Range-wide parallel climate-associated genomic clines in Atlantic salmon

Variable parallelism in the genomic basis of age at maturity across spatial scales in Atlantic Salmon

Complex traits often exhibit complex underlying genetic architectures resulting from a combination of evolution from standing variation, hard and soft sweeps, and alleles of varying effect size. Increasingly, studies implicate both large-effect loci and polygenic patterns underpinning adaptation, but the extent that common genetic architectures are utilized during repeated adaptation is not well understood. Sea age or age at maturation represents a significant life history trait in Atlantic Salmon (Salmo salar), the genetic basis of which has been studied extensively in European Atlantic populations, with repeated identification of large-effect loci. However, the genetic basis of sea age within North American Atlantic Salmon populations remains unclear, as does the potential for a parallel trans-Atlantic genomic basis to sea age. Here, we used a large single-nucleotide polymorphism (SNP) array and low-coverage whole-genome resequencing to explore the genomic basis of sea age variation in North American Atlantic Salmon. We found significant associations at the gene and SNP level with a large-effect locus (vgll3) previously identified in European populations, indicating genetic parallelism, but found that this pattern varied based on both sex and geographic region. We also identified nonrepeated sets of highly predictive loci associated with sea age among populations and sexes within North America, indicating polygenicity and low rates of genomic parallelism. Despite low genome-wide parallelism, we uncovered a set of conserved molecular pathways associated with sea age that were consistently enriched among comparisons, including calcium signaling, MapK signaling, focal adhesion, and phosphatidylinositol signaling. Together, our results indicate parallelism of the molecular basis of sea age in North American Atlantic Salmon across large-effect genes and molecular pathways despite population-specific patterns of polygenicity. These findings reveal roles for both contingency and repeated adaptation at the molecular level in the evolution of life history variation.

Rolling with the punches: Organism-environment interactions shape spatial pattern of adaptive differentiation in the widespread mantis shrimp Oratosquilla oratoria

Investigating spatial pattern of adaptive variation and its underlying processes can inform the adaptive potential distributed within species ranges, which is increasingly important in the context of a changing climate. A correct interpretation of adaptive variation pattern requires that population history and the ensuing population genetic structure are taken into account. Here we carried out such a study by integrating population genomic analyses, demographic model testing and species distribution modeling to investigate patterns and causes of adaptive differentiation in a widespread mantis shrimp, Oratosquilla oratoria, along a replicated, broad-scale temperature gradient in the northwestern Pacific (NWP). Our results supported a strong hierarchical ecogeographic structure dominated by habitat-linked divergence among O. oratoria populations accompanied with introgressive hybridization. A combined FST outlier and environmental correlation analyses revealed remarkable temperature-associated clines in allele frequency across paired North-South populations on Chinese and Japanese coasts, and identified a suite of loci associated with temperature adaptation. Further demographic model testing revealed the observed clinal variation derived partly from Pleistocene divergence followed by recent secondary contact. More importantly, the likelihood of hybridization is predicted to increase as climate change progresses, which would break barriers to gene flow and enable the spread of adaptive genetic variation. These results support that not only is temperature-driven adaptive differentiation occurs in O. oratoria but that such pattern is likely attributed to ancient adaptive variation, sustained by contemporary ocean conditions and a semi-permeable barrier to gene flow maintained by selection. They moreover provide genomic insights into the distribution of adaptive potential across O. oratoria' s species range. This work can serve as a case study to characterize adaptive diversity of marine species in the NWP by integrating environmental and genetic data at temporal and spatial scales in a population genomic framework, which would improve management and conservation actions under climate change.

A novel characterized multi-drug-resistant Pseudocitrobacter sp. isolated from a patient colonized while admitted to a tertiary teaching hospital

BACKGROUND

Reports of nosocomial infections typically describe recognised microorganisms. Here, a novel bacterial species was isolated, based on rectal swab screening for carbapenemases post-admission, then phenotypically and genetically characterized.

METHODS

Sensititre, Vitek and API kits, MALDI and Illumina MiSeq were employed before profiles and phylogeny were compared with other related species.

FINDINGS

Determined to be a possible Enterobacterales, the isolate was found to have 99.7% 16s rRNA identity to Pseudocitrobacter corydidari; an Asian cockroach-associated species. Given the highly conserved/low variability of 16S rRNA genes in Enterobacterales, average nucleotide identity (ANI) analysis compared the new isolate's genome with those of 18 Enterobacteriaceae species, including confirmed species of Pseudocitrobacter and unnamed Pseudocitrobacter species in the SILVA database. Of these, Pseudocitrobactercorydidari had the highest ANI at 0.9562. The published genome of the only known isolate of P.corydidari does not include Antimicrobial Resistance Genes (ARGs), with exception of potential drug efflux transporters. In contrast, our clinical isolate bears recognised antimicrobial resistance genes, including Klebsiella pneumoniae carbapenemase. The associated genome suggests resistance to carbapenems, β-lactams, sulfonamides, fluoroquinolones, macrolides, aminoglycosides and cephalosporins. Phenotypic antimicrobial resistance was confirmed.

CONCLUSION

Evident variations in ARG profiles, human colonization and origin in a clinically relevant niche that is geographically, physically and chemically disparate lend credibility for divergent evolution or, less likely, parallel evolution with P. corydidari. Genome data for this new species have been submitted to GENBANK using the proposed nomenclature Pseudocitrobacter limerickensis. The patient was colonized, rather than infected, and did not require antimicrobial treatment.

Multifaceted framework for defining conservation units: An example from Atlantic salmon (Salmo salar) in Canada

Conservation units represent important components of intraspecific diversity that can aid in prioritizing and protecting at-risk populations, while also safeguarding unique diversity that can contribute to species resilience. In Canada, identification and assessments of conservation units is done by the Committee on the Status of Endangered Wildlife in Canada (COSEWIC). COSEWIC can recognize conservation units below the species level (termed "designatable units"; DUs) if the unit has attributes that make it both discrete and evolutionarily significant. There are various ways in which a DU can meet criteria of discreteness and significance, and increasing access to "big data" is providing unprecedented information that can directly inform both criteria. Specifically, the incorporation of genomic data for an increasing number of non-model species is informing more COSEWIC assessments; thus, a repeatable, robust framework is needed for integrating these data into DU characterization. Here, we develop a framework that uses a multifaceted, weight of evidence approach to incorporate multiple data types, including genetic and genomic data, to inform COSEWIC DUs. We apply this framework to delineate DUs of Atlantic salmon (Salmo salar, L.), an economically, culturally, and ecologically significant species, that is also characterized by complex hierarchical population structure. Specifically, we focus on an in-depth example of how our approach was applied to a previously data limited region of northern Canada that was defined by a single large DU. Application of our framework with newly available genetic and genomic data led to subdividing this DU into three new DUs. Although our approach was developed to meet criteria of COSEWIC, it is widely applicable given similarities in the definitions of a conservation unit.

Trans-Arctic vicariance in Strongylocentrotus sea urchins

The sea urchins Strongylocentotus pallidus and S. droebachiensis first invaded the Atlantic Ocean from the Pacific following the opening of the Bering seaway in the late Miocene. While trans-Arctic dispersal during the Pleistocene is thought to have maintained species' integrity, a recent genomic analysis identified a reproductively isolated cryptic species within S. droebachiensis. Based on previous studies, the distribution of one of these lineages (S. droebachiensis W) includes the shallow water habitats of the northwest Atlantic and Pacific, while the other (S. droebachiensis E) is found throughout the shallow habitat in the northeast but is mostly restricted to deep habitats (>65 m) in the northwest Atlantic. However, since genetic variation within S. droebachiensis has been largely unstudied in the north Pacific and Arctic oceans, the biogeography of the cryptic species is not well known, and it is difficult to identify the mechanisms driving population subdivision and speciation. Here we use population genetic analyses to characterize the distribution of each species, and to test hypotheses about the role of vicariance in the evolution of systematic and genomic divergence within the genus. We collected individuals of all three Strongylocentrotus species (n = 365) from 10 previously unsampled locations in the northeast Pacific and north Atlantic (Labrador Sea and Norway), and generated mtDNA sequence data for a 418 bp fragment of cytochrome c oxidase subunit I (COI). To assess the biogeography of all three species, we combined our alignment with five previously published data sets (total n = 789) and used statistical parsimony and maximum likelihood to identify species and characterize their distribution within and among oceans. Patterns of haplotype sharing, pairwise F _ST , and hierarchical analyses of molecular variance (AMOVA) identified trans-Arctic dispersal in S. pallidus and S. droebachiensis W, but other than 5 previously reported singletons we failed to detect additional mtDNA haplotypes of S. droebachiensis E in the north Pacific. Within the Atlantic, patterns of habitat segregation suggests that temperature may play a role in limiting the distribution of S. droebachiensis E, particularly throughout the warmer coastal waters along the coast of Nova Scotia. Our results are consistent with the cycles of trans-Arctic dispersal and vicariance in S. pallidus and S. droebachiensis W, but we suggest that the evolution of Atlantic populations of S. droebachiensis E has been driven by persistent trans-Arctic vicariance that may date to the initial invasion in the late Pliocene.

Genomic evidence of recent European introgression into North American farmed and wild Atlantic salmon

Gene flow between wild and domestic populations has been repeatedly demonstrated across a diverse range of taxa. Ultimately, the genetic impacts of gene flow from domestic into wild populations depend both on the degree of domestication and the original source of the domesticated population. Atlantic salmon, Salmo salar, used in North American aquaculture are ostensibly of North American origin. However, evidence of European introgression into North American aquaculture salmon has accumulated in recent decades, even though the use of diploid European salmon has never been approved in Canada. The full extent of such introgression as well as the potential impacts on wild salmon in the Northwest Atlantic remains uncertain. Here, we extend previous work comparing North American and European wild salmon (n = 5799) using a 220 K SNP array to quantify levels of recent European introgression into samples of domestic salmon, aquaculture escapees, and wild salmon collected throughout Atlantic Canada. Analysis of North American farmed salmon (n = 403) and escapees (n = 289) displayed significantly elevated levels of European ancestry by comparison with wild individuals (p < 0.001). Of North American farmed salmon sampled between 2011 and 2018, ~17% had more than 10% European ancestry and several individuals exceeded 40% European ancestry. Samples of escaped farmed salmon similarly displayed elevated levels of European ancestry, with two individuals classified as 100% European. Analysis of juvenile salmon collected in rivers proximate to aquaculture locations also revealed evidence of elevated European ancestry and larger admixture tract in comparison to individuals collected at distance from aquaculture. Overall, our results demonstrate that even though diploid European salmon have never been approved for use in Canada, individuals of full and partial European ancestry have been in use over the last decade, and that some of these individuals have escaped and hybridized in the wild.

The genetics of adaptation in freshwater Eurasian shad (Alosa)

Studying the genetics of phenotypic convergence can yield important insights into adaptive evolution. Here, we conducted a comparative genomic study of four lineages (species and subspecies) of anadromous shad (Alosa) that have independently evolved life cycles entirely completed in freshwater. Three naturally diverged (A. fallax lacustris, A. f. killarnensis, and A. macedonica), and the fourth (A. alosa) was artificially landlocked during the last century. To conduct this analysis, we assembled and annotated a draft of the A. alosa genome and generated whole‐genome sequencing for 16 anadromous and freshwater populations of shad. Widespread evidence for parallel genetic changes in freshwater populations within lineages was found. In freshwater A. alosa, which have only been diverging for tens of generations, this shows that parallel adaptive evolution can rapidly occur. However, parallel genetic changes across lineages were comparatively rare. The degree of genetic parallelism was not strongly related to the number of shared polymorphisms between lineages, thus suggesting that other factors such as divergence among ancestral populations or environmental variation may influence genetic parallelism across these lineages. These overall patterns were exemplified by genetic differentiation involving a paralog of ATPase‐α1 that appears to be under selection in just two of the more distantly related lineages studied, A. f. lacustris and A. alosa. Our findings provide insights into the genetic architecture of adaptation and parallel evolution along a continuum of population divergence.

Ocean warming threatens key trophic interactions supporting a commercial fishery in a climate change hotspot

Worldwide, rising ocean temperatures are causing declines and range shifts in marine species. The direct effects of climate change on the biology of marine organisms are often well documented; yet, knowledge on the indirect effects, particularly through trophic interactions, is largely lacking. We provide evidence of ocean warming decoupling critical trophic interactions supporting a commercially important mollusc in a climate change hotspot. Dietary assessments of the Australian blacklip abalone (Haliotis rubra) indicate primary dependency on a widespread macroalgal species (Phyllospora comosa) which we show to be in state of decline due to ocean warming, resulting in abalone biomass reductions. Niche models suggest further declines in P. comosa over the coming decades and ongoing risks to H. rubra. This study highlights the importance of studies from climate change hotspots and understanding the interplay between climate and trophic interactions when determining the likely response of marine species to environmental changes.

Evolutionary Responses to Warming

Climate change is predicted to dramatically alter biological diversity and distributions, driving extirpations, extinctions, and extensive range shifts across the globe. Warming can also, however, lead to phenotypic or behavioural plasticity, as species adapt to new conditions. Recent genomic research indicates that some species are capable of rapid evolution as selection favours adaptive responses to environmental change and altered or novel niche spaces. New advances are providing mechanistic insights into how temperature might accelerate evolution in the Anthropocene. These discoveries highlight intriguing new research directions - such as using geothermal and polar systems combined with powerful genomic tools - that will help us to understand the processes underpinning adaptive evolution and better project how ecosystems will change in a warming world.

Genetic mixing for population management: From genetic rescue to provenancing

Animal and plant species around the world are being challenged by the deleterious effects of inbreeding, loss of genetic diversity, and maladaptation due to widespread habitat destruction and rapid climate change. In many cases, interventions will likely be needed to safeguard populations and species and to maintain functioning ecosystems. Strategies aimed at initiating, reinstating, or enhancing patterns of gene flow via the deliberate movement of genotypes around the environment are generating growing interest with broad applications in conservation and environmental management. These diverse strategies go by various names ranging from genetic or evolutionary rescue to provenancing and genetic resurrection. Our aim here is to provide some clarification around terminology and to how these strategies are connected and linked to underlying genetic processes. We draw on case studies from the literature and outline mechanisms that underlie how the various strategies aim to increase species fitness and impact the wider community. We argue that understanding mechanisms leading to species decline and community impact is a key to successful implementation of these strategies. We emphasize the need to consider the nature of source and recipient populations, as well as associated risks and trade-offs for the various strategies. This overview highlights where strategies are likely to have potential at population, species, and ecosystem scales, but also where they should probably not be attempted depending on the overall aims of the intervention. We advocate an approach where short- and long-term strategies are integrated into a decision framework that also considers nongenetic aspects of management.

Investigating Diadromy in Fishes and Its Loss in an -Omics Era

Diadromy, the predictable movements of individuals between marine and freshwater environments, is biogeographically and phylogenetically widespread across fishes. Thus, despite the high energetic and potential fitness costs involved in moving between distinct environments, diadromy appears to be an effective life history strategy. Yet, the origin and molecular mechanisms that underpin this migratory behavior are not fully understood. In this review, we aim first to summarize what is known about diadromy in fishes; this includes the phylogenetic relationship among diadromous species, a description of the main hypotheses regarding its origin, and a discussion of the presence of non-migratory populations within diadromous species. Second, we discuss how recent research based on -omics approaches (chiefly genomics, transcriptomics, and epigenomics) is beginning to provide answers to questions on the genetic bases and origin(s) of diadromy. Finally, we suggest future directions for -omics research that can help tackle questions on the evolution of diadromy.

Genetic data and climate niche suitability models highlight the vulnerability of a functionally important plant species from south-eastern Australia

Habitat fragmentation imperils the persistence of many functionally important species, with climate change a new threat to local persistence due to climate niche mismatching. Predicting the evolutionary trajectory of species essential to ecosystem function under future climates is challenging but necessary for prioritizing conservation investments. We use a combination of population genetics and niche suitability models to assess the trajectory of a functionally important, but highly fragmented, plant species from south-eastern Australia (Banksia marginata, Proteaceae). We demonstrate significant genetic structuring among, and high level of relatedness within, fragmented remnant populations, highlighting imminent risks of inbreeding. Population simulations, controlling for effective population size (N e), suggest that many remnant populations will suffer rapid declines in genetic diversity due to drift in the absence of intervention. Simulations were used to demonstrate how inbreeding and drift processes might be suppressed by assisted migration and population mixing approaches that enhance the size and connectivity of remnant populations. These analyses were complemented by niche suitability models that predicted substantial reductions of suitable habitat by 2080; ~30% of the current distribution of the species climate niche overlaps with the projected distribution of the species climate niche in the geographic region by the 2080s. Our study highlights the importance of conserving remnant populations and establishing new populations in areas likely to support B. marginata in the future, and adopting seed sourcing strategies that can help populations overcome the risks of inbreeding and maladaptation. We also argue that ecological replacement of B. marginata using climatically suited plant species might be needed in the future to maintain ecosystem processes where B. marginata cannot persist. We recommend the need for progressive revegetation policies and practices to prevent further deterioration of species such as B. marginata and the ecosystems they support.

Divergent and linked selection shape patterns of genomic differentiation between European and North American Atlantic salmon (Salmo salar)

As populations diverge many processes can shape genomic patterns of differentiation. Regions of high differentiation can arise due to divergent selection acting on selected loci, genetic hitchhiking of nearby loci, or through repeated selection against deleterious alleles (linked background selection); this divergence may then be further elevated in regions of reduced recombination. Atlantic salmon (Salmo salar) from Europe and North America diverged >600,000 years ago and despite some evidence of secondary contact, the majority of genetic data indicate substantial divergence between lineages. This deep divergence with potential gene flow provides an opportunity to investigate the role of different mechanisms that shape the genomic landscape during early speciation. Here, using 184,295 single nucleotide polymorphisms (SNPs) and 80 populations, we investigate the genomic landscape of differentiation across the Atlantic Ocean with a focus on highly differentiated regions and the processes shaping them. We found evidence of high (mean F_ST  = 0.26) and heterogeneous genomic differentiation between continents. Genomic regions associated with high trans-Atlantic differentiation ranged in size from single loci (SNPs) within important genes to large regions (1-3 Mbp) on four chromosomes (Ssa06, Ssa13, Ssa16 and Ssa19). These regions showed signatures consistent with selection, including high linkage disequilibrium, despite no significant reduction in recombination. Genes and functional enrichment of processes associated with differentiated regions may highlight continental differences in ocean navigation and parasite resistance. Our results provide insight into potential mechanisms underlying differences between continents, and evidence of near-fixed and potentially adaptive trans-Atlantic differences concurrent with a background of high genome-wide differentiation supports subspecies designation in Atlantic salmon.

Population Genomics in Rhamdia quelen (Heptapteridae, Siluriformes) Reveals Deep Divergence and Adaptation in the Neotropical Region

Rhamdia quelen, a Neotropical fish with hybridization between highly divergent mitochondrial DNA (mtDNA) lineages, represents an interesting evolutionary model. Previous studies suggested that there might be demographic differences between coastal lagoons and riverine environments, as well as divergent populations that could be reproductively isolated. Here, we investigated the genetic diversity pattern of this taxon in the Southern Neotropical Basin system that includes the La Plata Basin, Patos-Merin lagoon basin and the coastal lagoons draining to the SW Atlantic Ocean, through a population genomics approach using 2b-RAD-sequencing-derived single nucleotide polymorphisms (SNPs). The genomic scan identified selection footprints associated with divergence and suggested local adaptation environmental drivers. Two major genomic clusters latitudinally distributed in the Northern and Southern basins were identified, along with consistent signatures of divergent selection between them. Population structure based on the whole set of loci and on the presumptive neutral vs. adaptive loci showed deep genomic divergence between the two major clusters. Annotation of the most consistent SNPs under divergent selection revealed some interesting candidate genes for further functional studies. Moreover, signals of adaptation to a coastal lagoon environment mediated by purifying selection were found. These new insights provide a better understanding of the complex evolutionary history of R. quelen in the southernmost basin of the Neotropical region.

Local adaptation of a dominant coastal tree to freshwater availability and solar radiation suggested by genomic and ecophysiological approaches

Local adaptation is often a product of environmental variations in geographical space and has implications for biodiversity conservation. We investigated the role of latitudinal heterogeneity in climate on the organization of genetic and phenotypic variation in the dominant coastal tree Avicennia schaueriana. In a common garden experiment, samples from an equatorial region, with pronounced seasonality in precipitation, accumulated less biomass, and showed lower stomatal conductance and transpiration, narrower xylem vessels, smaller leaves and higher reflectance of long wavelengths by the stem epidermis than samples from a subtropical region, with seasonality in temperature and no dry season. Transcriptomic differences identified between trees sampled under field conditions at equatorial and subtropical sites, were enriched in functional categories such as responses to temperature, solar radiation, water deficit, photosynthesis and cell wall biosynthesis. Remarkably, the diversity based on genome-wide SNPs revealed a north-south genetic structure and signatures of selection were identified for loci associated with photosynthesis, anthocyanin accumulation and the responses to osmotic and hypoxia stresses. Our results suggest the existence of divergence in key resource-use characteristics, likely driven by seasonality in water deficit and solar radiation. These findings provide a basis for conservation plans and for predicting coastal plants responses to climate change.

The demographic history of Atlantic salmon (Salmo salar) across its distribution range reconstructed from approximate Bayesian computations

Understanding the dual roles of demographic and selective processes in the buildup of population divergence is one of the most challenging tasks in evolutionary biology. Here, we investigated the demographic history of Atlantic salmon across the entire species range using 2035 anadromous individuals from North America and Eurasia. By combining results from admixture graphs, geo-genetic maps, and an Approximate Bayesian Computation (ABC) framework, we validated previous hypotheses pertaining to secondary contact between European and Northern American populations, but also identified secondary contacts in European populations from different glacial refugia. We further identified the major sources of admixture from the southern range of North America into more northern populations along with a strong signal of secondary gene flow between genetic regional groups. We hypothesize that these patterns reflect the spatial redistribution of ancestral variation across the entire North American range. Results also support a role for linked selection and differential introgression that likely played an underappreciated role in shaping the genomic landscape of species in the Northern hemisphere. We conclude that studies between partially isolated populations should systematically include heterogeneity in selective and introgressive effects among loci to perform more rigorous demographic inferences of the divergence process.

Genomic signatures and correlates of widespread population declines in salmon

Global losses of biodiversity are occurring at an unprecedented rate, but causes are often unidentified. Genomic data provide an opportunity to isolate drivers of change and even predict future vulnerabilities. Atlantic salmon (Salmo salar) populations have declined range-wide, but factors responsible are poorly understood. Here, we reconstruct changes in effective population size (Ne) in recent decades for 172 range-wide populations using a linkage-based method. Across the North Atlantic, Ne has significantly declined in >60% of populations and declines are consistently temperature-associated. We identify significant polygenic associations with decline, involving genomic regions related to metabolic, developmental, and physiological processes. These regions exhibit changes in presumably adaptive diversity in declining populations consistent with contemporary shifts in body size and phenology. Genomic signatures of widespread population decline and associated risk scores allow direct and potentially predictive links between population fitness and genotype, highlighting the power of genomic resources to assess population vulnerability.

What can be learned by scanning the genome for molecular convergence in wild populations?

Convergent evolution, where independent lineages evolve similar phenotypes in response to similar challenges, can provide valuable insight into how selection operates and the limitations it encounters. However, it has only recently become possible to explore how convergent evolution is reflected at the genomic level. The overlapping outlier approach (OOA), where genome scans of multiple independent lineages are used to find outliers that overlap and therefore identify convergently evolving loci, is becoming popular. Here, we present a quantitative analysis of 34 studies that used this approach across many sampling designs, taxa, and sampling intensities. We found that OOA studies with increased biological sampling power within replicates have increased likelihood of finding overlapping, "convergent" signals of adaptation between them. When identifying convergent loci as overlapping outliers, it is tempting to assume that any false-positive outliers derived from individual scans will fail to overlap across replicates, but this cannot be guaranteed. We highlight how population demographics and genomic context can contribute toward both true convergence and false positives in OOA studies. We finish with an exploration of emerging methods that couple genome scans with phenotype and environmental measures, leveraging added information from genome data to more directly test hypotheses of the likelihood of convergent evolution.

Population genetic analysis reveals a geographically limited transition zone between two genetically distinct Atlantic salmon lineages in Norway

Atlantic salmon is characterized by a high degree of population genetic structure throughout its native range. However, while populations inhabiting rivers in Norway and Russia make up a significant proportion of salmon in the Atlantic, thus far, genetic studies in this region have only encompassed low to modest numbers of populations. Here, we provide the first "in-depth" investigation of population genetic structuring in the species in this region. Analysis of 18 microsatellites on >9,000 fish from 115 rivers revealed highly significant population genetic structure throughout, following a hierarchical pattern. The highest and clearest level of division separated populations north and south of the Lofoten region in northern Norway. In this region, only a few populations displayed intermediate genetic profiles, strongly indicating a geographically limited transition zone. This was further supported by a dedicated cline analysis. Population genetic structure was also characterized by a pattern of isolation by distance. A decline in overall genetic diversity was observed from the south to the north, and two of the microsatellites showed a clear decrease in number of alleles across the observed transition zone. Together, these analyses support results from previous studies, that salmon in Norway originate from two main genetic lineages, one from the Barents-White Sea refugium that recolonized northern Norwegian and adjacent Russian rivers, and one from the eastern Atlantic that recolonized the rest of Norway. Furthermore, our results indicate that local conditions in the limited geographic transition zone between the two observed lineages, characterized by open coastline with no obvious barriers to gene flow, are strong enough to maintain the genetic differentiation between them.

Standing geographic variation in eclosion time and the genomics of host race formation in Rhagoletis pomonella fruit flies

Taxa harboring high levels of standing variation may be more likely to adapt to rapid environmental shifts and experience ecological speciation. Here, we characterize geographic and host-related differentiation for 10,241 single nucleotide polymorphisms in Rhagoletis pomonella fruit flies to infer whether standing genetic variation in adult eclosion time in the ancestral hawthorn (Crataegus spp.)-infesting host race, as opposed to new mutations, contributed substantially to its recent shift to earlier fruiting apple (Malus domestica). Allele frequency differences associated with early vs. late eclosion time within each host race were significantly related to geographic genetic variation and host race differentiation across four sites, arrayed from north to south along a 430-km transect, where the host races co-occur in sympatry in the Midwest United States. Host fruiting phenology is clinal, with both apple and hawthorn trees fruiting earlier in the North and later in the South. Thus, we expected alleles associated with earlier eclosion to be at higher frequencies in northern populations. This pattern was observed in the hawthorn race across all four populations; however, allele frequency patterns in the apple race were more complex. Despite the generally earlier eclosion timing of apple flies and corresponding apple fruiting phenology, alleles on chromosomes 2 and 3 associated with earlier emergence were paradoxically at lower frequency in the apple than hawthorn host race across all four sympatric sites. However, loci on chromosome 1 did show higher frequencies of early eclosion-associated alleles in the apple than hawthorn host race at the two southern sites, potentially accounting for their earlier eclosion phenotype. Thus, although extensive clinal genetic variation in the ancestral hawthorn race exists and contributed to the host shift to apple, further study is needed to resolve details of how this standing variation was selected to generate earlier eclosing apple fly populations in the North.

Chromosomal fusion and life history-associated genomic variation contribute to within-river local adaptation of Atlantic salmon

Chromosomal inversions have been implicated in facilitating adaptation in the face of high levels of gene flow, but whether chromosomal fusions also have similar potential remains poorly understood. Atlantic salmon are usually characterized by population structure at multiple spatial scales; however, this is not the case for tributaries of the Miramichi River in North America. To resolve genetic relationships between populations in this system and the potential for known chromosomal fusions to contribute to adaptation, we genotyped 728 juvenile salmon using a 50 K SNP array. Consistent with previous work, we report extremely weak overall population structuring (Global F_ST  = 0.004) and failed to support hierarchical structure between the river's two main branches. We provide the first genomic characterization of a previously described polymorphic fusion between chromosomes 8 and 29. Fusion genomic characteristics included high LD, reduced heterozygosity in the fused homokaryotes, and strong divergence between the fused and the unfused rearrangement. Population structure based on fusion karyotype was five times stronger than neutral variation (F_ST  = 0.019), and the frequency of the fusion was associated with summer precipitation supporting a hypothesis that this rearrangement may contribute local adaptation despite weak neutral differentiation. Additionally, both outlier variation among populations and a polygenic framework for characterizing adaptive variation in relation to climate identified a 250-Kb region of chromosome 9, including the gene six6 that has previously been linked to age-at-maturity and run-timing for this species. Overall, our results indicate that adaptive processes, independent of major river branching, are more important than neutral processes for structuring these populations.

Environmental extremes drive population structure at the northern range limit of Atlantic salmon in North America

Conservation of exploited species requires an understanding of both genetic diversity and the dominant structuring forces, particularly near range limits, where climatic variation can drive rapid expansions or contractions of geographic range. Here, we examine population structure and landscape associations in Atlantic salmon (Salmo salar) across a heterogeneous landscape near the northern range limit in Labrador, Canada. Analysis of two amplicon-based data sets containing 101 microsatellites and 376 single nucleotide polymorphisms (SNPs) from 35 locations revealed clear differentiation between populations spawning in rivers flowing into a large marine embayment (Lake Melville) compared to coastal populations. The mechanisms influencing the differentiation of embayment populations were investigated using both multivariate and machine-learning landscape genetic approaches. We identified temperature as the strongest correlate with genetic structure, particularly warm temperature extremes and wider annual temperature ranges. The genomic basis of this divergence was further explored using a subset of locations (n = 17) and a 220K SNP array. SNPs associated with spatial structuring and temperature mapped to a diverse set of genes and molecular pathways, including regulation of gene expression, immune response, and cell development and differentiation. The results spanning molecular marker types and both novel and established methods clearly show climate-associated, fine-scale population structure across an environmental gradient in Atlantic salmon near its range limit in North America, highlighting valuable approaches for predicting population responses to climate change and managing species sustainability.

Range-wide parallel climate-associated genomic clines in Atlantic salmon

Clinal variation across replicated environmental gradients can reveal evidence of local adaptation, providing insight into the demographic and evolutionary processes that shape intraspecific diversity. Using 1773 genome-wide single nucleotide polymorphisms we evaluated latitudinal variation in allele frequency for 134 populations of North American and European Atlantic salmon (Salmo salar). We detected 84 (4.74%) and 195 (11%) loci showing clinal patterns in North America and Europe, respectively, with 12 clinal loci in common between continents. Clinal single nucleotide polymorphisms were evenly distributed across the salmon genome and logistic regression revealed significant associations with latitude and seasonal temperatures, particularly average spring temperature in both continents. Loci displaying parallel clines were associated with several metabolic and immune functions, suggesting a potential basis for climate-associated adaptive differentiation. These climate-based clines collectively suggest evidence of large-scale environmental associated differences on either side of the North Atlantic. Our results support patterns of parallel evolution on both sides of the North Atlantic, with evidence of both similar and divergent underlying genetic architecture. The identification of climate-associated genomic clines illuminates the role of selection and demographic processes on intraspecific diversity in this species and provides a context in which to evaluate the impacts of climate change.