RAD sequencing highlights polygenic discrimination of habitat ecotypes in the panmictic American eel

Genomic Footprints of Hybridisation in North Atlantic Eels (Anguilla anguilla and A. rostrata)

Understanding interspecific introgressive hybridisation and the biological significance of introgressed variation remains an important goal in population genomics. European (Anguilla anguilla) and American eel (A. rostrata) represent a remarkable case of hybridisation. Both are panmictic and spawn in partial sympatry in the Sargasso Sea, occasionally producing viable, fertile hybrids, primarily found in Iceland. We studied introgressive hybridisation from American into European eel using whole-genome sequences of 78 individuals, including European, American and 21 putative hybrid eels. Previous studies using few genetic markers could not resolve whether hybridisation involved simple unidirectional backcrossing or a more complex hybrid swarm scenario. However, local ancestry inference along individual chromosomes revealed that Icelandic hybrids were primarily F1 or first-generation backcrosses towards European eel, with some showing more complex backcrossing. All European eels outside Iceland contained short chromosomal blocks from American eel, indicating a porous genome. We found no evidence for previously hypothesised geographical gradients of introgression in European eel outside Iceland. Several chromosomal regions showed high interspecific divergence, but haplotype blocks introgressed from American eel were identified both within and outside these regions. There was little correspondence between regions of high relative (FST) and absolute divergence (dXY), with the former reflecting selective sweeps within species or reduced recombination rather than barrier loci. A single genomic region showed evidence of repeated introgression from American into European eel under positive selection in both species. The study illustrates that species can maintain genetic integrity despite porous genomes and that standing variation in one species can potentially be available for future adaptive responses in the other species.

Genomic structural variation in Barramundi Perch Lates calcarifer and potential roles in speciation and adaptation

Advancements in genome sequencing and assembly techniques have increased the documentation of structural variants in wild organisms. Of these variants, chromosomal inversions are especially prominent due to their large size and active recombination suppression between alternative homokaryotypes. This suppression enables the 2 forms of the inversion to be maintained and allows the preservation of locally adapted alleles. The Barramundi Perch (BP; Lates calcarifer) is a widespread species complex with 3 main genetic lineages located in the biogeographic regions of Australia and New Guinea (AUS + NG), Southeast Asia (SEA), and the Indian Subcontinent (IND). BP are typically considered to be a protandrous sequential hermaphrodite species that exhibits catadromy. Freshwater occupancy and intraspecific variation in life history (e.g. partially migratory populations) exist and provide opportunities for strongly divergent selection associated with, for example, salinity tolerance, swimming ability, and marine dispersal. Herein, we utilize genomic data generated from all 3 genetic lineages to identify and describe 3 polymorphic candidate chromosomal inversions. These candidate chromosomal inversions appear to be fixed for ancestral variants in the IND lineage and for inverted versions in the AUS + NG lineage and exhibit variation in all 3 inversions in the SEA lineage. BP have a diverse portfolio of life history options that includes migratory strategy as well as sexual system (i.e. hermaphroditism and gonochorism). We propose that the some of the life history variabilities observed in BP may be linked to inversions and, in doing so, we present genetic data that might be useful in enhancing aquaculture production and population management.

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.

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

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.

Contrasting Phylogeographic Patterns of Mitochondrial and Genome-Wide Variation in the Groundwater Amphipod Crangonyx islandicus That Survived the Ice Age in Iceland

The analysis of phylogeographic patterns has often been based on mitochondrial DNA variation, but recent analyses dealing with nuclear DNA have in some instances revealed mito-nuclear discordances and complex evolutionary histories. These enigmatic scenarios, which may involve stochastic lineage sorting, ancestral hybridization, past dispersal and secondary contacts, are increasingly scrutinized with a new generation of genomic tools such as RADseq, which also poses additional analytical challenges. Here, we revisited the previously inconclusive phylogeographic history, showing the mito-nuclear discordance of an endemic groundwater amphipod from Iceland, Crangonyx islandicus, which is the only metazoan known to have survived the Pleistocene beneath the glaciers. Previous studies based on three DNA markers documented a mitochondrial scenario with the main divergence occurring between populations in northern Iceland and an ITS scenario with the main divergence between the south and north. We used double digest restriction-site-associated DNA sequencing (ddRADseq) to clarify this mito-nuclear discordance by applying several statistical methods while estimating the sensitivity to different analytical approaches (data-type, differentiation indices and base call uncertainty). A majority of nuclear markers and methods support the ITS divergence. Nevertheless, a more complex scenario emerges, possibly involving introgression led by male-biased dispersal among northern locations or mitochondrial capture, which may have been further strengthened by natural selection.

New insights into detecting alizarin from autofluorescence in marked glass eels

Alizarin detection in fish fins is extensively employed because it is easy to use. However, in eels, the eelGFP fluorescent protein may impede the detection of the fluorescent markers in the eel tissues. The study tests the effectiveness of three of the most up-to-date alizarin-detecting technologies on the living body and fins of European glass eels (Anguilla anguilla L.). The findings demonstrated that the control group had a high autofluorescence at alizarin and eelGFP maxima bands. With fluorescence reflectance imaging (FRI), the eel living body autofluorescence impeded the detection of the marked eels. In contrast with experimental excitation-emission-matrix (EEM) fluorescence analyses, 99% of the marked eels were correctly assigned to their group from fluorescence analyses of their fin cellular contents. With epifluorometry (EPI), 100% of the marked eels were detected with the caudal fin tips when excited at 450–490 nm wavelengths due to a weaker autofluorescence signal. EEM and FRI assays unveiled an average fluorescence quenching 60% and 44% of the marked group respectively, in the alizarin and eelGFP maxima bands. The fluorescence quenching observed is discussed. Results will benefit experimental design by examining autofluorescence effects on mark detection and the development of non-invasive detection methods in this critically endangered species.

Polygenic discrimination of migratory phenotypes in an estuarine forage fish

Migration is a complex phenotypic trait with some species containing migratory and nonmigratory individuals. Such life history variation may be attributed in part to plasticity, epigenetics, or genetics. Although considered semianadromous, recent studies using otolith geochemistry have revealed life history variation within the critically endangered Delta Smelt. Broadly categorizable as migratory or freshwater residents, we examined Restriction site Associated DNA sequencing data to test for a relationship between genetic variation and migratory behaviors. As previously shown, we found no evidence for neutral population genetic structure within Delta Smelt; however, we found significant evidence for associations between genetic variants and life history phenotypes. Furthermore, discriminant analysis of principal components, hierarchical clustering, and machine learning resulted in accurate assignment of fish into the freshwater resident or migratory classes based on their genotypes. These results suggest the presence of adaptive genetic variants relating to life history variation within a panmictic population. Mechanisms that may lead to this observation are genotype dependent habitat choice and spatially variable selection, both of which could operate each generation and are not exclusive. Given that the population of cultured Delta Smelt are being used as a refugial population for conservation, as a supply for wild population supplementation, and currently represent the majority of all living individuals of this species, we recommend that the hatchery management strategy consider the frequencies of life history-associated alleles and how to maintain this important aspect of Delta Smelt biological variation while under captive propagation.

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.

Comparative genomics and signatures of selection in North Atlantic eels

Comparative genomic approaches can identify putative private and shared signatures of selection. We performed a comparative genomic study of North Atlantic eels, European eel (Anguilla Anguilla) and American eel (A. rostrata). The two sister species are nearly undistinguishable at the phenotypic level and despite a wide non-overlapping continental distribution, they spawn in partial sympatry in the Sargasso Sea. Taking advantage of the newly assembled and annotated genome, we used genome wide RAD sequencing data of 359 individuals retrieved from Sequence Nucleotide Archive and state-of-the-art statistic tests to identify putative genomic signatures of selection in North Atlantic eels. First, using the F_ST and XP-EHH methods, we detected apparent islands of divergence on a total of 7 chromosomes, particularly on chromosomes 6 and 10. Gene ontology analyses suggested candidate genes mainly related to energy production, development and regulation, which could reflect strong selection on traits related to eel migration and larval duration time. Gene effect prediction using SNPeff showed a high number of SNPs in noncoding regions, pointing to a possible regulatory role. Second, using the iHS method we detected shared regions under selection on a total of 11 chromosomes. Several hypotheses might account for the detection of shared islands of selection in North Atlantic eels, including parallel evolution due to adaptation to similar environments and introgression. Future comparative genomic studies will be needed to further clarify the causes and consequences of introgression, including the directionality of these introgression events.

Fish out of water: Genomic insights into persistence of rainbowfish populations in the desert

How populations of aquatic fauna persist in extreme desert environments is an enigma. Individuals often breed and disperse during favorable conditions. Theory predicts that adaptive capacity should be low in small populations, such as in desert fishes. We integrated satellite-derived surface water data and population genomic diversity from 20,294 single-nucleotide polymorphisms across 344 individuals to understand metapopulation persistence of the desert rainbowfish (Melanotaenia splendida tatei) in central Australia. Desert rainbowfish showed very small effective population sizes, especially at peripheral populations, and low connectivity between river catchments. Yet, there was no evidence of population-level inbreeding and a signal of possible adaptive divergence associated with aridity was detected. Candidate genes for local adaptation included functions related to environmental cues and stressful conditions. Eco-evolutionary modeling showed that positive selection in refugial subpopulations combined with connectivity during flood periods can enable retention of adaptive diversity. Our study suggests that adaptive variation can be maintained in small populations and integrate with neutral metapopulation processes to allow persistence in the desert.

Migrating silver eels return from the sea to the river of origin after a false start

The European eel's singular spawning migration from European waters towards the Sargasso Sea remains elusive, including the early phase of migration at sea. During spawning migration, the movement of freshwater resident eels from river to sea has been thought to be irreversible. We report the first recorded incidents of eels returning to the river of origin after spending up to a year in the marine environment. After migrating to the Baltic Sea, 21% of the silver eels, tagged with acoustic transmitters, returned to the Narva River. Half returned 11-12 months after moving to the sea, with 15 km being the longest upstream movement. The returned eels spent up to 33 days in the river and migrated to the sea again. The fastest specimen migrated to the outlet of the Baltic Sea in 68 days after the second start-roughly 1300 km. The surprising occurrence of returning migrants has implications for sustainable management and protection of this critically endangered species.

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.

Ecological adaptation in European eels is based on phenotypic plasticity

The relative role of genetic adaptation and phenotypic plasticity is of fundamental importance in evolutionary ecology [M. J. West-Eberhard, Proc. Natl. Acad. Sci. U.S.A. 102 (suppl. 1), 6543-6549 (2005)]. European eels have a complex life cycle, including transitions between life stages across ecological conditions in the Sargasso Sea, where spawning occurs, and those in brackish and freshwater bodies from northern Europe to northern Africa. Whether continental eel populations consist of locally adapted and genetically distinct populations or comprise a single panmictic population has received conflicting support. Here we use whole-genome sequencing and show that European eels belong to one panmictic population. A complete lack of geographical genetic differentiation is demonstrated. We postulate that this is possible because the most critical life stages-spawning and embryonic development-take place under near-identical conditions in the Sargasso Sea. We further show that within-generation selection, which has recently been proposed as a mechanism for genetic adaptation in eels, can only marginally change allele frequencies between cohorts of eels from different geographic regions. Our results strongly indicate plasticity as the predominant mechanism for how eels respond to diverse environmental conditions during postlarval stages, ultimately solving a long-standing question for a classically enigmatic species.

Community Parameters and Genome-Wide RAD-Seq Loci of Ceratothoa oestroides Imply Its Transfer between Farmed European Sea Bass and Wild Farm-Aggregating Fish

Wild fish assemblages that aggregate within commercial marine aquaculture sites for feeding and shelter have been considered as a primary source of pathogenic parasites vectored to farmed fish maintained in net pens at an elevated density. In order to evaluate whether Ceratothoa oestroides (Isopoda, Cymothoidae), a generalist and pestilent isopod that is frequently found in Adriatic and Greek stocks of farmed European sea bass (Dicentrarchus labrax), transfers between wild and farmed fish, a RAD-Seq (restriction-site-associated DNA sequencing)-mediated genetic screening approach was employed. The double-digest RAD-Seq of 310 C. oestroides specimens collected from farmed European sea bass (138) and different wild farm-aggregating fish (172) identified 313 robust SNPs that evidenced a close genetic relatedness between the “wild” and “farmed” genotypes. ddRAD-Seq proved to be an effective method for detecting the discrete genetic structuring of C. oestroides and genotype intermixing between two populations. The parasite prevalence in the farmed sea bass was 1.02%, with a mean intensity of 2.0 and mean abundance of 0.02, while in the wild fish, the prevalence was 8.1%; the mean intensity, 1.81; and the mean abundance, 0.15. Such differences are likely a consequence of human interventions during the farmed fish’s rearing cycle that, nevertheless, did not affect the transfer of C. oestroides.

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.

Phylogenetic analysis of Anguilla marmorata population in Thua Thien Hue, Vietnam based on the cytochrome C oxidase I (COI) gene fragments

The giant mottled eel is a species with high commercial value so overfishing, river management, and water pollution have negatively affected its movement and population numbers. Anguilla marmorata (eel) was listed in the Vietnam Red Data Book 2007 with a description of Vulnerability. This study used a barcode technique to analyze molecular characteristics and build genetic plants based on the cytochrome c oxidase I gene segment isolated from the mitochondrial genome of 48 individuals of A. marmorata collected in five different ecological regions of Thua Thien Hue, Vietnam. The isolated the cytochrome c oxidase I sequence has a length of 843 nucleotides, four base nucleotides of 30.03% Thymine, 25.15% Cytosine, 27.49% Adenine, and 17.43% Guanine. The percentage of Guanine + Cytosine content (42.58%) is acceptable, lower than the Adenine + Thymine content. The replacement capacity of Adenine and Guanine is 22.45% highest, the ratio between Thymine and Guanine; Cytosine and Guanine are the lowest at 2.72%. The establishment of genetically modified plants has shown the high genetic similarity of individuals in eel populations in Thua Thien Hue. The population of Anguilla marmorata eels in Thua Thien Hue, Vietnam is divided into two separate groups that are guided by the migration process and specific ecological. This is particularly important in building strategies to conserve and develop the gene for eel in Vietnam and Thua Thien Hue.

Genomic population structure of Striped Bass (Morone saxatilis) from the Gulf of St. Lawrence to Cape Fear River

Striped Bass, Morone saxatilis (Walbaum, 1792), is an anadromous fish species that supports fisheries throughout North America and is native to the North American Atlantic Coast. Due to long coastal migrations that span multiple jurisdictions, a detailed understanding of population genomics is required to untangle demographic patterns, understand local adaptation, and characterize population movements. This study used 1,256 single nucleotide polymorphism (SNP) loci to investigate genetic structure of 477 Striped Bass sampled from 15 locations spanning the North American Atlantic coast from the Gulf of St. Lawrence, Canada, to the Cape Fear River, United States. We found striking differences in neutral divergence among Canadian sites, which were isolated from each other and US populations, compared with US populations that were much less isolated. Our SNP dataset was able to assign 99% of Striped Bass back to six reporting groups, a 39% improvement over previous genetic markers. Using this method, we found (a) evidence of admixture within Saint John River, indicating that migrants from the United States and from Shubenacadie River occasionally spawn in the Saint John River; (b) Striped Bass collected in the Mira River, Cape Breton, Canada, were found to be of both Miramichi River and US origin; (c) juveniles in the newly restored Kennebec River population had small and nonsignificant differences from the Hudson River; and (d) tributaries within the Chesapeake Bay showed a mixture of homogeny and small differences among each other. This study introduces new hypotheses about the dynamic zoogeography of Striped Bass at its northern range and has important implications for the local and international management of this species.

Genetic variability and demographic history of Anguilla mossambica (Peters, 1852) from continental Africa and Madagascar

In this study, population genetic and demographic parameters were inferred using sequence data from 151 individuals of Anguilla mossambica originating from continental south and south-east Africa and Madagascar. The analyses were based on a 532 bp segment of the mitochondrial cytochrome b gene. The absence of genetic structuring was observed thereby supporting the hypothesis of panmixia for the endemic A. mossambica. The overall nucleotide diversity π = 0.002 and the haplotype diversity reached h = 0.691. Significant negative values from several tests of neutrality and mismatch analysis pointed to fluctuating historical population sizes. Bayesian averaging resulted in higher support for population growth models vs. a constant population-size model. Population decline and subsequent growth most likely predated the last glacial and were probably related to extended periods of extreme drought followed by wetter and more stable hydroclimate between 150 and 75,000 years before present (kBP). According to this scenario the female effective population size has increased since 110 kBP by c. two orders of magnitude to a recent level of about 650,000 (219,317-2,292,000).

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

The American Eel (Anguilla rostrata) has an exceptional life cycle characterized by panmictic reproduction at the species scale, random dispersal, and selection in a highly heterogeneous habitat extending from subtropical to subarctic latitudes. The genetic consequences of spatially-varying selection in this species have been investigated for decades, revealing subtle clines in allele frequency at a few loci that contrast with complete panmixia on the vast majority of the genome. Because reproduction homogenizes allele frequencies every generation, sampling size, and genomic coverage are critical to reach sufficient power to detect selected loci in this context. Here, we used a total of 710 individuals from 12 sites and 12,098 high-quality single nucleotide polymorphisms to re-evaluate the extent to which local selection affects the spatial distribution of genetic diversity in this species. We used environmental association methods to identify markers under spatially-varying selection, which indicated that selection affects ∼1.5% of the genome. We then evaluated the extent to which candidate markers collectively vary with environmental factors using additive polygenic scores. We found significant correlations between polygenic scores and latitude, longitude and temperature which are consistent with polygenic selection acting against maladapted genotypes in different habitats occupied by eels throughout their range of distribution. Gene functions associated with outlier markers were significantly enriched for the insulin signaling pathway, indicating that the trade-offs inherent to occupying such a large distribution range involve the regulation of metabolism. Overall, this study highlights the potential of the additive polygenic scores approach in detecting selective effects in a complex environment.

Whole-Genome Sequencing of 84 Japanese Eels Reveals Evidence against Panmixia and Support for Sympatric Speciation

The Japanese eel (Anguilla japonica), European eel (Anguilla anguilla), and American eel (Anguilla rostrata) are migratory, catadromous, temperate zone fish sharing several common life cycle features. The population genetics of panmixia in these eel species has already been investigated. Our extensive population genetics analysis was based on 1400 Gb of whole-genome sequence (WGS) data from 84 eels. It demonstrated that a Japanese eel group from the Kuma River differed from other populations of the same species. Even after removing the potential adapted/selected single nucleotide polymorphism (SNP) data, and with very small differences (fixation index [Fst] = 0.01), we obtained results consistently indicating that panmixia does not occur in Japanese eels. The life cycle of the Japanese eel is well-established and the Kuma River is in the center of its habitat. Nevertheless, simple reproductive isolation is not the probable cause of non-panmixia in this species. We propose that the combination of spawning area subdivision, philopatry, and habitat preference/avoidance accounts for the non-panmixia in the Japanese eel population. We named this hypothesis the “reproductive isolation like subset mapping” (RISM) model. This finding may be indicative of the initial stages of sympatric speciation in these eels.

Genomewide association analyses of fitness traits in captive-reared Chinook salmon: Applications in evaluating conservation strategies

A novel application of genomewide association analyses is to use trait-associated loci to monitor the effects of conservation strategies on potentially adaptive genetic variation. Comparisons of fitness between captive- and wild-origin individuals, for example, do not reveal how captive rearing affects genetic variation underlying fitness traits or which traits are most susceptible to domestication selection. Here, we used data collected across four generations to identify loci associated with six traits in adult Chinook salmon (Oncorhynchus tshawytscha) and then determined how two alternative management approaches for captive rearing affected variation at these loci. Loci associated with date of return to freshwater spawning grounds (return timing), length and weight at return, age at maturity, spawn timing, and daily growth coefficient were identified using 9108 restriction site-associated markers and random forest, an approach suitable for polygenic traits. Mapping of trait-associated loci, gene annotations, and integration of results across multiple studies revealed candidate regions involved in several fitness-related traits. Genotypes at trait-associated loci were then compared between two hatchery populations that were derived from the same source but are now managed as separate lines, one integrated with and one segregated from the wild population. While no broad-scale change was detected across four generations, there were numerous regions where trait-associated loci overlapped with signatures of adaptive divergence previously identified in the two lines. Many regions, primarily with loci linked to return and spawn timing, were either unique to or more divergent in the segregated line, suggesting that these traits may be responding to domestication selection. This study is one of the first to utilize genomic approaches to demonstrate the effectiveness of a conservation strategy, managed gene flow, on trait-associated-and potentially adaptive-loci. The results will promote the development of trait-specific tools to better monitor genetic change in captive and wild populations.

A practical introduction to Random Forest for genetic association studies in ecology and evolution

Large genomic studies are becoming increasingly common with advances in sequencing technology, and our ability to understand how genomic variation influences phenotypic variation between individuals has never been greater. The exploration of such relationships first requires the identification of associations between molecular markers and phenotypes. Here, we explore the use of Random Forest (RF), a powerful machine-learning algorithm, in genomic studies to discern loci underlying both discrete and quantitative traits, particularly when studying wild or nonmodel organisms. RF is becoming increasingly used in ecological and population genetics because, unlike traditional methods, it can efficiently analyse thousands of loci simultaneously and account for nonadditive interactions. However, understanding both the power and limitations of Random Forest is important for its proper implementation and the interpretation of results. We therefore provide a practical introduction to the algorithm and its use for identifying associations between molecular markers and phenotypes, discussing such topics as data limitations, algorithm initiation and optimization, as well as interpretation. We also provide short R tutorials as examples, with the aim of providing a guide to the implementation of the algorithm. Topics discussed here are intended to serve as an entry point for molecular ecologists interested in employing Random Forest to identify trait associations in genomic data sets.

Genomic associations with bill length and disease reveal drift and selection across island bird populations

Island species provide excellent models for investigating how selection and drift operate in wild populations, and for determining how these processes act to influence local adaptation and speciation. Here, we examine the role of selection and drift in shaping genomic and phenotypic variation across recently separated populations of Berthelot's pipit (Anthus berthelotii), a passerine bird endemic to three archipelagos in the Atlantic. We first characterized genetic diversity and population structuring that supported previous inferences of a history of recent colonizations and bottlenecks. We then tested for regions of the genome associated with the ecologically important traits of bill length and malaria infection, both of which vary substantially across populations in this species. We identified a SNP associated with variation in bill length among individuals, islands, and archipelagos; patterns of variation at this SNP suggest that both phenotypic and genotypic variation in bill length is largely shaped by founder effects. Malaria was associated with SNPs near/within genes involved in the immune response, but this relationship was not consistent among archipelagos, supporting the view that disease resistance is complex and rapidly evolving. Although we found little evidence for divergent selection at candidate loci for bill length and malaria resistance, genome scan analyses pointed to several genes related to immunity and metabolism as having important roles in divergence and adaptation. Our findings highlight the utility and challenges involved with combining association mapping and population genetic analysis in nonequilibrium populations, to disentangle the effects of drift and selection on shaping genotypes and phenotypes.

From conservation genetics to conservation genomics: a genome-wide assessment of blue whales (Balaenoptera musculus) in Australian feeding aggregations

Genetic datasets of tens of markers have been superseded through next-generation sequencing technology with genome-wide datasets of thousands of markers. Genomic datasets improve our power to detect low population structure and identify adaptive divergence. The increased population-level knowledge can inform the conservation management of endangered species, such as the blue whale (Balaenoptera musculus). In Australia, there are two known feeding aggregations of the pygmy blue whale (B. m. brevicauda) which have shown no evidence of genetic structure based on a small dataset of 10 microsatellites and mtDNA. Here, we develop and implement a high-resolution dataset of 8294 genome-wide filtered single nucleotide polymorphisms, the first of its kind for blue whales. We use these data to assess whether the Australian feeding aggregations constitute one population and to test for the first time whether there is adaptive divergence between the feeding aggregations. We found no evidence of neutral population structure and negligible evidence of adaptive divergence. We propose that individuals likely travel widely between feeding areas and to breeding areas, which would require them to be adapted to a wide range of environmental conditions. This has important implications for their conservation as this blue whale population is likely vulnerable to a range of anthropogenic threats both off Australia and elsewhere.

Ecological disturbance influences adaptive divergence despite high gene flow in golden perch (Macquaria ambigua): Implications for management and resilience to climate change

Populations that are adaptively divergent but maintain high gene flow may have greater resilience to environmental change as gene flow allows the spread of alleles that have already been tested elsewhere. In addition, populations naturally subjected to ecological disturbance may already hold resilience to future environmental change. Confirming this necessitates ecological genomic studies of high dispersal, generalist species. Here we perform one such study on golden perch (Macquaria ambigua) in the Murray-Darling Basin (MDB), Australia, using a genome-wide SNP data set. The MDB spans across arid to wet and temperate to subtropical environments, with low to high ecological disturbance in the form of low to high hydrological variability. We found high gene flow across the basin and three populations with low neutral differentiation. Genotype-environment association analyses detected adaptive divergence predominantly linked to an arid region with highly variable riverine flow, and candidate loci included functions related to fat storage, stress and molecular or tissue repair. The high connectivity of golden perch in the MDB will likely allow locally adaptive traits in its most arid and hydrologically variable environment to spread and be selected in localities that are predicted to become arid and hydrologically variable in future climates. High connectivity in golden perch is likely due to their generalist life history and efforts of fisheries management. Our study adds to growing evidence of adaptation in the face of gene flow and highlights the importance of considering ecological disturbance and adaptive divergence in biodiversity management.

Applications of random forest feature selection for fine-scale genetic population assignment

Genetic population assignment used to inform wildlife management and conservation efforts requires panels of highly informative genetic markers and sensitive assignment tests. We explored the utility of machine‐learning algorithms (random forest, regularized random forest and guided regularized random forest) compared with F_ST ranking for selection of single nucleotide polymorphisms (SNP) for fine‐scale population assignment. We applied these methods to an unpublished SNP data set for Atlantic salmon (Salmo salar) and a published SNP data set for Alaskan Chinook salmon (Oncorhynchus tshawytscha). In each species, we identified the minimum panel size required to obtain a self‐assignment accuracy of at least 90% using each method to create panels of 50–700 markers Panels of SNPs identified using random forest‐based methods performed up to 7.8 and 11.2 percentage points better than F_ST‐selected panels of similar size for the Atlantic salmon and Chinook salmon data, respectively. Self‐assignment accuracy ≥90% was obtained with panels of 670 and 384 SNPs for each data set, respectively, a level of accuracy never reached for these species using F_ST‐selected panels. Our results demonstrate a role for machine‐learning approaches in marker selection across large genomic data sets to improve assignment for management and conservation of exploited populations.

Differential gene expression in narrow- and broad-headed European glass eels (Anguilla anguilla) points to a transcriptomic link of head shape dimorphism with growth rate and chemotaxis

One of the major challenges in evolutionary biology is to understand the mechanisms underlying morphological dimorphism and plasticity, including the genomic basis of traits and links to ecology. At the yellow eel stage of the European eel (Anguilla anguilla), two morphotypes are found: broad- and narrow-heads. This dimorphism has been linked to dietary differences, with broad-heads feeding on harder, larger prey than narrow-heads. However, recent research showed that both morphotypes could be distinguished at the glass eel stage, the nonfeeding predecessor of the yellow eel stage, implying that nondietary factors play a role in the development of this head shape dimorphism. Here, we used transcriptome profiling (RNAseq) to identify differentially expressed genes between broad- and narrow-headed glass eels. We found 260 significantly differentially expressed genes between the morphotypes, of which most were related to defence and immune responses. Interestingly, two genes involved in growth (soma and igf2) were significantly upregulated in narrow-heads, while nine genes involved in chemotaxis showed significant differential expression. Thus, we found support for the observation that head shape is associated with somatic growth, with fast-growing eels developing a narrower head. Additionally, observations in the wild have shown that slow-growers prefer freshwater, while fast-growers prefer brackish water. The differential expression of genes involved in chemotaxis seems to indicate that glass eel growth rate and habitat choice are linked. We hypothesize that two levels of segregation could take place in the European eel: first according to habitat choice and second according to feeding preference.

Genetic architecture and balancing selection: the life and death of differentiated variants

Balancing selection describes any form of natural selection, which results in the persistence of multiple variants of a trait at intermediate frequencies within populations. By offering up a snapshot of multiple co-occurring functional variants and their interactions, systems under balancing selection can reveal the evolutionary mechanisms favouring the emergence and persistence of adaptive variation in natural populations. We here focus on the mechanisms by which several functional variants for a given trait can arise, a process typically requiring multiple epistatic mutations. We highlight how balancing selection can favour specific features in the genetic architecture and review the evolutionary and molecular mechanisms shaping this architecture. First, balancing selection affects the number of loci underlying differentiated traits and their respective effects. Control by one or few loci favours the persistence of differentiated functional variants by limiting intergenic recombination, or its impact, and may sometimes lead to the evolution of supergenes. Chromosomal rearrangements, particularly inversions, preventing adaptive combinations from being dissociated are increasingly being noted as features of such systems. Similarly, due to the frequency of heterozygotes maintained by balancing selection, dominance may be a key property of adaptive variants. High heterozygosity and limited recombination also influence associated genetic load, as linked recessive deleterious mutations may be sheltered. The capture of deleterious elements in a locus under balancing selection may reinforce polymorphism by further promoting heterozygotes. Finally, according to recent genomewide scans, balanced polymorphism might be more pervasive than generally thought. We stress the need for both functional and ecological studies to characterize the evolutionary mechanisms operating in these systems.

RAD sequencing resolves fine-scale population structure in a benthic invertebrate: implications for understanding phenotypic plasticity

The field of molecular ecology is transitioning from the use of small panels of classical genetic markers such as microsatellites to much larger panels of single nucleotide polymorphisms (SNPs) generated by approaches like RAD sequencing. However, few empirical studies have directly compared the ability of these methods to resolve population structure. This could have implications for understanding phenotypic plasticity, as many previous studies of natural populations may have lacked the power to detect genetic differences, especially over micro-geographic scales. We therefore compared the ability of microsatellites and RAD sequencing to resolve fine-scale population structure in a commercially important benthic invertebrate by genotyping great scallops (Pecten maximus) from nine populations around Northern Ireland at 13 microsatellites and 10 539 SNPs. The shells were then subjected to morphometric and colour analysis in order to compare patterns of phenotypic and genetic variation. We found that RAD sequencing was superior at resolving population structure, yielding higher Fst values and support for two distinct genetic clusters, whereas only one cluster could be detected in a Bayesian analysis of the microsatellite dataset. Furthermore, appreciable phenotypic variation was observed in size-independent shell shape and coloration, including among localities that could not be distinguished from one another genetically, providing support for the notion that these traits are phenotypically plastic. Taken together, our results suggest that RAD sequencing is a powerful approach for studying population structure and phenotypic plasticity in natural populations.

RAD sequencing resolves fine-scale population structure in a benthic invertebrate: implications for understanding phenotypic plasticity

The field of molecular ecology is transitioning from the use of small panels of classical genetic markers such as microsatellites to much larger panels of single nucleotide polymorphisms (SNPs) generated by approaches like RAD sequencing. However, few empirical studies have directly compared the ability of these methods to resolve population structure. This could have implications for understanding phenotypic plasticity, as many previous studies of natural populations may have lacked the power to detect genetic differences, especially over micro-geographic scales. We therefore compared the ability of microsatellites and RAD sequencing to resolve fine-scale population structure in a commercially important benthic invertebrate by genotyping great scallops (Pecten maximus) from nine populations around Northern Ireland at 13 microsatellites and 10 539 SNPs. The shells were then subjected to morphometric and colour analysis in order to compare patterns of phenotypic and genetic variation. We found that RAD sequencing was superior at resolving population structure, yielding higher F_st values and support for two distinct genetic clusters, whereas only one cluster could be detected in a Bayesian analysis of the microsatellite dataset. Furthermore, appreciable phenotypic variation was observed in size-independent shell shape and coloration, including among localities that could not be distinguished from one another genetically, providing support for the notion that these traits are phenotypically plastic. Taken together, our results suggest that RAD sequencing is a powerful approach for studying population structure and phenotypic plasticity in natural populations.

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.

Draft genome of the American Eel (Anguilla rostrata)

Freshwater eels (Anguilla sp.) have large economic, cultural, ecological and aesthetic importance worldwide, but they suffered more than 90% decline in global stocks over the past few decades. Proper genetic resources, such as sequenced, assembled and annotated genomes, are essential to help plan sustainable recoveries by identifying physiological, biochemical and genetic mechanisms that caused the declines or that may lead to recoveries. Here, we present the first sequenced genome of the American eel. This genome contained 305 043 contigs (N50 = 7397) and 79 209 scaffolds (N50 = 86 641) for a total size of 1.41 Gb, which is in the middle of the range of previous estimations for this species. In addition, protein-coding regions, including introns and flanking regions, are very well represented in the genome, as 95.2% of the 458 core eukaryotic genes and 98.8% of the 248 ultra-conserved subset were represented in the assembly and a total of 26 564 genes were annotated for future functional genomics studies. We performed a candidate gene analysis to compare three genes among all three freshwater eel species and, congruent with the phylogenetic relationships, Japanese eel (A. japanica) exhibited the most divergence. Overall, the sequenced genome presented in this study is a crucial addition to the presently available genetic tools to help guide future conservation efforts of freshwater eels.

Sewage treatment plant associated genetic differentiation in the blue mussel from the Baltic Sea and Swedish west coast

Human-derived environmental pollutants and nutrients that reach the aquatic environment through sewage effluents, agricultural and industrial processes are constantly contributing to environmental changes that serve as drivers for adaptive responses and evolutionary changes in many taxa. In this study, we examined how two types of point sources of aquatic environmental pollution, harbors and sewage treatment plants, affect gene diversity and genetic differentiation in the blue mussel in the Baltic Sea area and off the Swedish west coast (Skagerrak). Reference sites (REF) were geographically paired with sites from sewage treatments plant (STP) and harbors (HAR) with a nested sampling scheme, and genetic differentiation was evaluated using a high-resolution marker amplified fragment length polymorphism (AFLP). This study showed that genetic composition in the Baltic Sea blue mussel was associated with exposure to sewage treatment plant effluents. In addition, mussel populations from harbors were genetically divergent, in contrast to the sewage treatment plant populations, suggesting that there is an effect of pollution from harbors but that the direction is divergent and site specific, while the pollution effect from sewage treatment plants on the genetic composition of blue mussel populations acts in the same direction in the investigated sites.

Regional variation of gene regulation associated with storage lipid metabolism in American glass eels (Anguilla rostrata)

Variation in gene regulation may be involved in the differences observed for life history traits within species. American eel (Anguilla rostrata) is well known to harbor distinct ecotypes within a single panmictic population. We examined the expression of genes involved in the regulation of appetite as well as lipid and glycogen among glass eels migrating to different locations on the Canadian east coast and captured at two different periods of upstream migration. Gene expression levels of three reference and five candidate genes were analyzed by real-time PCR with Taqman probes in recently captured wild glass eels. All gene transcripts were detected in glass eels. Of the five candidate genes, bile salt activated and triacylglycerol lipases were respectively 7.65 and 3.25 times more expressed in glass eels from the St. Lawrence estuary than in those from Nova Scotia, and there was no effect related to the two-week difference in capture date. These two genes explained 82.41% of the dissimilarity between the two rivers. In contrast, glycogen phosphorylase, ghrelin, and leptin receptor genes showed no significant differences in gene transcription. These results confirmed at the molecular level an observation that was recently made at the phenotypic level that glass eels from the St. Lawrence estuary have a greater capacity to use lipid reserves to sustain their metabolic needs. These observations add to the body of evidence supporting the hypothesis that regional phenotypic variation observed in American eel is determined early in life and that part of this variation is likely under genetic control.