Can we rely on selected genetic markers for population identification? Evidence from coastal Atlantic cod

Ecology and Evolution, Год журнала: 2018, Номер 8(24), С. 12547 - 12558

Опубликована: Дек. 1, 2018

Abstract The use of genetic markers under putative selection in population studies carries the potential for erroneous identification populations and misassignment individuals to origin. Selected are nevertheless attractive, especially marine organisms that characterized by weak structure at neutral loci. Highly fecund species may tolerate cost strong selective mortality during early life stages, potentially leading a shift offspring genotypes away from parental proportions. In Atlantic cod, recent have uncovered different genotype clusters apparently representing phenotypically cryptic coexist coastal waters. Here, we tested if high‐graded SNP panel specifically designed classify individual cod origin be unreliable because natural acting on SNPs or their linked background. Temporal samples were collected two fjords, starting earliest stage (pelagic eggs) carried until late autumn (bottom‐settled juveniles), covering period summer high mortality. Despite study period, found no evidence selection, as both types occurred throughout season, already egg samples, there was season proportions one other type. We conclude marker panels represent valid useful tool identifying biological this highly presumably others.

Язык: Английский

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A Nanopore Based Chromosome-Level Assembly Representing Atlantic Cod from the Celtic Sea

G3 Genes Genomes Genetics, Год журнала: 2020, Номер 10(9), С. 2903 - 2910

Опубликована: Июль 9, 2020

Currently available genome assemblies for Atlantic cod (Gadus morhua) have been constructed from fish belonging to the Northeast Arctic Cod (NEAC) population; a migratory population feeding in Barents Sea. These crucial development of genetic markers which used study differentiation and adaptive evolution cod, pinpointing four discrete islands genomic divergence located on linkage groups 1, 2, 7 12. In this paper, we present high-quality reference male representing southern inhabiting Celtic sea. The assembly (gadMor_Celtic) was produced long-read nanopore data has combined contig length 686 Mb with an N50 10 Mb. Integrating contigs mapping information enabled us construct 23 chromosome sequences mapped high confidence latest NEAC (gadMor3) allowed characterize, extent not previously reported large chromosomal inversions most cases, inversion breakpoints could be within single contigs. Our results suggest presence 6, 11 21, although these remain confirmed. Further, identified specific repetitive element that is relatively enriched at predicted centromeric regions. gadMor_Celtic provides resource 'southern' complementary existing 'northern' based represents first step toward developing pan-genomic resources cod.

Язык: Английский

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Lobster reserves as a management tool in coastal waters: Two decades of experience in Norway

Marine Policy, Год журнала: 2021, Номер 136, С. 104908 - 104908

Опубликована: Дек. 17, 2021

The positive effects of reduced fishing pressure in marine protected areas (MPAs) are now well documented globally. Yet, evidence MPA benefits from long-term replicated before-after control-impact (BACI) studies and their usefulness protecting target species still rare, especially northern temperate areas. Scientific rigor the monitoring MPAs is considered important for obtaining trust compliance can increase interest enthusiasm conservation. Off coast southern Norway, a implementation process started up 2002. Based on comprehensive consultations with local fishers managers, four experimental lobster reserves were appointed 2004. Two years later (2006), came into effect as Norwegian Directorate Fisheries implemented regulations by-law Saltwater Act that effectively banned all fixed gear. Long-term adjacent control has enabled rigorous scientific evaluation these populations, including density, growth, demography, behavior, phenotypic diversity. As protection to manifest, attracted high public attention soon credible supplement traditional fisheries management. In period 2002 2021, more than 50 have been Norway. Here, we review experiences since designated, implemented, embraced by communities over two decades become an tool fishery Thoughts future along Norway discussed.

Язык: Английский

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Hierarchical genetic structure in an evolving species complex: Insights from genome wide ddRAD data in Sebastes mentella

PLoS ONE, Год журнала: 2021, Номер 16(5), С. e0251976 - e0251976

Опубликована: Май 27, 2021

The diverse biology and ecology of marine organisms may lead to complex patterns intraspecific diversity for both neutral adaptive genetic variation. Sebastes mentella displays a particular life-history as livebearers, which existence multiple ecotypes has been suspected complicate the population structure species. Double digest restriction-site associated DNA was used investigate in S. scan evidence selection. In total, 42,288 SNPs were detected 277 fish, 1,943 97 tentatively loci selected following stringent filtration. Unprecedented levels differentiation found among previously defined 'shallow pelagic', 'deep pelagic' 'demersal slope' ecotypes, with overall mean FST = 0.05 0.24 outlier SNPs, respectively. Bayesian computation estimated concurrent historical divergence these three local adaptation genome. Overall, findings imply that depth-defined habitat led reproductive isolation possibly radiation ecotypes. Additional sub-structuring within 'shallow' 'deep' pelagic Population assignment individual fish showed more than 94% agreement between results based on SNP generated microsatellite data, but data provided lower estimate hybridization by data. We identified panel only 21 discriminate populations mixed samples machine-learning algorithm. This first investigation clarifies mentella, provides novel high-resolution genomic tools future investigations. insights here can readily be incorporated into management serve template other exploited species exhibiting similar life history traits.

Язык: Английский

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Bayesian estimation of spatially varying mortality risk using tagged animal data

Methods in Ecology and Evolution, Год журнала: 2024, Номер 15(11), С. 2101 - 2117

Опубликована: Сен. 23, 2024

Abstract The survival of animals is impacted by landscapes spatially varying mortality factors including habitat type, predation risk or harvest risk, among others. Characterization these spatial processes important for managing animal populations and their habitats, yet this information has proved challenging to capture. Advances in telemetry now make it possible monitor tagged individuals' locations through time a wide range taxa, providing opportunity assess movement simultaneously time‐to‐event data. Existing modelling frameworks have largely ignored treated an animal's location as fixed at regional level. Here we present general model analysing data arising from telemetry. Our flexible Cox regression form can estimate the effects conventional non‐spatial (size, seasonality, etc.), covariates (e.g. type) variation not explained on mortality. We show how fit our using Bayesian methods demonstrate applications with several simulated examples two case studies. produced consistent unbiased parameter estimates throughout simulations variety hazards. In first study, 147 caribou British Columbia, Canada, revealed heterogeneous landscape elevation, likely response space use predators. second study involved dataset 390 acoustically Atlantic cod southern Norwegian fjord where marine protected area (MPA) was established during study. found that MPA led shift mostly fishing natural within risks had markedly different hazard patterns. widely used technologies characterize taxa. work provides new opportunities inform ecology management fish wildlife populations.

Язык: Английский

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