A genomic island linked to ecotype divergence in Atlantic cod

Genomic underpinnings of head and body shape in Arctic charr ecomorph pairs

Across its Holarctic range, Arctic charr (Salvelinus alpinus) populations have diverged into distinct trophic specialists across independent replicate lakes. The major aspect of divergence between ecomorphs is in head shape and body shape, which are ecomorphological traits reflecting niche use. However, whether the genomic underpinnings of these parallel divergences are consistent across replicates was unknown but key for resolving the substrate of parallel evolution. We investigated the genomic basis of head shape and body shape morphology across four benthivore-planktivore ecomorph pairs of Arctic charr in Scotland. Through genome-wide association analyses, we found genomic regions associated with head shape (89 SNPs) or body shape (180 SNPs) separately and 50 of these SNPs were strongly associated with both body and head shape morphology. For each trait separately, only a small number of SNPs were shared across all ecomorph pairs (3 SNPs for head shape and 10 SNPs for body shape). Signs of selection on the associated genomic regions varied across pairs, consistent with evolutionary demography differing considerably across lakes. Using a comprehensive database of salmonid QTLs newly augmented and mapped to a charr genome, we found several of the head- and body-shape-associated SNPs were within or near morphology QTLs from other salmonid species, reflecting a shared genetic basis for these phenotypes across species. Overall, our results demonstrate how parallel ecotype divergences can have both population-specific and deeply shared genomic underpinnings across replicates, influenced by differences in their environments and demographic histories.

How Fish Population Genomics Can Promote Sustainable Fisheries: A Road Map

Maintenance of genetic diversity in marine fishes targeted by commercial fishing is a grand challenge for the future. Most of these species are abundant and therefore important for marine ecosystems and food security. Here, we present a road map of how population genomics can promote sustainable fisheries. In these species, the development of reference genomes and whole genome sequencing is key, because genetic differentiation at neutral loci is usually low due to large population sizes and gene flow. First, baseline allele frequencies representing genetically differentiated populations within species must be established. These can then be used to accurately determine the composition of mixed samples, forming the basis for population demographic analysis to inform sustainably set fish quotas. SNP-chip analysis is a cost-effective method for determining baseline allele frequencies and for population identification in mixed samples. Finally, we describe how genetic marker analysis can transform stock identification and management.

Single Nucleotide Polymorphism Markers with Applications in Conservation and Exploitation of Aquatic Natural Populations

Simple Summary

In recent decades, societies, states and local authorities have become increasingly aware that for effective long-term management and protection of aquatic ecosystems and populations, it is necessary to take into account the genetic changes occurring in these populations. One type of high-resolution molecular marker suitable for studying the neutral and adaptive genetic diversity of populations is single nucleotide polymorphism (SNP). This review is an attempt to show the benefits of using SNPs to recognize natural populations of aquatic animals and detect the threats to them from accidentally or intentionally released farm animals, fishery and global climate changes. It is postulated that conservation actions should protect not only pristine natural populations that are endangered or overfished, but also protect populations of non-threatened species from unnecessarily released semi-domesticated animals. The enhancement of natural populations with farmed material usually reduces their genetic diversity. Experimental size-selective catches of artificially created populations have caused evolutionary changes in the life cycles of fishes. However, fishery-induced evolution in natural populations is difficult to observe. The negative measurable effects on populations can be expected when the number of breeding individuals is reduced below 100, which occurs very rarely in the sea and more often in fragmented freshwater streams, ponds and seasonal rivers.

Abstract

An increasing number of aquatic species have been studied for genetic polymorphism, which extends the knowledge on their natural populations. One type of high-resolution molecular marker suitable for studying the genetic diversity of large numbers of individuals is single nucleotide polymorphism (SNP). This review is an attempt to show the range of applications of SNPs in studies of natural populations of aquatic animals. In recent years, SNPs have been used in the genetic analysis of wild and enhanced fish and invertebrate populations in natural habitats, exploited migratory species in the oceans, migratory anadromous and freshwater fish and demersal species. SNPs have been used for the identification of species and their hybrids in natural environments, to study the genetic consequences of restocking for conservation purposes and the negative effects on natural populations of fish accidentally escaping from culture. SNPs are very useful for identifying genomic regions correlated with phenotypic variants relevant for wildlife protection, management and aquaculture. Experimental size-selective catches of populations created in tanks have caused evolutionary changes in life cycles of fishes. The research results have been discussed to clarify whether the fish populations in natural conditions can undergo changes due to selective harvesting targeting the fastest-growing fishes.

Genetic parallelism between European flat oyster populations at the edge of their natural range

Although all marine ecosystems have experienced global-scale losses, oyster reefs have shown the greatest. Therefore, substantial efforts have been dedicated to restoration of such ecosystems during the last two decades. In Europe, several pilot projects for the restoration of the native European flat oyster, Ostrea edulis, recently begun and recommendations to preserve genetic diversity and to conduct monitoring protocols have been made. In particular, an initial step is to test for genetic differentiation against homogeneity among the oyster populations potentially involved in such programs. Therefore, we conducted a new sampling of wild populations at the European scale and a new genetic analysis with 203 markers to (1) confirm and study in more detail the pattern of genetic differentiation between Atlantic and Mediterranean populations, (2) identify potential translocations that could be due to aquaculture practices and (3) investigate the populations at the fringe of the geographical range, since they seemed related despite their geographic distance. Such information should be useful to enlighten the choice of the animals to be translocated or reproduced in hatcheries for further restocking. After the confirmation of the general geographical pattern of genetic structure and the identification of one potential case of aquaculture transfer at a large scale, we were able to detect genomic islands of differentiation mainly in the form of two groups of linked markers, which could indicate the presence of polymorphic chromosomal rearrangements. Furthermore, we observed a tendency for these two islands and the most differentiated loci to show a parallel pattern of differentiation, grouping the North Sea populations with the Eastern Mediterranean and Black Sea populations, against geography. We discussed the hypothesis that this genetic parallelism could be the sign of a shared evolutionary history of the two groups of populations despite them being at the border of the distribution nowadays.

Hidden but revealed: After years of genetic studies behavioural monitoring combined with genomics uncover new insight into the population dynamics of Atlantic cod in Icelandic waters

Stock structure is of paramount importance for sustainable management of exploited resources. In that context, genetic markers have been used for more than two decades to resolve spatial structure of marine exploited resources and to fully fathom stock dynamics and interactions. While genetic markers such as allozymes and RFLP dominated the debate in the early era of genetics, technology advances have provided scientists with new tools every decade to better assess stock discrimination and interactions (i.e. gene flow). Here, we provide a review of genetic studies performed to understand stock structure of Atlantic cod in Icelandic waters, from the early allozyme approaches to the genomic work currently carried out. We further highlight the importance of the generation of a chromosome-anchored genome assembly together with whole-genome population data, which drastically changed our perception of the possible management units to consider. After nearly 60 years of genetic investigation of Atlantic cod structure in Icelandic waters, genetic (and later genomic) data combined with behavioural monitoring using Data Storage Tags shifted the attention from geographical population structures to behavioural ecotypes. This review also demonstrates the need for future research to further disentangle the impact of these ecotypes (and gene flow among them) on the population structure of Atlantic cod in Icelandic waters. It also highlights the importance of whole-genome data to unravel unexpected within-species diversity related to chromosomal inversions and associated supergenes, which are important to consider for future development of sustainable management programmes of the species within the North Atlantic.

Sweepstakes reproductive success via pervasive and recurrent selective sweeps

Highly fecund natural populations characterized by high early mortality abound, yet our knowledge about their recruitment dynamics is somewhat rudimentary. This knowledge gap has implications for our understanding of genetic variation, population connectivity, local adaptation, and the resilience of highly fecund populations. The concept of sweepstakes reproductive success, which posits a considerable variance and skew in individual reproductive output, is key to understanding the distribution of individual reproductive success. However, it still needs to be determined whether highly fecund organisms reproduce through sweepstakes and, if they do, the relative roles of neutral and selective sweepstakes. Here, we use coalescent-based statistical analysis of population genomic data to show that selective sweepstakes likely explain recruitment dynamics in the highly fecund Atlantic cod. We show that the Kingman coalescent (modelling no sweepstakes) and the Xi-Beta coalescent (modelling random sweepstakes), including complex demography and background selection, do not provide an adequate fit for the data. The Durrett-Schweinsberg coalescent, in which selective sweepstakes result from recurrent and pervasive selective sweeps of new mutations, offers greater explanatory power. Our results show that models of sweepstakes reproduction and multiple-merger coalescents are relevant and necessary for understanding genetic diversity in highly fecund natural populations. These findings have fundamental implications for understanding the recruitment variation of fish stocks and general evolutionary genomics of high-fecundity organisms.

Genomic differentiation in Pacific cod using P ool‐ S eq

Patterns of genetic differentiation across the genome can provide insight into selective forces driving adaptation. We used pooled whole genome sequencing, gene annotation, and environmental covariates to evaluate patterns of genomic differentiation and to investigate mechanisms responsible for divergence among proximate Pacific cod (Gadus macrocephalus) populations from the Bering Sea and Aleutian Islands and more distant Washington Coast cod. Samples were taken from eight spawning locations, three of which were replicated to estimate consistency in allele frequency estimation. A kernel smoothing moving weighted average of relative divergence (F_ST) identified 11 genomic islands of differentiation between the Aleutian Islands and Bering Sea samples. In some islands of differentiation, there was also elevated absolute divergence (d_XY) and evidence for selection, despite proximity and potential for gene flow. Similar levels of absolute divergence (d_XY) but roughly double the relative divergence (F_ST) were observed between the distant Bering Sea and Washington Coast samples. Islands of differentiation were much smaller than the four large inversions among Atlantic cod ecotypes. Islands of differentiation between the Bering Sea and Aleutian Island were associated with SNPs from five vision system genes, which can be associated with feeding, predator avoidance, orientation, and socialization. We hypothesize that islands of differentiation between Pacific cod from the Bering Sea and Aleutian Islands provide evidence for adaptive differentiation despite gene flow in this commercially important marine species.

Living apart together: Long-term coexistence of Baltic cod stocks associated with depth-specific habitat use

Coexistence of fish populations (= stocks) of the same species is a common phenomenon. In the Baltic Sea, two genetically divergent stocks of Atlantic cod (Gadus morhua), Western Baltic cod (WBC) and Eastern Baltic cod (EBC), coexist in the Arkona Sea. Although the relative proportions of WBC and EBC in this area are considered in the current stock assessments, the mixing dynamics and ecological mechanisms underlying coexistence are not well understood. In this study, a genetically validated otolith shape analysis was used to develop the most comprehensive time series of annual stock mixing data (1977–2019) for WBC and EBC. Spatio-temporal mixing analysis confirmed that the two stocks coexist in the Arkona Sea, albeit with fluctuating mixing proportions over the 43-year observation period. Depth-stratified analysis revealed a strong correlation between capture depth and stock mixing patterns, with high proportions of WBC in shallower waters (48–61% in <20m) and increasing proportions of EBC in deeper waters (50–86% in 40-70m). Consistent depth-specific mixing patterns indicate stable differences in depth distribution and habitat use of WBC and EBC that may thus underlie the long-term coexistence of the two stocks in the Arkona Sea. These differences were also reflected in significantly different proportions of WBC and EBC in fisheries applying passive gears in shallower waters (more WBC) and active gears in deeper waters (more EBC). This highlights the potential for fishing gear-specific exploitation of different stocks, and calls for stronger consideration of capture depth and gear type in stock assessments. This novel evidence provides the basis for improved approaches to research, monitoring and management of Baltic cod stocks.

Allopatric origin of sympatric whitefish morphs with insights on the genetic basis of their reproductive isolation

The European whitefish (Coregonus lavaretus) species complex is a classic example of recent adaptive radiation. Here, we examine a whitefish population introduced to northern Finnish Lake Tsahkal in the late 1960s, where three divergent morphs (viz. littoral, pelagic, and profundal feeders) were found 10 generations after. Using demographic modeling based on genomic data, we show that whitefish morphs evolved during a phase of strict isolation, refuting a rapid sympatric divergence scenario. The lake is now an artificial hybrid zone between morphs originated in allopatry. Despite their current syntopy, clear genetic differentiation remains between two of the three morphs. Using admixture mapping, we identify five SNPs associated with gonad weight variation, a proxy for sexual maturity and spawning time. We suggest that ecological adaptations in spawning time evolved in allopatry are currently maintaining partial reproductive isolation in the absence of other barriers to gene flow.

Retrospective genomics highlights changes in genetic composition of tiger sharks (Galeocerdo cuvier) and potential loss of a south-eastern Australia population

Over the last century, many shark populations have declined, primarily due to overexploitation in commercial, artisanal and recreational fisheries. In addition, in some locations the use of shark control programs also has had an impact on shark numbers. Still, there is a general perception that populations of large ocean predators cover wide areas and therefore their diversity is less susceptible to local anthropogenic disturbance. Here we report on temporal genomic analyses of tiger shark (Galeocerdo cuvier) DNA samples that were collected from eastern Australia over the past century. Using Single Nucleotide Polymorphism (SNP) loci, we documented a significant change in genetic composition of tiger sharks born between ~1939 and 2015. The change was most likely due to a shift over time in the relative contribution of two well-differentiated, but hitherto cryptic populations. Our data strongly indicate a dramatic shift in the relative contribution of these two populations to the overall tiger shark abundance on the east coast of Australia, possibly associated with differences in direct or indirect exploitation rates.

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

Ecological disruption due to human impacts is evident worldwide, and a key to mitigation lies in characterizing the underlying mechanisms of species and ecosystem stability. Here we show that three extensive “supergenes” are maintained in Atlantic cod by stabilizing selection, tying these genes to the persistence of a keystone species distributed across the northern Atlantic Ocean. Removal of this species has caused severe ecosystem reshuffling in several areas of its range. Genomic inference of historic stock sizes further shows that cod has been under pressure in the North Sea system since the Viking period, in line with zooarchaeological records. Expansion of fisheries in Northern Europe through the past millennium is well documented and supports the inferred long-term declines.

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

Supergene origin and maintenance in Atlantic cod

Supergenes are sets of genes that are inherited as a single marker and encode complex phenotypes through their joint action. They are identified in an increasing number of organisms, yet their origins and evolution remain enigmatic. In Atlantic cod, four megabase-scale supergenes have been identified and linked to migratory lifestyle and environmental adaptations. Here we investigate the origin and maintenance of these four supergenes through analysis of whole-genome-sequencing data, including a new long-read-based genome assembly for a non-migratory Atlantic cod individual. We corroborate the finding that chromosomal inversions underlie all four supergenes, and we show that they originated at different times between 0.40 and 1.66 million years ago. We reveal gene flux between supergene haplotypes where migratory and stationary Atlantic cod co-occur and conclude that this gene flux is driven by gene conversion, on the basis of an increase in GC content in exchanged sites. Additionally, we find evidence for double crossover between supergene haplotypes, leading to the exchange of an ~275 kilobase fragment with genes potentially involved in adaptation to low salinity in the Baltic Sea. Our results suggest that supergenes can be maintained over long timescales in the same way as hybridizing species, through the selective purging of introduced genetic variation.

Atlantic cod carries four supergenes linked to migratory lifestyle and environmental adaptations. Using whole-genome sequencing, the authors show that the genome inversions that underlie the supergenes originated at different times and show gene flux between supergene haplotypes.

Understanding population structure in an evolutionary context: population-specific FST and pairwise FST

Populations are shaped by their history. It is crucial to interpret population structure in an evolutionary context. Pairwise F_ST measures population structure, whereas population-specific F_ST measures deviation from the ancestral population. To understand the current population structure and a population’s history of range expansion, we propose a representation method that overlays population-specific F_ST estimates on a sampling location map, and on an unrooted neighbor-joining tree and a multi-dimensional scaling plot inferred from a pairwise F_ST distance matrix. We examined the usefulness of our procedure using simulations that mimicked population colonization from an ancestral population and by analyzing published human, Atlantic cod, and wild poplar data. Our results demonstrated that population-specific F_ST values identify the source population and trace the evolutionary history of its derived populations. Conversely, pairwise F_ST values represent the current population structure. By integrating the results of both estimators, we obtained a new picture of the population structure that incorporates evolutionary history. The generalized least squares estimate of genome-wide population-specific F_ST indicated that the wild poplar population expanded its distribution to the north, where daylight hours are long in summer, to coastal areas with abundant rainfall, and to the south where summers are dry. Genomic data highlight the power of the bias-corrected moment estimators of F_ST, whether global, pairwise, or population-specific, that provide unbiased estimates of F_ST. All F_ST moment estimators described in this paper have reasonable processing times and are useful in population genomics studies.

Low-coverage whole-genome sequencing reveals molecular markers for spawning season and sex identification in Gulf of Maine Atlantic cod (Gadus morhua, Linnaeus 1758)

Atlantic cod (Gadus morhua, Linnaeus 1758) in the western Gulf of Maine are managed as a single stock despite several lines of evidence supporting two spawning groups (spring and winter) that overlap spatially, while exhibiting seasonal spawning isolation. Low-coverage whole-genome sequencing was used to evaluate the genomic population structure of Atlantic cod spawning groups in the western Gulf of Maine and Georges Bank using 222 individuals collected over multiple years. Results indicated low total genomic differentiation, while also showing strong differentiation between spring and winter-spawning groups at specific regions of the genome. Guided regularized random forest and ranked F ST methods were used to select panels of single nucleotide polymorphisms (SNPs) that could reliably distinguish spring and winter-spawning Atlantic cod (88.5% assignment rate), as well as males and females (95.0% assignment rate) collected in the western Gulf of Maine. These SNP panels represent a valuable tool for fisheries research and management of Atlantic cod in the western Gulf of Maine that will aid investigations of stock production and support accuracy of future assessments.

Life-stage-dependent supergene haplotype frequencies and metapopulation neutral genetic patterns of Atlantic cod, Gadus morhua, from Canada's Northern cod stock region and adjacent areas

Among highly migratory fish species, nursery areas occupied by juveniles often differ from adult habitats. To better understand the spatial dynamics of Canada's Northern cod stock, juveniles caught off the east coast of Newfoundland and Labrador were compared to adults from the same region as well as individuals from other areas in Atlantic Canada using double-digest restriction site-associated DNA sequencing-derived single nucleotide polymorphisms. A reduced proportion of homozygotes with a chromosomal inversion located in linkage group 1 (LG1) was detected between juvenile and adult samples in the Northern cod stock region, potentially indicating age-dependent habitat use or ontogenetic selection for attributes associated with the many genes located in LG1. No selectively neutral genetic differences were found between samples from the Northern cod stock; nevertheless, significant differences were found between some of these samples and cod collected from St. Pierre Bank, Bay of Fundy, Browns Bank and the southern Scotian Shelf. Clustering analysis of variants at neutral loci provided evidence for three major genetic units: (a) the Newfoundland Atlantic Coast, (b) eastern and southern Gulf of St. Lawrence and Burgeo Bank and (c) the Bay of Fundy, Browns Bank and southern Scotian Shelf. Both adaptive and neutral population structure within the Northern cod stock should be considered by managers to promote demographic rebuilding of the stock.

The pantophysin gene and its relationship with survival in early life stages of Atlantic cod

Genetic markers are widely used in fisheries management around the world. While the genetic structure and markers selected are usually based on samples from the wild, very few controlled experiments have been carried out to investigate possible differences in influence on traits between markers. Here we examine the bi-allelic gene pantophysin (Pan I), widely used in the management of Atlantic cod, in a series of in vitro crosses under a range of temperatures. It has been proposed that this gene, or another tightly linked gene, may be under strong divergent selection. Resolving this issue is essential in order to interpret results when using this gene marker for stock management. We found no evidence of departure from the expected 1 : 2 : 1 Mendelian ratio for any of the three genotypes during the egg stage, while both the 6 and 12°C temperature regimes in tank experiments favoured the survival of the Pan IAA genotype. No difference in genotype survival was, however, found in a more natural mesocosm environment. Collectively, these results suggest that for the early life stages of Atlantic cod, and under the current experimental conditions, there is no strong consistent influence of Pan I genotype on survival. The results also emphasize the importance of varied experimental studies to verify the importance of environmental factors influencing genotype selection.

Small-scale population divergence is driven by local larval environment in a temperate amphibian

Genomic variation within and among populations is shaped by the interplay between natural selection and the effects of genetic drift and gene flow. Adaptive divergence can be found in small-scale natural systems even when population sizes are small, and the potential for gene flow is high, suggesting that local environments exert selection pressures strong enough to counteract the opposing effects of drift and gene flow. Here, we investigated genomic differentiation in nine moor frog (Rana arvalis) populations in a small-scale network of local wetlands using 16,707 ddRAD-seq SNPs, relating levels of differentiation with local environments, as well as with properties of the surrounding landscape. We characterized population structure and differentiation, and partitioned the effects of geographic distance, local larval environment, and landscape features on total genomic variation. We also conducted gene-environment association studies using univariate and multivariate approaches. We found small-scale population structure corresponding to 6-8 clusters. Local larval environment was the most influential component explaining 2.3% of the total genetic variation followed by landscape features (1.8%) and geographic distance (0.8%), indicative of isolation-by-environment, -by-landscape, and -by-distance, respectively. We identified 1000 potential candidate SNPs putatively under divergent selection mediated by the local larval environment. The candidate SNPs were involved in, among other biological functions, immune system function and development. Our results suggest that small-scale environmental differences can exert selection pressures strong enough to counteract homogenizing effects of gene flow and drift in this small-scale system, leading to observable population differentiation.

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

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

Footprints of local adaptation span hundreds of linked genes in the Atlantic silverside genome

The study of local adaptation in the presence of ongoing gene flow is the study of natural selection in action, revealing the functional genetic diversity most relevant to contemporary pressures. In addition to individual genes, genome‐wide architecture can itself evolve to enable adaptation. Distributed across a steep thermal gradient along the east coast of North America, Atlantic silversides (Menidia menidia) exhibit an extraordinary degree of local adaptation in a suite of traits, and the capacity for rapid adaptation from standing genetic variation, but we know little about the patterns of genomic variation across the species range that enable this remarkable adaptability. Here, we use low‐coverage, whole‐transcriptome sequencing of Atlantic silversides sampled along an environmental cline to show marked signatures of divergent selection across a gradient of neutral differentiation. Atlantic silversides sampled across 1371 km of the southern section of its distribution have very low genome‐wide differentiation (median F_ST = 0.006 across 1.9 million variants), consistent with historical connectivity and observations of recent migrants. Yet almost 14,000 single nucleotide polymorphisms (SNPs) are nearly fixed (F_ST > 0.95) for alternate alleles. Highly differentiated SNPs cluster into four tight linkage disequilibrium (LD) blocks that span hundreds of genes and several megabases. Variants in these LD blocks are disproportionately nonsynonymous and concentrated in genes enriched for multiple functions related to known adaptations in silversides, including variation in lipid storage, metabolic rate, and spawning behavior. Elevated levels of absolute divergence and demographic modeling suggest selection maintaining divergence across these blocks under gene flow. These findings represent an extreme case of heterogeneity in levels of differentiation across the genome, and highlight how gene flow shapes genomic architecture in continuous populations. Locally adapted alleles may be common features of populations distributed along environmental gradients, and will likely be key to conserving variation to enable future responses to environmental change.

SNP genotyping reveals substructuring in weakly differentiated populations of Atlantic cod (Gadus morhua) from diverse environments in the Baltic Sea

Atlantic cod (Gadus morhua) is one of the most important fish species in northern Europe for several reasons including its predator status in marine ecosystems, its historical role in fisheries, its potential in aquaculture and its strong public profile. However, due to over-exploitation in the North Atlantic and changes in the ecosystem, many cod populations have been reduced in size and genetic diversity. Cod populations in the Baltic Proper, Kattegat and North Sea have been analyzed using a species specific single nucleotide polymorphism (SNP) array. Using a subset of 8,706 SNPs, moderate genetic differences were found between subdivisions in three traditionally delineated cod management stocks: Kattegat, western and eastern Baltic. However, an FST measure of population differentiation based on allele frequencies from 588 outlier loci for 2 population groups, one including 5 western and the other 4 eastern Baltic populations, indicated high genetic differentiation. In this paper, differentiation has been demonstrated not only between, but also within western and eastern Baltic cod stocks for the first time, with salinity appearing to be the most important environmental factor influencing the maintenance of cod population divergence between the western and eastern Baltic Sea.

Northern European Salmo trutta (L.) populations are genetically divergent across geographical regions and environmental gradients

The salmonid fish Brown trout is iconic as a model for the application of conservation genetics to understand and manage local interspecific variation. However, there is still scant information about relationships between local and large-scale population structure, and to what extent geographical and environmental variables are associated with barriers to gene flow. We used information from 3,782 mapped SNPs developed for the present study and conducted outlier tests and gene-environment association (GEA) analyses in order to examine drivers of population structure. Analyses comprised >2,600 fish from 72 riverine populations spanning a central part of the species' distribution in northern Europe. We report hitherto unidentified genetic breaks in population structure, indicating strong barriers to gene flow. GEA loci were widely spread across genomic regions and showed correlations with climatic, abiotic and geographical parameters. In some cases, individual loci showed consistent GEA across the geographical regions Britain, Europe and Scandinavia. In other cases, correlations were observed only within a sub-set of regions, suggesting that locus-specific variation was associated with local processes. A paired-population sampling design allowed us to evaluate sampling effects on detection of outlier loci and GEA. Two widely applied methods for outlier detection (pcadapt and bayescan) showed low overlap in loci identified as statistical outliers across sub-sets of data. Two GEA analytical approaches (LFMM and RDA) showed good correspondence concerning loci associated with specific variables, but LFMM identified five times more statistically significant associations than RDA. Our results emphasize the importance of carefully considering the statistical methods applied for the hypotheses being tested in outlier analysis. Sampling design may have lower impact on results if the objective is to identify GEA loci and their population distribution. Our study provides new insights into trout populations, and results have direct management implications in serving as a tool for identification of conservation units.

Divergent selection and drift shape the genomes of two avian sister species spanning a saline-freshwater ecotone

The role of species divergence due to ecologically based divergent selection-or ecological speciation-in generating and maintaining biodiversity is a central question in evolutionary biology. Comparison of the genomes of phylogenetically related taxa spanning a selective habitat gradient enables discovery of divergent signatures of selection and thereby provides valuable insight into the role of divergent ecological selection in speciation. Tidal marsh ecosystems provide tractable opportunities for studying organisms' adaptations to selective pressures that underlie ecological divergence. Sharp environmental gradients across the saline-freshwater ecotone within tidal marshes present extreme adaptive challenges to terrestrial vertebrates. Here, we sequence 20 whole genomes of two avian sister species endemic to tidal marshes-the saltmarsh sparrow (Ammospiza caudacutus) and Nelson's sparrow (A. nelsoni)-to evaluate the influence of selective and demographic processes in shaping genome-wide patterns of divergence. Genome-wide divergence between these two recently diverged sister species was notably high (genome-wide F ST = 0.32). Against a background of high genome-wide divergence, regions of elevated divergence were widespread throughout the genome, as opposed to focused within islands of differentiation. These patterns may be the result of genetic drift resulting from past tidal march colonization events in conjunction with divergent selection to different environments. We identified several candidate genes that exhibited elevated divergence between saltmarsh and Nelson's sparrows, including genes linked to osmotic regulation, circadian rhythm, and plumage melanism-all putative candidates linked to adaptation to tidal marsh environments. These findings provide new insights into the roles of divergent selection and genetic drift in generating and maintaining biodiversity.

Novel signals of adaptive genetic variation in northwestern Atlantic cod revealed by whole-genome sequencing

Selection can create complex patterns of adaptive differentiation among populations in the wild that may be relevant to management. Atlantic cod in the Northwest Atlantic are at a fraction of their historical abundance and a lack of recovery within the Gulf of Maine has created concern regarding the misalignment of fisheries management structures with biological population structure. To address this and investigate genome-wide patterns of variation, we used low-coverage sequencing to perform a region-wide, whole-genome analysis of fine-scale population structure. We sequenced 306 individuals from 20 sampling locations in U.S. and Canadian waters, including the major spawning aggregations in the Gulf of Maine in addition to spawning aggregations from Georges Bank, southern New England, the eastern Scotian Shelf, and St. Pierre Bank. With genotype likelihoods estimated at almost 11 million loci, we found large differences in haplotype frequencies of previously described chromosomal inversions between Canadian and U.S. sampling locations and also among U.S. sampling locations. Our whole-genome resolution also revealed novel outlier peaks, some of which showed significant genetic differentiation among sampling locations. Comparisons between allochronic winter- and spring-spawning populations revealed highly elevated relative (FST ) and absolute (dxy ) genetic differentiation near genes involved in reproduction, particularly genes associated with the brain-pituitary-gonadal axis, which likely control timing of spawning, contributing to prezygotic isolation. We also found genetic differentiation associated with heat shock proteins and other genes of functional relevance, with complex patterns that may point to multifaceted selection pressures and local adaptation among spawning populations. We provide a high-resolution picture of U.S. Atlantic cod population structure, revealing greater complexity than is currently recognized in management. Our genome-scan approach likely underestimates the full suite of adaptive differentiation among sampling locations. Nevertheless, it should inform the revision of stock boundaries to preserve adaptive genetic diversity and evolutionary potential of cod populations.

Strong selection pressures maintain divergence on genomic islands in Atlantic cod (Gadus morhua L.) populations

Background

Two distinct populations have been extensively studied in Atlantic cod (Gadus morhua L.): the Northeast Arctic cod (NEAC) population and the coastal cod (CC) population. The objectives of the current study were to identify genomic islands of divergence and to propose an approach to quantify the strength of selection pressures using whole-genome single nucleotide polymorphism (SNP) data. After applying filtering criteria, information on 93 animals (9 CC individuals, 50 NEAC animals and 34 CC × NEAC crossbred individuals) and 3,123,434 autosomal SNPs were used.

Results

Four genomic islands of divergence were identified on chromosomes 1, 2, 7 and 12, which were mapped accurately based on SNP data and which extended in size from 11 to 18 Mb. These regions differed considerably between the two populations although the differences in the rest of the genome were small due to considerable gene flow between the populations. The estimates of selection pressures showed that natural selection was substantially more important than genetic drift in shaping these genomic islands. Our data confirmed results from earlier publications that suggested that genomic islands are due to chromosomal rearrangements that are under strong selection and reduce recombination between rearranged and non-rearranged segments.

Conclusions

Our findings further support the hypothesis that selection and reduced recombination in genomic islands may promote speciation between these two populations although their habitats overlap considerably and migrations occur between them.

The spatial scale of dispersal revealed by admixture tracts

Evaluating species dispersal across the landscape is essential to design appropriate management and conservation actions. However, technical difficulties often preclude direct measures of individual movement, while indirect genetic approaches rely on assumptions that sometimes limit their application. Here, we show that the temporal decay of admixture tracts lengths can be used to assess genetic connectivity within a population introgressed by foreign haplotypes. We present a proof-of-concept approach based on local ancestry inference in a high gene flow marine fish species, the European sea bass (Dicentrarchus labrax). Genetic admixture in the contact zone between Atlantic and Mediterranean sea bass lineages allows the introgression of Atlantic haplotype tracts within the Mediterranean Sea. Once introgressed, blocks of foreign ancestry are progressively eroded by recombination as they diffuse from the western to the eastern Mediterranean basin, providing a means to estimate dispersal. By comparing the length distributions of Atlantic tracts between two Mediterranean populations located at different distances from the contact zone, we estimated the average per-generation dispersal distance within the Mediterranean lineage to less than 50 km. Using simulations, we showed that this approach is robust to a range of demographic histories and sample sizes. Our results thus support that the length of admixture tracts can be used together with a recombination clock to estimate genetic connectivity in species for which the neutral migration-drift balance is not informative or simply does not exist.

Contrasting genomic shifts underlie parallel phenotypic evolution in response to fishing

Humans cause widespread evolutionary change in nature, but we still know little about the genomic basis of rapid adaptation in the Anthropocene. We tracked genomic changes across all protein-coding genes in experimental fish populations that evolved pronounced shifts in growth rates due to size-selective harvest over only four generations. Comparisons of replicate lines show parallel allele frequency shifts that recapitulate responses to size-selection gradients in the wild across hundreds of unlinked variants concentrated in growth-related genes. However, a supercluster of genes also rose rapidly in frequency and dominated the evolutionary dynamic in one replicate line but not in others. Parallel phenotypic changes thus masked highly divergent genomic responses to selection, illustrating how contingent rapid adaptation can be in the face of strong human-induced selection.

Identifying loci under positive selection in complex population histories

Detailed modeling of a species’ history is of prime importance for understanding how natural selection operates over time. Most methods designed to detect positive selection along sequenced genomes, however, use simplified representations of past histories as null models of genetic drift. Here, we present the first method that can detect signatures of strong local adaptation across the genome using arbitrarily complex admixture graphs, which are typically used to describe the history of past divergence and admixture events among any number of populations. The method—called graph-aware retrieval of selective sweeps (GRoSS)—has good power to detect loci in the genome with strong evidence for past selective sweeps and can also identify which branch of the graph was most affected by the sweep. As evidence of its utility, we apply the method to bovine, codfish, and human population genomic data containing panels of multiple populations related in complex ways. We find new candidate genes for important adaptive functions, including immunity and metabolism in understudied human populations, as well as muscle mass, milk production, and tameness in specific bovine breeds. We are also able to pinpoint the emergence of large regions of differentiation owing to inversions in the history of Atlantic codfish.

Population structure, demographic history and local adaptation of the grass carp

BACKGROUND

Genetic diversity within a species reflects population evolution, ecology, and ability to adapt. Genome-wide population surveys of both natural and introduced populations provide insights into genetic diversity, the evolutionary processes and the genetic basis underlying local adaptation. Grass carp is the most important freshwater foodfish species for food and water weed control. However, there is as yet no overall picture on genetic variations and population structure of this species, which is important for its aquaculture.

RESULTS

We used 43,310 SNPs to infer the population structure, evidence of local adaptation and sources of introduction. The overall genetic differentiation of this species was low. The native populations were differentiated into three genetic clusters, corresponding to the Yangtze, Pearl and Heilongjiang River Systems, respectively. The populations in Malaysia, India and Nepal were introduced from both the Yangtze and Pearl River Systems. Loci and genes involved in putative local selection for native locations were identified. Evidence of both positive and balancing selection was found in the introduced locations. Genes associated with loci under putative selection were involved in many biological functions. Outlier loci were grouped into clusters as genomic islands within some specific genomic regions, which likely agrees with the divergence hitchhiking scenario of divergence-with-gene-flow.

CONCLUSIONS

This study, for the first time, sheds novel insights on the population differentiation of the grass carp, genetics of its strong ability in adaption to diverse environments and sources of some introduced grass carp populations. Our data also suggests that the natural populations of the grass carp have been affected by the aquaculture besides neutral and adaptive forces.

Adaptive genetic variation underlies biocomplexity of Atlantic Cod in the Gulf of Maine and on Georges Bank

Atlantic cod (Gadus morhua) populations in the Gulf of Maine (GoM) are at a fraction of their historical abundance, creating economic hardships for fishermen and putting at risk the genetic diversity of the remaining populations. An understanding of the biocomplexity among GoM populations will allow for adaptive genetic diversity to be conserved to maximize the evolutionary potential and resilience of the fishery in a rapidly changing environment. We used restriction-site-associated DNA sequencing (RADseq) to characterize the population structure and adaptive genetic diversity of five spawning aggregations from the western GoM and Georges Bank. We also analyzed cod caught in the eastern GoM, an under-sampled area where spawning aggregations have been extirpated. Using 3,128 single nucleotide polymorphisms (SNPs), we confirmed the existence of three genetically separable spawning groups: (1) winter spawning cod from the western GoM, (2) spring spawning cod, also from the western GoM, and (3) Georges Bank cod. Non-spawning cod from the eastern GoM could not be decisively linked to either of the three spawning groups and may represent a unique component of the resource, a mixed sample, or cod from other unsampled source populations. The genetic differentiation among the three major spawning groups was primarily driven by loci putatively under selection, particularly loci in regions known to contain genomic inversions on linkage groups (LG) 7 and 12. These LGs have been found to be linked to thermal regime in cod across the Atlantic, and so it is possible that variation in timing of spawning in western GoM cod has resulted in temperature-driven adaptive divergence. This complex population structure and adaptive genetic differentiation could be crucial to ensuring the long-term productivity and resilience of the cod fishery, and so it should be considered in future management plans.

Genetic analyses reveal complex dynamics within a marine fish management area

Genetic data have great potential for improving fisheries management by identifying the fundamental management units-that is, the biological populations-and their mixing. However, so far, the number of practical cases of marine fisheries management using genetics has been limited. Here, we used Atlantic cod in the Baltic Sea to demonstrate the applicability of genetics to a complex management scenario involving mixing of two genetically divergent populations. Specifically, we addressed several assumptions used in the current assessment of the two populations. Through analysis of 483 single nucleotide polymorphisms (SNPs) distributed across the Atlantic cod genome, we confirmed that a model of mechanical mixing, rather than hybridization and introgression, best explained the pattern of genetic differentiation. Thus, the fishery is best monitored as a mixed-stock fishery. Next, we developed a targeted panel of 39 SNPs with high statistical power for identifying population of origin and analyzed more than 2,000 tissue samples collected between 2011 and 2015 as well as 260 otoliths collected in 2003/2004. These data provided high spatial resolution and allowed us to investigate geographical trends in mixing, to compare patterns for different life stages and to investigate temporal trends in mixing. We found similar geographical trends for the two time points represented by tissue and otolith samples and that a recently implemented geographical management separation of the two populations provided a relatively close match to their distributions. In contrast to the current assumption, we found that patterns of mixing differed between juveniles and adults, a signal likely linked to the different reproductive dynamics of the two populations. Collectively, our data confirm that genetics is an operational tool for complex fisheries management applications. We recommend focussing on developing population assessment models and fisheries management frameworks to capitalize fully on the additional information offered by genetically assisted fisheries monitoring.

Disentangling structural genomic and behavioural barriers in a sea of connectivity

Genetic divergence among populations arises through natural selection or drift and is counteracted by connectivity and gene flow. In sympatric populations, isolating mechanisms are thus needed to limit the homogenizing effects of gene flow to allow for adaptation and speciation. Chromosomal inversions act as an important mechanism maintaining isolating barriers, yet their role in sympatric populations and divergence with gene flow is not entirely understood. Here, we revisit the question of whether inversions play a role in the divergence of connected populations of the marine fish Atlantic cod (Gadus morhua), by exploring a unique data set combining whole‐genome sequencing data and behavioural data obtained with acoustic telemetry. Within a confined fjord environment, we find three genetically differentiated Atlantic cod types belonging to the oceanic North Sea population, the western Baltic population and a local fjord‐type cod. Continuous behavioural tracking over 4 year revealed temporally stable sympatry of these types within the fjord. Despite overall weak genetic differentiation consistent with high levels of gene flow, we detected significant frequency shifts of three previously identified inversions, indicating an adaptive barrier to gene flow. In addition, behavioural data indicated that North Sea cod and individuals homozygous for the LG12 inversion had lower fitness in the fjord environment. However, North Sea and fjord‐type cod also occupy different depths, possibly contributing to prezygotic reproductive isolation and representing a behavioural barrier to gene flow. Our results provide the first insights into a complex interplay of genomic and behavioural isolating barriers in Atlantic cod and establish a new model system towards an understanding of the role of genomic structural variants in adaptation and diversification.

Parallel pattern of differentiation at a genomic island shared between clinal and mosaic hybrid zones in a complex of cryptic seahorse lineages

Diverging semi-isolated lineages either meet in narrow clinal hybrid zones, or have a mosaic distribution associated with environmental variation. Intrinsic reproductive isolation is often emphasized in the former and local adaptation in the latter, although both reduce gene flow between groups. Rarely are these two patterns of spatial distribution reported in the same study system. Here, we report that the long-snouted seahorse Hippocampus guttulatus is subdivided into discrete panmictic entities by both types of hybrid zones. Along the European Atlantic coasts, a northern and a southern lineage meet in the southwest of France where they coexist in sympatry-i.e., in the same geographical zone-with little hybridization. In the Mediterranean Sea, two lineages have a mosaic distribution, associated with lagoon-like and marine habitats. A fifth lineage was identified in the Black Sea. Genetic homogeneity over large spatial scales contrasts with isolation maintained in sympatry or close parapatry at a fine scale. A high variation in locus-specific introgression rates provides additional evidence that partial reproductive isolation must be maintaining the divergence. We find that fixed differences between lagoon and marine populations in the Mediterranean Sea belong to the most differentiated SNPs between the two Atlantic lineages, against the genome-wide pattern of structure that mostly follow geography. These parallel outlier SNPs cluster on a single chromosome-wide island of differentiation. Since Atlantic lineages do not map to lagoon-sea habitat variation, genetic parallelism at the genomic island suggests a shared genetic barrier contributes to reproductive isolation in contrasting contexts-i.e., spatial versus ecological. We discuss how a genomic hotspot of parallel differentiation could have evolved and become associated both with space and with a patchy environment in a single study system.

Evolution of population structure in an estuarine-dependent marine fish

Restriction site-associated DNA (RAD) sequencing was used to characterize neutral and adaptive genetic variation among geographic samples of red drum, Sciaenops ocellatus, an estuarine-dependent fish found in coastal waters along the southeastern coast of the United States (Atlantic) and the northern Gulf of Mexico (Gulf). Analyses of neutral and outlier loci revealed three genetically distinct regional clusters: one in the Atlantic and two in the northern Gulf. Divergence in neutral loci indicated gradual genetic change and followed a linear pattern of isolation by distance. Divergence in outlier loci was at least an order of magnitude greater than divergence in neutral loci, and divergence between the regions in the Gulf was twice that of divergence between other regions. Discordance in patterns of genetic divergence between outlier and neutral loci is consistent with the hypothesis that the former reflects adaptive responses to environmental factors that vary on regional scales, while the latter largely reflects drift processes. Differences in basic habitat, initiated by glacial retreat and perpetuated by contemporary oceanic and atmospheric forces interacting with the geomorphology of the northern Gulf, followed by selection, appear to have led to reduced gene flow among red drum across the northern Gulf, reinforcing differences accrued during isolation and resulting in continued divergence across the genome. This same dynamic also may pertain to other coastal or nearshore fishes (18 species in 14 families) where genetically or morphologically defined sister taxa occur in the three regions.

Analysis of coastal cod (Gadus morhua L.) sampled on spawning sites reveals a genetic gradient throughout Norway's coastline

BACKGROUND

Atlantic cod (Gadus morhua L.) has formed the basis of many economically significant fisheries in the North Atlantic, and is one of the best studied marine fishes, but a legacy of overexploitation has depleted populations and collapsed fisheries in several regions. Previous studies have identified considerable population genetic structure for Atlantic cod. However, within Norway, which is the country with the largest remaining catch in the Atlantic, the population genetic structure of coastal cod (NCC) along the entire coastline has not yet been investigated. We sampled > 4000 cod from 55 spawning sites. All fish were genotyped with 6 microsatellite markers and Pan I (Dataset 1). A sub-set of the samples (1295 fish from 17 locations) were also genotyped with an additional 9 microsatellites (Dataset 2). Otoliths were read in order to exclude North East Arctic Cod (NEAC) from the analyses, as and where appropriate.

RESULTS

We found no difference in genetic diversity, measured as number of alleles, allelic richness, heterozygosity nor effective population sizes, in the north-south gradient. In both data sets, weak but significant population genetic structure was revealed (Dataset 1: global FST = 0.008, P < 0.0001. Dataset 2: global FST = 0.004, P < 0.0001). While no clear genetic groups were identified, genetic differentiation increased among geographically-distinct samples. Although the locus Gmo132 was identified as a candidate for positive selection, possibly through linkage with a genomic region under selection, overall trends remained when this locus was excluded from the analyses. The most common allele in loci Gmo132 and Gmo34 showed a marked frequency change in the north-south gradient, increasing towards the frequency observed in NEAC in the north.

CONCLUSION

We conclude that Norwegian coastal cod displays significant population genetic structure throughout its entire range, that follows a trend of isolation by distance. Furthermore, we suggest that a gradient of genetic introgression between NEAC and NCC contributes to the observed population genetic structure. The current management regime for coastal cod in Norway, dividing it into two stocks at 62°N, represents a simplification of the level of genetic connectivity among coastal cod in Norway, and needs revision.

Genetic mapping and comparative genomics to inform restoration enhancement and culture of southern flounder, Paralichthys lethostigma

BACKGROUND

Southern flounder, Paralichthys lethostigma, historically support a substantial fishery along the Atlantic and Gulf coasts of the southern United States. Low year-class strengths over the past few years in the western Gulf of Mexico have raised concern that spawning stocks may be overfished. Current management of the resource includes releasing hatchery-raised juveniles to restock bays and estuaries; additionally, there is a growing interest in the potential for commercial aquaculture of the species. Currently, genomic resources for southern flounder do not exist. Here, we used two hatchery-reared families and double-digest, restriction-site-associated DNA (ddRAD) sequencing to create a reduced-representation genomic library consisting of several thousand single nucleotide polymorphisms (SNPs) located throughout the genome.

RESULTS

The relative position of each SNP-containing locus was determined to create a high-density genetic map spanning the 24 linkage groups of the southern flounder genome. The consensus map was used to identify regions of shared synteny between southern flounder and seven other fish species for which genome assemblies are available. Finally, syntenic blocks were used to localize genes identified from transcripts in European flounder as potentially being involved in ecotoxicological and osmoregulatory responses, as well as QTLs associated with growth and disease resistance in Japanese flounder, on the southern flounder linkage map.

CONCLUSIONS

The information provided by the linkage map will enrich restoration efforts by providing a foundation for interpreting spatial genetic variation within the species, ultimately furthering an understanding of the adaptive potential and resilience of southern flounder to future changes in local environmental conditions. Further, the map will facilitate the use of genetic markers to enhance restoration and commercial aquaculture.

Environmental, population and life-stage plasticity in the visual system of Atlantic cod

The visual system is for many fishes essential in guiding behaviors, such as foraging, predator avoidance and mate choice. The marine environment is characterized by large spatio-temporal fluctuations in light intensity and spectral composition. However, visual capabilities are restricted by both space limitations set by eye size and by the genomic content of light-absorbing opsin genes. The rich array of visual opsins in teleosts may be used differentially to tune vision towards specific needs during ontogeny and to changing light. Yet, to what extent visual plasticity is a pre-programmed developmental event, or is triggered by photic environment, is unclear. Our previous studies on Atlantic cod revealed an evolutionary genomic loss of UV-sensitive sws1 and red-sensitive lws opsin families, while blue-sensitive sws2 and green-sensitive rh2 opsins had duplicated. The current study has taken an opsin expression approach to characterize visual plasticity in cod towards different spectral light during the larval stage, to maturation and extreme seasonal changes in the Barents Sea. Our data suggest that opsin plasticity in cod larvae is controlled by developmental programme rather than immediate light environment. The lack of expressional changes during maturation suggests a less important role for visual modulation related to mate choice. Although no seasonal effects on visual opsins were detected in migratory Northeast Arctic cod, the expressed opsin subset differed from the more stationary Norwegian coastal cod described in previous studies. Interestingly, these data provide the first indications of a population difference in actively used visual opsins associated with cod ecotypes.

Ancient chromosomal rearrangement associated with local adaptation of a postglacially colonized population of Atlantic Cod in the northwest Atlantic

Intraspecific diversity is central to the management and conservation of exploited species, yet knowledge of how this diversity is distributed and maintained in the genome of many marine species is lacking. Recent advances in genomic analyses allow for genome-wide surveys of intraspecific diversity and offer new opportunities for exploring genomic patterns of divergence. Here, we analysed genome-wide polymorphisms to measure genetic differentiation between an offshore migratory and a nonmigratory population and to define conservation units of Atlantic Cod (Gadus morhua) in coastal Labrador. A total of 141 individuals, collected from offshore sites and from a coastal site within Gilbert Bay, Labrador, were genotyped using an ~11k single nucleotide polymorphism array. Analyses of population structure revealed strong genetic differentiation between migratory offshore cod and nonmigratory Gilbert Bay cod. Genetic differentiation was elevated for loci within a chromosomal rearrangement found on linkage group 1 (LG1) that coincides with a previously found double inversion associated with migratory and nonmigratory ecotype divergence of cod in the northeast Atlantic. This inverted region includes several genes potentially associated with adaptation to differences in salinity and temperature, as well as influencing migratory behaviour. Our work provides evidence that a chromosomal rearrangement on LG1 is associated with parallel patterns of divergence between migratory and nonmigratory ecotypes on both sides of the Atlantic Ocean.

Genomic Changes Associated with Reproductive and Migratory Ecotypes in Sockeye Salmon (Oncorhynchus nerka)

Mechanisms underlying adaptive evolution can best be explored using paired populations displaying similar phenotypic divergence, illuminating the genomic changes associated with specific life history traits. Here, we used paired migratory [anadromous vs. resident (kokanee)] and reproductive [shore- vs. stream-spawning] ecotypes of sockeye salmon (Oncorhynchus nerka) sampled from seven lakes and two rivers spanning three catchments (Columbia, Fraser, and Skeena) in British Columbia, Canada to investigate the patterns and processes underlying their divergence. Restriction-site associated DNA sequencing was used to genotype this sampling at 7,347 single nucleotide polymorphisms, 334 of which were identified as outlier loci and candidates for divergent selection within at least one ecotype comparison. Sixty-eight of these outliers were present in two or more comparisons, with 33 detected across multiple catchments. Of particular note, one locus was detected as the most significant outlier between shore and stream-spawning ecotypes in multiple comparisons and across catchments (Columbia, Fraser, and Snake). We also detected several genomic islands of divergence, some shared among comparisons, potentially showing linked signals of differential selection. The single nucleotide polymorphisms and genomic regions identified in our study offer a range of mechanistic hypotheses associated with the genetic basis of O. nerka life history variation and provide novel tools for informing fisheries management.

Trans-oceanic genomic divergence of Atlantic cod ecotypes is associated with large inversions

Chromosomal rearrangements such as inversions can play a crucial role in maintaining polymorphism underlying complex traits and contribute to the process of speciation. In Atlantic cod (Gadus morhua), inversions of several megabases have been identified that dominate genomic differentiation between migratory and nonmigratory ecotypes in the Northeast Atlantic. Here, we show that the same genomic regions display elevated divergence and contribute to ecotype divergence in the Northwest Atlantic as well. The occurrence of these inversions on both sides of the Atlantic Ocean reveals a common evolutionary origin, predating the >100 000-year-old trans-Atlantic separation of Atlantic cod. The long-term persistence of these inversions indicates that they are maintained by selection, possibly facilitated by coevolution of genes underlying complex traits. Our data suggest that migratory behaviour is derived from more stationary, ancestral ecotypes. Overall, we identify several large genomic regions—each containing hundreds of genes—likely involved in the maintenance of genomic divergence in Atlantic cod on both sides of the Atlantic Ocean.

Ancient DNA reveals the Arctic origin of Viking Age cod from Haithabu, Germany

Knowledge of the range and chronology of historic trade and long-distance transport of natural resources is essential for determining the impacts of past human activities on marine environments. However, the specific biological sources of imported fauna are often difficult to identify, in particular if species have a wide spatial distribution and lack clear osteological or isotopic differentiation between populations. Here, we report that ancient fish-bone remains, despite being porous, brittle, and light, provide an excellent source of endogenous DNA (15-46%) of sufficient quality for whole-genome reconstruction. By comparing ancient sequence data to that of modern specimens, we determine the biological origin of 15 Viking Age (800-1066 CE) and subsequent medieval (1066-1280 CE) Atlantic cod (Gadus morhua) specimens from excavation sites in Germany, Norway, and the United Kingdom. Archaeological context indicates that one of these sites was a fishing settlement for the procurement of local catches, whereas the other localities were centers of trade. Fish from the trade sites show a mixed ancestry and are statistically differentiated from local fish populations. Moreover, Viking Age samples from Haithabu, Germany, are traced back to the North East Arctic Atlantic cod population that has supported the Lofoten fisheries of Norway for centuries. Our results resolve a long-standing controversial hypothesis and indicate that the marine resources of the North Atlantic Ocean were used to sustain an international demand for protein as far back as the Viking Age.

Population-genomic inference of the strength and timing of selection against gene flow

The interplay of divergent selection and gene flow is key to understanding how populations adapt to local environments and how new species form. Here, we use DNA polymorphism data and genome-wide variation in recombination rate to jointly infer the strength and timing of selection, as well as the baseline level of gene flow under various demographic scenarios. We model how divergent selection leads to a genome-wide negative correlation between recombination rate and genetic differentiation among populations. Our theory shows that the selection density (i.e., the selection coefficient per base pair) is a key parameter underlying this relationship. We then develop a procedure for parameter estimation that accounts for the confounding effect of background selection. Applying this method to two datasets from Mimulus guttatus, we infer a strong signal of adaptive divergence in the face of gene flow between populations growing on and off phytotoxic serpentine soils. However, the genome-wide intensity of this selection is not exceptional compared with what M. guttatus populations may typically experience when adapting to local conditions. We also find that selection against genome-wide introgression from the selfing sister species M. nasutus has acted to maintain a barrier between these two species over at least the last 250 ky. Our study provides a theoretical framework for linking genome-wide patterns of divergence and recombination with the underlying evolutionary mechanisms that drive this differentiation.

Highly localized divergence within supergenes in Atlantic cod (Gadus morhua) within the Gulf of Maine

BACKGROUND

Atlantic cod (Gadus morhua), is known to vary genetically across the North Atlantic, Greenland, and Newfoundland. This genetic variation occurs both spatially and temporally through decades of heavy fishing, and is concentrated in three linkage disequilibrium blocks, previously defined by pedigreed linkage mapping analysis. Variation within these genomic regions is correlated with both seawater temperature and behavioral ecotype. The full extent and nature of these linkage groups is important information for interpreting cod genetic structure as a tool for future fisheries management.

RESULTS

We conducted whole genome sequencing for 31 individual cod from three sub-populations in the Gulf of Maine. Across the genome, we found 3,390,654 intermediate to high frequency Single Nucleotide Polymorphisms (SNPs). We show that pairwise linkage analysis among these SNPs is a powerful tool to detect linkage disequilibrium clusters by recovering the three previously detected linkage groups and identifying the 1031 genes contained therein. Across these genes, we found significant population differentiation among spawning groups in the Gulf of Maine and between Georges Bank and Gulf of Maine. Coordinated divergence among these genes and their differentiation at both short and long spatial scales suggests that they are acting as linked supergenes in local adaptation of cod populations.

CONCLUSIONS

Differentiation between SNPs in linkage disequilibrium blocks is the major signal of genetic differentiation between all groups tested within the Gulf of Maine. Our data provide a map of genes contained in these blocks, allowing an enhanced search for neutral genetic structure for demographic inference and fisheries modeling. Patterns of selection and the history of populations may be possible to identify in cod using this description of linkage disequilibrium blocks and future data sets to robustly separate neutral and selected genetic markers.

Genomic islands of divergence linked to ecotypic variation in sockeye salmon

Regions of the genome displaying elevated differentiation (genomic islands of divergence) are thought to play an important role in local adaptation, especially in populations experiencing high gene flow. However, the characteristics of these islands as well as the functional significance of genes located within them remain largely unknown. Here, we used data from thousands of SNPs aligned to a linkage map to investigate genomic islands of divergence in three ecotypes of sockeye salmon (Oncorhynchus nerka) from a single drainage in southwestern Alaska. We found ten islands displaying high differentiation among ecotypes. Conversely, neutral structure observed throughout the rest of the genome was low and not partitioned by ecotype. One island on linkage group So13 was particularly large and contained six SNPs with F_ST  > 0.14 (average F_ST of neutral SNPs = 0.01). Functional annotation revealed that the peak of this island contained a nonsynonymous mutation in a gene involved in growth in other species (TULP4). The islands that we discovered were relatively small (80-402 Kb), loci found in islands did not show reduced levels of diversity, and loci in islands displayed slightly elevated linkage disequilibrium. These attributes suggest that the islands discovered here were likely generated by divergence hitchhiking; however, we cannot rule out the possibility that other mechanisms may have produced them. Our results suggest that islands of divergence serve an important role in local adaptation with gene flow and represent a significant advance towards understanding the genetic basis of ecotypic differentiation.

Saving the spandrels? Adaptive genomic variation in conservation and fisheries management

As highlighted by many of the papers in this issue, research on the genomic basis of adaptive phenotypic variation in natural populations has made spectacular progress in the past few years, largely due to the advances in sequencing technology and analysis. Without question, the resulting genomic data will improve the understanding of regions of the genome under selection and extend knowledge of the genetic basis of adaptive evolution. What is far less clear, but has been the focus of active discussion, is how such information can or should transfer into conservation practice to complement more typical conservation applications of genetic data. Before such applications can be realized, the evolutionary importance of specific targets of selection relative to the genome-wide diversity of the species as a whole must be evaluated. The key issues for the incorporation of adaptive genomic variation in conservation and management are discussed here, using published examples of adaptive genomic variation associated with specific phenotypes in salmonids and other taxa to highlight practical considerations for incorporating such information into conservation programmes. Scenarios are described in which adaptive genomic data could be used in conservation or restoration, constraints on its utility and the importance of validating inferences drawn from new genomic data before applying them in conservation practice. Finally, it is argued that an excessive focus on preserving the adaptive variation that can be measured, while ignoring the vast unknown majority that cannot, is a modern twist on the adaptationist programme that Gould and Lewontin critiqued almost 40 years ago.

On the maintenance of genetic variation and adaptation to environmental change: considerations from population genomics in fishes

The first goal of this paper was to overview modern approaches to local adaptation, with a focus on the use of population genomics data to detect signals of natural selection in fishes. Several mechanisms are discussed that may enhance the maintenance of genetic variation and evolutionary potential, which have been overlooked and should be considered in future theoretical development and predictive models: the prevalence of soft sweeps, polygenic basis of adaptation, balancing selection and transient polymorphisms, parallel evolution, as well as epigenetic variation. Research on fish population genomics has provided ample evidence for local adaptation at the genome level. Pervasive adaptive evolution, however, seems to almost never involve the fixation of beneficial alleles. Instead, adaptation apparently proceeds most commonly by soft sweeps entailing shifts in frequencies of alleles being shared between differentially adapted populations. One obvious factor contributing to the maintenance of standing genetic variation in the face of selective pressures is that adaptive phenotypic traits are most often highly polygenic, and consequently the response to selection should derive mostly from allelic co-variances among causative loci rather than pronounced allele frequency changes. Balancing selection in its various forms may also play an important role in maintaining adaptive genetic variation and the evolutionary potential of species to cope with environmental change. A large body of literature on fishes also shows that repeated evolution of adaptive phenotypes is a ubiquitous evolutionary phenomenon that seems to occur most often via different genetic solutions, further adding to the potential options of species to cope with a changing environment. Moreover, a paradox is emerging from recent fish studies whereby populations of highly reduced effective population sizes and impoverished genetic diversity can apparently retain their adaptive potential in some circumstances. Although more empirical support is needed, several recent studies suggest that epigenetic variation could account for this apparent paradox. Therefore, epigenetic variation should be fully integrated with considerations pertaining to role of soft sweeps, polygenic and balancing selection, as well as repeated adaptation involving different genetic basis towards improving models predicting the evolutionary potential of species to cope with a changing world.

Cunningham's skinks show low genetic connectivity and signatures of divergent selection across its distribution

Establishing corridors of connecting habitat has become a mainstay conservation strategy to maintain gene flow and facilitate climate‐driven range shifts. Yet, little attention has been given to ascertaining the extent to which corridors will benefit philopatric species, which might exhibit localized adaptation. Measures of genetic connectivity and adaptive genetic variation across species’ ranges can help fill this knowledge gap. Here, we characterized the spatial genetic structure of Cunningham's skink (Egernia cunninghami), a philopatric species distributed along Australia's Great Dividing Range, and assessed evidence of localized adaptation. Analysis of 4,274 SNPs from 94 individuals sampled at four localities spanning 500 km and 4° of latitude revealed strong genetic structuring at neutral loci (mean F_ST ± SD = 0.603 ± 0.237) among the localities. Putatively neutral SNPs and those under divergent selection yielded contrasting spatial patterns, with the latter identifying two genetically distinct clusters. Given low genetic connectivity of the four localities, we suggest that the natural movement rate of this species is insufficient to keep pace with spatial shifts to its climate envelope, irrespective of habitat availability. In addition, our finding of localized adaptation highlights the risk of outbreeding depression should the translocation of individuals be adopted as a conservation management strategy.