Weak genetic structure despite strong genomic signal in lesser sandeel in the North Sea

Putting Structural Variants Into Practice: The Role of Chromosomal Inversions in the Management of Marine Environments

Major threats to marine species and ecosystems include overfishing, invasive species, pollution and climate change. The changing climate not only imposes direct threats through the impacts of severe marine heatwaves, cyclones and ocean acidification but also complicates fisheries and invasive species management by driving species range shifts. The dynamic nature of these threats means that the future of our oceans will depend on the ability of species to adapt. This has led to calls for genetic interventions focussed on enhancing species' adaptive capacity, including translocations, restocking and selective breeding. Assessing the benefits and risks of such approaches requires an improved understanding of the genetic architecture of adaptive variation, not only in relation to climate-resilient phenotypes but also locally adapted populations and the fitness of hybrids. Large structural genetic variants such as chromosomal inversions play an important role in local adaptation by linking multiple adaptive loci. Consequently, inversions are likely to be particularly important when managing for adaptive capacity. However, under some circumstances, they also accumulate deleterious mutations, potentially increasing the risk of inbreeding depression. Genetic management that takes account of these dual roles on fitness is likely to be more effective at ensuring population persistence. We summarise evolutionary factors influencing adaptive and deleterious variation of inversions, review inversions found in marine taxa, and provide a framework to predict the consequences of ignoring inversions in key management scenarios. We conclude by describing practical methods to bridge the gap between evolutionary theory and practical application of inversions in conservation.

Connections Across Open Water: A Bi-Organelle, Genomics-Scale Assessment of Atlantic-Wide Population Dynamics in a Pelagic, Endangered Apex Predator Shark (Isurus oxyrinchus)

Large-bodied pelagic sharks are key regulators of oceanic ecosystem stability, but highly impacted by severe overfishing. One such species, the shortfin mako shark (Isurus oxyrinchus), a globally widespread, highly migratory predator, has undergone dramatic population reductions and is now Endangered (IUCN Red List), with Atlantic Ocean mako sharks in particular assessed by fishery managers as overfished and in need of urgent, improved management attention. Genomic-scale population assessments for this apex predator species have not been previously available to inform management planning; thus, we investigated the population genetics of mako sharks across the Atlantic using a bi-organelle genomics approach. Complete mitochondrial genome (mitogenome) sequences and genome-wide SNPs from sharks distributed across the Atlantic revealed contrasting patterns of population structure across marker types. Consistent with this species' long-distance migratory capabilities, SNPs showed high connectivity and Atlantic panmixia overall. In contrast, there was matrilineal population genetic structure across Northern and Southern Hemispheres, suggesting at least large regional-scale female philopatry. Linkage disequilibrium network analysis indicated that makos possess a chromosomal inversion that occurs Atlantic wide, a genome feature that may be informative for evolutionary investigations concerning adaptations and the global history of this iconic species. Mitogenome diversity in Atlantic makos was high compared to other elasmobranchs assessed at the mitogenome level, and nuclear diversity was high compared to the two other, highly migratory pelagic shark species assessed with SNPs. These results support management efforts for shortfin makos on at least Northern versus Southern Hemisphere scales to preserve their matrilineal genetic distinctiveness. The overall comparative genetic diversity findings provide a baseline for future comparative assessments and monitoring of genetic diversity, as called for by the United Nations Convention on Biological Diversity, and cautious optimism regarding the health and recovery potential of Atlantic shortfin makos if further population declines can be halted.

A Faroese perspective on decoding life for sustainable use of nature and protection of biodiversity

Biodiversity is under pressure, mainly due to human activities and climate change. At the international policy level, it is now recognised that genetic diversity is an important part of biodiversity. The availability of high-quality reference genomes gives the best basis for using genetics and genetic diversity towards the global aims of (1) the protection of species, biodiversity, and nature, and (2) the management of biodiversity for achieving sustainable harvesting of nature. Protecting biodiversity is a global responsibility, also resting on small nations, like the Faroe Islands. Being in the middle of the North Atlantic Ocean and having large fisheries activity, the nation has a particular responsibility towards maritime matters. We here provide the reasoning behind the Genome Atlas of Faroese Ecology (Gen@FarE), a project based on our participation in the European Reference Genome Atlas consortium (ERGA). Gen@FarE has three major aims: (1) To acquire high-quality genomes of all eukaryotic species in the Faroe Islands and Faroese waters. (2) To establish population genetics for species of commercial or ecological interest. (3) To establish an information databank for all Faroese species, combined with a citizen science registration database, making it possible for the public to participate in acquiring and maintaining the overview of Faroese species in both terrestrial and marine environments. Altogether, we believe that this will enhance the society's interest in and awareness of biodiversity, thereby protecting the foundations of our lives. Furthermore, the combination of a wide and highly competent ERGA umbrella and more targeted national projects will help fulfil the formal and moral responsibilities that all nations, also those with limited resources, have in protecting biodiversity and achieving sustainability in harvesting from nature.

Genetics in the Ocean's Twilight Zone: Population Structure of the Glacier Lanternfish Across Its Distribution Range

The mesopelagic zone represents one of the few habitats that remains relatively untouched from anthropogenic activities. Among the many species inhabiting the north Atlantic mesopelagic zone, glacier lanternfish (Benthosema glaciale) is the most abundant and widely distributed. This species has been regarded as a potential target for a dedicated fishery despite the scarce knowledge of its population genetic structure. Here, we investigated its genetic structure across the North Atlantic and into the Mediterranean Sea using 121 SNPs, which revealed strong differentiation among three main groups: the Mediterranean Sea, oceanic samples, and Norwegian fjords. The Mediterranean samples displayed less than half the genetic variation of the remaining ones. Very weak or nearly absent genetic structure was detected among geographically distinct oceanic samples across the North Atlantic, which contrasts with the low motility of the species. In contrast, a longitudinal gradient of differentiation was observed in the Mediterranean Sea, where genetic connectivity is known to be strongly shaped by oceanographic processes such as current patterns and oceanographic discontinuities. In addition, 12 of the SNPs, in linkage disequilibrium, drove a three clusters' pattern detectable through Principal Component Analysis biplot matching the genetic signatures generally associated with large chromosomal rearrangements, such as inversions. The arrangement of this putative inversion showed frequency differences between open-ocean and more confined water bodies such as the fjords and the Mediterranean, as it was fixed in the latter for the second most common arrangement of the fjord's samples. However, whether genetic differentiation was driven by local adaptation, secondary contact, or a combination of both factors remains undetermined. The major finding of this study is that B. glaciale in the North Atlantic-Mediterranean is divided into three major genetic units, information that should be combined with demographic properties to outline the management of this species prior to any eventual fishery attempt.

Unidirectional trans-Atlantic gene flow and a mixed spawning area shape the genetic connectivity of Atlantic bluefin tuna

The commercially important Atlantic bluefin tuna (Thunnus thynnus), a large migratory fish, has experienced notable recovery aided by accurate resource assessment and effective fisheries management efforts. Traditionally, this species has been perceived as consisting of eastern and western populations, spawning respectively in the Mediterranean Sea and the Gulf of Mexico, with mixing occurring throughout the Atlantic. However, recent studies have challenged this assumption by revealing weak genetic differentiation and identifying a previously unknown spawning ground in the Slope Sea used by Atlantic bluefin tuna of uncertain origin. To further understand the current and past population structure and connectivity of Atlantic bluefin tuna, we have assembled a unique dataset including thousands of genome-wide single-nucleotide polymorphisms (SNPs) from 500 larvae, young of the year and spawning adult samples covering the three spawning grounds and including individuals of other Thunnus species. Our analyses support two weakly differentiated but demographically connected ancestral populations that interbreed in the Slope Sea. Moreover, we also identified signatures of introgression from albacore (Thunnus alalunga) into the Atlantic bluefin tuna genome, exhibiting varied frequencies across spawning areas, indicating strong gene flow from the Mediterranean Sea towards the Slope Sea. We hypothesize that the observed genetic differentiation may be attributed to increased gene flow caused by a recent intensification of westward migration by the eastern population, which could have implications for the genetic diversity and conservation of western populations. Future conservation efforts should consider these findings to address potential genetic homogenization in the species.

Genomic survey of edible cockle (Cerastoderma edule) in the Northeast Atlantic: A baseline for sustainable management of its wild resources

Knowledge on correlations between environmental factors and genome divergence between populations of marine species is crucial for sustainable management of fisheries and wild populations. The edible cockle (Cerastoderma edule) is a marine bivalve distributed along the Northeast Atlantic coast of Europe and is an important resource from both commercial and ecological perspectives. We performed a population genomics screening using 2b-RAD genotyping on 9309 SNPs localized in the cockle's genome on a sample of 536 specimens pertaining to 14 beds in the Northeast Atlantic Ocean to analyse the genetic structure with regard to environmental variables. Larval dispersal modelling considering species behaviour and interannual/interseasonal variation in ocean conditions was carried out as an essential background to which compare genetic information. Cockle populations in the Northeast Atlantic displayed low but significant geographical differentiation between populations (F ST = 0.0240; p < 0.001), albeit not across generations. We identified 742 and 36 outlier SNPs related to divergent and balancing selection in all the geographical scenarios inspected, and sea temperature and salinity were the main environmental correlates suggested. Highly significant linkage disequilibrium was detected at specific genomic regions against the very low values observed across the whole genome. Two main genetic groups were identified, northwards and southwards of French Brittany. Larval dispersal modelling suggested a barrier for larval dispersal linked to the Ushant front that could explain these two genetic clusters. Further genetic subdivision was observed using outlier loci and considering larval advection. The northern group was divided into the Irish/Celtic Seas and the English Channel/North Sea, while the southern group was divided into three subgroups. This information represents the baseline for the management of cockles, designing conservation strategies, founding broodstock for depleted beds and producing suitable seed for aquaculture production.

Distinct genetic clustering in the weakly differentiated polar cod, Boreogadus saida Lepechin, 1774 from East Siberian Sea to Svalbard

The 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.

Evolution at two time frames: ancient structural variants involved in post-glacial divergence of the European plaice (Pleuronectes platessa)

Changing environmental conditions can lead to population diversification through differential selection on standing genetic variation. Structural variant (SV) polymorphisms provide examples of ancient alleles that in time become associated with novel environmental gradients. The European plaice (Pleuronectes platessa) is a marine flatfish showing large allele-frequency differences at two putative SVs associated with environmental variation. In this study, we explored the contribution of these SVs to population structure across the North East Atlantic. We compared genome-wide population structure using sets of RAD-sequencing SNPs with the spatial structure of the SVs. We found that in contrast to the rest of the genome, the SVs were only weakly associated with an isolation-by-distance pattern. Indeed, both SVs showed important variation in haplogroup frequencies, with the same haplogroup increasing both along the salinity gradient of the Baltic Sea, and found in high frequency in the northern-range margin of the Atlantic. Phylogenetic analyses suggested that the SV alleles are much older than the age of the Baltic Sea itself. These results suggest that the SVs are older than the age of the environmental gradients with which they currently co-vary. Altogether, our results suggest that the plaice SVs were shaped by evolutionary processes occurring at two time frames, firstly following their origin, ancient spread and maintenance in the ancestral populations, and secondly related to their current association with more recently formed environmental gradients such as those found in the North Sea-Baltic Sea transition zone.

Consequences of Single-Locus and Tightly Linked Genomic Architectures for Evolutionary Responses to Environmental Change

Genetic and genomic architectures of traits under selection are key factors influencing evolutionary responses. Yet, knowledge of their impacts has been limited by a widespread assumption that most traits are controlled by unlinked polygenic architectures. Recent advances in genome sequencing and eco-evolutionary modeling are unlocking the potential for integrating genomic information into predictions of population responses to environmental change. Using eco-evolutionary simulations, we demonstrate that hypothetical single-locus control of a life history trait produces highly variable and unpredictable harvesting-induced evolution relative to the classically applied multilocus model. Single-locus control of complex traits is thought to be uncommon, yet blocks of linked genes, such as those associated with some types of structural genomic variation, have emerged as taxonomically widespread phenomena. Inheritance of linked architectures resembles that of single loci, thus enabling single-locus-like modeling of polygenic adaptation. Yet, the number of loci, their effect sizes, and the degree of linkage among them all occur along a continuum. We review how linked architectures are often associated, directly or indirectly, with traits expected to be under selection from anthropogenic stressors and are likely to play a large role in adaptation to environmental disturbance. We suggest using single-locus models to explore evolutionary extremes and uncertainties when the trait architecture is unknown, refining parameters as genomic information becomes available, and explicitly incorporating linkage among loci when possible. By overestimating the complexity (e.g., number of independent loci) of the genomic architecture of traits under selection, we risk underestimating the complexity (e.g., nonlinearity) of their evolutionary dynamics.

Time matters: genetic composition and evaluation of effective population size in temperate coastal fish species

Background

Extensive knowledge on the genetic characterization of marine organisms has been assembled, mainly concerning the spatial distribution and structuring of populations. Temporal monitoring assesses not only the stability in genetic composition but also its trajectory over time, providing critical information for the accurate forecast of changes in genetic diversity of marine populations, particularly important for both fisheries and endangered species management. We assessed fluctuations in genetic composition among different sampling periods in the western Portuguese shore in three fish species.

Methods

White seabream Diplodus sargus, sand smelt Atherina presbyter and shanny Lipophrys pholis were chosen, because of their genetic patterns in distinct ecological environments, insight into historical and contemporary factors influencing population effective size (N_e), and degree of commercial exploitation. Samples were obtained near Lisbon between 2003 and 2014 and screened for genetic variation with mitochondrial and nuclear markers. Analyses included genealogies, genetic diversities, temporal structures and contemporary N_e.

Results

For mtDNA no temporal structure was detected, while for nDNA significant differences were recorded between some sampling periods for the shanny and the sand smelt. Haplotype networks revealed deep genealogies, with various levels of diversification. The shanny revealed a smaller N_e/generation when compared to the other species, which, in turn, revealed no evidence of genetic drift for most study periods. These results highlight the fact that temporal variations in genetic pool composition should be considered when evaluating the population structure of fish species with long distance dispersal, which are more vulnerable to recruitment fluctuations.

Weak genetic structure despite strong genomic signal in lesser sandeel in the North Sea

Sandeels are an ecologically important group of fishes; they are a key part of the food chain serving as food for marine mammals, seabirds and fish. Sandeels are further targeted by a large industrial fishery, which has led to concern about ecosystem effects. In the North Sea, the lesser sandeel Ammodytes marinus is by far the most prevalent species of sandeel in the fishery. Management of sandeel in the North Sea plus the Kattegat is currently divided into seven geographical areas, based on subtle differences in demography, population dynamics and results from simulations of larval dispersal. However, little is known about the underlying genetic population structure. In this study, we used 2,522 SNPs derived from restriction site-associated DNA sequencing (RADseq) typed in 429 fish representing four main sandeel management areas. Our main results showed (a) a lack of a clear spatially defined genetic structure across the majority of genetic markers and (b) the existence of a group of at least 13 SNPs under strong linkage disequilibrium which together separate North Sea sandeel into three haplotype clusters, suggestive of one or more structural variants in the genome. Analyses of the spatial distribution of these putative structural variants suggest at least partial reproductive isolation of sandeel in the western management area along the Scottish coast, supporting a separate management. Our results highlight the importance of the application of a large number of markers to be able to detect weak patterns of differentiation. This study contributes to increasing the genetic knowledge of this important exploited species, and results can be used to improve our understanding of population dynamics and stock structure.