and Environmental Sciences Centre; ISPA - Instituto Universitário, Rua Jardim do Tabaco 34, 1149-041, Lisboa, Portugal.
| | - Regina L Cunha
- Centre of Marine Sciences, CCMAR, University of Algarve, Gambelas, 8005-139, Faro, Portugal
| | - Ana Ramos
- Centre of Marine Sciences, CCMAR, University of Algarve, Gambelas, 8005-139, Faro, Portugal
| | - Rita Castilho
- Centre of Marine Sciences, CCMAR, University of Algarve, Gambelas, 8005-139, Faro, Portugal
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14
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Masmoudi MB, Chaoui L, Topçu NE, Hammami P, Kara MH, Aurelle D. Contrasted levels of genetic diversity in a benthic Mediterranean octocoral: Consequences of different demographic histories? Ecol Evol 2016; 6:8665-8678. [PMID: 28035258 PMCID: PMC5192949 DOI: 10.1002/ece3.2490] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Revised: 08/17/2016] [Accepted: 08/18/2016] [Indexed: 01/17/2023] Open
Abstract
Understanding the factors explaining the observed patterns of genetic diversity is an important question in evolutionary biology. We provide the first data on the genetic structure of a Mediterranean octocoral, the yellow gorgonian Eunicella cavolini, along with insights into the demographic history of this species. We sampled populations in four areas of the Mediterranean Sea: continental France, Algeria, Turkey, and the Balearic and Corsica islands. Along French coasts, three sites were sampled at two depths (20 and 40 m). We demonstrated a high genetic structure in this species (overall FST = 0.13), and most pairwise differentiation tests were significant. We did not detect any difference between depths at the same site. Clustering analyses revealed four differentiated groups corresponding to the main geographical areas. The levels of allelic richness and heterozygosity were significantly different between regions, with highest diversity in Algeria and lowest levels in Turkey. The highest levels of private allelic richness were observed in Algeria followed by Turkey. Such contrasted patterns of genetic diversity were not observed in other Mediterranean octocorals and could be the result of different evolutionary histories. We also provide new empirical evidence of contrasting results between tests and model‐based studies of demographic history. Our results have important consequences for the management of this species.
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Affiliation(s)
- Moutassem Billah Masmoudi
- Aix Marseille Univ Univ Avignon CNRS IRD IMBE Marseille France; Laboratoire Bioressources Marines Université d'Annaba Badji Mokhtar Annaba Algérie
| | - Lamya Chaoui
- Laboratoire Bioressources Marines Université d'Annaba Badji Mokhtar Annaba Algérie
| | - Nur Eda Topçu
- İstanbul Üniversitesi Su Ürünleri Fakültesi İstanbul Turkey
| | - Pachka Hammami
- Aix Marseille UnivUniv Avignon CNRS IRD IMBE Marseille France; CIRAD UMR CMAEE Montpellier France
| | - Mohamed Hichem Kara
- Laboratoire Bioressources Marines Université d'Annaba Badji Mokhtar Annaba Algérie
| | - Didier Aurelle
- Aix Marseille Univ Univ Avignon CNRS IRD IMBE Marseille France
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15
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Le Moan A, Gagnaire PA, Bonhomme F. Parallel genetic divergence among coastal-marine ecotype pairs of European anchovy explained by differential introgression after secondary contact. Mol Ecol 2016; 25:3187-202. [PMID: 27027737 DOI: 10.1111/mec.13627] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 02/28/2016] [Accepted: 03/15/2016] [Indexed: 12/19/2022]
Abstract
Ecophenotypic differentiation among replicate ecotype pairs within a species complex is often attributed to independent outcomes of parallel divergence driven by adaptation to similar environmental contrasts. However, the extent to which parallel phenotypic and genetic divergence patterns have emerged independently is increasingly questioned by population genomic studies. Here, we document the extent of genetic differentiation within and among two geographic replicates of the coastal and marine ecotypes of the European anchovy (Engraulis encrasicolus) gathered from Atlantic and Mediterranean locations. Using a genome-wide data set of RAD-derived SNPs, we show that habitat type (marine vs. coastal) is the most important component of genetic differentiation among populations of anchovy. By analysing the joint allele frequency spectrum of each coastal-marine ecotype pair, we show that genomic divergence patterns between ecotypes can be explained by a postglacial secondary contact following a long period of allopatric isolation (c. 300 kyrs). We found strong support for a model including heterogeneous migration among loci, suggesting that secondary gene flow has eroded past differentiation at different rates across the genome. Markers experiencing reduced introgression exhibited strongly correlated differentiation levels among Atlantic and Mediterranean regions. These results support that partial reproductive isolation and parallel genetic differentiation among replicate pairs of anchovy ecotypes are largely due to a common divergence history prior to secondary contact. They moreover provide comprehensive insights into the origin of a surprisingly strong fine-scale genetic structuring in a high gene flow marine fish, which should improve stock management and conservation actions.
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Affiliation(s)
- A Le Moan
- Université Montpellier 2, Place Eugène Bataillon, Montpellier, 34095, France.,ISEM - CNRS, UMR 5554, SMEL, 2 rue des Chantiers, Sète, 34200, France
| | - P-A Gagnaire
- Université Montpellier 2, Place Eugène Bataillon, Montpellier, 34095, France.,ISEM - CNRS, UMR 5554, SMEL, 2 rue des Chantiers, Sète, 34200, France
| | - F Bonhomme
- Université Montpellier 2, Place Eugène Bataillon, Montpellier, 34095, France.,ISEM - CNRS, UMR 5554, SMEL, 2 rue des Chantiers, Sète, 34200, France
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16
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Boissin E, Micu D, Janczyszyn-Le Goff M, Neglia V, Bat L, Todorova V, Panayotova M, Kruschel C, Macic V, Milchakova N, Keskin Ç, Anastasopoulou A, Nasto I, Zane L, Planes S. Contemporary genetic structure and postglacial demographic history of the black scorpionfish, Scorpaena porcus, in the Mediterranean and the Black Seas. Mol Ecol 2016; 25:2195-209. [PMID: 26989881 DOI: 10.1111/mec.13616] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Revised: 02/09/2016] [Accepted: 03/11/2016] [Indexed: 12/24/2022]
Abstract
Understanding the distribution of genetic diversity in the light of past demographic events linked with climatic shifts will help to forecast evolutionary trajectories of ecosystems within the current context of climate change. In this study, mitochondrial sequences and microsatellite loci were analysed using traditional population genetic approaches together with Bayesian dating and the more recent approximate Bayesian computation scenario testing. The genetic structure and demographic history of a commercial fish, the black scorpionfish, Scorpaena porcus, was investigated throughout the Mediterranean and Black Seas. The results suggest that the species recently underwent population expansions, in both seas, likely concomitant with the warming period following the Last Glacial Maximum, 20 000 years ago. A weak contemporaneous genetic differentiation was identified between the Black Sea and the Mediterranean Sea. However, the genetic diversity was similar for populations of the two seas, suggesting a high number of colonizers entered the Black Sea during the interglacial period and/or the presence of a refugial population in the Black Sea during the glacial period. Finally, within seas, an east/west genetic differentiation in the Adriatic seems to prevail, whereas the Black Sea does not show any structured spatial genetic pattern of its population. Overall, these results suggest that the Black Sea is not that isolated from the Mediterranean, and both seas revealed similar evolutionary patterns related to climate change and changes in sea level.
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Affiliation(s)
- E Boissin
- EPHE, PSL Research University, UPVD, CNRS, USR 3278 CRIOBE, Perpignan, F-66360, France.,Laboratoire d'Excellence CRIOBE, BP 1013, 98729, Papetoai, Moorea, Polynésie Française
| | - D Micu
- National Institute of Marine Research and Development, Grigore Antipa, Constanta, 900581, Romania
| | - M Janczyszyn-Le Goff
- EPHE, PSL Research University, UPVD, CNRS, USR 3278 CRIOBE, Perpignan, F-66360, France.,Laboratoire d'Excellence CRIOBE, BP 1013, 98729, Papetoai, Moorea, Polynésie Française
| | - V Neglia
- EPHE, PSL Research University, UPVD, CNRS, USR 3278 CRIOBE, Perpignan, F-66360, France.,Laboratoire d'Excellence CRIOBE, BP 1013, 98729, Papetoai, Moorea, Polynésie Française
| | - L Bat
- Department of Marine Biology and Ecology, Faculty of Fisheries, Sinop University, Sinop, TR57000, Turkey
| | - V Todorova
- IO-BAS - Institute of Oceanology, PO Box 152, Varna, 9000, Bulgaria
| | - M Panayotova
- IO-BAS - Institute of Oceanology, PO Box 152, Varna, 9000, Bulgaria
| | - C Kruschel
- University of Zadar, Ul. Mihovila Pavlinovića, Zadar, 23000, Croatia
| | - V Macic
- Institute of Marine Biology Kotor (IBMK), Dobrota bb, PO Box 69, Kotor, 85330, Montenegro
| | - N Milchakova
- Institute of Marine Biological Research (IMBR), 2 Nakhimov ave., Sevastopol, 299011, Russia
| | - Ç Keskin
- Faculty of Fisheries, Istanbul University, Ordu St 200, Istanbul, TR-34470, Turkey
| | - A Anastasopoulou
- Hellenic Centre for Marine Research, 46.7 km Athinon-Souniou Av., Anavyssos, 19013, Greece
| | - I Nasto
- Department of Biology, Faculty of Technical Sciences, Vlora University, Vlora, 9401, Albania
| | - L Zane
- Department of Biology, University of Padova, via U. Bassi/58B, Padova, I-35121, Italy
| | - S Planes
- EPHE, PSL Research University, UPVD, CNRS, USR 3278 CRIOBE, Perpignan, F-66360, France.,Laboratoire d'Excellence CRIOBE, BP 1013, 98729, Papetoai, Moorea, Polynésie Française
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17
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Castilho R, Silva G. The European anchovy, a genetically highly diverse species displays null within-sample haplotype diversity on a single study? MITOCHONDRIAL DNA PART B-RESOURCES 2016; 1:60-61. [PMID: 33644327 PMCID: PMC7871658 DOI: 10.1080/23802359.2015.1137823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The European anchovy has been the focus of numerous population genetic studies, most of which exposing high levels of haplotype diversity. However, Keskin and Atar (2012) revealed rather singular results of null haplotype diversities. We therefore call for caution when considering these findings.
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Affiliation(s)
- Rita Castilho
- CCMAR, Centro de Ciências do Mar, Universidade do Algarve, Campus de Gambelas, Faro, Portugal
| | - Gonçalo Silva
- MARE - Marine and Environmental Sciences Centre, ISPA - Instituto Universitário, Departamento de Biociências, R. Jardim do Tabaco, Lisboa, Portugal
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18
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Tonay AM, Yazıcı Ö, Dede A, Bilgin S, Danyer E, Aytemiz I, Maracı Ö, Öztürk AA, Öztürk B, Bilgin R. Is there a distinct harbor porpoise subpopulation in the Marmara Sea? Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:558-564. [PMID: 27159712 DOI: 10.3109/24701394.2016.1155118] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Genetic population structure of geographically isolated endangered Black Sea harbor porpoise (Phocoena phocoena relicta) is little known in Turkish waters, especially in the Turkish Straits System (TSS- Marmara Sea, Bosphorus and Dardanelles), which connects the Black Sea and the Aegean Sea. Mitochondrial DNA sequences of 70 new individuals sampled in the Turkish Black Sea, TSS and Aegean Sea, revealed five new haplotypes from the Black Sea. The findings support the idea that harbor porpoises from the Black Sea dispersed into the Aegean through the TSS. Considering signatures of population expansion, all subpopulations showed a signature of population expansion. The network data and the Фst calculations indicated that the Marmara Sea subpopulation was significantly differentiated from all of the other subpopulations, and supports the notion of its isolated. The finding of a potential management unit (MU) within an already heavily impacted subpopulation as a whole suggests that the individuals of P. p. relicta inhabiting the Marmara Sea require a very rigorous conservation strategy to ensure the survival of this subpopulation, represented by its unique haplotype.
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Affiliation(s)
- Arda M Tonay
- a Faculty of Fisheries , Istanbul University , Laleli , Istanbul , Turkey.,b Turkish Marine Research Foundation (TUDAV) , Beykoz , Istanbul , Turkey
| | - Özge Yazıcı
- c Institute of Environment Sciences , Boğaziçi University , Bebek , Istanbul , Turkey
| | - Ayhan Dede
- a Faculty of Fisheries , Istanbul University , Laleli , Istanbul , Turkey.,b Turkish Marine Research Foundation (TUDAV) , Beykoz , Istanbul , Turkey
| | - Sabri Bilgin
- d Faculty of Fisheries , Sinop University , Sinop , Turkey
| | - Erdem Danyer
- b Turkish Marine Research Foundation (TUDAV) , Beykoz , Istanbul , Turkey.,e Faculty of Veterinary , Istanbul University , Avcılar , Istanbul , Turkey
| | - Işıl Aytemiz
- b Turkish Marine Research Foundation (TUDAV) , Beykoz , Istanbul , Turkey.,e Faculty of Veterinary , Istanbul University , Avcılar , Istanbul , Turkey
| | - Öncü Maracı
- c Institute of Environment Sciences , Boğaziçi University , Bebek , Istanbul , Turkey
| | - Ayaka A Öztürk
- a Faculty of Fisheries , Istanbul University , Laleli , Istanbul , Turkey.,b Turkish Marine Research Foundation (TUDAV) , Beykoz , Istanbul , Turkey
| | - Bayram Öztürk
- a Faculty of Fisheries , Istanbul University , Laleli , Istanbul , Turkey.,b Turkish Marine Research Foundation (TUDAV) , Beykoz , Istanbul , Turkey
| | - Raşit Bilgin
- c Institute of Environment Sciences , Boğaziçi University , Bebek , Istanbul , Turkey
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19
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Pappalardo AM, Federico C, Sabella G, Saccone S, Ferrito V. A COI Nonsynonymous Mutation as Diagnostic Tool for Intraspecific Discrimination in the European Anchovy Engraulis encrasicolus (Linnaeus). PLoS One 2015; 10:e0143297. [PMID: 26599908 PMCID: PMC4657973 DOI: 10.1371/journal.pone.0143297] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 11/03/2015] [Indexed: 12/01/2022] Open
Abstract
The European anchovy, Engraulis encrasicolus, is currently one of the principal target species for commercial fisheries in Europe. In this study, the mitochondrial Control Region (CR) and the Cytochrome Oxidase I (COI) mitochondrial gene were analyzed in 74 specimens of E. encrasicolus from four localities in the central Mediterranean. In both populations, the two markers revealed the presence of two main haplogroups, A and B, already detected in previous investigations of different classes of molecular markers. Both CR and COI markers consistently identified two haplogroups. The COI sequence analysis identified a non-synonymous transversion (T to G) at position 116 of the translated sequence, resulting in an amino acid change. All COI sequences of haplogroup A had an amino acid sequence with alanine in this position, while serine was present in the same position in haplogroup B. The two haplogroups A and B were also discriminated by the variable number of TACA elements at the 5’-end of the mitochondrial CR. The selection tests applied to the COI dataset revealed that codon 116 was not under positive selection, that seven amino acid changes were under purifying selection, and that two amino acids were under episodic positive selection.
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Affiliation(s)
- Anna Maria Pappalardo
- Department of Biological, Geological and Environmental Sciences, Sec. Animal Biology “M. La Greca”, University of Catania, Catania, Italy
| | - Concetta Federico
- Department of Biological, Geological and Environmental Sciences, Sec. Animal Biology “M. La Greca”, University of Catania, Catania, Italy
| | - Giorgio Sabella
- Department of Biological, Geological and Environmental Sciences, Sec. Animal Biology “M. La Greca”, University of Catania, Catania, Italy
| | - Salvatore Saccone
- Department of Biological, Geological and Environmental Sciences, Sec. Animal Biology “M. La Greca”, University of Catania, Catania, Italy
| | - Venera Ferrito
- Department of Biological, Geological and Environmental Sciences, Sec. Animal Biology “M. La Greca”, University of Catania, Catania, Italy
- * E-mail:
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Silva G, Lima FP, Martel P, Castilho R. Thermal adaptation and clinal mitochondrial DNA variation of European anchovy. Proc Biol Sci 2015; 281:rspb.2014.1093. [PMID: 25143035 DOI: 10.1098/rspb.2014.1093] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Natural populations of widely distributed organisms often exhibit genetic clinal variation over their geographical ranges. The European anchovy, Engraulis encrasicolus, illustrates this by displaying a two-clade mitochondrial structure clinally arranged along the eastern Atlantic. One clade has low frequencies at higher latitudes, whereas the other has an anti-tropical distribution, with frequencies decreasing towards the tropics. The distribution pattern of these clades has been explained as a consequence of secondary contact after an ancient geographical isolation. However, it is not unlikely that selection acts on mitochondria whose genes are involved in relevant oxidative phosphorylation processes. In this study, we performed selection tests on a fragment of 1044 bp of the mitochondrial cytochrome b gene using 455 individuals from 18 locations. We also tested correlations of six environmental features: temperature, salinity, apparent oxygen utilization and nutrient concentrations of phosphate, nitrate and silicate, on a compilation of mitochondrial clade frequencies from 66 sampling sites comprising 2776 specimens from previously published studies. Positive selection in a single codon was detected predominantly (99%) in the anti-tropical clade and temperature was the most relevant environmental predictor, contributing with 59% of the variance in the geographical distribution of clade frequencies. These findings strongly suggest that temperature is shaping the contemporary distribution of mitochondrial DNA clade frequencies in the European anchovy.
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Affiliation(s)
- Gonçalo Silva
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, Campus de Gambelas, Faro 8005-139, Portugal
| | - Fernando P Lima
- CIBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Campus Agrário de Vairão, Vairão 4485-661, Portugal
| | - Paulo Martel
- Centro de Biomedicina Molecular e Estrutural Instituto de Biotecnologia e Bioengenharia (CBME-Associate Laboratory), Universidade do Algarve, Campus de Gambelas, Faro 8005-139, Portugal
| | - Rita Castilho
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, Campus de Gambelas, Faro 8005-139, Portugal
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21
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Past and present drivers of population structure in a small coastal fish, the European long snouted seahorse Hippocampus guttulatus. CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0728-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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22
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Population genetic structure of chub mackerel Scomber japonicus in the Northwestern Pacific inferred from microsatellite analysis. Mol Biol Rep 2014; 42:373-82. [PMID: 25366174 DOI: 10.1007/s11033-014-3777-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2013] [Accepted: 09/22/2014] [Indexed: 10/24/2022]
Abstract
Marine pelagic fishes are usually characterized by subtle but complex patterns of genetic differentiation, which are influenced by both historical process and contemporary gene flow. Genetic population differentiation of chub mackerel, Scomber japonicus, was examined across most of its range in the Northwestern Pacific by screening variation of eight microsatellite loci. Our genetic analysis detected a weak but significant genetic structure of chub mackerel, which was characterized by areas of gene flow and isolation by distance. Consistent with previous estimates of stock structure, we found genetic discontinuity between Japan and China samples. Local-scale pattern of genetic differentiation was observed between samples from the Bohai Sea and North Yellow Sea and those from the East China Sea, which we ascribed to differences in spawning time and migratory behavior. Furthermore, the observed homogeneity among collections of chub mackerel from the East and South China Seas could be the result of an interaction between biological characteristics and marine currents. The present study underlies the importance of understanding the biological significance of genetic differentiation to establish management strategies for exploited fish populations.
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Gubili C, Sims DW, Veríssimo A, Domenici P, Ellis J, Grigoriou P, Johnson AF, McHugh M, Neat F, Satta A, Scarcella G, Serra-Pereira B, Soldo A, Genner MJ, Griffiths AM. A tale of two seas: contrasting patterns of population structure in the small-spotted catshark across Europe. ROYAL SOCIETY OPEN SCIENCE 2014; 1:140175. [PMID: 26064555 PMCID: PMC4448844 DOI: 10.1098/rsos.140175] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Accepted: 10/14/2014] [Indexed: 06/04/2023]
Abstract
Elasmobranchs represent important components of marine ecosystems, but they can be vulnerable to overexploitation. This has driven investigations into the population genetic structure of large-bodied pelagic sharks, but relatively little is known of population structure in smaller demersal taxa, which are perhaps more representative of the biodiversity of the group. This study explores spatial population genetic structure of the small-spotted catshark (Scyliorhinus canicula), across European seas. The results show significant genetic differences among most of the Mediterranean sample collections, but no significant structure among Atlantic shelf areas. The data suggest the Mediterranean populations are likely to have persisted in a stable and structured environment during Pleistocene sea-level changes. Conversely, the Northeast Atlantic populations would have experienced major changes in habitat availability during glacial cycles, driving patterns of population reduction and expansion. The data also provide evidence of male-biased dispersal and female philopatry over large spatial scales, implying complex sex-determined differences in the behaviour of elasmobranchs. On the basis of this evidence, we suggest that patterns of connectivity are determined by trends of past habitat stability that provides opportunity for local adaptation in species exhibiting philopatric behaviour, implying that resilience of populations to fisheries and other stressors may differ across the range of species.
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Affiliation(s)
- Chrysoula Gubili
- School of Environment and Life Sciences, University of Salford, Salford, Greater Manchester M5 4WU, UK
| | - David W. Sims
- Marine Biological Association of the United Kingdom, The Laboratory, Plymouth PL1 2PB, UK
| | - Ana Veríssimo
- CIBIO-U.P., Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Rua Padre Armando Quintas, Vairão 4485-661, Portugal
| | | | - Jim Ellis
- Centre for Environment, Fisheries and Aquaclture Science (CEFAS), Pakefield Road, Lowestoft, Suffolk NR33 0HT, UK
| | - Panagiotis Grigoriou
- Cretaquarium, Thalassocosmos, Hellenic Centre for Marine Research (HCMR), PO Box 2214, Heraklion Crete 71003, Greece
| | - Andrew F. Johnson
- Center for Marine Biodiversity and Conservation, Scripps Institution of Oceanography 0202, University of California, 9500 Gilman Drive, San Diego, CA 92083-0202, USA
| | - Matthew McHugh
- Marine and Estuarine Ecology Unit, School of Biological Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Francis Neat
- Marine Scotland—Science, Marine Laboratory, PO Box 101, Aberdeen AB11 9DB, UK
| | - Andrea Satta
- CNR-IAMC Località Sa Mardini, Torregrande 09170, Italy
| | - Giuseppe Scarcella
- ISMAR-CNR—Istituto di Scienze Marine, Consiglio Nazionale delle Ricerche, Largo Fiera della Pesca 2, Ancona 60125, Italy
| | - Bárbara Serra-Pereira
- Departamento do Mar e Recursos Marinhos, IPMA, Instituto Português do Mar e da Atmosfera, Av. Brasilia, Lisboa 1449-006, Portugal
| | - Alen Soldo
- Department of Marine Studies, University of Split, Livanjska 5, Split 21000, Croatia
| | - Martin J. Genner
- School of Biological Sciences, University of Bristol, Bristol Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Andrew M. Griffiths
- Marine Biological Association of the United Kingdom, The Laboratory, Plymouth PL1 2PB, UK
- School of Biological Sciences, University of Bristol, Bristol Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
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SNP discovery in European anchovy (Engraulis encrasicolus, L) by high-throughput transcriptome and genome sequencing. PLoS One 2013; 8:e70051. [PMID: 23936375 PMCID: PMC3731364 DOI: 10.1371/journal.pone.0070051] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 06/13/2013] [Indexed: 11/29/2022] Open
Abstract
Increased throughput in sequencing technologies has facilitated the acquisition of detailed genomic information in non-model species. The focus of this research was to discover and validate SNPs derived from the European anchovy (Engraulis encrasicolus) transcriptome, a species with no available reference genome, using next generation sequencing technologies. A cDNA library was constructed from four tissues of ten fish individuals corresponding to three populations of E. encrasicolus, and Roche 454 GS FLX Titanium sequencing yielded 19,367 contigs. Additionally, the European anchovy genome was sequenced for the same ten individuals using an Illumina HiSeq2000. Using a computational pipeline for combining transcriptome and genome information, a total of 18,994 SNPs met the necessary minor allele frequency and depth filters. A series of further stringent filters were applied to identify those SNPs likely to succeed in genotyping assays, and for filtering of those in potential duplicated genome regions. A novel method for detecting potential intron-exon boundaries in areas of putative SNPs has also been applied in silico to improve genotyping success. In all, 2,317 filtered putative transcriptome SNPs suitable for genotyping primer design were identified. From those, a subset of 530 were selected, with the genotyping results showing the highest reported conversion and validation rates (91.3% and 83.2%, respectively) reported to date for a non-model species. This study represents a promising strategy to discover genotypable SNPs in the exome of non-model organisms. The genomic resource generated for E. encrasicolus, both in terms of sequences and novel markers, will be informative for research into this species with applications including traceability studies, population genetic analyses and aquaculture.
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Ragionieri L, Schubart CD. Population genetics, gene flow, and biogeographical boundaries ofCarcinus aestuarii(Crustacea: Brachyura: Carcinidae) along the European Mediterranean coast. Biol J Linn Soc Lond 2013. [DOI: 10.1111/bij.12099] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Lapo Ragionieri
- RNA Biology Laboratory; Department of Biology & CESAM; University of Aveiro; 3810-193; Aveiro; Portugal
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26
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Fadhlaoui-Zid K, Knittweis L, Aurelle D, Nafkha C, Ezzeddine S, Fiorentino F, Ghmati H, Ceriola L, Jarboui O, Maltagliati F. Genetic structure of Octopus vulgaris (Cephalopoda, Octopodidae) in the central Mediterranean Sea inferred from the mitochondrial COIII gene. C R Biol 2012. [DOI: 10.1016/j.crvi.2012.10.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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27
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Zarraonaindia I, Iriondo M, Albaina A, Pardo MA, Manzano C, Grant WS, Irigoien X, Estonba A. Multiple SNP markers reveal fine-scale population and deep phylogeographic structure in European anchovy (Engraulis encrasicolus L.). PLoS One 2012; 7:e42201. [PMID: 22860082 PMCID: PMC3408476 DOI: 10.1371/journal.pone.0042201] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Accepted: 07/02/2012] [Indexed: 12/29/2022] Open
Abstract
Geographic surveys of allozymes, microsatellites, nuclear DNA (nDNA) and mitochondrial DNA (mtDNA) have detected several genetic subdivisions among European anchovy populations. However, these studies have been limited in their power to detect some aspects of population structure by the use of a single or a few molecular markers, or by limited geographic sampling. We use a multi-marker approach, 47 nDNA and 15 mtDNA single nucleotide polymorphisms (SNPs), to analyze 626 European anchovies from the whole range of the species to resolve shallow and deep levels of population structure. Nuclear SNPs define 10 genetic entities within two larger genetically distinctive groups associated with oceanic variables and different life-history traits. MtDNA SNPs define two deep phylogroups that reflect ancient dispersals and colonizations. These markers define two ecological groups. One major group of Iberian-Atlantic populations is associated with upwelling areas on narrow continental shelves and includes populations spawning and overwintering in coastal areas. A second major group includes northern populations in the North East (NE) Atlantic (including the Bay of Biscay) and the Mediterranean and is associated with wide continental shelves with local larval retention currents. This group tends to spawn and overwinter in oceanic areas. These two groups encompass ten populations that differ from previously defined management stocks in the Alboran Sea, Iberian-Atlantic and Bay of Biscay regions. In addition, a new North Sea-English Channel stock is defined. SNPs indicate that some populations in the Bay of Biscay are genetically closer to North Western (NW) Mediterranean populations than to other populations in the NE Atlantic, likely due to colonizations of the Bay of Biscay and NW Mediterranean by migrants from a common ancestral population. Northern NE Atlantic populations were subsequently established by migrants from the Bay of Biscay. Populations along the Iberian-Atlantic coast appear to have been founded by secondary waves of migrants from a southern refuge.
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Affiliation(s)
- Iratxe Zarraonaindia
- Laboratory of Genetics, Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Sarriena auzoa z/g, Leioa (Bizkaia), Spain
- * E-mail:
| | - Mikel Iriondo
- Laboratory of Genetics, Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Sarriena auzoa z/g, Leioa (Bizkaia), Spain
| | - Aitor Albaina
- Laboratory of Genetics, Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Sarriena auzoa z/g, Leioa (Bizkaia), Spain
| | - Miguel Angel Pardo
- AZTI-Tecnalia, Food Research Unit, Parque Tecnológico de Bizkaia, Astondo Bidea, Edif. 609, Derio (Bizkaia), Spain
| | - Carmen Manzano
- Laboratory of Genetics, Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Sarriena auzoa z/g, Leioa (Bizkaia), Spain
| | - W. Stewart Grant
- Commercial Fisheries Division, Alaska Department of Fish and Game, Anchorage, Alaska, United States of America
| | - Xabier Irigoien
- AZTI-Tecnalia, Marine Research Division, Herrera Kaia Portualde z/g, Pasaia (Gipuzkoa), Spain
| | - Andone Estonba
- Laboratory of Genetics, Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Sarriena auzoa z/g, Leioa (Bizkaia), Spain
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Keski˙n E, Atar HH. Genetic structuring of European anchovy (Engraulis encrasicolus) populations through mitochondrial DNA sequences. ACTA ACUST UNITED AC 2012; 23:62-9. [DOI: 10.3109/19401736.2011.653798] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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29
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DeFaveri J, Zanella LN, Zanella D, Mrakovčić M, Merilä J. Phylogeography of isolated freshwater three-spined stickleback Gasterosteus aculeatus populations in the Adriatic Sea basin. JOURNAL OF FISH BIOLOGY 2012; 80:61-85. [PMID: 22220890 DOI: 10.1111/j.1095-8649.2011.03147.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Analyses of mitochondrial (mt) DNA and microsatellite variation were carried out to examine the relationships between 10 freshwater populations of three-spined sticklebacks Gasterosteus aculeatus along the eastern coast of the Adriatic Sea. Partial sequences of the mtDNA control region and cytochrome b gene, in addition to 15 microsatellite loci, were used to analyse populations from four isolated river catchments. Results uncovered an Adriatic lineage that was clearly divergent from the European lineage, and confirmed that the most divergent and ancient populations are located within the Adriatic lineage as compared with other European populations. Two northern Adriatic populations formed independent clades within the European mitochondrial lineage, suggesting different colonization histories of the different Adriatic populations. Nuclear marker analyses also indicated deep divergence between Adriatic and European populations, albeit with some discordance between the mtDNA phylogeny of the northern Adriatic populations, further highlighting the strong differentiation among the Adriatic populations. The southern populations within the Adriatic lineage were further organized into distinct clades corresponding to respective river catchments and sub-clades corresponding to river tributaries, reflecting a high degree of population structuring within a small geographic region, concurrent with suggestions of existence of several microrefugia within the Balkan Peninsula. The highly divergent clades and haplotypes unique to the southern Adriatic populations further suggest, in accordance with an earlier, more limited survey, that southern Adriatic populations represent an important reservoir for ancient genetic diversity of G. aculeatus.
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Affiliation(s)
- J DeFaveri
- Ecological Genetics Research Unit, Department of Biological Sciences, FI-00014, University of Helsinki, Helsinki, Finland.
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Mejri R, Arculeo M, Hassine OKB, Brutto SL. Genetic architecture of the marbled goby Pomatoschistus marmoratus (Perciformes, Gobiidae) in the Mediterranean Sea. Mol Phylogenet Evol 2010; 58:395-403. [PMID: 21167289 DOI: 10.1016/j.ympev.2010.12.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Revised: 11/26/2010] [Accepted: 12/03/2010] [Indexed: 11/19/2022]
Abstract
The marbled goby Pomatoschistus marmoratus, a species inhabiting coastal Mediterranean lagoons, has been studied by measuring its mitochondrial DNA variation. This analysis revealed a Mediterranean west vs east split and, subsequently, an eastern differentiation among the Libyan-Tunisian Gulf, the Adriatic Sea and the Aegean Sea. The high cohesion between the samples collected in the vast area of western Mediterranean contrasts with the genetic mosaic of the more sub-structured eastern Mediterranean. This western homogeneity can not yet be fully explained even if a human-mediated migratory flow, due to a maritime traffic, has been posited. The pattern in the eastern basin revealed a genetic architecture possibly due to the non-migratory habit of the gobid. Within this perspective, the role of the Mediterranean lagoon habitat should be related to how much it amplifies the effects of historical (e.g. past sea-level changes) and environmental (e.g. present-day hydrographic regime) processes as regards the genetic structure of the inhabiting species.
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Affiliation(s)
- Randa Mejri
- Unité de Recherche de Biologie, Ecologie et Parasitologie des Organismes Aquatiques, Département de Biologie, Tunis El Manar 2092, Tunisia
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PAKAKI V, MAGOULAS A, KASAPIDIS P. New polymorphic microsatellite loci for population studies in the European anchovy,
Engraulis encrasicolus
(L.). Mol Ecol Resour 2009; 9:1406-9. [DOI: 10.1111/j.1755-0998.2009.02681.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- V. PAKAKI
- Institute of Marine Biology and Genetics, Hellenic Centre for Marine Research, PO Box 2214, 71003 Heraklion, Greece
| | - A. MAGOULAS
- Institute of Marine Biology and Genetics, Hellenic Centre for Marine Research, PO Box 2214, 71003 Heraklion, Greece
| | - P. KASAPIDIS
- Institute of Marine Biology and Genetics, Hellenic Centre for Marine Research, PO Box 2214, 71003 Heraklion, Greece
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32
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VIRGILIO M, FAUVELOT C, COSTANTINI F, ABBIATI M, BACKELJAU T. Phylogeography of the common ragwormHediste diversicolor(Polychaeta: Nereididae) reveals cryptic diversity and multiple colonization events across its distribution. Mol Ecol 2009; 18:1980-94. [DOI: 10.1111/j.1365-294x.2009.04170.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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BEARZI GIOVANNI, FORTUNA CATERINAMARIA, REEVES RANDALLR. Ecology and conservation of common bottlenose dolphinsTursiops truncatusin the Mediterranean Sea. Mamm Rev 2009. [DOI: 10.1111/j.1365-2907.2008.00133.x] [Citation(s) in RCA: 122] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Mitochondrial DNA variation in the caramote prawn Penaeus (Melicertus) kerathurus across a transition zone in the Mediterranean Sea. Genetica 2008; 136:439-47. [PMID: 19109695 DOI: 10.1007/s10709-008-9344-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2008] [Accepted: 12/06/2008] [Indexed: 10/21/2022]
Abstract
In this study we analysed mitochondrial DNA variation in Penaeus kerathurus prawns collected from seven locations along a transect across the Siculo-Tunisian region in order to verify if any population structuring exists over a limited geographical scale and to delineate the putative transition zone with sufficient accuracy. Partial DNA sequences of COI and 16S genes were analysed. In contrast to the highly conservative 16S gene, the COI sequences exhibited sufficient diversity for population analysis. The COI gene revealed low levels of haplotype and nucleotide diversities. The size of the annual landings of this commercial species suggests large population sizes. Hence, the low genetic diversity detected in this study could indicate a possible reduction in effective population sizes in the past. We detected significant genetic differentiation between eastern and western populations likely due to restricted gene flow across the Siculo-Tunisian boundary. We discuss the different evolutionary forces that may have shaped the genetic variation and suggest that the genetic divide is probably maintained by present-day dispersal limitation.
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Luttikhuizen PC, Campos J, Bleijswijk JV, Peijnenburg KT, van der Veer HW. Phylogeography of the common shrimp, Crangon crangon (L.) across its distribution range. Mol Phylogenet Evol 2008; 46:1015-30. [DOI: 10.1016/j.ympev.2007.11.011] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2007] [Revised: 10/19/2007] [Accepted: 11/15/2007] [Indexed: 10/22/2022]
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Gonzalez EG, Zardoya R. Relative role of life-history traits and historical factors in shaping genetic population structure of sardines (Sardina pilchardus). BMC Evol Biol 2007; 7:197. [PMID: 17953768 PMCID: PMC2204010 DOI: 10.1186/1471-2148-7-197] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2007] [Accepted: 10/22/2007] [Indexed: 12/04/2022] Open
Abstract
Background Marine pelagic fishes exhibit rather complex patterns of genetic differentiation, which are the result of both historical processes and present day gene flow. Comparative multi-locus analyses based on both nuclear and mitochondrial genetic markers are probably the most efficient and informative approach to discerning the relative role of historical events and life-history traits in shaping genetic heterogeneity. The European sardine (Sardina pilchardus) is a small pelagic fish with a relatively high migratory capability that is expected to show low levels of genetic differentiation among populations. Previous genetic studies based on meristic and mitochondrial control region haplotype frequency data supported the existence of two sardine subspecies (S. p. pilchardus and S. p. sardina). Results We investigated genetic structure of sardine among nine locations in the Atlantic Ocean and Mediterranean Sea using allelic size variation of eight specific microsatellite loci. Bayesian clustering and assignment tests, maximum likelihood estimates of migration rates, as well as classical genetic-variance-based methods (hierarchical AMOVA test and RST pairwise comparisons) supported a single evolutionary unit for sardines. These analyses only detected weak but significant genetic differentiation, which followed an isolation-by-distance pattern according to Mantel test. Conclusion We suggest that the discordant genetic structuring patterns inferred based on mitochondrial and microsatellite data might indicate that the two different classes of molecular markers may be reflecting different and complementary aspects of the evolutionary history of sardine. Mitochondrial data might be reflecting past isolation of sardine populations into two distinct groupings during Pleistocene whereas microsatellite data reveal the existence of present day gene flow among populations, and a pattern of isolation by distance.
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Affiliation(s)
- Elena G Gonzalez
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC, José Gutiérrez Abascal, 2; 28006 Madrid, Spain.
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Patarnello T, Volckaert FAMJ, Castilho R. Pillars of Hercules: is the Atlantic-Mediterranean transition a phylogeographical break? Mol Ecol 2007; 16:4426-44. [PMID: 17908222 DOI: 10.1111/j.1365-294x.2007.03477.x] [Citation(s) in RCA: 407] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The geological history of the Mediterranean Sea, its hydrography and connection with the Atlantic Ocean have been well documented. Despite a wealth of historical and oceanographic data, the Atlantic-Mediterranean transition remains controversial at the biological level as there are discordant results regarding the biogeographical separation between the Atlantic and Mediterranean biota. The opening of the Strait of Gibraltar at the end of the Messinian Salinity Crisis (some 5.33 million years ago), removed the land barrier that impeded the marine biota allowing it to disperse freely into the Mediterranean Sea. However, present day genetic patterns suggest a limitation to gene flow for some marine species, preventing population admixture. In the last few years, a large number of studies have challenged the hypothesis of the Strait of Gibraltar representing a phylogeographical break. A review of more than 70 papers reveals no obvious relationship between either dispersal ability or life history, and observed patterns of partial or complete genetic isolation between Atlantic and Mediterranean populations. We re-analysed a selection of this large body of data (20 studies in total) in order to provide a homogeneous and coherent view on the generality of the phylogeographical patterns and the presence of a phylogeographical barrier. This offered the opportunity to summarize the state of the art on this matter and reach some general conclusions on the evolutionary history across the Atlantic-Mediterranean range. Geographically, some species in the transition zone showed step changes of allele frequencies associated with the Almeria-Oran Front rather than with the Strait of Gibraltar itself. A major part of the data describe evolutionary events well within the time frame of the Quaternary age as very few taxa pre-date closure of the Tethys Sea. Results point to a combined signature of vicariance, palaeoclimate fluctuation and life-history traits on the Atlantic-Mediterranean phylogeographical patterns. Principal component analysis failed to show any particular association between biological traits and genetic variables. It would argue that organismal determinism may play a far less significant role than marine biogeographers have generally believed.
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Affiliation(s)
- Tomaso Patarnello
- Dipartimento di Sanità Pubblica Patologia Comparata e Igiene Veterinaria, Agripolis, Università di Padova, Viale dell'Università, 16, I-35020 Legnaro (Pd), Italy.
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Zane L, Marcato S, Bargelloni L, Bortolotto E, Papetti C, Simonato M, Varotto V, Patarnello T. Demographic history and population structure of the Antarctic silverfish Pleuragramma antarcticum. Mol Ecol 2006; 15:4499-511. [PMID: 17107479 DOI: 10.1111/j.1365-294x.2006.03105.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The Antarctic silverfish Pleuragramma antarcticum (Nototheniidae) is the most abundant pelagic fish inhabiting Antarctic waters. In this study we investigated, through partial sequencing of the D-loop mitochondrial region, samples collected at four different locations in the Southern Ocean, three in the Atlantic and one in the Pacific sector. Sampling was replicated in two different years at two locations. Sequence analysis showed a remarkably high polymorphism, with 110 haplotypes over the 256 investigated specimens, and about 80% of haplotypes occurring only once. Neutrality tests indicated that all samples were not at mutation-drift equilibrium, and suggested a past population expansion. This result was supported by the presence of a star-like topology in the D-loop gene tree, and by results of mismatch distribution. The start of the expansion was dated, using a specifically calibrated clock, between 111 and 126 thousand years ago. This value corresponds to the start of the cooling period that led to the last glaciation peak, and is in close agreement with a recently suggested range expansion for pelagic Antarctic ecosystems. Analysis of molecular variation indicated a small, though highly significant, value of differentiation between samples. This result, together with the lack of association between clades and geographical locations, indicates a weak population structure for the species.
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Affiliation(s)
- L Zane
- Dipartimento di Biologia, Università di Padova, Via G. Colombo, 3, I-35121 Padova, Italy
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