The Population Genetic Organization of Pacific Cod Gadus macrocephalus in the North Pacific Based on Microsatellite Analysis

Смирнова, М. А.; Orlova, S. Yu.; Орлов, А. М.

doi:10.1134/s0032945219040155

Cited by 6 publications

(7 citation statements)

References 33 publications

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“…Our RAD sequencing results add to previous microsatellite studies (Canino et al, 2010; Gwak & Nakayama, 2011; Kim et al, 2010; Smirnova et al, 2019; Suda et al, 2017) to provide a more complete picture of Pacific cod population structure in the marginal seas of the northwestern Pacific (Figure 1). Pacific cod around the Korean Peninsula form three genetically distinct populations, as demonstrated by our results and by Gwak and Nakayama (2011): one along the western coast in the Yellow Sea, one on the southern coast within the Tsushima Warm Current, and one on the northeastern coast in the East Sea.…”

Section: Discussionsupporting

confidence: 74%

“…Our RAD sequencing results add to previous microsatellite studies (Canino et al, 2010;Gwak & Nakayama, 2011;Kim et al, 2010;Smirnova et al, 2019;Suda et al, 2017) Tsushima Warm Current (Suda et al, 2017) and thus could be part of the southern Korean population identified here (Figure 1), although there is no direct comparison of samples across the Korea Strait.…”

Section: Demographic History Regional Oceanography and Local Adaptati...supporting

confidence: 68%

“…Quality filtering and demultiplexing of raw sequences, de novo construction of a reference database of RAD loci, SNP discovery, and genotyping, was completed using a combination of the Stacks v1.44 pipeline (Catchen et al, 2011(Catchen et al, , 2013, Bowtie (Langmead et al, 2009), and NCBI's Basic Local Alignment Search Tool, BLAST (Altschul et al, 1990), according to the procedures outlined in Drinan et al (2018) and Brieuc et al (2014). Final F I G U R E 1 Map of sampling sites around the Korean Peninsula used for this study (labeled points), augmented with results from previous genetic analyses in the surrounding region (Canino et al, 2010;Smirnova et al, 2019;Suda et al, 2017). Point coloration represents the putative populations of each site according to the genetic structure described by RAD loci (this study) and microsatellite DNA (msDNA; previous studies).…”

Section: Sample and Data Collectionmentioning

confidence: 99%

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Genetic structure and dispersal in peripheral populations of a marine fish (Pacific cod, Gadus macrocephalus) and their importance for adaptation to climate change

Fisher

Helser

Sukyung

et al. 2021

Ecology and Evolution

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Small and isolated peripheral populations, which are often remnants of glacial refugia, offer an opportunity to determine the magnitude and direction of fine‐scale connectivity in high gene flow marine species. When located at the equatorial edge of a species’ range, these populations may also harbor genetic diversity related to survival and reproduction at higher temperatures, a critical resource for marine species facing warming ocean temperatures. Pacific cod (Gadus macrocephalus), a marine fish in the North Pacific, has already experienced major shifts in biomass and distribution linked to climate change. We estimated the magnitude and direction of connectivity between peripheral populations of Pacific cod at the southern edge of the species’ range, by conducting restriction site‐associated DNA (RAD) sequencing and individual assignment on fish collected around the Korean Peninsula during the spawning season. Three populations on the western, eastern, and southern Korean coasts were highly differentiated (FST = 0.025–0.042) and relatively small (Ne = 433–1,777). Ten putative dispersers and estimates of contemporary migration rates revealed asymmetrical, west‐to‐east movement around the Korean Peninsula, at a higher rate than predicted by indirect estimates of connectivity (FST). Allele frequencies at 87 RAD loci were decisively correlated with strong marine temperature gradients between the warmer southern coast and the cooler waters of the eastern and western coasts. Despite relatively small sample sizes, our data suggest asymmetrical dispersal and gene flow, potentially involving adaptive alleles, between peripheral populations inhabiting markedly different thermal regimes. Our study emphasizes the conservation value of peripheral populations in high gene flow marine fish species.

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Section: Discussionsupporting

confidence: 74%

Section: Demographic History Regional Oceanography and Local Adaptati...supporting

confidence: 68%

Section: Sample and Data Collectionmentioning

confidence: 99%

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Genetic structure and dispersal in peripheral populations of a marine fish (Pacific cod, Gadus macrocephalus) and their importance for adaptation to climate change

Fisher

Helser

Sukyung

et al. 2021

Ecology and Evolution

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“…Pacific cod are found demersally throughout the Western Pacific as far south as the Korean Peninsula, northward to the Bering and Chukchi Sea, throughout the Aleutian Islands and southward along the eastern Pacific as far as northern California. Populations at the southern edges of both the eastern and western Pacific show deep genetic divergence from northern populations (Canino et al, 2010), and studies of neutrally evolving loci have identified moderately genetically differentiated populations of Pacific cod (F ST < 0.02) throughout the North Pacific that display a general isolation-by-distance pattern indicating somewhat limited dispersal (e.g., Cunningham et al, 2009;Drinan et al, 2018;Smirnova et al, 2018Smirnova et al, , 2019).…”

Section: Introductionmentioning

confidence: 99%

Evidence for selection and spatially distinct patterns found in a putative zona pellucida gene in Pacific cod, and implications for management

Spies

Drinan

Petrou

et al. 2021

Ecology and Evolution

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Genetic differentiation has been observed in marine species even when no obvious barriers to gene flow exist, and understanding such differentiation is essential for effective fisheries management. Highly differentiated outlier loci can provide information on how genetic variation might not only contribute to local adaptation but may also be affected by historical demographic events. A locus which aligned to a predicted zona pellucida sperm-binding protein 3 gene (ZP3) in Atlantic cod (Gadus morhua) was previously identified as the highest outlier based on F ST in a RADseq study of Pacific cod (Gadus macrocephalus) across the West Coast of North America.However, because of the limited length of the RAD sequence and restricted geographic area of sampling, no conclusion on the functional significance of the observed variation was possible. In other marine species, ZP3 is involved in reproductive isolation, local adaptation, and has neofunctionalized as an antifreeze gene, and so it may provide important insights in functional population structure of Pacific cod. Here, we sequenced a 544-bp region of ZP3 in 230 Pacific cod collected from throughout their geographic range. We observed striking patterns of spatial structuring of ZP3 haplotypes, with a sharp break near Kodiak, Alaska, USA where populations within ~200 km of each other are nearly fixed for different haplotypes, contrasting a pattern of isolation by distance at other genetic markers in this region (F ST = 0.003).Phylogenetic analysis of ZP3 haplotypes revealed that the more southern haplotypes appear to be ancestral, with the northern haplotype evolving more recently, potentially in response to a novel selective pressure as Pacific cod recolonized northern latitudes after glaciation. The sharp break in haplotype frequencies suggests strong selective pressures are operating on small spatial scales and illustrates that selection can create high divergence even in marine species with ample opportunities for gene flow.

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“…Pacific cod is a wide-ranging species that can be found from the southern tip of the Korean Peninsula (Yellow Sea) in the western North Pacific Ocean across the Aleutian Islands and as far north as the Chukchi Sea and south to the California coast in the eastern North Pacific Ocean. Genetic research has shown that there is limited connectivity among spawning groups of Pacific cod, as well as a strong isolation by distance signal across its North American range [5][6][7][8][9]. Genetic work has shown strong support for significant differences between Bering Sea and Aleutian Islands cod, as well as the possibility for additional differentiation within spawning stocks found along the Aleutian Archipelago [5,6].…”

mentioning

confidence: 99%

Seasonal migratory patterns of Pacific cod (Gadus macrocephalus) in the Aleutian Islands

et al. 2021

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Background Pacific cod (Gadus macrocephalus) is an ecologically important species that supports a valuable commercial fishery throughout Alaska waters. Although its life history includes seasonal movement for spawning and feeding, little is known about its movement ecology. Here, we present results from the first study to use pop-up satellite archival tags (PSATs) to track the within-year movements of Pacific cod to understand their potential seasonal movement patterns within the Aleutian Islands. This study was part of a cooperative research project; tagging was conducted onboard commercial vessels during the winter fishing season while Pacific cod were aggregated to spawn in the central Aleutian Islands. Results Of the 36 PSATs deployed, we were able to obtain movement data from 13 Pacific cod that were at liberty between 60 and 360 days. We determined that three tagged Pacific cod were predated on by marine mammals and three were recaptured by the commercial fishery. Geolocation models were produced for four migrating individuals. Eight Pacific cod moved to a productive foraging ground near Seguam Island located 64 to 344 km from their release site and presumed spawning ground within a few weeks of their release. These movements indicate that some Pacific cod in the Aleutian Islands undergo seasonal migration. Three Pacific cod remained near their release locations (within 50 km) for more than 75 days suggesting the existence of partial migration in the population. Two Pacific cod undertook larger movements (378 and 394 km) during which they swam over deep passes and crossed several management boundaries highlighting the potential connectedness of Pacific cod throughout the Aleutian Islands. Conclusions This study provided important initial insights into the seasonal movement patterns of Pacific cod in the Aleutian Islands. Most tracked Pacific cod (77%) undertook migrations in the middle of March (64–394 km) from their winter spawning areas to summer foraging areas, but a few individuals remained in their capture location suggesting a partial migration strategy. Their ability to cross deep passes that were previously seen as potential barriers to movement has expanded our understanding of population connectivity.

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The Population Genetic Organization of Pacific Cod Gadus macrocephalus in the North Pacific Based on Microsatellite Analysis

Cited by 6 publications

References 33 publications

Genetic structure and dispersal in peripheral populations of a marine fish (Pacific cod, Gadus macrocephalus) and their importance for adaptation to climate change

Genetic structure and dispersal in peripheral populations of a marine fish (Pacific cod, Gadus macrocephalus) and their importance for adaptation to climate change

Evidence for selection and spatially distinct patterns found in a putative zona pellucida gene in Pacific cod, and implications for management

Seasonal migratory patterns of Pacific cod (Gadus macrocephalus) in the Aleutian Islands

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