RAD-Seq Reveals Patterns of Additive Polygenic Variation Caused by Spatially-Varying Selection in the American Eel (Anguilla rostrata)

Effects of dissolved oxygen changes in the benthic environment on phosphorus flux at the sediment-water interface in a coastal brackish lake

In semi-enclosed coastal brackish lakes, changes in dissolved oxygen in the bottom layer due to salinity stratification can affect the flux of phosphorus (P) at the sediment-water interface, resulting in short- and long-term water quality fluctuations in the water column. In this study, the physicochemical properties of the water layers and sediments at five sites in Saemangeum Lake were analyzed in spring and autumn for four years, and phosphorus release experiments from sediments were conducted for 20 days under oxic and anoxic conditions during the same period. Sediment total phosphorus (T-P) decreased in autumn compared to spring due to mineralization of organic bound phosphorus, which was the most dominant P fraction. This may be related to the increase in the ratio of PO4-P to T-P in bottom waters in autumn, when hypoxia was frequently observed. The difference in P fluxes between oxic and anoxic conditions indicated that during autumn, as compared to spring, the release of phosphorus could have a more immediate impact on the water column during the formation of hypoxia/anoxia. The main factors influencing changes in P fluxes from sediments were identified through redundancy analysis. Additionally, based on the results of multiple regression analysis, sediment TOC, sediment non-apatite phosphorus, porewater pH, and porewater PO4-P were determined to be the most significant factors affecting P fluxes from sediments, depending on the season or redox conditions. Recently, the increased influx of seawater into Saemangeum Lake has been shown to contribute to water quality improvements in the water column due to a strong dilution effect. However, the sediment environment has shifted towards a more reduced state, leading to increased P release under anoxic conditions. Therefore, for future water quality management within the lake, it is necessary to consistently address the recurring hypoxia and continuously monitor phosphorus dynamics.

Genomic signatures of climate adaptation in bank voles

Evidence for divergent selection and adaptive variation across the landscape can provide insight into a species' ability to adapt to different environments. However, despite recent advances in genomics, it remains difficult to detect the footprints of climate-mediated selection in natural populations. Here, we analysed ddRAD sequencing data (21,892 SNPs) in conjunction with geographic climate variation to search for signatures of adaptive differentiation in twelve populations of the bank vole (Clethrionomys glareolus) distributed across Europe. To identify the loci subject to selection associated with climate variation, we applied multiple genotype-environment association methods, two univariate and one multivariate, and controlled for the effect of population structure. In total, we identified 213 candidate loci for adaptation, 74 of which were located within genes. In particular, we identified signatures of selection in candidate genes with functions related to lipid metabolism and the immune system. Using the results of redundancy analysis, we demonstrated that population history and climate have joint effects on the genetic variation in the pan-European metapopulation. Furthermore, by examining only candidate loci, we found that annual mean temperature is an important factor shaping adaptive genetic variation in the bank vole. By combining landscape genomic approaches, our study sheds light on genome-wide adaptive differentiation and the spatial distribution of variants underlying adaptive variation influenced by local climate in bank voles.

Panmixia in the American eel extends to its tropical range of distribution: Biological implications and policymaking challenges

The American eel (Anguilla rostrata) has long been regarded as a panmictic fish and has been confirmed as such in the northern part of its range. In this paper, we tested for the first time whether panmixia extends to the tropical range of the species. To do so, we first assembled a reference genome (975 Mbp, 19 chromosomes) combining long (PacBio and Nanopore and short (Illumina paired-end) reads technologies to support both this study and future research. To test for population structure, we estimated genotype likelihoods from low-coverage whole-genome sequencing of 460 American eels, collected at 21 sampling sites (in seven geographic regions) ranging from Canada to Trinidad and Tobago. We estimated genetic distance between regions, performed ADMIXTURE-like clustering analysis and multivariate analysis, and found no evidence of population structure, thus confirming that panmixia extends to the tropical range of the species. In addition, two genomic regions with putative inversions were observed, both geographically widespread and present at similar frequencies in all regions. We discuss the implications of lack of genetic population structure for the species. Our results are key for the future genomic research in the American eel and the implementation of conservation measures throughout its geographic range. Additionally, our results can be applied to fisheries management and aquaculture of the species.

Re-thinking the environment in landscape genomics

Detecting the extrinsic selective pressures shaping genomic variation is critical for a better understanding of adaptation and for forecasting evolutionary responses of natural populations to changing environmental conditions. With increasing availability of geo-referenced environmental data, landscape genomics provides unprecedented insights into how genomic variation and underlying gene functions affect traits potentially under selection. Yet, the robustness of genotype-environment associations used in landscape genomics remains tempered due to various limitations, including the characteristics of environmental data used, sampling designs employed, and statistical frameworks applied. Here, we argue that using complementary or new environmental data sources and well-informed sampling designs may help improve the detection of selective pressures underlying patterns of local adaptation in various organisms and environments.

Redundancy analysis, genome-wide association studies and the pigmentation of brown trout (Salmo trutta L.)

The association of molecular variants with phenotypic variation is a main issue in biology, often tackled with genome-wide association studies (GWAS). GWAS are challenging, with increasing, but still limited, use in evolutionary biology. We used redundancy analysis (RDA) as a complimentary ordination approach to single- and multitrait GWAS to explore the molecular basis of pigmentation variation in brown trout (Salmo trutta) belonging to wild populations impacted by hatchery fish. Based on 75,684 single nucleotide polymorphic (SNP) markers, RDA, single- and multitrait GWAS allowed the extraction of 337 independent colour patterning loci (CPLs) associated with trout pigmentation traits, such as the number of red and black spots on flanks. Collectively, these CPLs (i) mapped onto 35 out of 40 brown trout linkage groups indicating a polygenic genomic architecture of pigmentation, (ii) were found to be associated with 218 candidate genes, including 197 genes formerly mentioned in the literature associated to skin pigmentation, skin patterning, differentiation or structure notably in a close relative, the rainbow trout (Onchorhynchus mykiss), and (iii) related to functions relevant to pigmentation variation (e.g., calcium- and ion-binding, cell adhesion). Annotated CPLs include genes with well-known pigmentation effects (e.g., PMEL, SLC45A2, SOX10), but also markers associated with genes formerly found expressed in rainbow or brown trout skins. RDA was also shown to be useful to investigate management issues, especially the dynamics of trout pigmentation submitted to several generations of hatchery introgression.

Neutral and adaptive loci reveal fine‐scale population structure in Eleginops maclovinus from north Patagonia

Patagonia is an understudied area, especially when it comes to population genomic studies with relevance to fishery management. However, the dynamic and heterogeneous landscape in this area can harbor an important but cryptic genetic population structure. Once such information is revealed, it can be integrated into the management of infrequently investigated species. Eleginops maclovinus is a protandrous hermaphrodite species with economic importance for local communities that are currently managed as a single genetic unit. In this study, we sampled five locations distributed across a salinity cline from Northern Patagonia to investigate the genetic population structure of E. maclovinus. We used restriction site‐associated DNA (RAD) sequencing and outlier tests to obtain neutral and adaptive loci, using F_ST and GEA approaches. We identified a spatial pattern of structuration with gene flow and spatial selection by environmental association. Neutral and adaptive loci showed two and three genetic groups, respectively. The effective population sizes estimated ranged from 572 (Chepu) to 14,454 (Chaitén) and were influenced more by locality than by salinity cline. We found loci putatively associated with salinity suggesting that salinity may act as a selective driver in E. maclovinus populations. These results suggest a complex interaction between genetic drift, gene flow, and natural selection in this area. Our findings also suggest several evolutionary significant units in this area, and the information should be integrated into the management of this species. We discussed the significance of these results for fishery management and suggest future directions to improve our understanding of how E. maclovinus has adapted to the dynamic waters of Northern Patagonia.

Genome-wide methylation in the panmictic European eel (Anguilla anguilla)

The role of methylation in adaptive, developmental and speciation processes has attracted considerable interest, but interpretation of results is complicated by diffuse boundaries between genetic and non-genetic variation. We studied whole genome genetic and methylation variation in the European eel, distributed from subarctic to subtropical environments, but with panmixia precluding genetically based local adaptation beyond single-generation responses. Overall methylation was 70.9%, with hypomethylation predominantly found in promoters and first exons. Redundancy analyses involving juvenile glass eels showed 0.06% and 0.03% of the variance at SNPs to be explained by localities and environmental variables, respectively, with GO terms of genes associated with outliers primarily involving neural system functioning. For CpGs 2.98% and 1.36% of variance was explained by localities and environmental variables. Differentially methylated regions particularly included genes involved in developmental processes, with hox clusters featuring prominently. Life stage (adult versus glass eels) was the most important source of inter-individual variation in methylation, likely reflecting both ageing and developmental processes. Demethylation of transposable elements relative to pure European eel was observed in European X American eel hybrids, possibly representing postzygotic barriers in this system characterized by prolonged speciation and ongoing gene flow. Whereas the genetic data are consistent with a role of single-generation selective responses, the methylation results underpin the importance of epigenetics in the life cycle of eels and suggests interactions between local environments, development and phenotypic variation mediated by methylation variation. Eels are remarkable by having retained eight hox clusters, and the results suggest important roles of methylation at hox genes for adaptive processes.

Genomic signatures for latitudinal selection in the tropical eel Anguilla marmorata

Selection acting across environmental gradients, such as latitudes, can cause spatial structuring of genomic variants even within panmictic populations. In this study, we focused on the within-generation latitudinal selection between northernmost and southernmost individuals of the North Pacific population of a tropical eel Anguilla marmorata, which shares its northernmost distribution with a temperate eel Anguilla japonica. Whole-genome sequencing data indicated that the northernmost and southernmost individuals of A. marmorata belong to a single panmictic population, as suggested by previous studies. On the contrary, parts of genomic regions across multiple chromosomes exhibited significant genetic differentiation between the northernmost and southernmost individuals, and in these genomic regions, the genotypes of the northernmost individuals were similar to those of A. japonica. These findings suggested within-generation latitudinal selection of A. marmorata, which might have led to genetic closeness between northernmost A. marmorata and A. japonica.

Genome-Wide Investigation of the Multiple Origins Hypothesis for Deep-Spawning Kokanee Salmon (Oncorhynchus nerka) across its Pan-Pacific Distribution

Salmonids have emerged as important study systems for investigating molecular processes underlying parallel evolution given their tremendous life history variation. Kokanee, the resident form of anadromous sockeye salmon (Oncorhynchus nerka), have evolved multiple times across the species' pan-Pacific distribution, exhibiting multiple reproductive ecotypes including those that spawn in streams, on lake-shores, and at lake depths >50 m. The latter has only been detected in 5 locations in Japan and British Columbia, Canada. Here, we investigated the multiple origins hypothesis for deep-spawning kokanee, using 9721 single nucleotide polymorphisms distributed across the genome analyzed for the vast majority of known populations in Japan (Saiko Lake) and Canada (Anderson, Seton, East Barrière Lakes) relative to stream-spawning populations in both regions. We detected 397 outlier loci, none of which were robustly identified in paired-ecotype comparisons in Japan and Canada independently. Bayesian clustering and principal components analyses based on neutral loci revealed 6 distinct clusters, largely associated with geography or translocation history, rather than ecotype. Moreover, a high level of divergence between Canadian and Japanese populations, and between deep- and stream-spawning populations regionally, suggests the deep-spawning ecotype independently evolved on the 2 continents. On a finer level, Japanese kokanee populations exhibited low estimates of heterozygosity, significant levels of inbreeding, and reduced effective population sizes relative to Canadian populations, likely associated with transplantation history. Along with preliminary evidence for hybridization between deep- and stream-spawning ecotypes in Saiko Lake, these findings should be considered within the context of on-going kokanee fisheries management in Japan.

Landscape genomics of the streamside salamander: Implications for species management in the face of environmental change

Understanding spatial patterns of genetic differentiation and local adaptation is critical in a period of rapid environmental change. Climate change and anthropogenic development have led to population declines and shifting geographic distributions in numerous species. The streamside salamander, Ambystoma barbouri, is an endemic amphibian with a small geographic range that predominantly inhabits small, ephemeral streams. As A. barbouri is listed as near‐threatened by the IUCN, we describe range‐wide patterns of genetic differentiation and adaptation to assess the species’ potential to respond to environmental change. We use outlier scans and genetic‐environment association analyses to identify genomic variation putatively underlying local adaptation across the species’ geographic range. We find evidence for adaptation with a polygenic architecture and a set of candidate SNPs that identify genes putatively contributing to local adaptation. Our results build on earlier work that suggests that some A. barbouri populations are locally adapted despite evidence for asymmetric gene flow between the range core and periphery. Taken together, the body of work describing the evolutionary genetics of range limits in A. barbouri suggests that the species may be unlikely to respond naturally to environmental challenges through a range shift or in situ adaptation. We suggest that management efforts such as assisted migration may be necessary in future.

Genetic and phenotypic variation exhibit both predictable and stochastic patterns across an intertidal fish metapopulation

Interactions among selection, gene flow, and drift affect the trajectory of adaptive evolution. In natural populations, the direction and magnitude of these processes can be variable across different spatial, temporal, or ontogenetic scales. Consequently, variability in evolutionary processes affects the predictability or stochasticity of microevolutionary outcomes. We studied an intertidal fish, Bathygobius cocosensis (Bleeker, 1854), to understand how space, time, and life stage structure genetic and phenotypic variation in a species with potentially extensive dispersal and a complex life cycle (larval dispersal preceding benthic recruitment). We sampled juvenile and adult life stages, at three sites, over three years. Genome-wide SNPs uncovered a pattern of chaotic genetic patchiness, that is, weak-but-significant patchy spatial genetic structure that was variable through time and between life stages. Outlier locus analyses suggested that targets of spatially divergent selection were mostly temporally variable, though a significant number of spatial outlier loci were shared between life stages. Head shape, a putatively ecologically responsive (adaptive) phenotype in B. cocosensis also exhibited high temporal variability within sites. However, consistent spatial relationships between sites indicated that environmental similarities among sites may generate predictable phenotype distributions across space. Our study highlights the complex microevolutionary dynamics of marine systems, where consideration of multiple ecological dimensions can reveal both predictable and stochastic patterns in the distributions of genetic and phenotypic variation. Such considerations probably apply to species that possess short, complex life cycles, have large dispersal potential and fecundities, and that inhabit heterogeneous environments.

Microgeographical adaptation corresponds to elevational distributions of congeneric montane grasshoppers

Local adaptation can occur at small spatial scales relative to the dispersal capacity of species. Alpine ecosystems have sharp environmental clines that offer an opportunity to investigate the effects of fine-scale shifts in species' niche breadth on adaptive genetic processes. Here we examine two grasshopper species endemic to the Australian Alps (Kosciuscola spp.) that differ in elevational niche breadth: one broader, K. usitatus (1400-2200 m), and one narrower, K. tristis (1600-2000 m). We examine signatures of selection with respect to environmental and morphological variables in two mountain regions using F_ST outlier tests and environmental association analyses (EAAs) applied to single nucleotide polymorphism (SNP) data (K. usitatus: 9017 SNPs, n = 130; K. tristis: 7363 SNPs, n = 135). Stronger genetic structure was found in the more narrowly distributed K. tristis, which showed almost twice the number of SNPs under putative selection (10.8%) compared with K. usitatus (5.3%). When examining SNPs in common across species (n = 3058), 260 SNPs (8.5%) were outliers shared across species, and these were mostly associated with elevation, a proxy for temperature, suggesting parallel adaptive processes in response to climatic drivers. Additive polygenic scores (an estimate of the cumulative signal of selection across all candidate loci) were nonlinearly and positively correlated with elevation in both species. However, a steeper correlation in K. tristis indicated a stronger signal of spatially varying selection towards higher elevations. Our study illustrates that the niche breadth of co-occurring and related species distributed along the same environmental cline is associated with differences in patterns of microgeographical adaptation.

Genomic Signatures of Selection along a Climatic Gradient in the Northern Range Margin of the White-Footed Mouse (Peromyscus leucopus)

Identifying genetic variation involved in thermal adaptation is likely to yield insights into how species adapt to different climates. Physiological and behavioral responses associated with overwintering (e.g., torpor) are thought to serve important functions in climate adaptation. In this study, we use 2 isolated Peromyscus leucopus lineages on the northern margin of the species range to identify single nucleotide polymorphisms (SNPs) showing a strong environmental association and test for evidence of parallel evolution. We found signatures of clinal selection in each lineage, but evidence of parallelism was limited, with only 2 SNPs showing parallel allele frequencies across transects. These parallel SNPs map to a gene involved in protection against iron-dependent oxidative stress (Fxn) and to a gene with unknown function but containing a forkhead-associated domain (Fhad1). Furthermore, within transects, we find significant clinal patterns in genes enriched for functions associated with glycogen homeostasis, synaptic function, intracellular Ca2+ balance, H3 histone modification, as well as the G2/M transition of cell division. Our results are consistent with recent literature on the cellular and molecular basis of climate adaptation in small mammals and provide candidate genomic regions for further study.

Local thermal adaptation and limited gene flow constrain future climate responses of a marine ecosystem engineer

Rising ocean temperatures and extreme temperature events have precipitated declines and local extinctions in many marine species globally, but patterns of loss are often uneven across species ranges for reasons that are poorly understood. Knowledge of the extent of local adaptation and gene flow may explain such patterns and help predict future trajectories under scenarios of climate change. We test the extent to which local differentiation in thermal tolerance is influenced by gene flow and local adaptation using a widely distributed intertidal seaweed (Hormosira banksii) from temperate Australia. Population surveys across ~2,000 km of the species range revealed strong genetic structuring at regional and local scales (global F ST = 0.243) reflecting extremely limited gene flow, while common garden experiments (14-day exposures to 15, 18, 21°C) revealed strong site differences in early development and mortality in response to elevated temperature. Embryos from many sites spanning a longitudinal thermal gradient showed suppressed development and increased mortality to elevated water temperatures, but populations originating from warmer and more variable thermal environments tended to be less susceptible to warming. Notably, there was significant local-scale variation in the thermal responses of embryos within regions which was corroborated by the finding of small-scale genetic differences. We expect the observed genetic and phenotypic differentiation to lead to uneven responses to warming sea surface temperatures in this important marine foundation species. The study highlights the challenges of predicting species responses to thermal stress and the importance of management strategies that incorporate evolutionary potential for "climate-proofing" marine ecosystems.

Insights into the neutral and adaptive processes shaping the spatial distribution of genomic variation in the economically important Moroccan locust (Dociostaurus maroccanus)

Understanding the processes that shape neutral and adaptive genomic variation is a fundamental step to determine the demographic and evolutionary dynamics of pest species. Here, we use genomic data obtained via restriction site-associated DNA sequencing to investigate the genetic structure of Moroccan locust (Dociostaurus maroccanus) populations from the westernmost portion of the species distribution (Iberian Peninsula and Canary Islands), infer demographic trends, and determine the role of neutral versus selective processes in shaping spatial patterns of genomic variation in this pest species of great economic importance. Our analyses showed that Iberian populations are characterized by high gene flow, whereas the highly isolated Canarian populations have experienced strong genetic drift and loss of genetic diversity. Historical demographic reconstructions revealed that all populations have passed through a substantial genetic bottleneck around the last glacial maximum (~21 ka BP) followed by a sharp demographic expansion at the onset of the Holocene, indicating increased effective population sizes during warm periods as expected from the thermophilic nature of the species. Genome scans and environmental association analyses identified several loci putatively under selection, suggesting that local adaptation processes in certain populations might not be impeded by widespread gene flow. Finally, all analyses showed few differences between outbreak and nonoutbreak populations. Integrated pest management practices should consider high population connectivity and the potential importance of local adaptation processes on population persistence.

Within-Generation Polygenic Selection Shapes Fitness-Related Traits across Environments in Juvenile Sea Bream

Understanding the genetic underpinnings of fitness trade-offs across spatially variable environments remains a major challenge in evolutionary biology. In Mediterranean gilthead sea bream, first-year juveniles use various marine and brackish lagoon nursery habitats characterized by a trade-off between food availability and environmental disturbance. Phenotypic differences among juveniles foraging in different habitats rapidly appear after larval settlement, but the relative role of local selection and plasticity in phenotypic variation remains unclear. Here, we combine phenotypic and genetic data to address this question. We first report correlations of opposite signs between growth and condition depending on juvenile habitat type. Then, we use single nucleotide polymorphism (SNP) data obtained by Restriction Associated DNA (RAD) sequencing to search for allele frequency changes caused by a single generation of spatially varying selection between habitats. We found evidence for moderate selection operating at multiple loci showing subtle allele frequency shifts between groups of marine and brackish juveniles. We identified subsets of candidate outlier SNPs that, in interaction with habitat type, additively explain up to 3.8% of the variance in juvenile growth and 8.7% in juvenile condition; these SNPs also explained significant fraction of growth rate in an independent larval sample. Our results indicate that selective mortality across environments during early-life stages involves complex trade-offs between alternative growth strategies.

Interaction among soil physicochemical properties, bacterial community structure, and arsenic contamination: Clay-induced change in long-term arsenic contaminated soils

Pyrosequencing analyses to determine soil bacterial communities were conducted with forty-two soil samples collected from rice paddy and forest/farmland soils (Group A and B, respectively) at a long-term As-contaminated site. Soil physicochemical properties, such as the concentrations of As, Fe, Al, and Mn, pH, organic matter content, and clay content, were found to be significantly different with land use, and more importantly, strongly affected the bacterial community structure of the soil samples. When fitting the soil properties onto a nonmetric multidimensional scale plot of soil bacterial communities, clay content was found to be the most important factor in clustering the bacterial communities (R² = 0.4831, p-value = 0.001). Phylum Chloroflexi (-1.03 of bioplot score) and Planctomycetes (1.31 of bioplot score) showed a significant relationship with clay content in soil samples. Interestingly, thebacterial phylotypes linked to clay content were only found in the soil samples of group B with low clay content, and had a strong relationship to As contamination in the redundancy analysis and the correlation analysis.Our results suggest that clay content seems to be negatively related to As contamination in soils, which, in turn, strongly influences the structure of bacterial communities in As-contaminated soil.

Gold nanoparticles and angiogenesis: molecular mechanisms and biomedical applications

Angiogenesis is the formation of new blood vessels from pre-existing vessels. It is a highly regulated process as determined by the interplay between pro-angiogenic and anti-angiogenic factors. Under certain conditions the balance between angiogenesis stimulators and inhibitors is altered, which results in a shift from physiological to pathological angiogenesis. Therefore, the goal of therapeutic targeting of angiogenic process is to normalize vasculature in target tissues by enhancing angiogenesis in disease conditions of reduced vascularity and blood flow, such as tissue ischemia, or alternatively to inhibit excessive and abnormal angiogenesis in disorders like cancer. Gold nanoparticles (AuNPs) are special particles that are generated by nanotechnology and composed of an inorganic core containing gold which is encircled by an organic monolayer. The ability of AuNPs to alter vasculature has captured recent attention in medical literature as potential therapeutic agents for the management of pathologic angiogenesis. This review provides an overview of the effects of AuNPs on angiogenesis and the molecular mechanisms and biomedical applications associated with their effects. In addition, the main synthesis methods, physical properties, uptake mechanisms, and toxicity of AuNPs are briefly summarized.

The conundrum of species delimitation: a genomic perspective on a mitogenetically super-variable butterfly

The Palaearctic butterfly Melitaea didyma stands out as one of the most striking cases of intraspecific genetic differentiation detected in Lepidoptera: 11 partially sympatric mitochondrial lineages have been reported, displaying levels of divergence of up to 7.4%. To better understand the evolutionary processes underlying the diversity observed in mtDNA, we compared mtDNA and genome-wide SNP data using double-digest restriction site-associated DNA sequencing (ddRADseq) results from 93 specimens of M. didyma ranging from Morocco to eastern Kazakhstan. We found that, between ddRADseq and mtDNA results, there is a match only in populations that probably remained allopatric for long periods of time. Other mtDNA lineages may have resulted from introgression events and were probably affected by Wolbachia infection. The five main ddRADseq clades supported by STRUCTURE were parapatric or allopatric and showed high pairwise F_ST values, but some were also estimated to display various levels of gene flow. Melitaea didyma represents one of the first cases of deep mtDNA splits among European butterflies assessed by a genome-wide DNA analysis and reveals that the interpretation of patterns remains challenging even when a high amount of genomic data is available. These findings actualize the ongoing debate of species delimitation in allopatry, an issue probably of relevance to a significant proportion of global biodiversity.

RAD genotyping reveals fine-scale population structure and provides evidence for adaptive divergence in a commercially important fish from the northwestern Pacific Ocean

Exploring factors shaping genetic structure of marine fish is challenging due to fewer barriers to gene flow in the ocean. However, genome-wide sequence data can greatly enhance our ability to delineate previously unidentified population structure as well as potential adaptive divergence. The small yellow croaker (Larimichthys polyactis) is a commercially important fish species with high gene flow and its overwintering populations experience heterogeneous environment, suggesting possible population differentiation and adaptive divergence. To delineate patterns of population structure as well as test for signatures of local adaptation, a total of 68,666 quality filtered SNP markers were identified for 80 individuals from four overwintering populations by using restriction site-associated DNA sequencing (RAD-seq). Significant genetic differentiation among overwintering populations from the Central Yellow Sea, the South Yellow Sea and the North East China Sea were detected (Pair-wise F_ST: 0.00036–0.00390), which were consistent with population division of overwintering groups inferred from traditional ecological approaches. In addition, a total of 126 unique SNPs were detected to be significantly associated with environmental parameters (temperature, salinity and turbidity). These candidate SNPs were involved in multiple pathways such as energy metabolism and phagocytosis, suggesting they may play key roles in growth and innate immunity. Our results suggested the existence of hitherto unrecognized cryptic population structure and local adaptation in this high gene flow marine fish and thus gain new insights into the design of management strategies.

Evolutionary genomics of gypsy moth populations sampled along a latitudinal gradient

The European gypsy moth (Lymantria dispar L.) was first introduced to Massachusetts in 1869 and within 150 years has spread throughout eastern North America. This large-scale invasion across a heterogeneous landscape allows examination of the genetic signatures of adaptation potentially associated with rapid geographical spread. We tested the hypothesis that spatially divergent natural selection has driven observed changes in three developmental traits that were measured in a common garden for 165 adult moths sampled from six populations across a latitudinal gradient covering the entirety of the range. We generated genotype data for 91,468 single nucleotide polymorphisms based on double digest restriction-site associated DNA sequencing and used these data to discover genome-wide associations for each trait, as well as to test for signatures of selection on the discovered architectures. Genetic structure across the introduced range of gypsy moth was low in magnitude (F_ST  = 0.069), with signatures of bottlenecks and spatial expansion apparent in the rare portion of the allele frequency spectrum. Results from applications of Bayesian sparse linear mixed models were consistent with the presumed polygenic architectures of each trait. Further analyses indicated spatially divergent natural selection acting on larval development time and pupal mass, with the linkage disequilibrium component of this test acting as the main driver of observed patterns. The populations most important for these signals were two range-edge populations established less than 30 generations ago. We discuss the importance of rapid polygenic adaptation to the ability of non-native species to invade novel environments.

Evolutionary Toxicogenomics of the Striped Killifish (Fundulus majalis) in the New Bedford Harbor (Massachusetts, USA)

In this paper, we used a Genotyping-by-Sequencing (GBS) approach to find and genotype more than 4000 genome-wide SNPs (Single Nucleotide Polymorphisms) from striped killifish exposed to a variety of polychlorinated biphenyls (PCBs) and other aromatic pollutants in New Bedford Harbor (NBH, Massachusetts, USA). The aims of this study were to identify the genetic consequences of exposure to aquatic pollutants and detect genes that may be under selection. Low genetic diversity (H_E and π) was found in the site exposed to the highest pollution level, but the pattern of genetic diversity did not match the pollution levels. Extensive connectivity was detected among sampling sites, which suggests that balanced gene flow may explain the lack of genetic variation in response to pollution levels. Tests for selection identified 539 candidate outliers, but many of the candidate outliers were not shared among tests. Differences among test results likely reflect different test assumptions and the complex pollutant mixture. Potentially, selectively important loci are associated with 151 SNPs, and enrichment analysis suggests a likely involvement of these genes with pollutants that occur in NBH. This result suggests that selective processes at genes targeted by pollutants may be occurring, even at a small geographical scale, and may allow the local striped killifish to resist the high pollution levels.

Seascape genomics of eastern oyster (Crassostrea virginica) along the Atlantic coast of Canada

Interactions between environmental factors and complex life-history characteristics of marine organisms produce the genetic diversity and structure observed within species. Our main goal was to test for genetic differentiation among eastern oyster populations from the coastal region of Canadian Maritimes against expected genetic homogeneity caused by historical events, taking into account spatial and environmental (temperature, salinity, turbidity) variation. This was achieved by genotyping 486 individuals originating from 13 locations using RADSeq. A total of 11,321 filtered SNPs were used in a combination of population genomics and environmental association analyses. We revealed significant neutral genetic differentiation (mean F ST = 0.009) between sampling locations, and the occurrence of six major genetic clusters within the studied system. Redundancy analyses (RDAs) revealed that spatial and environmental variables explained 3.1% and 4.9% of the neutral genetic variation and 38.6% and 12.2% of the putatively adaptive genetic variation, respectively. These results indicate that these environmental factors play a role in the distribution of both neutral and putatively adaptive genetic diversity in the system. Moreover, polygenic selection was suggested by genotype-environment association analysis and significant correlations between additive polygenic scores and temperature and salinity. We discuss our results in the context of their conservation and management implications for the eastern oyster.

Comparison of Migratory and Resident Populations of Brown Trout Reveals Candidate Genes for Migration Tendency

Candidate genes associated with migration have been identified in multiple taxa: including salmonids, many of whom perform migrations requiring a series of physiological changes associated with the freshwater–saltwater transition. We screened over 5,500 SNPs for signatures of selection related to migratory behavior of brown trout Salmo trutta by focusing on ten differentially migrating freshwater populations from two watersheds (the Koutajoki and the Oulujoki). We found eight outlier SNPs potentially associated with migratory versus resident life history using multiple (≥3) outlier detection approaches. Comparison of three migratory versus resident population pairs in the Koutajoki watershed revealed seven outlier SNPs, of which three mapped close to genes ZNF665-like, GRM4-like, and PCDH8-like that have been previously associated with migration and smoltification in salmonids. Two outlier SNPs mapped to genes involved in mucus secretion (ST3GAL1-like) and osmoregulation (C14orf37-like). The last two strongly supported outlier SNPs mapped to thermally induced genes (FNTA1-like, FAM134C-like). Within the Oulujoki, the only consistent outlier SNP mapped close to a gene (EZH2) that is associated with compensatory growth in fasted trout. Our results suggest that a relatively small yet common set of genes responsible for physiological functions associated with resident and migratory life histories is evolutionarily conserved.