Population‐level inferences from environmental DNA—Current status and future perspectives

Evolutionary Applications, Год журнала: 2019, Номер 13(2), С. 245 - 262

Опубликована: Окт. 20, 2019

Environmental DNA (eDNA) extracted from water samples has recently shown potential as a valuable source of population genetic information for aquatic macroorganisms. This approach offers several advantages compared with conventional tissue-based methods, including the fact that eDNA sampling is noninvasive and generally more cost-efficient. Currently, approaches have been limited to single-marker studies mitochondrial (mtDNA), relationship between haplotype composition true still needs be thoroughly verified. will require testing bioinformatic statistical software correct erroneous sequences, well biases random variation in relative sequence abundances. However, eDNA-based methods far-reaching both basic applied research. In this paper, we present brief overview achievements genetics date, outline prospects future developments field, estimation nuclear (nuDNA) epigenetic information. We discuss challenges associated opposed those individual tissue assess whether might offer additional types unobtainable samples. Lastly, provide recommendations determining an would useful suitable choice different research settings. limit our discussion largely contemporary systems, but advantages, challenges, perspectives can large degree generalized spatial temporal focus.

Язык: Английский

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Disentangling structural genomic and behavioural barriers in a sea of connectivity

Molecular Ecology, Год журнала: 2019, Номер 28(6), С. 1394 - 1411

Опубликована: Янв. 11, 2019

Abstract Genetic divergence among populations arises through natural selection or drift and is counteracted by connectivity gene flow. In sympatric populations, isolating mechanisms are thus needed to limit the homogenizing effects of flow allow for adaptation speciation. Chromosomal inversions act as an important mechanism maintaining barriers, yet their role in with not entirely understood. Here, we revisit question whether play a connected marine fish Atlantic cod ( Gadus morhua ), exploring unique data set combining whole‐genome sequencing behavioural obtained acoustic telemetry. Within confined fjord environment, find three genetically differentiated types belonging oceanic North Sea population, western Baltic population local fjord‐type cod. Continuous tracking over 4 year revealed temporally stable sympatry these within fjord. Despite overall weak genetic differentiation consistent high levels flow, detected significant frequency shifts previously identified inversions, indicating adaptive barrier addition, indicated that individuals homozygous LG 12 inversion had lower fitness environment. However, also occupy different depths, possibly contributing prezygotic reproductive isolation representing Our results provide first insights into complex interplay genomic barriers establish new model system towards understanding structural variants diversification.

Язык: Английский

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Stabilizing selection on Atlantic cod supergenes through a millennium of extensive exploitation

Proceedings of the National Academy of Sciences, Год журнала: 2022, Номер 119(8)

Опубликована: Фев. 14, 2022

Life on Earth has been characterized by recurring cycles of ecological stasis and disruption, relating biological eras to geological climatic transitions through the history our planet. Due increasing degree abruption caused human influences many advocate that we now have entered era Anthropocene, or "the age man." Considering ongoing mass extinction ecosystem reshuffling observed worldwide, a better understanding drivers will be requisite for identifying routes intervention mitigation. Ecosystem stability may rely one few keystone species, loss such species could potentially detrimental effects. The Atlantic cod (Gadus morhua) historically highly abundant is considered in ecosystems northern Ocean. Collapses stocks both sides reported effects include vast reshuffling. By whole-genome resequencing demonstrate stabilizing selection maintains three extensive "supergenes" cod, linking these genes persistence stasis. Genomic inference historic effective population sizes shows continued declines North Sea-Skagerrak-Kattegat system past millennia, consistent with an early onset marine Anthropocene industrialization commercialization fisheries throughout medieval period.

Язык: Английский

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Stable coexistence of genetically divergent Atlantic cod ecotypes at multiple spatial scales

Evolutionary Applications, Год журнала: 2018, Номер 11(9), С. 1527 - 1539

Опубликована: Апрель 20, 2018

Coexistence in the same habitat of closely related yet genetically different populations is a phenomenon that challenges our understanding local population structure and adaptation. Identifying underlying mechanisms for such coexistence can yield new insight into adaptive evolution, diversification potential organisms to adapt persist response changing environment. Recent studies have documented cryptic, sympatric Atlantic cod (Gadus morhua) coastal areas. We analysed genetic origin 6,483 individual sampled annually over 14 years from 125 locations along Norwegian Skagerrak coast document stable two divergent ecotypes throughout study area period. A "fjord" ecotype dominated numbers deep inside fjords while "North Sea" was only type found offshore North Sea. Both coexisted similar proportions habitats at all spatial scales. The size-at-age Sea on average exceeded fjord by 20% length 80% weight across habitats. Different growth size among individuals types might be one several ecologically significant variables allow within habitat. Management plans, biodiversity initiatives other mitigation strategies do not account mixture species are unlikely meet objectives sustainability fish fisheries.

Язык: Английский

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The International Union for Conservation of Nature Red List does not account for intraspecific diversity

ICES Journal of Marine Science, Год журнала: 2024, Номер 81(5), С. 815 - 822

Опубликована: Апрель 8, 2024

Abstract The International Union for Conservation of Nature (IUCN) Red List identifies threatened and endangered species is a key instrument in global biodiversity conservation efforts. Our understanding the structure value genetic below level rapidly increasing. Nonetheless, IUCN assessment criteria overlook variation within species. Here, we address this blind spot discuss principles status classification relative to intraspecific biodiversity. We focus on coastal species, which thrive heterogeneous environments known drive differentiation. focal example Atlantic cod sugar kelp, have contrasting life histories, are ecologically economically important constituents ecosystem, currently not classified as Norway Canada. expose population structure, presence ecotypes genetic-environment covariation, well loss that threatens these Because makeup directly influences their resilience, omitting information from assessments can result adaptive capacity future stressors, such climate change. Consequently, recognizing preserving emerges vital species’ abilities adapt survive ocean conditions.

Язык: Английский

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Reduced‐Representation Sequencing Detects Trans‐Arctic Connectivity and Local Adaptation in Polar Cod (Boreogadus saida)

Molecular Ecology, Год журнала: 2025, Номер unknown

Опубликована: Март 5, 2025

Information on connectivity and genetic structure of marine organisms remains sparse in frontier ecosystems such as the Arctic Ocean. Filling these knowledge gaps becomes increasingly urgent, is undergoing rapid physical, ecological socio-economic changes. The abundant widely distributed polar cod (Boreogadus saida) highly adapted to waters, its larvae juveniles live close association with sea ice. Through a reduced-representation sequencing approach, this study explored spatial at circum-Arctic scale. Genomic variation was partitioned into neutral adaptive components respectively investigate local adaptation. Based 922 high-quality single nucleotide polymorphism (SNP) markers genotyped 611 cod, broad-scale differentiation detected among three groups: (i) Beaufort -Chukchi seas, (ii) all regions connected by Transpolar Drift, ranging from Laptev Sea Iceland, including European (iii) West Greenland. Patterns suggested broadscale oceanographic ice drift features (i.e., Gyre Drift) important drivers connectivity. 35 outlier loci indicated divergence Greenland Beaufort-Chukchi Seas populations, possibly driven environmental conditions. decline changing ocean currents can alter or disrupt between groups, potentially undermining their resilience climate change, even putative refugia, Central Ocean Archipelago.

Язык: Английский

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Modular chromosome rearrangements reveal parallel and nonparallel adaptation in a marine fish

Ecology and Evolution, Год журнала: 2020, Номер 10(2), С. 638 - 653

Опубликована: Янв. 1, 2020

Abstract Genomic architecture and standing variation can play a key role in ecological adaptation contribute to the predictability of evolution. In Atlantic cod ( Gadus morhua ), four large chromosomal rearrangements have been associated with gradients migratory behavior regional analyses. However, degree parallelism, extent independent inheritance, functional distinctiveness these remain poorly understood. Here, we use 12K single nucleotide polymorphism (SNP) array demonstrate extensive individual rearrangement genotype within populations across species range, suggesting that local fine‐scale is enabled by inheritance. Our results significant association migration phenotype environmental range. Individual exhibit modularity, but also contain loci showing multiple associations. Clustering genetic distance trees reduced differentiation range are consistent shared as source contemporary adaptive diversity cod. Conversely, find haplotypes LG12 LG1 rearranged region diverged Atlantic, despite Exchange structurally variable genomic regions, well selective pressures, has likely facilitated stocks. highlight importance enabling marine species.

Язык: Английский

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Combining population genomics with demographic analyses highlights habitat patchiness and larval dispersal as determinants of connectivity in coastal fish species

Molecular Ecology, Год журнала: 2022, Номер 31(9), С. 2562 - 2577

Опубликована: Март 1, 2022

Abstract Gene flow shapes spatial genetic structure and the potential for local adaptation. Among marine animals with nonmigratory adults, presence or absence of a pelagic larval stage is thought to be key determinant in shaping gene populations. In addition, distribution suitable habitats expected influence biological populations their connectivity patterns. We used whole genome sequencing study demographic history reduced representation (double‐digest restriction associated DNA) data analyse broadnosed pipefish ( Syngnathus typhle ). Its main habitat eelgrass beds, which are patchily distributed along area southern Norway. Demographic among was inferred from long‐term (~30‐year) population counts that uncovered rapid decline correlations abundance distance as short ~2 km. These findings were contrasted two other fish species have (corkwing wrasse, Symphodus melops ; black goby, Gobius niger For these latter species, we found wider scales weaker isolation‐by‐distance patterns, except where both experienced strong barrier flow, seemingly due lack habitat. Our verify expectations fragmented promote structure, while larvae increases perhaps over extensive gaps.

Язык: Английский

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Global, regional, and cryptic population structure in a high gene-flow transatlantic fish

PLoS ONE, Год журнала: 2023, Номер 18(3), С. e0283351 - e0283351

Опубликована: Март 20, 2023

Lumpfish ( Cyclopterus lumpus ) is a transatlantic marine fish displaying large population sizes and high potential for dispersal gene-flow. These features are expected to result in weak structure. Here, we investigated genetic structure of lumpfish throughout its natural distribution the North Atlantic using two approaches: I) 4,393 genome wide SNPs 95 individuals from 10 locations, II) 139 discriminatory 1,669 40 locations. Both approaches identified extensive structuring with major split between East West distinct Baltic Sea population, as well further differentiation English Channel, Iceland, Greenland. The loci displayed ~2–5 times higher divergence than approach, revealing evidence local substructures. Isfjorden Svalbard were highly but resembled most Kattegat area transition zone, formed previously undescribed group. Also, subdivision was detected within America, Greenland, Barents Sea, Norway. Although have considerable gene-flow, observed levels suggests that this species may natal homing behavior populations adaptive differences. This fine-scale calls consideration when defining management units exploitation stocks decisions related sourcing moving cleaner use salmonid aquaculture.

Язык: Английский

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Ecological interactions between farmed Atlantic salmon and wild Atlantic cod populations in Norway: A review of risk sources and knowledge gaps

Reviews in Aquaculture, Год журнала: 2024, Номер 16(3), С. 1333 - 1350

Опубликована: Фев. 27, 2024

Abstract Aquaculture provides an important and expanding source of protein rich healthy food to the world. However, minimize environmental harm from aquaculture, interactions with wild fish communities need be thoroughly assessed. Here, we characterize existing knowledge pertaining such interactions, exemplified Atlantic salmon ( Salmo salar ) farming in open net pens along Norwegian coast potential consequences for cod Gadus morhua populations. Importantly, fishery also a rich, high quality economic value. We identify seven risk sources that may affect behaviour, physiology, survival cod. Of particular importance is large amount waste feed causes aggregate around farms, thereby altering multitude ecological including predation disease transmission. Moreover, altered pellets alter physiological processes cause mortality vulnerable life‐stages More research needed on mechanisms thresholds harm. As most fisheries are found northern Norway, where climate change rapid, expect stronger potentially more harmful between as aquaculture continues expand. hope our analysis will inspire further research, farmed but general. Such fundamental development management systems can reduce impact environment.

Язык: Английский

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