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Graham BA, Hipfner JM, Wellband KW, Ito M, Burg TM. Genetic-environment associations explain genetic differentiation and variation between western and eastern North Pacific rhinoceros auklet ( Cerorhinca monocerata) breeding colonies. Ecol Evol 2024; 14:e11534. [PMID: 38994218 PMCID: PMC11237344 DOI: 10.1002/ece3.11534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 05/03/2024] [Accepted: 05/13/2024] [Indexed: 07/13/2024] Open
Abstract
Animals are strongly connected to the environments they live in and may become adapted to local environments. Examining genetic-environment associations of key indicator species, like seabirds, provides greater insights into the forces that drive evolution in marine systems. Here we examined a RADseq dataset of 19,213 SNPs for 99 rhinoceros auklets (Cerorhinca monocerata) from five western Pacific and 10 eastern Pacific breeding colonies. We used partial redundancy analyses to identify candidate adaptive loci and to quantify the effects of environmental variation on population genetic structure. We identified 262 candidate adaptive loci, which accounted for 3.0% of the observed genetic variation among western Pacific and eastern Pacific breeding colonies. Genetic variation was more strongly associated with pH and maximum current velocity, than maximum sea surface temperature. Genetic-environment associations explain genetic differences between western and eastern Pacific populations; however, genetic variation within the western and eastern Pacific Ocean populations appears to follow a pattern of isolation-by-distance. This study represents a first to quantify the relationship between environmental and genetic variation for this widely distributed marine species and provides greater insights into the evolutionary forces that act on marine species.
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Affiliation(s)
- Brendan A Graham
- Department of Biological Sciences University of Lethbridge Lethbridge Alberta Canada
- Institute of Arctic Biology University of Alaska Fairbanks Fairbanks Alaska USA
| | - J Mark Hipfner
- Wildlife Research Division Environment and Climate Change Canada Delta British Columbia Canada
| | - Kyle W Wellband
- Fisheries and Oceans Canada West Vancouver British Columbia Canada
| | - Motohiro Ito
- Faculty of Life Sciences Toyo University Bunkyō-ku Japan
| | - Theresa M Burg
- Department of Biological Sciences University of Lethbridge Lethbridge Alberta Canada
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Strøm JF, Bøhn T, Skjaeraasen JE, Gjelland KØ, Karlsen Ø, Johansen T, Hanebrekke T, Bjørn PA, Olsen EM. Movement diversity and partial sympatry of coastal and Northeast Arctic cod ecotypes at high latitudes. J Anim Ecol 2023; 92:1966-1978. [PMID: 37485731 DOI: 10.1111/1365-2656.13989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 07/04/2023] [Indexed: 07/25/2023]
Abstract
Movement diversity within species represent an important but often neglected, component of biodiversity that affects ecological and genetic interactions, as well as the productivity of exploited systems. By combining individual tracking data from acoustic telemetry with novel genetic analyses, we describe the movement diversity of two Atlantic cod Gadus morhua ecotypes in two high-latitude fjord systems: the highly migratory Northeast Arctic cod (NEA cod) that supports the largest cod fishery in the world, and the more sedentary Norwegian coastal cod, which is currently in a depleted state. As predicted, coastal cod displayed a higher level of fjord residency than NEA cod. Of the cod tagged during the spawning season, NEA cod left the fjords permanently to a greater extent and earlier compared to coastal cod, which to a greater extent remained resident and left the fjords temporarily. Despite this overall pattern, horizontal movements atypical for the ecotypes were common with some NEA cod remaining within the fjords year-round and some coastal cod displaying a low fjord fidelity. Fjord residency and exit timing also differed with spawning status and body size, with spawning cod and large individuals tagged during the feeding season more prone to leave the fjords and earlier than non-spawning and smaller individuals. While our results confirm a lower fjord dependency for NEA cod, they highlight a movement diversity within each ecotype and sympatric residency between ecotypes, previously undetected by population-level monitoring. This new knowledge is relevant for the management, which should base their fisheries advice for these interacting ecotypes on their habitat use and seasonal movements.
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Affiliation(s)
| | - Thomas Bøhn
- Institute of Marine Research, Tromsø, Norway
| | | | - Karl Øystein Gjelland
- Department of Arctic Ecology, Norwegian Institute of Nature Research (NINA), Tromsø, Norway
| | | | | | | | | | - Esben Moland Olsen
- Institute of Marine Research, His, Norway
- Department of Natural Sciences, Centre for Coastal Research, University of Agder, Kristiansand, Norway
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3
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Rutle KH, Skern‐Mauritzen R, Nilsen F, Mateos‐Rivera A, Eide AGS, Jansson E, Quintela M, Besnier F, Allyon F, Fjørtoft HB, Glover KA. Aquaculture-driven evolution of the salmon louse mtDNA genome. Evol Appl 2023; 16:1328-1344. [PMID: 37492153 PMCID: PMC10363823 DOI: 10.1111/eva.13572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 05/17/2023] [Accepted: 06/06/2023] [Indexed: 07/27/2023] Open
Abstract
Resistance toward the antiparasitic pyrethroid, deltamethrin, is reported in the Atlantic salmon louse (Lepeophtheirus salmonis salmonis), a persistent ectoparasite of farmed and wild salmonids. The resistance mechanism is linked to mitochondrial DNA (mtDNA), where genetic markers for resistance have been identified. Here, we investigated how widespread pyrethroid use in aquaculture may have influenced mtDNA variation in lice, and the dispersion of resistant haplotypes across the North Atlantic, using historical (2000-2002 "pre-resistance") and contemporary (2014-2017 "post-resistance") samples. To study this, we sequenced ATPase 6 and cytochrome b, genotyped two genetic markers for deltamethrin resistance, and genotyped microsatellites as "neutral" controls of potential population bottlenecks. Overall, we observed a modest reduction in mtDNA diversity in the period 2000-2017, but no reduction in microsatellite variation was observed. The reduction in mtDNA variation was especially distinct in two of the contemporary samples, fixed for one and two haplotypes, respectively. By contrast, all historical samples consisted of close to one mtDNA haplotype per individual. No population genetic structure was detected among the historical samples for mtDNA nor microsatellites. By contrast, significant population genetic differentiation was observed for mtDNA among some of the contemporary samples. However, the observed population genetic structure was tightly linked with the pattern of deltamethrin resistance, and we therefore conclude that it primarily reflects the transient mosaic of pyrethroid usage in time and space. Two historically undetected mtDNA haplotypes dominated in the contemporary samples, both of which were linked to deltamethrin resistance, demonstrating primarily two origins of deltamethrin resistance in the North Atlantic. Collectively, these data demonstrate that the widespread use of pyrethroids in commercial aquaculture has substantially altered the patterns of mtDNA diversity in lice across the North Atlantic, and that long-distance dispersion of resistance is rapid due to high level of genetic connectivity that is observed in this species.
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Affiliation(s)
| | | | - Frank Nilsen
- Department of Biological SciencesUniversity of BergenBergenNorway
| | | | | | | | | | | | | | - Helene Børretzen Fjørtoft
- Department of Biological SciencesUniversity of BergenBergenNorway
- Department of Biological Sciences in AalesundNorwegian University of Science and TechnologyAalesundNorway
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Dysin AP, Shcherbakov YS, Nikolaeva OA, Terletskii VP, Tyshchenko VI, Dementieva NV. Salmonidae Genome: Features, Evolutionary and Phylogenetic Characteristics. Genes (Basel) 2022; 13:genes13122221. [PMID: 36553488 PMCID: PMC9778375 DOI: 10.3390/genes13122221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/19/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022] Open
Abstract
The salmon family is one of the most iconic and economically important fish families, primarily possessing meat of excellent taste as well as irreplaceable nutritional and biological value. One of the most common and, therefore, highly significant members of this family, the Atlantic salmon (Salmo salar L.), was not without reason one of the first fish species for which a high-quality reference genome assembly was produced and published. Genomic advancements are becoming increasingly essential in both the genetic enhancement of farmed salmon and the conservation of wild salmon stocks. The salmon genome has also played a significant role in influencing our comprehension of the evolutionary and functional ramifications of the ancestral whole-genome duplication event shared by all Salmonidae species. Here we provide an overview of the current state of research on the genomics and phylogeny of the various most studied subfamilies, genera, and individual salmonid species, focusing on those studies that aim to advance our understanding of salmonid ecology, physiology, and evolution, particularly for the purpose of improving aquaculture production. This review should make potential researchers pay attention to the current state of research on the salmonid genome, which should potentially attract interest in this important problem, and hence the application of new technologies (such as genome editing) in uncovering the genetic and evolutionary features of salmoniforms that underlie functional variation in traits of commercial and scientific importance.
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Affiliation(s)
- Artem P. Dysin
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
- Correspondence:
| | - Yuri S. Shcherbakov
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Olga A. Nikolaeva
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Valerii P. Terletskii
- All-Russian Research Veterinary Institute of Poultry Science-Branch of the Federal Scientific Center, All-Russian Research and Technological Poultry Institute (ARRVIPS), Lomonosov, 198412 St. Petersburg, Russia
| | - Valentina I. Tyshchenko
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Natalia V. Dementieva
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
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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.
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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
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