1
|
Coelho JFR, Mendes LDF, Di Dario F, Carvalho PH, Dias RM, Lima SMQ, Verba JT, Pereira RJ. Integration of genomic and ecological methods inform management of an undescribed, yet highly exploited, sardine species. Proc Biol Sci 2024; 291:20232746. [PMID: 38444338 PMCID: PMC10915539 DOI: 10.1098/rspb.2023.2746] [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: 12/05/2023] [Accepted: 02/06/2024] [Indexed: 03/07/2024] Open
Abstract
Assessing genetic diversity within species is key for conservation strategies in the context of human-induced biotic changes. This is important in marine systems, where many species remain undescribed while being overfished, and conflicts between resource-users and conservation agencies are common. Combining niche modelling with population genomics can contribute to resolving those conflicts by identifying management units and understanding how past climatic cycles resulted in current patterns of genetic diversity. We addressed these issues on an undescribed but already overexploited species of sardine of the genus Harengula. We find that the species distribution is determined by salinity and depth, with a continuous distribution along the Brazilian mainland and two disconnected oceanic archipelagos. Genomic data indicate that such biogeographic barriers are associated with two divergent intraspecific lineages. Changes in habitat availability during the last glacial cycle led to different demographic histories among stocks. One coastal population experienced a 3.6-fold expansion, whereas an island-associated population contracted 3-fold, relative to the size of the ancestral population. Our results indicate that the island population should be managed separately from the coastal population, and that a Marine Protected Area covering part of the island population distribution can support the viability of this lineage.
Collapse
Affiliation(s)
- Jéssica Fernanda Ramos Coelho
- Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Avenida Senador Salgado Filho S/N, Campus Universitário, 59078-970, Natal/RN, Brazil
| | - Liana de Figueiredo Mendes
- Departamento de Ecologia, Universidade Federal do Rio Grande do Norte, Avenida Senador Salgado Filho S/N, Campus Universitário, 59078-970, Natal/RN, Brazil
| | - Fabio Di Dario
- Instituto de Biodiversidade e Sustentabilidade - Universidade Federal do Rio de Janeiro, Avenida São José do Barreto, 764, 27965-045, Macaé/RJ, Brazil
| | - Pedro Hollanda Carvalho
- Instituto de Biodiversidade e Sustentabilidade - Universidade Federal do Rio de Janeiro, Avenida São José do Barreto, 764, 27965-045, Macaé/RJ, Brazil
| | - Ricardo Marques Dias
- Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista - São Cristóvão, 20940-040, Rio de Janeiro/RJ, Brazil
| | - Sergio Maia Queiroz Lima
- Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Avenida Senador Salgado Filho S/N, Campus Universitário, 59078-970, Natal/RN, Brazil
| | - Julia Tovar Verba
- Evolutionary Biology, Ludwig Maximilian University of Munich, Grosshaderner Strasse 2, 82152, Planegg-Martinsried, Germany
| | - Ricardo J. Pereira
- Evolutionary Biology, Ludwig Maximilian University of Munich, Grosshaderner Strasse 2, 82152, Planegg-Martinsried, Germany
- Department of Zoology, State Museum of Natural History Stuttgart, Rosenstein 1–3, 70191, Stuttgart, Germany
| |
Collapse
|
2
|
Fuentes‐Pardo AP, Stanley R, Bourne C, Singh R, Emond K, Pinkham L, McDermid JL, Andersson L, Ruzzante DE. Adaptation to seasonal reproduction and environment-associated factors drive temporal and spatial differentiation in northwest Atlantic herring despite gene flow. Evol Appl 2024; 17:e13675. [PMID: 38495946 PMCID: PMC10940790 DOI: 10.1111/eva.13675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 03/19/2024] Open
Abstract
Understanding how marine organisms adapt to local environments is crucial for predicting how populations will respond to global climate change. The genomic basis, environmental factors and evolutionary processes involved in local adaptation are however not well understood. Here we use Atlantic herring, an abundant, migratory and widely distributed marine fish with substantial genomic resources, as a model organism to evaluate local adaptation. We examined genomic variation and its correlation with environmental variables across a broad environmental gradient, for 15 spawning aggregations in Atlantic Canada and the United States. We then compared our results with available genomic data of northeast Atlantic populations. We confirmed that population structure lies in a fraction of the genome including likely adaptive genetic variants of functional importance. We discovered 10 highly differentiated genomic regions distributed across four chromosomes. Nine regions show strong association with seasonal reproduction. One region, corresponding to a known inversion on chromosome 12, underlies a latitudinal pattern discriminating populations north and south of a biogeographic transition zone on the Scotian Shelf. Genome-environment associations indicate that winter seawater temperature best correlates with the latitudinal pattern of this inversion. The variation at two so-called 'islands of divergence' related to seasonal reproduction appear to be private to the northwest Atlantic. Populations in the northwest and northeast Atlantic share variation at four of these divergent regions, simultaneously displaying significant diversity in haplotype composition at another four regions, which includes an undescribed structural variant approximately 7.7 Mb long on chromosome 8. Our results suggest that the timing and geographic location of spawning and early development may be under diverse selective pressures related to allelic fitness across environments. Our study highlights the role of genomic architecture, ancestral haplotypes and selection in maintaining adaptive divergence in species with large population sizes and presumably high gene flow.
Collapse
Affiliation(s)
- Angela P. Fuentes‐Pardo
- Department of BiologyDalhousie UniversityHalifaxNova ScotiaCanada
- Department of Medical Biochemistry and MicrobiologyUppsala UniversityUppsalaSweden
| | - Ryan Stanley
- Fisheries and Oceans CanadaMaritimes RegionDartmouthNova ScotiaCanada
| | - Christina Bourne
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt John'sNewfoundland and LabradorCanada
| | - Rabindra Singh
- Fisheries and Oceans CanadaSt. Andrews Biological StationSt. AndrewsNew BrunswickCanada
| | - Kim Emond
- Fisheries and Oceans CanadaMaurice Lamontagne InstituteMont‐JoliQuebecCanada
| | - Lisa Pinkham
- Department of Marine ResourcesWest Boothbay HarborMaineUSA
| | - Jenni L. McDermid
- Fisheries and Oceans CanadaGulf Fisheries CentreMonctonNew BrunswickCanada
| | - Leif Andersson
- Department of Medical Biochemistry and MicrobiologyUppsala UniversityUppsalaSweden
- Department of Veterinary Integrative BiosciencesTexas A&M UniversityCollege StationTexasUSA
| | | |
Collapse
|
3
|
Martínez-García L, Ferrari G, Cuevas A, Atmore LM, López-Arias B, Culling M, Llorente-Rodríguez L, Morales-Muñiz A, Roselló-Izquierdo E, Quirós JA, Marlasca-Martín R, Hänfling B, Hutchinson WF, Jakobsen KS, Jentoft S, Orton D, Star B, Barrett JH. Ancient DNA evidence for the ecological globalization of cod fishing in medieval and post-medieval Europe. Proc Biol Sci 2022; 289:20221107. [PMID: 36259206 DOI: 10.1098/rspb.2022.1107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Understanding the historical emergence and growth of long-range fisheries can provide fundamental insights into the timing of ecological impacts and the development of coastal communities during the last millennium. Whole-genome sequencing approaches can improve such understanding by determining the origin of archaeological fish specimens that may have been obtained from historic trade or distant water. Here, we used genome-wide data to individually infer the biological source of 37 ancient Atlantic cod specimens (ca 1050-1950 CE) from England and Spain. Our findings provide novel genetic evidence that eleventh- to twelfth-century specimens from London were predominantly obtained from nearby populations, while thirteenth- to fourteenth-century specimens were derived from distant sources. Our results further suggest that Icelandic cod was indeed exported to London earlier than previously reported. Our observations confirm the chronology and geography of the trans-Atlantic cod trade from Newfoundland to Spain starting by the early sixteenth century. Our findings demonstrate the utility of whole-genome sequencing and ancient DNA approaches to describe the globalization of marine fisheries and increase our understanding regarding the extent of the North Atlantic fish trade and long-range fisheries in medieval and early modern times.
Collapse
Affiliation(s)
- Lourdes Martínez-García
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo 0315, Norway
| | - Giada Ferrari
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo 0315, Norway.,Royal Botanic Garden Edinburgh, Edinburgh EH3 5NZ, UK
| | - Angélica Cuevas
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo 0315, Norway
| | - Lane M Atmore
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo 0315, Norway
| | - Begoña López-Arias
- Laboratorio de Arqueozoología LAZ-UAM, Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Mark Culling
- Evolutionary Biology Group, Department of Biological Sciences, University of Hull, Hull HU6 7RX, UK
| | - Laura Llorente-Rodríguez
- Laboratory for Archaezoological Studies, Faculty of Archaeology, University of Leiden, Leiden 2311 EZ, The Netherlands
| | - Arturo Morales-Muñiz
- Laboratorio de Arqueozoología LAZ-UAM, Universidad Autónoma de Madrid, Madrid 28049, Spain
| | | | - Juan Antonio Quirós
- Department of Geography, Prehistory and Archaeology, University of the Basque Country, Vitoria-Gasteiz 48940, Spain
| | | | - Bernd Hänfling
- Institute for Biodiversity and Freshwater Conservation, UHI-Inverness, Inverness, UK
| | - William F Hutchinson
- Evolutionary Biology Group, Department of Biological Sciences, University of Hull, Hull HU6 7RX, UK
| | - Kjetill S Jakobsen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo 0315, Norway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo 0315, Norway
| | - David Orton
- BioArCh, Department of Archaeology, University of York, York, UK
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo 0315, Norway
| | - James H Barrett
- Department of Archaeology and Cultural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim 7012, Norway
| |
Collapse
|
4
|
Kim D, Taylor AT, Near TJ. Phylogenomics and species delimitation of the economically important Black Basses (Micropterus). Sci Rep 2022; 12:9113. [PMID: 35668124 PMCID: PMC9170712 DOI: 10.1038/s41598-022-11743-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 04/28/2022] [Indexed: 01/25/2023] Open
Abstract
Informed management and conservation efforts are vital to sustainable recreational fishing and biodiversity conservation. Because the taxonomic rank of species is important in conservation and management strategies, success of these efforts depends on accurate species delimitation. The Black Basses (Micropterus) are an iconic lineage of freshwater fishes that include some of the world’s most popular species for recreational fishing and world's most invasive species. Despite their popularity, previous studies to delimit species and lineages in Micropterus suffer from insufficient geographic coverage and uninformative molecular markers. Our phylogenomic analyses of ddRAD data result in the delimitation of 19 species of Micropterus, which includes 14 described species, the undescribed but well-known Altamaha, Bartram’s, and Choctaw basses, and two additional undescribed species currently classified as Smallmouth Bass (M. dolomieu). We provide a revised delimitation of species in the Largemouth Bass complex that necessitates a change in scientific nomenclature: Micropterus salmoides is retained for the Florida Bass and Micropterus nigricans is elevated from synonymy for the Largemouth Bass. The new understanding of diversity, distribution, and systematics of Black Basses will serve as important basis for the management and conservation of this charismatic and economically important clade of fishes.
Collapse
Affiliation(s)
- Daemin Kim
- Department of Ecology and Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT, 06511, USA.
| | - Andrew T Taylor
- Department of Biology, University of Central Oklahoma, Edmond, OK, 73034, USA.,Department of Biology, University of North Georgia, Dahlonega, GA, 30597, USA
| | - Thomas J Near
- Department of Ecology and Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT, 06511, USA.,Peabody Museum, Yale University, New Haven, CT, 06511, USA
| |
Collapse
|
5
|
Breistein B, Dahle G, Johansen T, Besnier F, Quintela M, Jorde PE, Knutsen H, Westgaard JI, Nedreaas K, Farestveit E, Glover KA. Geographic variation in gene‐flow from a genetically distinct migratory ecotype drives population genetic structure of coastal Atlantic cod (
Gadus morhua
L.). Evol Appl 2022; 15:1162-1176. [PMID: 35899259 PMCID: PMC9309456 DOI: 10.1111/eva.13422] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 05/10/2022] [Accepted: 05/12/2022] [Indexed: 11/30/2022] Open
Affiliation(s)
- B. Breistein
- Institute of Marine Research Bergen Norway
- Department of Biology University of Bergen Bergen Norway
| | - G. Dahle
- Institute of Marine Research Bergen Norway
- Department of Biology University of Bergen Bergen Norway
| | | | - F. Besnier
- Institute of Marine Research Bergen Norway
| | | | - P. E. Jorde
- Institute of Marine Research Flødevigen Norway
| | - H. Knutsen
- Institute of Marine Research Flødevigen Norway
- Centre for Coastal Research, Department of Natural Sciences University of Agder Norway
| | | | | | | | - K. A. Glover
- Institute of Marine Research Bergen Norway
- Department of Biology University of Bergen Bergen Norway
| |
Collapse
|
6
|
Martínez-García L, Ferrari G, Hufthammer AK, Jakobsen KS, Jentoft S, Barrett JH, Star B. Ancient DNA reveals a southern presence of the Northeast Arctic cod during the Holocene. Biol Lett 2022; 18:20220021. [PMID: 35506242 PMCID: PMC9065953 DOI: 10.1098/rsbl.2022.0021] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Climate change has been implicated in an increased number of distributional shifts of marine species during the last century. Nonetheless, it is unclear whether earlier climatic fluctuations had similar impacts. We use ancient DNA to investigate the long-term spawning distribution of the Northeast Arctic cod (skrei) which performs yearly migrations from the Barents Sea towards spawning grounds along the Norwegian coast. The distribution of these spawning grounds has shifted northwards during the last century, which is thought to be associated with food availability and warming temperatures. We genetically identify skrei specimens from Ruskeneset in west Norway, an archaeological site located south of their current spawning range. Remarkably, 14C analyses date these specimens to the late Holocene, when temperatures were warmer than present-day conditions. Our results either suggest that temperature is not the only driver influencing the spawning distribution of Atlantic cod, or could be indicative of uncertainty in palaeoclimate reconstructions in this region. Regardless, our findings highlight the utility of aDNA to reconstruct the historical distribution of economically important fish populations and reveal the complexity of long-term ecological interactions in the marine environment.
Collapse
Affiliation(s)
- Lourdes Martínez-García
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Blindernveien 31, NO-0371 Oslo, Norway
| | - Giada Ferrari
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Blindernveien 31, NO-0371 Oslo, Norway
| | - Anne Karin Hufthammer
- Department of Natural HistoryThe University Museum, , University of Bergen, N-5020 Bergen, Norway
| | - Kjetill S Jakobsen
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Blindernveien 31, NO-0371 Oslo, Norway
| | - Sissel Jentoft
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Blindernveien 31, NO-0371 Oslo, Norway
| | - James H Barrett
- Department of Archaeology and Cultural History, NTNU University Museum, Erling Skakkes 47b, Trondheim, Norway
| | - Bastiaan Star
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Blindernveien 31, NO-0371 Oslo, Norway
| |
Collapse
|
7
|
Stabilizing selection on Atlantic cod supergenes through a millennium of extensive exploitation. Proc Natl Acad Sci U S A 2022; 119:2114904119. [PMID: 35165196 PMCID: PMC8872764 DOI: 10.1073/pnas.2114904119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2022] [Indexed: 12/21/2022] Open
Abstract
Ecological disruption due to human impacts is evident worldwide, and a key to mitigation lies in characterizing the underlying mechanisms of species and ecosystem stability. Here we show that three extensive “supergenes” are maintained in Atlantic cod by stabilizing selection, tying these genes to the persistence of a keystone species distributed across the northern Atlantic Ocean. Removal of this species has caused severe ecosystem reshuffling in several areas of its range. Genomic inference of historic stock sizes further shows that cod has been under pressure in the North Sea system since the Viking period, in line with zooarchaeological records. Expansion of fisheries in Northern Europe through the past millennium is well documented and supports the inferred long-term declines. Life on Earth has been characterized by recurring cycles of ecological stasis and disruption, relating biological eras to geological and climatic transitions through the history of our planet. Due to the increasing degree of ecological abruption caused by human influences many advocate that we now have entered the geological era of the Anthropocene, or “the age of man.” Considering the ongoing mass extinction and ecosystem reshuffling observed worldwide, a better understanding of the drivers of ecological stasis will be a requisite for identifying routes of intervention and mitigation. Ecosystem stability may rely on one or a few keystone species, and the loss of such species could potentially have detrimental effects. The Atlantic cod (Gadus morhua) has historically been highly abundant and is considered a keystone species in ecosystems of the northern Atlantic Ocean. Collapses of cod stocks have been observed on both sides of the Atlantic and reported to have detrimental effects that include vast ecosystem reshuffling. By whole-genome resequencing we demonstrate that stabilizing selection maintains three extensive “supergenes” in Atlantic cod, linking these genes to species persistence and ecological stasis. Genomic inference of historic effective population sizes shows continued declines for cod in the North Sea–Skagerrak–Kattegat system through the past millennia, consistent with an early onset of the marine Anthropocene through industrialization and commercialization of fisheries throughout the medieval period.
Collapse
|
8
|
Matschiner M, Barth JMI, Tørresen OK, Star B, Baalsrud HT, Brieuc MSO, Pampoulie C, Bradbury I, Jakobsen KS, Jentoft S. Supergene origin and maintenance in Atlantic cod. Nat Ecol Evol 2022; 6:469-481. [PMID: 35177802 PMCID: PMC8986531 DOI: 10.1038/s41559-022-01661-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 01/10/2022] [Indexed: 12/19/2022]
Abstract
Supergenes are sets of genes that are inherited as a single marker and encode complex phenotypes through their joint action. They are identified in an increasing number of organisms, yet their origins and evolution remain enigmatic. In Atlantic cod, four megabase-scale supergenes have been identified and linked to migratory lifestyle and environmental adaptations. Here we investigate the origin and maintenance of these four supergenes through analysis of whole-genome-sequencing data, including a new long-read-based genome assembly for a non-migratory Atlantic cod individual. We corroborate the finding that chromosomal inversions underlie all four supergenes, and we show that they originated at different times between 0.40 and 1.66 million years ago. We reveal gene flux between supergene haplotypes where migratory and stationary Atlantic cod co-occur and conclude that this gene flux is driven by gene conversion, on the basis of an increase in GC content in exchanged sites. Additionally, we find evidence for double crossover between supergene haplotypes, leading to the exchange of an ~275 kilobase fragment with genes potentially involved in adaptation to low salinity in the Baltic Sea. Our results suggest that supergenes can be maintained over long timescales in the same way as hybridizing species, through the selective purging of introduced genetic variation. Atlantic cod carries four supergenes linked to migratory lifestyle and environmental adaptations. Using whole-genome sequencing, the authors show that the genome inversions that underlie the supergenes originated at different times and show gene flux between supergene haplotypes.
Collapse
Affiliation(s)
- Michael Matschiner
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway. .,Department of Palaeontology and Museum, University of Zurich, Zurich, Switzerland. .,Natural History Museum, University of Oslo, Oslo, Norway.
| | - Julia Maria Isis Barth
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Ole Kristian Tørresen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Helle Tessand Baalsrud
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Marine Servane Ono Brieuc
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | | | - Ian Bradbury
- Fisheries and Oceans Canada, St John's, Newfoundland and Labrador, Canada
| | - Kjetill Sigurd Jakobsen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway.
| |
Collapse
|
9
|
Delaval A, Frost M, Bendall V, Hetherington SJ, Stirling D, Hoarau G, Jones CS, Noble LR. Population and seascape genomics of a critically endangered benthic elasmobranch, the blue skate Dipturus batis. Evol Appl 2022; 15:78-94. [PMID: 35126649 PMCID: PMC8792474 DOI: 10.1111/eva.13327] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 11/16/2021] [Accepted: 11/22/2021] [Indexed: 11/28/2022] Open
Abstract
The blue skate (Dipturus batis) has a patchy distribution across the North-East Atlantic Ocean, largely restricted to occidental seas around the British Isles following fisheries-induced population declines and extirpations. The viability of remnant populations remains uncertain and could be impacted by continued fishing and by-catch pressure, and the projected impacts of climate change. We genotyped 503 samples of D. batis, obtained opportunistically from the widest available geographic range, across 6 350 single nucleotide polymorphisms (SNPs) using a reduced-representation sequencing approach. Genotypes were used to assess the species' contemporary population structure, estimate effective population sizes and identify putative signals of selection in relation to environmental variables using a seascape genomics approach. We identified genetic discontinuities between inshore (British Isles) and offshore (Rockall and Faroe Island) populations, with differentiation most pronounced across the deep waters of the Rockall Trough. Effective population sizes were largest in the Celtic Sea and Rockall, but low enough to be of potential conservation concern among Scottish and Faroese sites. Among the 21 candidate SNPs under positive selection was one significantly correlated with environmental variables predicted to be affected by climate change, including bottom temperature, salinity and pH. The paucity of well-annotated elasmobranch genomes precluded us from identifying a putative function for this SNP. Nevertheless, our findings suggest that climate change could inflict a strong selective force upon remnant populations of D. batis, further constraining its already-restricted habitat. Furthermore, the results provide fundamental insights on the distribution, behaviour and evolutionary biology of D. batis in the North-East Atlantic that will be useful for the establishment of conservation actions for this and other critically endangered elasmobranchs.
Collapse
Affiliation(s)
| | - Michelle Frost
- School of Biological SciencesUniversity of AberdeenAberdeenUK
| | - Victoria Bendall
- Centre for EnvironmentFisheries and Aquaculture ScienceLowestoftUK
| | | | | | - Galice Hoarau
- Faculty of Biosciences and AquacultureNord UniversityBodøNorway
| | | | - Leslie R. Noble
- Faculty of Biosciences and AquacultureNord UniversityBodøNorway
- School of Biological SciencesUniversity of AberdeenAberdeenUK
| |
Collapse
|
10
|
Distinct genetic clustering in the weakly differentiated polar cod, Boreogadus saida Lepechin, 1774 from East Siberian Sea to Svalbard. Polar Biol 2021. [DOI: 10.1007/s00300-021-02911-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
AbstractThe cold-adapted polar cod Boreogadus saida, a key species in Arctic ecosystems, is vulnerable to global warming and ice retreat. In this study, 1257 individuals sampled in 17 locations within the latitudinal range of 75–81°N from Svalbard to East Siberian Sea were genotyped with a dedicated suite of 116 single-nucleotide polymorphic loci (SNP). The overall pattern of isolation by distance (IBD) found was driven by the two easternmost samples (East Siberian Sea and Laptev Sea), whereas no differentiation was registered in the area between the Kara Sea and Svalbard. Eleven SNP under strong linkage disequilibrium, nine of which could be annotated to chromosome 2 in Atlantic cod, defined two genetic groups of distinct size, with the major cluster containing seven-fold larger number of individuals than the minor. No underlying geographic basis was evident, as both clusters were detected throughout all sampling sites in relatively similar proportions (i.e. individuals in the minor cluster ranging between 4 and 19% on the location basis). Similarly, females and males were also evenly distributed between clusters and age groups. A differentiation was, however, found regarding size at age: individuals belonging to the major cluster were significantly longer in the second year. This study contributes to increasing the population genetic knowledge of this species and suggests that an appropriate management should be ensured to safeguard its diversity.
Collapse
|
11
|
Thomson AI, Archer FI, Coleman MA, Gajardo G, Goodall‐Copestake WP, Hoban S, Laikre L, Miller AD, O’Brien D, Pérez‐Espona S, Segelbacher G, Serrão EA, Sjøtun K, Stanley MS. Charting a course for genetic diversity in the UN Decade of Ocean Science. Evol Appl 2021; 14:1497-1518. [PMID: 34178100 PMCID: PMC8210796 DOI: 10.1111/eva.13224] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 03/04/2021] [Accepted: 03/04/2021] [Indexed: 02/06/2023] Open
Abstract
The health of the world's oceans is intrinsically linked to the biodiversity of the ecosystems they sustain. The importance of protecting and maintaining ocean biodiversity has been affirmed through the setting of the UN Sustainable Development Goal 14 to conserve and sustainably use the ocean for society's continuing needs. The decade beginning 2021-2030 has additionally been declared as the UN Decade of Ocean Science for Sustainable Development. This program aims to maximize the benefits of ocean science to the management, conservation, and sustainable development of the marine environment by facilitating communication and cooperation at the science-policy interface. A central principle of the program is the conservation of species and ecosystem components of biodiversity. However, a significant omission from the draft version of the Decade of Ocean Science Implementation Plan is the acknowledgment of the importance of monitoring and maintaining genetic biodiversity within species. In this paper, we emphasize the importance of genetic diversity to adaptive capacity, evolutionary potential, community function, and resilience within populations, as well as highlighting some of the major threats to genetic diversity in the marine environment from direct human impacts and the effects of global climate change. We then highlight the significance of ocean genetic diversity to a diverse range of socioeconomic factors in the marine environment, including marine industries, welfare and leisure pursuits, coastal communities, and wider society. Genetic biodiversity in the ocean, and its monitoring and maintenance, is then discussed with respect to its integral role in the successful realization of the 2030 vision for the Decade of Ocean Science. Finally, we suggest how ocean genetic diversity might be better integrated into biodiversity management practices through the continued interaction between environmental managers and scientists, as well as through key leverage points in industry requirements for Blue Capital financing and social responsibility.
Collapse
Affiliation(s)
| | | | - Melinda A. Coleman
- New South Wales FisheriesNational Marine Science CentreCoffs HarbourNSWAustralia
- National Marine Science CentreSouthern Cross UniversityCoffs HarbourNSWAustralia
- Oceans Institute and School of Biological SciencesUniversity of Western AustraliaCrawleyWAAustralia
| | - Gonzalo Gajardo
- Laboratory of Genetics, Aquaculture & BiodiversityUniversidad de Los LagosOsornoChile
| | | | - Sean Hoban
- Centre for Tree ScienceThe Morton ArboretumLisleILUSA
| | - Linda Laikre
- Centre for Tree ScienceThe Morton ArboretumLisleILUSA
- The Wildlife Analysis UnitThe Swedish Environmental Protection AgencyStockholmSweden
| | - Adam D. Miller
- School of Life and Environmental SciencesCentre for Integrative EcologyDeakin UniversityGeelongVicAustralia
- Deakin Genomics CentreDeakin UniversityGeelongVic.Australia
| | | | - Sílvia Pérez‐Espona
- The Royal (Dick) School of Veterinary Studies and The Roslin InstituteMidlothianUK
| | - Gernot Segelbacher
- Chair of Wildlife Ecology and ManagementUniversity FreiburgFreiburgGermany
| | - Ester A. Serrão
- CCMARCentre of Marine SciencesFaculty of Sciences and TechnologyUniversity of AlgarveFaroPortugal
| | - Kjersti Sjøtun
- Department of Biological SciencesUniversity of BergenBergenNorway
| | | |
Collapse
|
12
|
Otterå H, Johansen T, Folkvord A, Dahle G, Solvang Bingh MK, Westgaard JI, Glover KA. The pantophysin gene and its relationship with survival in early life stages of Atlantic cod. ROYAL SOCIETY OPEN SCIENCE 2020; 7:191983. [PMID: 33204437 PMCID: PMC7657904 DOI: 10.1098/rsos.191983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 09/21/2020] [Indexed: 06/11/2023]
Abstract
Genetic markers are widely used in fisheries management around the world. While the genetic structure and markers selected are usually based on samples from the wild, very few controlled experiments have been carried out to investigate possible differences in influence on traits between markers. Here we examine the bi-allelic gene pantophysin (Pan I), widely used in the management of Atlantic cod, in a series of in vitro crosses under a range of temperatures. It has been proposed that this gene, or another tightly linked gene, may be under strong divergent selection. Resolving this issue is essential in order to interpret results when using this gene marker for stock management. We found no evidence of departure from the expected 1 : 2 : 1 Mendelian ratio for any of the three genotypes during the egg stage, while both the 6 and 12°C temperature regimes in tank experiments favoured the survival of the Pan IAA genotype. No difference in genotype survival was, however, found in a more natural mesocosm environment. Collectively, these results suggest that for the early life stages of Atlantic cod, and under the current experimental conditions, there is no strong consistent influence of Pan I genotype on survival. The results also emphasize the importance of varied experimental studies to verify the importance of environmental factors influencing genotype selection.
Collapse
Affiliation(s)
- Håkon Otterå
- Institute of Marine Research, POB 1870, 5817 Bergen, Norway
| | - Torild Johansen
- Institute of Marine Research, Tromsø Division, Framsenteret 9296 Tromsø, Norway
| | - Arild Folkvord
- Institute of Marine Research, POB 1870, 5817 Bergen, Norway
- Department of Biological Sciences, University of Bergen, Thormøhlensgt. 53, 5020Bergen
| | - Geir Dahle
- Institute of Marine Research, POB 1870, 5817 Bergen, Norway
| | | | - Jon-Ivar Westgaard
- Institute of Marine Research, Tromsø Division, Framsenteret 9296 Tromsø, Norway
| | - Kevin A. Glover
- Institute of Marine Research, POB 1870, 5817 Bergen, Norway
- Department of Biological Sciences, University of Bergen, Thormøhlensgt. 53, 5020Bergen
| |
Collapse
|