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Dimens PV, Jones KL, Margulies D, Scholey V, Cusatti S, McPeak B, Hildahl TE, Saillant EAE. Genomic resources for the Yellowfin tuna Thunnus albacares. Mol Biol Rep 2024; 51:232. [PMID: 38281308 DOI: 10.1007/s11033-023-09117-6] [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: 07/08/2023] [Accepted: 12/06/2023] [Indexed: 01/30/2024]
Abstract
BACKGROUND The Yellowfin tuna (Thunnus albacares) is a large tuna exploited by major fisheries in tropical and subtropical waters of all oceans except the Mediterranean Sea. Genomic studies of population structure, adaptive variation or of the genetic basis of phenotypic traits are needed to inform fisheries management but are currently limited by the lack of a reference genome for this species. Here we report a draft genome assembly and a linkage map for use in genomic studies of T. albacares. METHODS AND RESULTS Illumina and PacBio SMRT sequencing were used in combination to generate a hybrid assembly that comprises 743,073,847 base pairs contained in 2,661 scaffolds. The assembly has a N50 of 351,587 and complete and partial BUSCO scores of 86.47% and 3.63%, respectively. Double-digest restriction associated DNA (ddRAD) was used to genotype the 2 parents and 164 of their F1 offspring resulting from a controlled breeding cross, retaining 19,469 biallelic single nucleotide polymorphism (SNP) loci. The SNP loci were used to construct a linkage map that features 24 linkage groups that represent the 24 chromosomes of yellowfin tuna. The male and female maps span 1,243.8 cM and 1,222.9 cM, respectively. The map was used to anchor the assembly in 24 super-scaffolds that contain 79% of the yellowfin tuna genome. Gene prediction identified 46,992 putative genes 20,203 of which could be annotated via gene ontology. CONCLUSIONS The draft reference will be valuable to interpret studies of genome wide variation in T. albacares and other Scombroid species.
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Affiliation(s)
- Pavel V Dimens
- School of Ocean Science and Engineering, The University of Southern Mississippi, Ocean Springs, MS, 39564, USA
| | | | - Daniel Margulies
- Inter-American Tropical Tuna Commission, 8901 La Jolla Shores Drive, La Jolla, CA, 92037, USA
| | - Vernon Scholey
- Inter-American Tropical Tuna Commission, 8901 La Jolla Shores Drive, La Jolla, CA, 92037, USA
| | - Susana Cusatti
- Inter-American Tropical Tuna Commission, 8901 La Jolla Shores Drive, La Jolla, CA, 92037, USA
| | - Brooke McPeak
- School of Ocean Science and Engineering, The University of Southern Mississippi, Ocean Springs, MS, 39564, USA
| | - Tami E Hildahl
- School of Ocean Science and Engineering, The University of Southern Mississippi, Ocean Springs, MS, 39564, USA
| | - Eric A E Saillant
- School of Ocean Science and Engineering, The University of Southern Mississippi, Ocean Springs, MS, 39564, USA.
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2
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Artetxe-Arrate I, Brophy D, Dettman DL, Lastra-Luque P, Varela JL, Oray I, Arrizabalaga H, Fraile I. Otolith-temperature estimates in Atlantic bluefin tuna (Thunnus thynnus) from the Mediterranean Sea: Insights from clumped isotope measurements. MARINE ENVIRONMENTAL RESEARCH 2024; 193:106283. [PMID: 38128348 DOI: 10.1016/j.marenvres.2023.106283] [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: 10/04/2023] [Revised: 11/16/2023] [Accepted: 11/20/2023] [Indexed: 12/23/2023]
Abstract
The subpopulation and/or contingent structure of Atlantic bluefin tuna (Thunnus thynnus) within the Mediterranean Sea is undefined, leading to uncertainty regarding the best strategy for an effective assessment and management of this highly exploited stock. This study aimed to reconstruct temperatures experienced by Atlantic bluefin tuna during the early life period (<3.5 months) using clumped isotope temperature proxy, an innovative geothermometer for carbonates, that does not require previous knowledge of other environmental parameters such as water oxygen composition. We examined otolith chemistry in fish captured from 3 different areas of the Mediterranean Sea and adjacent waters. We found that mean seasonal temperature estimates from clumped isotopes did not differ significantly from satellite derived and otolith oxygen stable isotopic ratios derived temperatures, except for the central Mediterranean Sea, were clumped isotopes derived temperatures were significantly higher than satellite derived temperatures. However, the sensitivity of the clumped isotope thermometer was found to be lower than that based on oxygen fractionation equation, with high variance observed in the clumped isotopes derived temperature estimates. We also observed that clumped isotope derived temperatures were undistinguishable among bluefin tuna captured in the Gibraltar Strait, the central, and eastern Mediterranean Sea. In this paper, we discuss the major sources of uncertainty in temperature reconstructions using bluefin tuna otoliths.
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Affiliation(s)
- I Artetxe-Arrate
- AZTI, Marine Research, AZTI Basque Research and Alliance, Txatxarramendi ugartea z/g, 48395, Sukarrieta, Bizkaia, Spain.
| | - D Brophy
- Marine and Freshwater Research Centre, Atlantic Technological University - Galway City, Wellpark Road, Galway, H91 DY9Y, Ireland
| | - D L Dettman
- Environmental Isotope Laboratory, Department of Geosciences, University of Arizona, Tucson, AZ, 85721, USA
| | - P Lastra-Luque
- AZTI, Marine Research, AZTI Basque Research and Alliance, Txatxarramendi ugartea z/g, 48395, Sukarrieta, Bizkaia, Spain
| | - J L Varela
- Departamento de Biología, Universidad de Cádiz, Campus de Excelencia Internacional del Mar (CEI·MAR), Av. República Saharaui s/n, 11510, Puerto Real, Cádiz, Spain
| | - I Oray
- Istanbul University, Faculty of Aquatic Sciences, Vezneciler, Istanbul, Turkey
| | - H Arrizabalaga
- AZTI, Marine Research, AZTI Basque Research and Alliance, Txatxarramendi ugartea z/g, 48395, Sukarrieta, Bizkaia, Spain
| | - I Fraile
- AZTI, Marine Research, AZTI Basque Research and Alliance, Txatxarramendi ugartea z/g, 48395, Sukarrieta, Bizkaia, Spain
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3
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Díaz-Arce N, Gagnaire PA, Richardson DE, Walter JF, Arnaud-Haond S, Fromentin JM, Brophy D, Lutcavage M, Addis P, Alemany F, Allman R, Deguara S, Fraile I, Goñi N, Hanke AR, Karakulak FS, Pacicco A, Quattro JM, Rooker JR, Arrizabalaga H, Rodríguez-Ezpeleta N. Unidirectional trans-Atlantic gene flow and a mixed spawning area shape the genetic connectivity of Atlantic bluefin tuna. Mol Ecol 2024; 33:e17188. [PMID: 37921120 DOI: 10.1111/mec.17188] [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: 06/21/2023] [Revised: 10/02/2023] [Accepted: 10/19/2023] [Indexed: 11/04/2023]
Abstract
The commercially important Atlantic bluefin tuna (Thunnus thynnus), a large migratory fish, has experienced notable recovery aided by accurate resource assessment and effective fisheries management efforts. Traditionally, this species has been perceived as consisting of eastern and western populations, spawning respectively in the Mediterranean Sea and the Gulf of Mexico, with mixing occurring throughout the Atlantic. However, recent studies have challenged this assumption by revealing weak genetic differentiation and identifying a previously unknown spawning ground in the Slope Sea used by Atlantic bluefin tuna of uncertain origin. To further understand the current and past population structure and connectivity of Atlantic bluefin tuna, we have assembled a unique dataset including thousands of genome-wide single-nucleotide polymorphisms (SNPs) from 500 larvae, young of the year and spawning adult samples covering the three spawning grounds and including individuals of other Thunnus species. Our analyses support two weakly differentiated but demographically connected ancestral populations that interbreed in the Slope Sea. Moreover, we also identified signatures of introgression from albacore (Thunnus alalunga) into the Atlantic bluefin tuna genome, exhibiting varied frequencies across spawning areas, indicating strong gene flow from the Mediterranean Sea towards the Slope Sea. We hypothesize that the observed genetic differentiation may be attributed to increased gene flow caused by a recent intensification of westward migration by the eastern population, which could have implications for the genetic diversity and conservation of western populations. Future conservation efforts should consider these findings to address potential genetic homogenization in the species.
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Affiliation(s)
- Natalia Díaz-Arce
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Sukarrieta, Spain
| | | | - David E Richardson
- Northeast Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration (NOAA), Narragansett, Rhode Island, USA
| | - John F Walter
- Southeast Fisheries Sciences Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration (NOAA), Miami, Florida, USA
| | | | | | - Deirdre Brophy
- Marine and Freshwater Research Center, Atlantic Technological University (ATU), Galway City, Ireland
| | - Molly Lutcavage
- Large Pelagics Research Center, School for the Environment, University of Massachusetts Boston, Gloucester, Massachusetts, USA
| | - Piero Addis
- Department of Environmental and Life Science, University of Cagliari, Cagliari, Italy
| | - Francisco Alemany
- International Commission for the Conservation of Atlantic Tunas, GBYP, Madrid, Spain
| | - Robert Allman
- National Marine Fisheries Service, Southeast Fisheries Science Center, Panama City Laboratory, Panama City, Florida, USA
| | | | - Igaratza Fraile
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Pasaia, Spain
| | - Nicolas Goñi
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Pasaia, Spain
| | - Alex R Hanke
- St Andrews Biological Station, Fisheries and Oceans Canada, St. Andrews, New Brunswick, Canada
| | | | - Ashley Pacicco
- Cooperative Institute for Marine and Atmospheric Studies Rosenstiel School of Marine, Atmospheric and Earth Science, University of Miami, Miami, Florida, USA
| | - Joseph M Quattro
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, USA
| | - Jay R Rooker
- Department of Marine Biology, Texas A&M University at Galveston, Galveston, Texas, USA
| | - Haritz Arrizabalaga
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Pasaia, Spain
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4
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Kottillil S, Rao C, Bowen BW, Shanker K. Phylogeography of sharks and rays: a global review based on life history traits and biogeographic partitions. PeerJ 2023; 11:e15396. [PMID: 37283899 PMCID: PMC10239618 DOI: 10.7717/peerj.15396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 04/20/2023] [Indexed: 06/08/2023] Open
Abstract
Considerable research exists on the life history traits, evolutionary history, and environmental factors that shape the population genetic structure of marine organisms, including sharks and rays. Conservation concerns are particularly strong for this group as they are highly susceptible to anthropogenic stressors due to a combination of life history traits including late maturity and low fecundity. Here, we provide a review and synthesis of the global phylogeography of sharks and rays. We examined existing data for 40 species of sharks belonging to 17 genera and 19 species of rays belonging to 11 genera. Median joining haplotype networks were constructed for each species for the mtDNA cytochrome C oxidase subunit I (COI), and an Analysis of Molecular Variance (AMOVA) was conducted to understand patterns of genetic diversity and structure across the three major ocean basins-the Indian, Atlantic and Pacific Oceans. Haplotype networks showed very shallow coalescence in most species, a finding previously reported for marine teleosts. Star topologies were predominant among sharks while complex mutational topologies predominated among rays, a finding we attribute to extremely limited dispersal in the early life history of rays. Population structuring varied amongst species groups, apparently due to differences in life history traits including reproductive philopatry, site fidelity, pelagic habitat, migratory habits, and dispersal ability. In comparison to reef-associated and demersal species, pelagic and semi pelagic species showed lower levels of structure between and within ocean basins. As expected, there is variation between taxa and groups, but there are also some broad patterns that can guide management and conservation strategies.
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Affiliation(s)
- Sudha Kottillil
- Centre for Ecological Sciences, Indian Institute of Science, Bengaluru, Karnataka, India
- Department of Energy and Environment, TERI School of Advanced Studies, New Delhi, India
| | - Chetan Rao
- Dakshin Foundation, Bengaluru, Karnataka, India
| | - Brian W. Bowen
- Hawai‘i Institute of Marine Biology, University of Hawaii, Kaneohe, Hawai‘i, United States of America
| | - Kartik Shanker
- Centre for Ecological Sciences, Indian Institute of Science, Bengaluru, Karnataka, India
- Dakshin Foundation, Bengaluru, Karnataka, India
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5
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Zhao X, Huang Y, Bian C, You X, Zhang X, Chen J, Wang M, Hu C, Xu Y, Xu J, Shi Q. Whole genome sequencing of the fast-swimming Southern bluefin tuna (Thunnus maccoyii). Front Genet 2022; 13:1020017. [DOI: 10.3389/fgene.2022.1020017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022] Open
Abstract
The economically important Southern bluefin tuna (Thunnus maccoyii) is a world-famous fast-swimming fish, but its genomic information is limited. Here, we performed whole genome sequencing and assembled a draft genome for Southern bluefin tuna, aiming to generate useful genetic data for comparative functional prediction. The final genome assembly is 806.54 Mb, with scaffold and contig N50 values of 3.31 Mb and 67.38 kb, respectively. Genome completeness was evaluated to be 95.8%. The assembled genome contained 23,403 protein-coding genes and 236.1 Mb of repeat sequences (accounting for 29.27% of the entire assembly). Comparative genomics analyses of this fast-swimming tuna revealed that it had more than twice as many hemoglobin genes (18) as other relatively slow-moving fishes (such as seahorse, sunfish, and tongue sole). These hemoglobin genes are mainly localized in two big clusters (termed as “MNˮ and “LAˮ respectively), which is consistent with other reported fishes. However, Thr39 of beta-hemoglobin in the MN cluster, conserved in other fishes, was mutated as cysteine in tunas including the Southern bluefin tuna. Since hemoglobins are reported to transport oxygen efficiently for aerobic respiration, our genomic data suggest that both high copy numbers of hemoglobin genes and an adjusted function of the beta-hemoglobin may support the fast-swimming activity of tunas. In summary, we produced a primary genome assembly and predicted hemoglobin-related roles for the fast-swimming Southern bluefin tuna.
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6
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Andrews AJ, Puncher GN, Bernal-Casasola D, Di Natale A, Massari F, Onar V, Toker NY, Hanke A, Pavey SA, Savojardo C, Martelli PL, Casadio R, Cilli E, Morales-Muñiz A, Mantovani B, Tinti F, Cariani A. Ancient DNA SNP-panel data suggests stability in bluefin tuna genetic diversity despite centuries of fluctuating catches in the eastern Atlantic and Mediterranean. Sci Rep 2021; 11:20744. [PMID: 34671077 PMCID: PMC8528830 DOI: 10.1038/s41598-021-99708-9] [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: 05/07/2021] [Accepted: 09/25/2021] [Indexed: 11/10/2022] Open
Abstract
Atlantic bluefin tuna (Thunnus thynnus; BFT) abundance was depleted in the late 20th and early 21st century due to overfishing. Historical catch records further indicate that the abundance of BFT in the Mediterranean has been fluctuating since at least the 16th century. Here we build upon previous work on ancient DNA of BFT in the Mediterranean by comparing contemporary (2009–2012) specimens with archival (1911–1926) and archaeological (2nd century BCE–15th century CE) specimens that represent population states prior to these two major periods of exploitation, respectively. We successfully genotyped and analysed 259 contemporary and 123 historical (91 archival and 32 archaeological) specimens at 92 SNP loci that were selected for their ability to differentiate contemporary populations or their association with core biological functions. We found no evidence of genetic bottlenecks, inbreeding or population restructuring between temporal sample groups that might explain what has driven catch fluctuations since the 16th century. We also detected a putative adaptive response, involving the cytoskeletal protein synemin which may be related to muscle stress. However, these results require further investigation with more extensive genome-wide data to rule out demographic changes due to overfishing, and other natural and anthropogenic factors, in addition to elucidating the adaptive drivers related to these.
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Affiliation(s)
- Adam J Andrews
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy. .,Department of Cultural Heritage, University of Bologna, Ravenna, Italy.
| | - Gregory N Puncher
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy. .,Department of Biological Sciences, Canadian Rivers Institute, University of New Brunswick, Saint John, NB, Canada.
| | - Darío Bernal-Casasola
- Department of History, Geography and Philosophy, Faculty of Philosophy and Letters, University of Cádiz, Cádiz, Spain
| | | | - Francesco Massari
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy
| | - Vedat Onar
- Osteoarcheology Practice and Research Centre and Faculty of Veterinary Medicine, Istanbul University-Cerrahpaşa, Avcılar, Istanbul, Turkey
| | - Nezir Yaşar Toker
- Osteoarcheology Practice and Research Centre and Faculty of Veterinary Medicine, Istanbul University-Cerrahpaşa, Avcılar, Istanbul, Turkey
| | - Alex Hanke
- St. Andrews Biological Station, Fisheries and Oceans Canada, St. Andrews, NB, Canada
| | - Scott A Pavey
- Department of Biological Sciences, Canadian Rivers Institute, University of New Brunswick, Saint John, NB, Canada
| | | | | | - Rita Casadio
- Biocomputing Group, University of Bologna, Bologna, Italy
| | - Elisabetta Cilli
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | | | - Barbara Mantovani
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Fausto Tinti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy
| | - Alessia Cariani
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy
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7
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Christiansen H, Heindler FM, Hellemans B, Jossart Q, Pasotti F, Robert H, Verheye M, Danis B, Kochzius M, Leliaert F, Moreau C, Patel T, Van de Putte AP, Vanreusel A, Volckaert FAM, Schön I. Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing. BMC Genomics 2021; 22:625. [PMID: 34418978 PMCID: PMC8380342 DOI: 10.1186/s12864-021-07917-3] [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: 04/02/2021] [Accepted: 07/26/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Genome-wide data are invaluable to characterize differentiation and adaptation of natural populations. Reduced representation sequencing (RRS) subsamples a genome repeatedly across many individuals. However, RRS requires careful optimization and fine-tuning to deliver high marker density while being cost-efficient. The number of genomic fragments created through restriction enzyme digestion and the sequencing library setup must match to achieve sufficient sequencing coverage per locus. Here, we present a workflow based on published information and computational and experimental procedures to investigate and streamline the applicability of RRS. RESULTS In an iterative process genome size estimates, restriction enzymes and size selection windows were tested and scaled in six classes of Antarctic animals (Ostracoda, Malacostraca, Bivalvia, Asteroidea, Actinopterygii, Aves). Achieving high marker density would be expensive in amphipods, the malacostracan target taxon, due to the large genome size. We propose alternative approaches such as mitogenome or target capture sequencing for this group. Pilot libraries were sequenced for all other target taxa. Ostracods, bivalves, sea stars, and fish showed overall good coverage and marker numbers for downstream population genomic analyses. In contrast, the bird test library produced low coverage and few polymorphic loci, likely due to degraded DNA. CONCLUSIONS Prior testing and optimization are important to identify which groups are amenable for RRS and where alternative methods may currently offer better cost-benefit ratios. The steps outlined here are easy to follow for other non-model taxa with little genomic resources, thus stimulating efficient resource use for the many pressing research questions in molecular ecology.
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Affiliation(s)
- Henrik Christiansen
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium.
| | - Franz M Heindler
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
| | - Bart Hellemans
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
| | - Quentin Jossart
- Marine Biology Group, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | | | - Henri Robert
- OD Nature, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Marie Verheye
- OD Nature, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Bruno Danis
- Marine Biology Laboratory, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Marc Kochzius
- Marine Biology Group, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Frederik Leliaert
- Marine Biology Research Group, Ghent University, Ghent, Belgium.,Meise Botanic Garden, Meise, Belgium
| | - Camille Moreau
- Marine Biology Laboratory, Université Libre de Bruxelles (ULB), Brussels, Belgium.,Université de Bourgogne Franche-Comté (UBFC) UMR CNRS 6282 Biogéosciences, Dijon, France
| | - Tasnim Patel
- OD Nature, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Anton P Van de Putte
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium.,OD Nature, Royal Belgian Institute of Natural Sciences, Brussels, Belgium.,Marine Biology Laboratory, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Ann Vanreusel
- Marine Biology Research Group, Ghent University, Ghent, Belgium
| | - Filip A M Volckaert
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
| | - Isa Schön
- OD Nature, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
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8
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Yüncü E, Açan SC, Onar V, Karakulak FS, Gökoğlu M, Alıçlı TZ, Chiriboga F, Togan İ, Özer F. Demography of swordfish (Xiphias gladius Linneus) populations from the coasts of Turkey, based on mitochondrial DNA and microsatellites. JOURNAL OF FISH BIOLOGY 2021; 99:37-48. [PMID: 33559126 DOI: 10.1111/jfb.14696] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 02/08/2021] [Indexed: 06/12/2023]
Abstract
The genetic diversity of the Mediterranean swordfish (Xiphias gladius Linneus) has not been explored extensively at its easternmost range so far. In this study, modern X. gladius samples from the eastern part of the Mediterranean basin, north of the Aegean Sea (Aegean-2013, n = 26) and the Mediterranean coast of Turkey (N.Levantine-2013, n = 42) were studied genetically, along with ancient samples from Yenikapı excavation (n = 6). Partial mitochondrial DNA control region sequences (entire sequences, clade I and clade II) were evaluated spatially and temporally together with previously published sequences (Alvarado Bremer et al., Molecular Phylogenetics and Evolution, 2005, 36, 169-187; Viñas et al., ICES Journal of Marine Science, 2010, 67, 1222-1229; Righi et al., Diversity, 2020, 12, 170) from the rest of the Mediterranean Sea. Pair-wise FST and pair-wise AMOVA tests showed that, in general, groups of eastern populations and western Mediterranean populations have not genetically differed from each other significantly nearly in the past 20 years. Therefore, the results direct reconsideration of previous descriptions of population sub-structure within the Mediterranean and support high gene flow throughout the region. On the contrary, the results of this study confirmed the existence of genetic diversity differences between western and eastern Mediterranean, with eastern being low. One-tailed permutation tests revealed that θ, which is directly proportional to long-term female effective population size (Ne), decreased significantly (P < 0.05) in both regions over the past two decades. On the Turkish coasts, θ is not significantly different from that of the nearly contemporary eastern Mediterranean population. Nonetheless, θ of the ancient sample was consistently and significantly (P < 0.001) higher than those of the eastern and western Mediterranean populations in clade I and clade II. Furthermore, it contains two mitochondrial haplotypes that are not observed in modern samples, suggesting that the Ne of X. gladius in the eastern was high in Byzantium times. Eight microsatellite loci were also genotyped in modern samples. The microsatellite-based present Ne estimate of the pooled Aegean-2013 and N.Levantine-2013 populations was lower than 1000 according to the upper limit of 95% c.i. and possibly even lower than 100 according to the mean of posterior distribution of the present Ne estimate calculated by the software package MSVAR. These alarming genetic signals for the sustainability of X. gladius on the coasts of Turkey are in agreement with the nearly collapsing X. gladius fisheries as depicted also in the fisheries statistics. Overall, congruent with the previous studies, the data presented here show that sustainability of the X. gladius population in Mediterranean is under major threat. Therefore, X. gladius around the Turkish coasts need an immediate stringent action and management plan.
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Affiliation(s)
- Eren Yüncü
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Sinan Can Açan
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Vedat Onar
- Department of Anatomy, Faculty of Veterinary Medicine, Istanbul University-Cerrahpaşa, Istanbul, Turkey
| | - F Saadet Karakulak
- Department of Fisheries Technology Management, Faculty of Aquatic Sciences, Istanbul University, Istanbul, Turkey
| | - Mehmet Gökoğlu
- Department of Aquaculture, Faculty of Fisheries, Akdeniz University, Antalya, Turkey
| | - Turgut Zahit Alıçlı
- Department of Fisheries Technology Management, Faculty of Aquatic Sciences, Istanbul University, Istanbul, Turkey
| | - Fidel Chiriboga
- Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, ETH Zurich, Zurich, Switzerland
| | - İnci Togan
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Füsun Özer
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
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9
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Johnstone C, Pérez M, Malca E, Quintanilla JM, Gerard T, Lozano-Peral D, Alemany F, Lamkin J, García A, Laiz-Carrión R. Genetic connectivity between Atlantic bluefin tuna larvae spawned in the Gulf of Mexico and in the Mediterranean Sea. PeerJ 2021; 9:e11568. [PMID: 34178457 PMCID: PMC8210807 DOI: 10.7717/peerj.11568] [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: 10/16/2020] [Accepted: 05/16/2021] [Indexed: 12/11/2022] Open
Abstract
The highly migratory Atlantic bluefin tuna (ABFT) is currently managed as two distinct stocks, in accordance with natal homing behavior and population structuring despite the absence of barriers to gene flow. Larval fish are valuable biological material for tuna molecular ecology. However, they have hardly been used to decipher the ABFT population structure, although providing the genetic signal from successful breeders. For the first time, cooperative field collection of tuna larvae during 2014 in the main spawning area for each stock, the Gulf of Mexico (GOM) and the Mediterranean Sea (MED), enabled us to assess the ABFT genetic structure in a precise temporal and spatial frame exclusively through larvae. Partitioning of genetic diversity at nuclear microsatellite loci and in the mitochondrial control region in larvae spawned contemporarily resulted in low significant fixation indices supporting connectivity between spawners in the main reproduction area for each population. No structuring was detected within the GOM after segregating nuclear diversity in larvae spawned in two hydrographically distinct regions, the eastern GOM (eGOM) and the western GOM (wGOM), with the larvae from eGOM being more similar to those collected in the MED than the larvae from wGOM. We performed clustering of genetically characterized ABFT larvae through Bayesian analysis and by Discriminant Analysis of Principal Components (DAPC) supporting the existence of favorable areas for mixing of ABFT spawners from Western and Eastern stocks, leading to gene flow and apparent connectivity between weakly structured populations. Our findings suggest that the eastern GOM is more prone for the mixing of breeders from the two ABFT populations. Conservation of this valuable resource exploited for centuries calls for intensification of tuna ichthyoplankton research and standardization of genetic tools for monitoring population dynamics.
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Affiliation(s)
- Carolina Johnstone
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, Consejo Superior de Investigaciones Científicas, Fuengirola, Málaga, Spain
| | - Montse Pérez
- Centro Oceanográfico de Vigo, Instituto Español de Oceanografía, Consejo Superior de Investigaciones Científicas, Vigo, Pontevedra, Spain
| | - Estrella Malca
- Cooperative Institute for Marine and Atmospheric Studies, University of Miami, Miami, Florida, United States of America.,Southeast Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Miami, Florida, United States of America
| | - José María Quintanilla
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, Consejo Superior de Investigaciones Científicas, Fuengirola, Málaga, Spain
| | - Trika Gerard
- Southeast Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Miami, Florida, United States of America
| | - Diego Lozano-Peral
- Centro de Supercomputación y Bioinnovación, Servicios Centrales de Apoyo a la Investigación, Universidad de Málaga, Málaga, Spain
| | - Francisco Alemany
- International Commision for the Conservation of Atlantic Tunas, Madrid, Spain
| | - John Lamkin
- Southeast Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Miami, Florida, United States of America
| | - Alberto García
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, Consejo Superior de Investigaciones Científicas, Fuengirola, Málaga, Spain
| | - Raúl Laiz-Carrión
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, Consejo Superior de Investigaciones Científicas, Fuengirola, Málaga, Spain
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10
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Vaux F, Bohn S, Hyde JR, O'Malley KG. Adaptive markers distinguish North and South Pacific Albacore amid low population differentiation. Evol Appl 2021; 14:1343-1364. [PMID: 34025772 PMCID: PMC8127716 DOI: 10.1111/eva.13202] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 12/19/2022] Open
Abstract
Albacore (Thunnus alalunga) support an economically valuable global fishery, but surprisingly little is known about the population structure of this highly migratory species. Physical tagging data suggest that Albacore from the North and South Pacific Ocean are separate stocks, but results from previous genetic studies did not support this two stock hypothesis. In addition, observed biological differences among juveniles suggest that there may be population substructure in the North Pacific. We used double-digest restriction site-associated DNA sequencing to assess population structure among 308 Albacore caught in 12 sample areas across the Pacific Ocean (10 North, 2 South). Since Albacore are highly migratory and spawning areas are unknown, sample groups were not assumed to be equivalent to populations and the genetic data were analyzed iteratively. We tested for putatively adaptive differences among groups and for genetic variation associated with sex. Results indicated that Albacore in the North and South Pacific can be distinguished using 84 putatively adaptive loci, but not using the remaining 12,788 presumed neutral sites. However, two individuals likely represent F1 hybrids between the North and South Pacific populations, and 43 Albacore potentially exhibit lower degrees of mixed ancestry. In addition, four or five cross-hemisphere migrants were potentially identified. No genetic evidence was found for population substructure within the North Pacific, and no loci appeared to distinguish males from females. Potential functions for the putatively adaptive loci were identified, but an annotated Albacore genome is required for further exploration. Future research should try to locate spawning areas so that life history, demography, and genetic population structure can be linked and spatiotemporal patterns can be investigated.
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Affiliation(s)
- Felix Vaux
- State Fisheries Genomics LabCoastal Oregon Marine Experiment StationDepartment of Fisheries and WildlifeHatfield Marine Science CenterOregon State UniversityNewportORUSA
- Department of ZoologyUniversity of OtagoDunedinNew Zealand
| | - Sandra Bohn
- State Fisheries Genomics LabCoastal Oregon Marine Experiment StationDepartment of Fisheries and WildlifeHatfield Marine Science CenterOregon State UniversityNewportORUSA
| | - John R. Hyde
- Southwest Fisheries Science CenterNational Marine Fisheries ServiceLa JollaCAUSA
| | - Kathleen G. O'Malley
- State Fisheries Genomics LabCoastal Oregon Marine Experiment StationDepartment of Fisheries and WildlifeHatfield Marine Science CenterOregon State UniversityNewportORUSA
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11
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Brophy D, Rodríguez-Ezpeleta N, Fraile I, Arrizabalaga H. Combining genetic markers with stable isotopes in otoliths reveals complexity in the stock structure of Atlantic bluefin tuna (Thunnus thynnus). Sci Rep 2020; 10:14675. [PMID: 32895410 PMCID: PMC7477220 DOI: 10.1038/s41598-020-71355-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 08/13/2020] [Indexed: 11/09/2022] Open
Abstract
Atlantic bluefin tuna (Thunnus thynnus) from the two main spawning populations in the Mediterranean and Gulf of Mexico occur together in the western, central and eastern Atlantic. Stock composition of catches from mixing areas is uncertain, presenting a major challenge to the sustainable management of the fisheries. This study combines genetic and chemical markers to develop an integrated method of population assignment. Stable isotope signatures (δ13C and δ18O) in the otolith core of adults from the two main spawning populations (adult baselines) showed less overlap than those of yearlings (12-18 months old) from western and eastern nursery areas suggesting that some exchange occurs towards the end of the yearling phase. The integrated model combined δ18O with four genetic markers (SNPs) to distinguish the adult baselines with greater accuracy than chemical or genetic markers alone. When used to assign individuals from the mixing areas to their population of origin, the integrated model resolved some (but not all) discrepancies between the chemistry and genetic methods. Some individuals in the mixing area had otolith δ18O values and genetic profiles which when taken together, were not representative of either population. These fish may originate from another Atlantic spawning area or may represent population contingents that move away from the main spawning areas during the first year of life. This complexity in stock structure is not captured by the current two-stock model.
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Affiliation(s)
- Deirdre Brophy
- Marine and Freshwater Research Centre, Galway Mayo Institute of Technology, Dublin road, Galway, H91 T8NW, Ireland.
| | | | - Igaratza Fraile
- Marine Research Division, AZTI, Txatxarramendi Ugartea Z/G, 48395, Sukarrieta, Bizkaia, Spain
| | - Haritz Arrizabalaga
- Marine Research Division, AZTI, Txatxarramendi Ugartea Z/G, 48395, Sukarrieta, Bizkaia, Spain
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