1
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Caccavo JA, Arantes LS, Celemín E, Mbedi S, Sparmann S, Mazzoni CJ. Whole-genome resequencing improves the utility of otoliths as a critical source of DNA for fish stock research and monitoring. Mol Ecol Resour 2024:e14013. [PMID: 39233613 DOI: 10.1111/1755-0998.14013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 07/23/2024] [Accepted: 08/15/2024] [Indexed: 09/06/2024]
Abstract
Fish ear bones, known as otoliths, are often collected in fisheries to assist in management, and are a common sample type in museum and national archives. Beyond their utility for ageing, morphological and trace element analysis, otoliths are a repository of valuable genomic information. Previous work has shown that DNA can be extracted from the trace quantities of tissue remaining on the surface of otoliths, despite the fact that they are often stored dry at room temperature. However, much of this work has used reduced representation sequencing methods in clean lab conditions, to achieve adequate yields of DNA, libraries and ultimately single-nucleotide polymorphisms (SNPs). Here, we pioneer the use of small-scale (spike-in) sequencing to screen contemporary otolith samples prepared in regular molecular biology (in contrast to clean) laboratories for contamination and quality levels, submitting for whole-genome resequencing only samples above a defined endogenous DNA threshold. Despite the typically low quality and quantity of DNA extracted from otoliths, we are able to produce whole-genome libraries and ultimately sets of filtered, unlinked and even putatively adaptive SNPs of ample numbers for downstream uses in population, climate and conservation genomics. By comparing with a set of tissue samples from the same species, we are able to highlight the quality and efficacy of otolith samples from DNA extraction and library preparation, to bioinformatic preprocessing and SNP calling. We provide detailed schematics, protocols and scripts of our approach, such that it can be adopted widely by the community, improving the use of otoliths as a source of valuable genomic data.
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Affiliation(s)
- Jilda Alicia Caccavo
- Berlin Center for Genomics in Biodiversity Research, BeGenDiv, Berlin, Germany
- Department of Evolutionary Genetics, Leibniz-Institut für Zoo- und Wildtierforschung, IZW, Berlin, Germany
| | - Larissa S Arantes
- Berlin Center for Genomics in Biodiversity Research, BeGenDiv, Berlin, Germany
- Department of Evolutionary Genetics, Leibniz-Institut für Zoo- und Wildtierforschung, IZW, Berlin, Germany
| | - Enrique Celemín
- Institute of Biochemistry and Biology, Evolutionary Biology & Systematic Zoology, University of Potsdam, Potsdam, Germany
| | - Susan Mbedi
- Berlin Center for Genomics in Biodiversity Research, BeGenDiv, Berlin, Germany
- Museum für Naturkunde, Berlin, Germany
| | - Sarah Sparmann
- Berlin Center for Genomics in Biodiversity Research, BeGenDiv, Berlin, Germany
- Leibniz-Institut für Gewässerökologie und Binnenfischerei (IGB), Berlin, Germany
| | - Camila J Mazzoni
- Berlin Center for Genomics in Biodiversity Research, BeGenDiv, Berlin, Germany
- Department of Evolutionary Genetics, Leibniz-Institut für Zoo- und Wildtierforschung, IZW, Berlin, Germany
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2
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Pampoulie C, Berg PR, Jentoft S. Hidden but revealed: After years of genetic studies behavioural monitoring combined with genomics uncover new insight into the population dynamics of Atlantic cod in Icelandic waters. Evol Appl 2023; 16:223-233. [PMID: 36793686 PMCID: PMC9923494 DOI: 10.1111/eva.13471] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 05/29/2022] [Accepted: 08/18/2022] [Indexed: 11/27/2022] Open
Abstract
Stock structure is of paramount importance for sustainable management of exploited resources. In that context, genetic markers have been used for more than two decades to resolve spatial structure of marine exploited resources and to fully fathom stock dynamics and interactions. While genetic markers such as allozymes and RFLP dominated the debate in the early era of genetics, technology advances have provided scientists with new tools every decade to better assess stock discrimination and interactions (i.e. gene flow). Here, we provide a review of genetic studies performed to understand stock structure of Atlantic cod in Icelandic waters, from the early allozyme approaches to the genomic work currently carried out. We further highlight the importance of the generation of a chromosome-anchored genome assembly together with whole-genome population data, which drastically changed our perception of the possible management units to consider. After nearly 60 years of genetic investigation of Atlantic cod structure in Icelandic waters, genetic (and later genomic) data combined with behavioural monitoring using Data Storage Tags shifted the attention from geographical population structures to behavioural ecotypes. This review also demonstrates the need for future research to further disentangle the impact of these ecotypes (and gene flow among them) on the population structure of Atlantic cod in Icelandic waters. It also highlights the importance of whole-genome data to unravel unexpected within-species diversity related to chromosomal inversions and associated supergenes, which are important to consider for future development of sustainable management programmes of the species within the North Atlantic.
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Affiliation(s)
| | - Paul Ragnar Berg
- Norwegian Institute for Water ResearchOsloNorway
- Department of Natural Sciences, Centre for Coastal Research (CCR)University of AgderKristiansandNorway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary SynthesisOsloNorway
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3
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Jansson E, Faust E, Bekkevold D, Quintela M, Durif C, Halvorsen KT, Dahle G, Pampoulie C, Kennedy J, Whittaker B, Unneland L, Post S, André C, Glover KA. Global, regional, and cryptic population structure in a high gene-flow transatlantic fish. PLoS One 2023; 18:e0283351. [PMID: 36940210 PMCID: PMC10027230 DOI: 10.1371/journal.pone.0283351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 03/07/2023] [Indexed: 03/21/2023] Open
Abstract
Lumpfish (Cyclopterus lumpus) is a transatlantic marine fish displaying large population sizes and a high potential for dispersal and gene-flow. These features are expected to result in weak population structure. Here, we investigated population genetic structure of lumpfish throughout its natural distribution in the North Atlantic using two approaches: I) 4,393 genome wide SNPs and 95 individuals from 10 locations, and II) 139 discriminatory SNPs and 1,669 individuals from 40 locations. Both approaches identified extensive population genetic structuring with a major split between the East and West Atlantic and a distinct Baltic Sea population, as well as further differentiation of lumpfish from the English Channel, Iceland, and Greenland. The discriminatory loci displayed ~2-5 times higher divergence than the genome wide approach, revealing further evidence of local population substructures. Lumpfish from Isfjorden in Svalbard were highly distinct but resembled most fish from Greenland. The Kattegat area in the Baltic transition zone, formed a previously undescribed distinct genetic group. Also, further subdivision was detected within North America, Iceland, West Greenland, Barents Sea, and Norway. Although lumpfish have considerable potential for dispersal and gene-flow, the observed high levels of population structuring throughout the Atlantic suggests that this species may have a natal homing behavior and local populations with adaptive differences. This fine-scale population structure calls for consideration when defining management units for exploitation of lumpfish stocks and in decisions related to sourcing and moving lumpfish for cleaner fish use in salmonid aquaculture.
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Affiliation(s)
- Eeva Jansson
- Institute of Marine Research, Nordnes, Bergen, Norway
| | - Ellika Faust
- Department of Marine Sciences - Tjärnö Marine Laboratory, University of Gothenburg, Strömstad, Sweden
| | - Dorte Bekkevold
- DTU-Aqua National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark
| | | | - Caroline Durif
- Institute of Marine Research, Austevoll Research Station, Storebø, Norway
| | | | - Geir Dahle
- Institute of Marine Research, Nordnes, Bergen, Norway
| | | | - James Kennedy
- Marine and Freshwater Research Institute, Hafnarfjörður, Iceland
| | - Benjamin Whittaker
- Department of Biosciences, Centre for Sustainable Aquatic Research, Swansea University, Swansea, United Kingdom
| | | | - Søren Post
- Greenland Institute of Natural Resources, Nuuk, Greenland
| | - Carl André
- Department of Marine Sciences - Tjärnö Marine Laboratory, University of Gothenburg, Strömstad, Sweden
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4
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Righi T, Splendiani A, Fioravanti T, Petetta A, Candelma M, Gioacchini G, Gillespie K, Hanke A, Carnevali O, Caputo Barucchi V. Mediterranean swordfish ( Xiphias gladius Linnaeus, 1758) population structure revealed by microsatellite DNA: genetic diversity masked by population mixing in shared areas. PeerJ 2020; 8:e9518. [PMID: 33194325 PMCID: PMC7394060 DOI: 10.7717/peerj.9518] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 06/19/2020] [Indexed: 11/20/2022] Open
Abstract
Background The Mediterranean swordfish stock is overfished and considered not correctly managed. Elucidating the patterns of the Mediterranean swordfish population structure constitutes an essential prerequisite for effective management of this fishery resource. To date, few studies have investigated intra-Mediterranean swordfish population structure, and their conclusions are controversial. Methods A panel of 20 microsatellites DNA was used to investigate fine-scale population structuring of swordfish from six main fishing areas of the Mediterranean Sea. Results This study provides evidence to reject the hypothesis of a single swordfish population within the Mediterranean Sea. DAPC analysis revealed the presence of three genetic clusters and a high level of admixture within the Mediterranean Sea. Genetic structure was supported by significant FST values while mixing was endorsed by the heterozygosity deficit observed in sampling localities indicative of a possible Wahlund effect, by sampling admixture individuals. Overall, our tests reject the hypothesis of a single swordfish population within the Mediterranean Sea. Homing towards the Mediterranean breeding areas may have generated a weak degree of genetic differentiation between populations even at the intra-basin scale.
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Affiliation(s)
- Tommaso Righi
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Andrea Splendiani
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Tatiana Fioravanti
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Andrea Petetta
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Michela Candelma
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Giorgia Gioacchini
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Kyle Gillespie
- Fisheries and Oceans Canada, St. Andrews Biological Station, Ottawa, Canada
| | - Alex Hanke
- Fisheries and Oceans Canada, St. Andrews Biological Station, Ottawa, Canada
| | - Oliana Carnevali
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Vincenzo Caputo Barucchi
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
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5
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Anisakid nematode larvae in the liver of Atlantic cod Gadus morhua L. from West Greenland. Parasitol Res 2020; 119:3233-3241. [PMID: 32656658 DOI: 10.1007/s00436-020-06807-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 07/06/2020] [Indexed: 10/23/2022]
Abstract
Anisakid nematode larvae occur frequently in the liver of Atlantic cod, but merely few infection data from cod in waters around Greenland exist. The present study reports the occurrence of third-stage anisakid larvae in the livers of 200 Atlantic cod caught on fishing grounds along the West coast of Greenland (fjord systems of Maniitsoq) in May, June, August and September 2017. Classical and molecular helminthological techniques were used to identify the nematodes. A total of 200 cod livers were examined, and 194 were infected with third-stage nematode larvae (overall prevalence of infection 97%) with a mean intensity of 10.3 (range between 1 and 44 parasites per fish). Prevalences recorded were 96% for Anisakis simplex (s.l.), 55% for Pseudoterranova decipiens (s.l.) and 8% for Contracaecum osculatum (s.l.). Sequencing the mtDNA cox2 from 8 out of 23 these latter larvae conferred these to C. osculatum sp. B. A clear seasonal variation was observed, with a rise in A. simplex (s.l.) and P. decipiens (s.l.) occurrence in June and August and a decline in September. The study may serve as a baseline for future investigations using the three anisakids as biological indicators in Greenland waters.
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6
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Hawkins AD, Picciulin M. The importance of underwater sounds to gadoid fishes. THE JOURNAL OF THE ACOUSTICAL SOCIETY OF AMERICA 2019; 146:3536. [PMID: 31795661 DOI: 10.1121/1.5134683] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 10/30/2019] [Indexed: 06/10/2023]
Abstract
The codfish family includes more than 500 species that vary greatly in their abundance in areas like the North Sea and are widely fished. Gadoids (codfish) gather at particular locations to spawn, where they exhibit complex reproductive behavior with visual and acoustic displays. Calls have been described from seven species, including the Atlantic cod and haddock. They vocalize by means of a specialized apparatus, consisting of rapidly contracting striated muscles (the drumming muscles) attached to the gas-filled swim bladder. Several gadoids, such as the ling and the Greenland cod, possess drumming muscles and are likely to make sounds. Non-vocal gadoids, such as the poor cod, lack these muscles. It is suggested that the sonic apparatus was present in the early species of the gadoids, with some species having lost their sonic ability. Interestingly, silent gadoids are mainly small schooling fishes. Gadoid species are most sensitive to sounds from 30 to 500 Hz. Gadoid hearing can be masked by ambient sound but also by anthropogenic sounds, which may therefore adversely affect their reproduction, with potential effects upon discrete local stocks. Listening for gadoid sounds provides a reliable, non-invasive way of locating spawning sites, which can enhance the protection of reproducing fish from human impacts.
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Affiliation(s)
- Anthony D Hawkins
- Aquatic Noise Trust, Kincraig, Blairs, Aberdeen AB12 5YT, United Kingdom
| | - Marta Picciulin
- Department of Environmental Sciences, Informatics and Statistics, Ca' Foscari University of Venice, Via Torino 155, 30172 Venezia Mestre, Italy
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7
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Barth JMI, Villegas-Ríos D, Freitas C, Moland E, Star B, André C, Knutsen H, Bradbury I, Dierking J, Petereit C, Righton D, Metcalfe J, Jakobsen KS, Olsen EM, Jentoft S. Disentangling structural genomic and behavioural barriers in a sea of connectivity. Mol Ecol 2019; 28:1394-1411. [PMID: 30633410 PMCID: PMC6518941 DOI: 10.1111/mec.15010] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 12/21/2018] [Accepted: 12/27/2018] [Indexed: 12/17/2022]
Abstract
Genetic divergence among populations arises through natural selection or drift and is counteracted by connectivity and gene flow. In sympatric populations, isolating mechanisms are thus needed to limit the homogenizing effects of gene flow to allow for adaptation and speciation. Chromosomal inversions act as an important mechanism maintaining isolating barriers, yet their role in sympatric populations and divergence with gene flow is not entirely understood. Here, we revisit the question of whether inversions play a role in the divergence of connected populations of the marine fish Atlantic cod (Gadus morhua), by exploring a unique data set combining whole‐genome sequencing data and behavioural data obtained with acoustic telemetry. Within a confined fjord environment, we find three genetically differentiated Atlantic cod types belonging to the oceanic North Sea population, the western Baltic population and a local fjord‐type cod. Continuous behavioural tracking over 4 year revealed temporally stable sympatry of these types within the fjord. Despite overall weak genetic differentiation consistent with high levels of gene flow, we detected significant frequency shifts of three previously identified inversions, indicating an adaptive barrier to gene flow. In addition, behavioural data indicated that North Sea cod and individuals homozygous for the LG12 inversion had lower fitness in the fjord environment. However, North Sea and fjord‐type cod also occupy different depths, possibly contributing to prezygotic reproductive isolation and representing a behavioural barrier to gene flow. Our results provide the first insights into a complex interplay of genomic and behavioural isolating barriers in Atlantic cod and establish a new model system towards an understanding of the role of genomic structural variants in adaptation and diversification.
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Affiliation(s)
- Julia M I Barth
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway.,Zoological Institute, University of Basel, Basel, Switzerland
| | - David Villegas-Ríos
- Department of Ecology and Marine Resources, Mediterranean Institute for Advanced Studies, IMEDEA CSIC-UIB, Esporles, Spain.,Department of Ecology and Marine Resources, Institute of Marine Research, (IIM CSIC), Vigo, Spain
| | - Carla Freitas
- Institute for Marine Research, Flødevigen, Norway.,Centre for Coastal Research, University of Agder, Agder, Norway.,Oceanic Observatory of Madeira, Funchal, Portugal
| | - Even Moland
- Institute for Marine Research, Flødevigen, Norway.,Centre for Coastal Research, University of Agder, Agder, Norway
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Carl André
- Department of Marine Sciences - Tjärnö, University of Gothenburg, Gothenburg, Sweden
| | - Halvor Knutsen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway.,Institute for Marine Research, Flødevigen, Norway.,Centre for Coastal Research, University of Agder, Agder, Norway
| | - Ian Bradbury
- Science Branch, Fisheries and Oceans Canada, St. John's, Newfoundland and Labrador, Canada
| | - Jan Dierking
- GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | | | - David Righton
- Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Lowestoft, UK
| | - Julian Metcalfe
- Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Lowestoft, UK
| | - Kjetill S Jakobsen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Esben M Olsen
- Institute for Marine Research, Flødevigen, Norway.,Centre for Coastal Research, University of Agder, Agder, Norway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
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8
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Árnason E, Halldórsdóttir K. Codweb: Whole-genome sequencing uncovers extensive reticulations fueling adaptation among Atlantic, Arctic, and Pacific gadids. SCIENCE ADVANCES 2019; 5:eaat8788. [PMID: 30906856 PMCID: PMC6426462 DOI: 10.1126/sciadv.aat8788] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Accepted: 02/04/2019] [Indexed: 05/11/2023]
Abstract
Introgressive hybridization creates networks of genetic relationships across species. Among marine fish of the Gadidae family, Pacific cod and walleye pollock are separate invasions of an Atlantic cod ancestor into the Pacific. Cods are ecological success stories, and their ecologies allow them to support the largest fisheries of the world. The enigmatic walleye pollock differs morphologically, behaviorally, and ecologically from its relatives, representing a niche shift. Here, we apply whole-genome sequencing to Pacific, Arctic, and Atlantic gadids and reveal extensive introgression among them with the ABBA-BABA test and pseudolikelihood phylogenetic network analysis. We propose that walleye pollock resulted from extensive adaptive introgression or homoploid hybrid speciation. The path of evolution of these taxa is more web than a tree. Their ability to invade and expand into new habitats and become ecologically successful may depend on genes acquired through adaptive introgression or hybrid speciation.
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Affiliation(s)
- Einar Árnason
- Institute of Life and Environmental Sciences, University of Iceland, Sturlugata 7, 101 Reykjavík, Iceland
- Department of Organismal and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Katrín Halldórsdóttir
- Institute of Life and Environmental Sciences, University of Iceland, Sturlugata 7, 101 Reykjavík, Iceland
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9
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Fairweather R, Bradbury IR, Helyar SJ, de Bruyn M, Therkildsen NO, Bentzen P, Hemmer‐Hansen J, Carvalho GR. Range-wide genomic data synthesis reveals transatlantic vicariance and secondary contact in Atlantic cod. Ecol Evol 2018; 8:12140-12152. [PMID: 30598806 PMCID: PMC6303715 DOI: 10.1002/ece3.4672] [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: 07/25/2018] [Revised: 09/20/2018] [Accepted: 09/24/2018] [Indexed: 11/11/2022] Open
Abstract
Recent advances in genetic and genomic analysis have greatly improved our understanding of spatial population structure in marine species. However, studies addressing phylogeographic patterns at oceanic spatial scales remain rare. In Atlantic cod (Gadus morhua), existing range-wide examinations suggest significant transatlantic divergence, although the fine-scale contemporary distribution of populations and potential for secondary contact are largely unresolved. Here, we explore transatlantic phylogeography in Atlantic cod using a data-synthesis approach, integrating multiple genome-wide single-nucleotide polymorphism (SNP) datasets representative of different regions to create a single range-wide dataset containing 1,494 individuals from 54 locations and genotyped at 796 common loci. Our analysis highlights significant transatlantic divergence and supports the hypothesis of westward post-glacial colonization of Greenland from the East Atlantic. Accordingly, our analysis suggests the presence of transatlantic secondary contact off eastern North America and supports existing perspectives on the phylogeographic history of Atlantic cod with an unprecedented combination of genetic and geographic resolution. Moreover, we demonstrate the utility of integrating distinct SNP databases of high comparability.
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Affiliation(s)
- Robert Fairweather
- Department of BiologyDalhousie UniversityHalifaxNova ScotiaCanada
- School of Biological SciencesBangor UniversityBangorUK
| | - Ian R. Bradbury
- Science Branch, Department of FisheriesSt John’s, Newfoundland and LabradorCanada
| | - Sarah J. Helyar
- Institute of Global Food SecurityQueen’s University BelfastBelfastUK
| | - Mark de Bruyn
- School of Biological SciencesBangor UniversityBangorUK
- School of Life and Environmental SciencesThe University of SydneySydneyNew South WalesAustralia
| | | | - Paul Bentzen
- Department of BiologyDalhousie UniversityHalifaxNova ScotiaCanada
| | - Jakob Hemmer‐Hansen
- Section for Marine Living Resources, National Institute for Aquatic ResourcesTechnical University of DenmarkSilkeborgDenmark
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10
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McDowell JR, Brightman HL. High level of genetic connectivity in a deep-water reef fish, Caulolatilus microps. JOURNAL OF FISH BIOLOGY 2018; 93:766-777. [PMID: 30168143 DOI: 10.1111/jfb.13779] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 08/02/2018] [Indexed: 06/08/2023]
Abstract
The life-history characteristics of blueline tilefish make them particularly vulnerable to overfishing. Although North Carolina, U.S.A. was previously considered to be the northern extent of the range of C. microps, concentrations have recently been discovered in Virginia and Maryland, with reports as far north as Montauk, New York. Attempts to manage the fishery have been hampered by a lack of information about whether the U.S. East Coast includes multiple stocks. To assess the appropriateness of alternate management options, we used 25 variable microsatellite loci and sequencing of the mitochondrial (mt)DNA control region (CR) to evaluate the genetic structure of 490 C. microps sampled from across the U.S. East Coast range. Pairwise comparisons of genetic differentiation among collection locations based on both nuclear microsatellite and mtCR sequence data were all low and non significant. No significant autocorrelation was observed across multiple distance classes, consistent with widespread dispersal., Although the assumed sedentary nature of adult C. microps suggests population structuring, the genetic data were consistent with the presence of sufficient gene flow to prevent the accumulation of significant genetic differences and supports management of C. microps as a single stock along the U.S. East Coast.
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Affiliation(s)
- Jan R McDowell
- Department of Fisheries Science, Virginia Institute of Marine Science, College of William & Mary, Gloucester Point, Virginia
| | - Heid L Brightman
- Department of Fisheries Science, Virginia Institute of Marine Science, College of William & Mary, Gloucester Point, Virginia
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11
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Carroll EL, Bruford MW, DeWoody JA, Leroy G, Strand A, Waits L, Wang J. Genetic and genomic monitoring with minimally invasive sampling methods. Evol Appl 2018; 11:1094-1119. [PMID: 30026800 PMCID: PMC6050181 DOI: 10.1111/eva.12600] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 01/02/2018] [Indexed: 12/12/2022] Open
Abstract
The decreasing cost and increasing scope and power of emerging genomic technologies are reshaping the field of molecular ecology. However, many modern genomic approaches (e.g., RAD-seq) require large amounts of high-quality template DNA. This poses a problem for an active branch of conservation biology: genetic monitoring using minimally invasive sampling (MIS) methods. Without handling or even observing an animal, MIS methods (e.g., collection of hair, skin, faeces) can provide genetic information on individuals or populations. Such samples typically yield low-quality and/or quantities of DNA, restricting the type of molecular methods that can be used. Despite this limitation, genetic monitoring using MIS is an effective tool for estimating population demographic parameters and monitoring genetic diversity in natural populations. Genetic monitoring is likely to become more important in the future as many natural populations are undergoing anthropogenically driven declines, which are unlikely to abate without intensive adaptive management efforts that often include MIS approaches. Here, we profile the expanding suite of genomic methods and platforms compatible with producing genotypes from MIS, considering factors such as development costs and error rates. We evaluate how powerful new approaches will enhance our ability to investigate questions typically answered using genetic monitoring, such as estimating abundance, genetic structure and relatedness. As the field is in a period of unusually rapid transition, we also highlight the importance of legacy data sets and recommend how to address the challenges of moving between traditional and next-generation genetic monitoring platforms. Finally, we consider how genetic monitoring could move beyond genotypes in the future. For example, assessing microbiomes or epigenetic markers could provide a greater understanding of the relationship between individuals and their environment.
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Affiliation(s)
- Emma L. Carroll
- Scottish Oceans Institute and Sea Mammal Research UnitUniversity of St AndrewsSt AndrewsUK
| | - Mike W. Bruford
- Cardiff School of Biosciences and Sustainable Places Research InstituteCardiff UniversityCardiff, WalesUK
| | - J. Andrew DeWoody
- Department of Forestry and Natural Resources and Department of Biological SciencesPurdue UniversityWest LafayetteINUSA
| | - Gregoire Leroy
- Animal Production and Health DivisionFood and Agriculture Organization of the United NationsRomeItaly
| | - Alan Strand
- Grice Marine LaboratoryDepartment of BiologyCollege of CharlestonCharlestonSCUSA
| | - Lisette Waits
- Department of Fish and Wildlife SciencesUniversity of IdahoMoscowIDUSA
| | - Jinliang Wang
- Institute of ZoologyZoological Society of LondonLondonUK
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12
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Wright PJ, Régnier T, Gibb FM, Augley J, Devalla S. Assessing the role of ontogenetic movement in maintaining population structure in fish using otolith microchemistry. Ecol Evol 2018; 8:7907-7920. [PMID: 30250672 PMCID: PMC6144964 DOI: 10.1002/ece3.4186] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 04/10/2018] [Accepted: 04/22/2018] [Indexed: 01/03/2023] Open
Abstract
Identifying the mechanisms maintaining population structure in marine fish species with more than a single dispersing life stage is challenging because of the difficulty in tracking all life stages. Here, a two-stage otolith microchemistry approach to examining life-stage movement was adopted, tracking a year-class from the juvenile to adult stage and inferring larval sources from clustering, in order to consider the mechanisms maintaining population structuring in North Sea cod. Clustering of near-core chemistry identified four clusters, two of which had either a southern or northern affinity and were similar to juvenile edge chemistry. The other two clusters, common to the central North Sea, had intermediate chemical composition and may have reflected either larval mixing in this region or a lack of geographic heterogeneity in the elemental signature. From the comparison of whole juvenile and the corresponding component of adult otoliths, adults from the southern North Sea mostly recruited from adjacent nursery grounds. In contrast, many adults in the northern North Sea had a juvenile chemistry consistent with the Skagerrak and juveniles from the northern Skagerrak site had a near-core chemistry consistent with the northern North Sea. Similarities in otolith chemistry were consistent with retention of early life stages at a regional level and also juvenile and adult fidelity. The links between the northern North Sea and Skagerrak indicate natal homing, which when considered in the context of genetic evidence is suggestive of philopatry. The approach used here should be useful in exploring the mechanisms underlying population structuring in other species with multiple dispersive life stages and calcified hard parts.
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Affiliation(s)
| | | | | | - Julian Augley
- Marine Scotland ScienceAberdeenUK
- Present address:
Fios GenomicsNine Edinburgh BioquarterEdinburghUK
| | - Sandhya Devalla
- Marine Scotland ScienceAberdeenUK
- Present address:
Environmental and Biochemical SciencesThe James Hutton InstituteCraigiebucklerAberdeenUK
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Reconciling differences in natural tags to infer demographic and genetic connectivity in marine fish populations. Sci Rep 2018; 8:10343. [PMID: 29985467 PMCID: PMC6037741 DOI: 10.1038/s41598-018-28701-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 06/22/2018] [Indexed: 11/08/2022] Open
Abstract
Processes regulating population connectivity are complex, ranging from extrinsic environmental factors to intrinsic individual based features, and are a major force shaping the persistence of fish species and population responses to harvesting and environmental change. Here we developed an integrated assessment of demographic and genetic connectivity of European flounder Platichthys flesus in the northeast Atlantic (from the Norwegian to the Portuguese coast) and Baltic Sea. Specifically, we used a Bayesian infinite mixture model to infer the most likely number of natal sources of individuals based on otolith near core chemical composition. Simultaneously, we characterised genetic connectivity via microsatellite DNA markers, and evaluated how the combined use of natural tags informed individual movement and long-term population exchange rates. Individual markers provided different insights on movement, with otolith chemistry delineating Norwegian and Baltic Sea sources, whilst genetic markers showed a latitudinal pattern which distinguished southern peripheral populations along the Iberian coast. Overall, the integrated use of natural tags resulted in outcomes that were not readily anticipated by individual movement or gene flow markers alone. Our ecological and evolutionary approach provided a synergistic view on connectivity, which will be paramount to align biological and management units and safeguard species' biocomplexity.
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Dahle G, Quintela M, Johansen T, Westgaard JI, Besnier F, Aglen A, Jørstad KE, Glover KA. Analysis of coastal cod (Gadus morhua L.) sampled on spawning sites reveals a genetic gradient throughout Norway's coastline. BMC Genet 2018; 19:42. [PMID: 29986643 PMCID: PMC6036686 DOI: 10.1186/s12863-018-0625-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 05/18/2018] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Atlantic cod (Gadus morhua L.) has formed the basis of many economically significant fisheries in the North Atlantic, and is one of the best studied marine fishes, but a legacy of overexploitation has depleted populations and collapsed fisheries in several regions. Previous studies have identified considerable population genetic structure for Atlantic cod. However, within Norway, which is the country with the largest remaining catch in the Atlantic, the population genetic structure of coastal cod (NCC) along the entire coastline has not yet been investigated. We sampled > 4000 cod from 55 spawning sites. All fish were genotyped with 6 microsatellite markers and Pan I (Dataset 1). A sub-set of the samples (1295 fish from 17 locations) were also genotyped with an additional 9 microsatellites (Dataset 2). Otoliths were read in order to exclude North East Arctic Cod (NEAC) from the analyses, as and where appropriate. RESULTS We found no difference in genetic diversity, measured as number of alleles, allelic richness, heterozygosity nor effective population sizes, in the north-south gradient. In both data sets, weak but significant population genetic structure was revealed (Dataset 1: global FST = 0.008, P < 0.0001. Dataset 2: global FST = 0.004, P < 0.0001). While no clear genetic groups were identified, genetic differentiation increased among geographically-distinct samples. Although the locus Gmo132 was identified as a candidate for positive selection, possibly through linkage with a genomic region under selection, overall trends remained when this locus was excluded from the analyses. The most common allele in loci Gmo132 and Gmo34 showed a marked frequency change in the north-south gradient, increasing towards the frequency observed in NEAC in the north. CONCLUSION We conclude that Norwegian coastal cod displays significant population genetic structure throughout its entire range, that follows a trend of isolation by distance. Furthermore, we suggest that a gradient of genetic introgression between NEAC and NCC contributes to the observed population genetic structure. The current management regime for coastal cod in Norway, dividing it into two stocks at 62°N, represents a simplification of the level of genetic connectivity among coastal cod in Norway, and needs revision.
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Affiliation(s)
- Geir Dahle
- Institute of Marine Research (IMR), Postbox 1870, N-5817 Bergen, Norway
- Department of Biology, University of Bergen, Bergen, Norway
| | - María Quintela
- Institute of Marine Research (IMR), Postbox 1870, N-5817 Bergen, Norway
| | - Torild Johansen
- Institute of Marine Research (IMR), Postbox 6404, N-9019 Tromsø, Norway
| | | | - François Besnier
- Institute of Marine Research (IMR), Postbox 1870, N-5817 Bergen, Norway
| | - Asgeir Aglen
- Institute of Marine Research (IMR), Postbox 1870, N-5817 Bergen, Norway
| | - Knut E. Jørstad
- Institute of Marine Research (IMR), Postbox 1870, N-5817 Bergen, Norway
| | - Kevin A. Glover
- Institute of Marine Research (IMR), Postbox 1870, N-5817 Bergen, Norway
- Department of Biology, University of Bergen, Bergen, Norway
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Rogers LA, Salomon AK, Connors B, Krkošek M. Collapse, Tipping Points, and Spatial Demographic Structure Arising from the Adopted Migrant Life History. Am Nat 2018; 192:49-61. [PMID: 29897803 DOI: 10.1086/697488] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The roles of dispersal and recruitment have long been a focal point in ecology and conservation. The adopted migrant hypothesis proposes a life history in which social learning transmits migratory knowledge between generations of iteroparous fish. Specifically, juveniles disperse from the parental spawning site, encounter and recruit to a local adult population, and learn migration routes between spawning and foraging habitats by following older, experienced fish. Although the adopted migrant life history may apply to many species of pelagic marine fishes, there is scant theoretical or empirical work on the consequent population dynamics. We developed and analyzed a mathematical model of this life history in which the recruitment of juveniles depends on the relative abundance of the local populations and recruitment overlap, which measures the ease with which juveniles are recruited by a nonparental population. We demonstrate that the adopted migrant life history can maintain spatial demographic structure among local populations, that it can also predispose local populations to collapse when a tipping point is crossed, and that recovery after collapse is impaired by reduced recruitment at small local population sizes.
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O’Corry-Crowe G, Suydam R, Quakenbush L, Potgieter B, Harwood L, Litovka D, Ferrer T, Citta J, Burkanov V, Frost K, Mahoney B. Migratory culture, population structure and stock identity in North Pacific beluga whales (Delphinapterus leucas). PLoS One 2018; 13:e0194201. [PMID: 29566001 PMCID: PMC5863979 DOI: 10.1371/journal.pone.0194201] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 02/27/2018] [Indexed: 01/31/2023] Open
Abstract
The annual return of beluga whales, Delphinapterus leucas, to traditional seasonal locations across the Arctic may involve migratory culture, while the convergence of discrete summering aggregations on common wintering grounds may facilitate outbreeding. Natal philopatry and cultural inheritance, however, has been difficult to assess as earlier studies were of too short a duration, while genetic analyses of breeding patterns, especially across the beluga's Pacific range, have been hampered by inadequate sampling and sparse information on wintering areas. Using a much expanded sample and genetic marker set comprising 1,647 whales, spanning more than two decades and encompassing all major coastal summering aggregations in the Pacific Ocean, we found evolutionary-level divergence among three geographic regions: the Gulf of Alaska, the Bering-Chukchi-Beaufort Seas, and the Sea of Okhotsk (Φst = 0.11-0.32, Rst = 0.09-0.13), and likely demographic independence of (Fst-mtDNA = 0.02-0.66), and in many cases limited gene flow (Fst-nDNA = 0.0-0.02; K = 5-6) among, summering groups within regions. Assignment tests identified few immigrants within summering aggregations, linked migrating groups to specific summering areas, and found that some migratory corridors comprise whales from multiple subpopulations (PBAYES = 0.31:0.69). Further, dispersal is male-biased and substantial numbers of closely related whales congregate together at coastal summering areas. Stable patterns of heterogeneity between areas and consistently high proportions (~20%) of close kin (including parent-offspring) sampled up to 20 years apart within areas (G = 0.2-2.9, p>0.5) is the first direct evidence of natal philopatry to migration destinations in belugas. Using recent satellite telemetry findings on belugas we found that the spatial proximity of winter ranges has a greater influence on the degree of both individual and genetic exchange than summer ranges (rwinter-Fst-mtDNA = 0.9, rsummer-Fst-nDNA = 0.1). These findings indicate widespread natal philopatry to summering aggregation and entire migratory circuits, and provide compelling evidence that migratory culture and kinship helps maintain demographically discrete beluga stocks that can overlap in time and space.
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Affiliation(s)
- Greg O’Corry-Crowe
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, Florida, United States of America
| | - Robert Suydam
- North Slope Borough Department of Wildlife Management, Barrow, Alaska, United States of America
| | - Lori Quakenbush
- Alaska Department of Fish and Game, Fairbanks, Alaska, United States of America
| | - Brooke Potgieter
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, Florida, United States of America
| | - Lois Harwood
- Fisheries and Oceans Canada, Yellowknife, Northwest Territories, Canada
| | - Dennis Litovka
- Marine Mammal Laboratory, ChukotTINRO, Anadyr, Chukotka, Russia
| | - Tatiana Ferrer
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, Florida, United States of America
| | - John Citta
- Alaska Department of Fish and Game, Fairbanks, Alaska, United States of America
| | - Vladimir Burkanov
- North Pacific Wildlife Consulting, Marine Mammal Laboratory, Seattle, Washington, United States of America
| | - Kathy Frost
- University of Alaska, School of Fisheries and Ocean Science, Kailua Kona, Hawaii, United States of America
| | - Barbara Mahoney
- National Marine Fisheries Service, Anchorage, Alaska, United States of America
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17
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O'Corry-Crowe G, Suydam R, Quakenbush L, Potgieter B, Harwood L, Litovka D, Ferrer T, Citta J, Burkanov V, Frost K, Mahoney B. Migratory culture, population structure and stock identity in North Pacific beluga whales (Delphinapterus leucas). PLoS One 2018; 13:e0194201. [PMID: 29566001 DOI: 10.1371/journal.pone.019420116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 02/27/2018] [Indexed: 05/27/2023] Open
Abstract
The annual return of beluga whales, Delphinapterus leucas, to traditional seasonal locations across the Arctic may involve migratory culture, while the convergence of discrete summering aggregations on common wintering grounds may facilitate outbreeding. Natal philopatry and cultural inheritance, however, has been difficult to assess as earlier studies were of too short a duration, while genetic analyses of breeding patterns, especially across the beluga's Pacific range, have been hampered by inadequate sampling and sparse information on wintering areas. Using a much expanded sample and genetic marker set comprising 1,647 whales, spanning more than two decades and encompassing all major coastal summering aggregations in the Pacific Ocean, we found evolutionary-level divergence among three geographic regions: the Gulf of Alaska, the Bering-Chukchi-Beaufort Seas, and the Sea of Okhotsk (Φst = 0.11-0.32, Rst = 0.09-0.13), and likely demographic independence of (Fst-mtDNA = 0.02-0.66), and in many cases limited gene flow (Fst-nDNA = 0.0-0.02; K = 5-6) among, summering groups within regions. Assignment tests identified few immigrants within summering aggregations, linked migrating groups to specific summering areas, and found that some migratory corridors comprise whales from multiple subpopulations (PBAYES = 0.31:0.69). Further, dispersal is male-biased and substantial numbers of closely related whales congregate together at coastal summering areas. Stable patterns of heterogeneity between areas and consistently high proportions (~20%) of close kin (including parent-offspring) sampled up to 20 years apart within areas (G = 0.2-2.9, p>0.5) is the first direct evidence of natal philopatry to migration destinations in belugas. Using recent satellite telemetry findings on belugas we found that the spatial proximity of winter ranges has a greater influence on the degree of both individual and genetic exchange than summer ranges (rwinter-Fst-mtDNA = 0.9, rsummer-Fst-nDNA = 0.1). These findings indicate widespread natal philopatry to summering aggregation and entire migratory circuits, and provide compelling evidence that migratory culture and kinship helps maintain demographically discrete beluga stocks that can overlap in time and space.
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Affiliation(s)
- Greg O'Corry-Crowe
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, Florida, United States of America
| | - Robert Suydam
- North Slope Borough Department of Wildlife Management, Barrow, Alaska, United States of America
| | - Lori Quakenbush
- Alaska Department of Fish and Game, Fairbanks, Alaska, United States of America
| | - Brooke Potgieter
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, Florida, United States of America
| | - Lois Harwood
- Fisheries and Oceans Canada, Yellowknife, Northwest Territories, Canada
| | - Dennis Litovka
- Marine Mammal Laboratory, ChukotTINRO, Anadyr, Chukotka, Russia
| | - Tatiana Ferrer
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, Florida, United States of America
| | - John Citta
- Alaska Department of Fish and Game, Fairbanks, Alaska, United States of America
| | - Vladimir Burkanov
- North Pacific Wildlife Consulting, Marine Mammal Laboratory, Seattle, Washington, United States of America
| | - Kathy Frost
- University of Alaska, School of Fisheries and Ocean Science, Kailua Kona, Hawaii, United States of America
| | - Barbara Mahoney
- National Marine Fisheries Service, Anchorage, Alaska, United States of America
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19
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Bentzen P, Bradbury IR. Don't bet against the natal homing abilities of marine fishes. Mol Ecol 2017; 25:2691-2. [PMID: 27306459 DOI: 10.1111/mec.13591] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 02/12/2016] [Indexed: 11/26/2022]
Abstract
Whether marine fishes are capable of homing to their natal areas has long been something of an enigma. For some estuarine species or sharks (which have extended nondispersal juvenile stages or are born as relatively large, fully formed juveniles), the answer is clearly 'yes' (Thorrold et al. ; Feldheim et al. ), but for most marine fishes, the issue is much more mysterious. Many species have free-floating eggs, and most have pelagic, passively dispersing larvae. It is challenging to imagine how adult fish might navigate to a region of the ocean they experienced only as eggs or larvae, and easier to assume that such dispersal leads inexorably to high gene flow, and even panmixia. One way to resolve the conundrum would be to track fish from hatching to reproduction, but for marine fishes with tiny eggs and drifting larvae, this is notoriously difficult to do (Bradbury & Laurel ). In this issue of Molecular Ecology, Bonanomi et al. () use a creative approach to solve this challenge for Atlantic cod (Gadus morhua) populations that mingle in the vicinity of Greenland. They show that cod that disperse more than a 1000 km away from Iceland as eggs and larvae, then spend years growing on the far side of Greenland, while mixing with two local populations, return as adults to spawning areas near Iceland - and further, that this behaviour has remained stable over more than six decades. They manage this feat with a clever use of historical cod tracking data, modern genomic data and genetic analysis of decades-old DNA obtained from archived materials. Their results have important implications for our view of the biocomplexity of marine fish populations, and how we should manage them.
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Affiliation(s)
- Paul Bentzen
- Marine Gene Probe Laboratory, Department of Biology, Dalhousie University, 1355 Oxford Street, Halifax, NS, Canada, B3H 4R2
| | - Ian R Bradbury
- Salmonids Section, Science Branch, Department of Fisheries and Oceans Canada, 80 East White Hills Road, St. John's, NF, Canada, A1C 5X1
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20
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Barth JMI, Berg PR, Jonsson PR, Bonanomi S, Corell H, Hemmer-Hansen J, Jakobsen KS, Johannesson K, Jorde PE, Knutsen H, Moksnes PO, Star B, Stenseth NC, Svedäng H, Jentoft S, André C. Genome architecture enables local adaptation of Atlantic cod despite high connectivity. Mol Ecol 2017. [DOI: 10.1111/mec.14207] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Julia M. I. Barth
- Department of Biosciences; Centre for Ecological and Evolutionary Synthesis (CEES); University of Oslo; Oslo Norway
| | - Paul R. Berg
- Department of Biosciences; Centre for Ecological and Evolutionary Synthesis (CEES); University of Oslo; Oslo Norway
- Faculty of Medicine; Centre for Molecular Medicine Norway (NCMM); University of Oslo; Oslo Norway
| | - Per R. Jonsson
- Department of Marine Sciences - Tjärnö; University of Gothenburg; Strömstad Sweden
| | - Sara Bonanomi
- Section for Marine Living Resources; National Institute of Aquatic Resources; Technical University of Denmark; Silkeborg Denmark
- National Research Council (CNR); Fisheries Section; Institute of Marine Sciences (ISMAR); Ancona Italy
| | - Hanna Corell
- Department of Marine Sciences - Tjärnö; University of Gothenburg; Strömstad Sweden
| | - Jakob Hemmer-Hansen
- Section for Marine Living Resources; National Institute of Aquatic Resources; Technical University of Denmark; Silkeborg Denmark
| | - Kjetill S. Jakobsen
- Department of Biosciences; Centre for Ecological and Evolutionary Synthesis (CEES); University of Oslo; Oslo Norway
| | - Kerstin Johannesson
- Department of Marine Sciences - Tjärnö; University of Gothenburg; Strömstad Sweden
| | - Per Erik Jorde
- Department of Biosciences; Centre for Ecological and Evolutionary Synthesis (CEES); University of Oslo; Oslo Norway
| | - Halvor Knutsen
- Department of Biosciences; Centre for Ecological and Evolutionary Synthesis (CEES); University of Oslo; Oslo Norway
- Institute of Marine Research; Flødevigen; His Norway
- Department of Natural Sciences; Centre for Coastal Research; University of Agder; Kristiansand Norway
| | - Per-Olav Moksnes
- Department of Marine Sciences; University of Gothenburg; Gothenburg Sweden
| | - Bastiaan Star
- Department of Biosciences; Centre for Ecological and Evolutionary Synthesis (CEES); University of Oslo; Oslo Norway
| | - Nils Chr. Stenseth
- Department of Biosciences; Centre for Ecological and Evolutionary Synthesis (CEES); University of Oslo; Oslo Norway
- Department of Natural Sciences; Centre for Coastal Research; University of Agder; Kristiansand Norway
| | - Henrik Svedäng
- Swedish Institute for the Marine Environment (SIME); Gothenburg Sweden
| | - Sissel Jentoft
- Department of Biosciences; Centre for Ecological and Evolutionary Synthesis (CEES); University of Oslo; Oslo Norway
- Department of Natural Sciences; Centre for Coastal Research; University of Agder; Kristiansand Norway
| | - Carl André
- Department of Marine Sciences - Tjärnö; University of Gothenburg; Strömstad Sweden
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22
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Population structure and persistence of Pacific herring following the Great Tohoku earthquake. CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0918-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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23
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Garcia-Mayoral E, Olsen M, Hedeholm R, Post S, Nielsen EE, Bekkevold D. Genetic structure of West Greenland populations of lumpfish Cyclopterus lumpus. JOURNAL OF FISH BIOLOGY 2016; 89:2625-2642. [PMID: 27753091 DOI: 10.1111/jfb.13167] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 09/06/2016] [Indexed: 06/06/2023]
Abstract
In this study, 11 microsatellite markers were used to determine the structure of West Greenlandic lumpfish Cyclopterus lumpus populations across six spawning locations spanning >1500 km and compared with neighbouring populations in Canada and Iceland. To evaluate whether data allow for identification of origin of C. lumpus in Greenlandic waters, genetic assignment analysis was performed for 86 C. lumpus sampled on a feeding migration. Significant structuring with isolation by distance was observed in the West Greenland samples and two major subpopulations, north and south, were suggested. Based on FST values, closer relationships were observed between Greenland and Canada, than Greenland and Iceland. Surprisingly, the North Greenland population showed more similarities with Canadian samples, than did the geographically closer south-west Greenland population. Origin could be assigned for a high proportion of non-spawning fish and demonstrated a marked east-west spatial separation of fish of Greenlandic and Icelandic genotypes.
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Affiliation(s)
- E Garcia-Mayoral
- Danish Technical University, National Institue for Aquatic Resources, Vejlsøvej 39, 8600, Silkeborg, Denmark
| | - M Olsen
- Greenland Institute of Natural Resources, Kivioq 2, 3900, Nuuk, Greenland
| | - R Hedeholm
- Greenland Institute of Natural Resources, Kivioq 2, 3900, Nuuk, Greenland
| | - S Post
- Greenland Institute of Natural Resources, Kivioq 2, 3900, Nuuk, Greenland
| | - E E Nielsen
- Danish Technical University, National Institue for Aquatic Resources, Vejlsøvej 39, 8600, Silkeborg, Denmark
| | - D Bekkevold
- Danish Technical University, National Institue for Aquatic Resources, Vejlsøvej 39, 8600, Silkeborg, Denmark
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Drinan DP, Galindo HM, Loher T, Hauser L. Subtle genetic population structure in Pacific halibut Hippoglossus stenolepis. JOURNAL OF FISH BIOLOGY 2016; 89:2571-2594. [PMID: 27714808 DOI: 10.1111/jfb.13148] [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: 04/04/2016] [Accepted: 08/25/2016] [Indexed: 06/06/2023]
Abstract
Pacific halibut Hippoglossus stenolepis from 10 sampling locations throughout their range were investigated for signs of population structure. Two genetic data sets were created: (1) all individuals (n = 828) at few anonymous microsatellite markers (number of loci = 16); (2) fewer individuals (n = 435) genotyped at anonymous as well as expressed sequence-tag linked microsatellites (number of loci = 61). A combination of multidimensional scaling plots, discriminant analysis of principal components and pairwise differentiation estimates suggested that samples from the Aleutian Islands, particularly the western Aleutian Islands, were genetically distinct from samples collected in other regions. In addition, outlier analyses found that two markers linked to expressed sequence tags may be under directional selection and could explain the differentiation among samples. These results confirm findings from previous research and suggest that population structure may exist within a current management unit (i.e. International Pacific Halibut Commission Regulatory Area 4B).
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Affiliation(s)
- D P Drinan
- School of Aquatic and Fishery Sciences, University of Washington, Box 355020, Seattle, WA, 98195, U.S.A
| | - H M Galindo
- School of Aquatic and Fishery Sciences, University of Washington, Box 355020, Seattle, WA, 98195, U.S.A
| | - T Loher
- International Pacific Halibut Commission, 2320 West Commodore Way, Suite 300, Seattle, WA, 98199, U.S.A
| | - L Hauser
- School of Aquatic and Fishery Sciences, University of Washington, Box 355020, Seattle, WA, 98195, U.S.A
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