Genetic basis of adult migration timing in anadromous steelhead discovered through multivariate association testing

Archaeogenomic analysis of Chesapeake Atlantic sturgeon illustrates shaping of its populations in recovery from severe overexploitation

Atlantic sturgeon (Acipenser oxyrinchus ssp. oxyrinchus) has been a food resource in North America for millennia. However, industrial-scale fishing activities following the establishment of European colonies led to multiple collapses of sturgeon stocks, driving populations such as those in the Chesapeake area close to extinction. While recent conservation efforts have been successful in restoring census numbers, little is known regarding genomic consequences of the population bottleneck. Here, we characterize its effect on present-day population structuring and genomic diversity in James River populations. To establish a pre-collapse baseline, we collected genomic data from archaeological remains from Middle Woodland Maycock's Point (c. 200-900 CE), as well as Jamestown and Williamsburg colonial sites. Demographic analysis of recovered mitogenomes reveals a historical collapse in effective population size, also reflected in diminished present-day mitogenomic diversity and structure. We infer that James River fall- and spring-spawning populations likely took shape in recent years of population recovery, where genetic drift enhanced the degree of population structure. The mismatch of mitogenomic lineages to geographical-seasonal groupings implies that despite their homing instinct and differential adaptation manifested as season-specific behaviour, colonization of new rivers has been a key ecological strategy for Atlantic sturgeon over evolutionary timescales.

Historical and contemporary processes driving the origin and structure of an admixed population within a contact zone between subspecies of a north temperate diadromous fish

Hybridization between divergent lineages can result in losses of distinct evolutionary taxa. Alternatively, hybridization can lead to increased genetic variability that may fuel local adaptation and the generation of novel traits and/or taxa. Here, we examined single-nucleotide polymorphisms generated using genotyping-by-sequencing in a population of Dolly Varden char (Pisces: Salmonidae) that is highly admixed within a contact zone between two subspecies (Salvelinus malma malma, Northern Dolly Varden [NDV] and S. m. lordi, Southern Dolly Varden [SDV]) in southwestern Alaska to assess the spatial distribution of hybrids and to test hypotheses on the origin of the admixed population. Ancestry analysis revealed that this admixed population is composed of advanced generation hybrids between NDV and SDV or advanced backcrosses to SDV; no F1 hybrids were detected. Coalescent-based demographic modelling supported the origin of this population about 55,000 years ago by secondary contact between NDV and SDV with low levels of contemporary gene flow. Ancestry in NDV and SDV varies within the watershed and ancestry in NDV was positively associated with distance upstream from the sea, contingent on habitat-type sampled, and negatively associated with the number of migrations that individual fish made to the sea. Our results suggest that divergence between subspecies over hundreds of thousands of years may not be associated with significant reproductive isolation, but that elevated diversity owing to hybridization may have contributed to adaptive divergence in habitat use and life history.

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

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

Genetic parentage reveals the (un)natural history of Central Valley hatchery steelhead

Populations composed of individuals descended from multiple distinct genetic lineages often feature significant differences in phenotypic frequencies. We considered hatchery production of steelhead, the migratory anadromous form of the salmonid species Oncorhynchus mykiss, and investigated how differences among genetic lineages and environmental variation impacted life history traits. We genotyped 23,670 steelhead returning to the four California Central Valley hatcheries over 9 years from 2011 to 2019, confidently assigning parentage to 13,576 individuals to determine age and date of spawning and rates of iteroparity and repeat spawning within each year. We found steelhead from different genetic lineages showed significant differences in adult life history traits despite inhabiting similar environments. Differences between coastal and Central Valley steelhead lineages contributed to significant differences in age at return, timing of spawning, and rates of iteroparity among programs. In addition, adaptive genomic variation associated with life history development in this species varied among hatchery programs and was associated with the age of steelhead spawners only in the coastal lineage population. Environmental variation likely contributed to variations in phenotypic patterns observed over time, as our study period spanned both a marine heatwave and a serious drought in California. Our results highlight evidence of a strong genetic component underlying known phenotypic differences in life history traits between two steelhead lineages.

Contrasting patterns of sequence variation in steelhead populations reflect distinct evolutionary processes

Multiple evolutionary processes influence genome-wide allele frequencies and quantifying effects of genetic drift, and multiple forms of selection remain challenging in natural populations. Here, we investigate variation at major effect loci in contrast to patterns of neutral drift across a wide collection of steelhead (Oncorhynchus mykiss) populations that have declined in abundance due to anthropogenic impacts. Whole-genome resequencing of 74 populations of steelhead revealed genome-wide patterns (~8 million SNPs) consistent with expected neutral population structure. However, allelic variation at major effect loci associated with adult migration timing (chromosome 28: GREB1L/ROCK1) and age at maturity (chromosome 25: SIX6) reflected how selection has acted on phenotypic variation in contrast with neutral structure. Variation at major effect loci was influenced by evolutionary processes with differing signals between the strongly divergent Coastal and Inland lineages, while allele frequencies within and among populations within the Inland lineage have been driven by local natural selection as well as recent anthropogenic influences. Recent anthropogenic effects appeared to have influenced the frequency of major effect alleles including artificial selection for specific traits in hatchery stocks with subsequent gene flow into natural populations. Selection from environmental factors at various scales has also likely influenced variation for major effect alleles. These results reveal evolutionary mechanisms that influence allele frequencies at major effect loci that are critical for conservation of phenotypic traits and life history variation of this protected species.

Distinct patterns of inheritance shape life-history traits in steelhead trout

Life-history variation is the raw material of adaptation, and understanding its genetic and environmental underpinnings is key to designing effective conservation strategies. We used large-scale genetic pedigree reconstruction of anadromous steelhead trout (Oncorhynchus mykiss) from the Russian River, CA, USA, to elucidate sex-specific patterns of life-history traits and their heritability. SNP data from adults returning from sea over a 14-year period were used to identify 13,474 parent-offspring trios. These pedigrees were used to determine age structure, size distributions and family sizes for these fish, as well as to estimate the heritability of two key life-history traits, spawn date and age at maturity (first reproduction). Spawn date was highly heritable (h2  = 0.73) and had a cross-sex genetic correlation near unity. We provide the first estimate of heritability for age at maturity in ocean-going fish from this species and found it to be highly heritable (h2 from 0.29 to 0.62, depending on sex and method), with a much lower genetic correlation across sexes. We also evaluated genotypes at a migration-associated inversion polymorphism and found sex-specific correlations with age at maturity. The significant heritability of these two key reproductive traits in these imperiled fish, and their patterns of inheritance in the two sexes, is consistent with predictions of both natural and sexually antagonistic selection (sexes experience opposing selection pressures). This emphasizes the importance of anthropogenic factors, including hatchery practices and ecosystem modifications, in shaping the fitness of this species, thus providing important guidance for management and conservation efforts.

A homology guide for Pacific salmon genus Oncorhynchus resolves patterns of ohnolog retention, resolution and local adaptation following the salmonid-specific whole-genome duplication event

Salmonid fishes have emerged as a tractable model to study whole-genome duplications (WGDs) as this group has undergone four rounds of WGDs. While most of the salmonid genome has returned to a diploid state, a significant proportion of genes are maintained as duplicates and are referred to as ohnologs. The fact that much of the modern salmonid gene repertoire is comprised of ohnologs, while other genes have returned to their singleton state creates complications for genetic studies by obscuring homology relationships. The difficulty this creates is particularly prominent in Pacific salmonids belonging to genus Oncorhynchus who are the focus of intense genetics-based conservation and management efforts owing to the important ecological and cultural roles these fish play. To address this gap, we generated a homology guide for six species of Oncorhynchus with available genomes and used this guide to describe patterns of ohnolog retention and resolution. Overall, we find that ohnologs comprise approximately half of each species modern gene repertoires, which are functionally enriched for genes involved in DNA binding, while the less numerous singleton genes are heavily enriched in dosage-sensitive processes such as mitochondrial metabolism. Additionally, by reanalyzing published expression data from locally adapted strains of O. mykiss, we show that numerous ohnologs exhibit adaptive expression profiles; however, ohnologs are not more likely to display adaptive signatures than either paralogs or singletons. Finally, we demonstrate the utility of our homology guide by investigating the evolutionary relationship among genes highlighted as playing a role in salmonid life-history traits or gene editing targets.

Long-distance migration is a major factor driving local adaptation at continental scale in Coho salmon

Inferring the genomic basis of local adaptation is a long-standing goal of evolutionary biology. Beyond its fundamental evolutionary implications, such knowledge can guide conservation decisions for populations of conservation and management concern. Here, we investigated the genomic basis of local adaptation in the Coho salmon (Oncorhynchus kisutch) across its entire North American range. We hypothesized that extensive spatial variation in environmental conditions and the species' homing behaviour may promote the establishment of local adaptation. We genotyped 7829 individuals representing 217 sampling locations at more than 100,000 high-quality RADseq loci to investigate how recombination might affect the detection of loci putatively under selection and took advantage of the precise description of the demographic history of the species from our previous work to draw accurate population genomic inferences about local adaptation. The results indicated that genetic differentiation scans and genetic-environment association analyses were both significantly affected by variation in recombination rate as low recombination regions displayed an increased number of outliers. By taking these confounding factors into consideration, we revealed that migration distance was the primary selective factor driving local adaptation and partial parallel divergence among distant populations. Moreover, we identified several candidate single nucleotide polymorphisms associated with long-distance migration and altitude including a gene known to be involved in adaptation to altitude in other species. The evolutionary implications of our findings are discussed along with conservation applications.

Going the distance to test local adaptation in Coho salmon

The mechanisms underlying local adaptation, where populations evolve traits that confer advantages to the local environment, is a central topic for understanding evolution in natural systems. Conservation goals for species at risk often include defining population boundaries by identifying gene diversity, genetic differentiation, and adaptation to local environments. In this issue of Molecular Ecology, Rougemont et al. (2022) combine genome-wide SNP data with an extensive set of landscape variables to study the genomic mechanisms of local adaptation in the entire North American range of Coho salmon (Oncorhynchus kisutch), representing one of the largest studies of its kind. Migration distance, defined as the distance adult Coho salmon migrate from the ocean to their freshwater spawning ground, was found to be the primary factor driving local adaptation in this species. With climatic changes altering flow regimes and therefore the success of Coho salmon to return to spawning grounds, understanding environmental drivers and the genomic basis for migration is essential in the conservation of anadromous salmonids.

Whole genome resequencing identifies local adaptation associated with environmental variation for redband trout

Aquatic ectotherms are predicted to harbour genomic signals of local adaptation resulting from selective pressures driven by the strong influence of climate conditions on body temperature. We investigated local adaptation in redband trout (Oncorhynchus mykiss gairdneri) using genome scans for 547 samples from 11 populations across a wide range of habitats and thermal gradients in the interior Columbia River. We estimated allele frequencies for millions of single nucleotide polymorphism loci (SNPs) across populations using low-coverage whole genome resequencing, and used population structure outlier analyses to identify genomic regions under divergent selection between populations. Twelve genomic regions showed signatures of local adaptation, including two regions associated with genes known to influence migration and developmental timing in salmonids (GREB1L, ROCK1, SIX6). Genotype-environment association analyses indicated that diurnal temperature variation was a strong driver of local adaptation, with signatures of selection driven primarily by divergence of two populations in the northern extreme of the subspecies range. We also found evidence for adaptive differences between high-elevation desert vs. montane habitats at a smaller geographical scale. Finally, we estimated vulnerability of redband trout to future climate change using ecological niche modelling and genetic offset analyses under two climate change scenarios. These analyses predicted substantial habitat loss and strong genetic shifts necessary for adaptation to future habitats, with the greatest vulnerability predicted for high-elevation desert populations. Our results provide new insight into the complexity of local adaptation in salmonids, and important predictions regarding future responses of redband trout to climate change.

Genomic correlates for migratory direction in a free-ranging cervid

Animal migrations are some of the most ubiquitous and one of the most threatened ecological processes globally. A wide range of migratory behaviours occur in nature, and this behaviour is not uniform among and within species, where even individuals in the same population can exhibit differences. While the environment largely drives migratory behaviour, it is necessary to understand the genetic mechanisms influencing migration to elucidate the potential of migratory species to cope with novel conditions and adapt to environmental change. In this study, we identified genes associated with a migratory trait by undertaking pooled genome-wide scans on a natural population of migrating mule deer. We identified genomic regions associated with variation in migratory direction, including FITM1, a gene linked to the formation of lipids, and DPPA3, a gene linked to epigenetic modifications of the maternal line. Such a genetic basis for a migratory trait contributes to the adaptive potential of the species and might affect the flexibility of individuals to change their behaviour in the face of changes in their environment.

The genomic basis of reproductive and migratory behaviour in a polymorphic salmonid

Recent ecotypic differentiation provides unique opportunities to investigate the genomic basis and architecture of local adaptation, while offering insights into how species form and persist. Sockeye salmon (Oncorhynchus nerka) exhibit migratory and resident ("kokanee") ecotypes, which are further distinguished into shore-spawning and stream-spawning reproductive ecotypes. Here, we analysed 36 sockeye (stream-spawning) and kokanee (stream- and shore-spawning) genomes from a system where they co-occur and have recent common ancestry (Okanagan Lake/River in British Columbia, Canada) to investigate the genomic basis of reproductive and migratory behaviour. Examination of the genomic landscape of differentiation, differences in allele frequencies and genotype-phenotype associations revealed three main blocks of sequence differentiation on chromosomes 7, 12 and 20, associated with migratory behaviour, spawning location and spawning timing. Structural variants identified in these same areas suggest they could contribute to ecotypic differentiation directly as causal variants or via maintenance of their genomic architecture through recombination suppression mechanisms. Genes in these regions were related to spatial memory and swimming endurance (SYNGAP, TPM3), as well as eye and brain development (including SIX6), potentially associated with differences in migratory behaviour and visual habitats across spawning locations, respectively. Additional genes (GREB1L, ROCK1) identified here have been associated with timing of migration in other salmonids and could explain variation in timing of O. nerka spawning. Together, these results based on the joint analysis of sequence and structural variation represent a significant advance in our understanding of the genomic landscape of ecotypic differentiation at different stages in the speciation continuum.

Non-Lethal Sampling Supports Integrative Movement Research in Freshwater Fish

Freshwater ecosystems and fishes are enormous resources for human uses and biodiversity worldwide. However, anthropogenic climate change and factors such as dams and environmental contaminants threaten these freshwater systems. One way that researchers can address conservation issues in freshwater fishes is via integrative non-lethal movement research. We review different methods for studying movement, such as with acoustic telemetry. Methods for connecting movement and physiology are then reviewed, by using non-lethal tissue biopsies to assay environmental contaminants, isotope composition, protein metabolism, and gene expression. Methods for connecting movement and genetics are reviewed as well, such as by using population genetics or quantitative genetics and genome-wide association studies. We present further considerations for collecting molecular data, the ethical foundations of non-lethal sampling, integrative approaches to research, and management decisions. Ultimately, we argue that non-lethal sampling is effective for conducting integrative, movement-oriented research in freshwater fishes. This research has the potential for addressing critical issues in freshwater systems in the future.

Influence of environmental conditions at spawning sites and migration routes on adaptive variation and population connectivity in Chinook salmon

Many species that undergo long breeding migrations, such as anadromous fishes, face highly heterogeneous environments along their migration corridors and at their spawning sites. These environmental challenges encountered at different life stages may act as strong selective pressures and drive local adaptation. However, the relative influence of environmental conditions along the migration corridor compared with the conditions at spawning sites on driving selection is still unknown. In this study, we performed genome-environment associations (GEA) to understand the relationship between landscape and environmental conditions driving selection in seven populations of the anadromous Chinook salmon (Oncorhynchus tshawytscha)-a species of important economic, social, cultural, and ecological value-in the Columbia River basin. We extracted environmental variables for the shared migration corridors and at distinct spawning sites for each population, and used a Pool-seq approach to perform whole genome resequencing. Bayesian and univariate GEA tests with migration-specific and spawning site-specific environmental variables indicated many more candidate SNPs associated with environmental conditions at the migration corridor compared with spawning sites. Specifically, temperature, precipitation, terrain roughness, and elevation variables of the migration corridor were the most significant drivers of environmental selection. Additional analyses of neutral loci revealed two distinct clusters representing populations from different geographic regions of the drainage that also exhibit differences in adult migration timing (summer vs. fall). Tests for genomic regions under selection revealed a strong peak on chromosome 28, corresponding to the GREB1L/ROCK1 region that has been identified previously in salmonids as a region associated with adult migration timing. Our results show that environmental variation experienced throughout migration corridors imposed a greater selective pressure on Chinook salmon than environmental conditions at spawning sites.

A candidate chromosome inversion in Arctic charr (Salvelinus alpinus) identified by population genetic analysis techniques

The "genomics era" has allowed questions to be asked about genome organization and genome architecture of non-model species at a rate not previously seen. Analyses of these genome-wide datasets have documented many examples of novel structural variants (SVs) such as chromosomal inversions, copy number variants, and chromosomal translocations, many of which have been linked to adaptation. The salmonids are a taxonomic group with abundant genome-wide datasets due to their importance in aquaculture and fisheries. However, the number of documented SVs in salmonids is surprisingly low and is most likely due to removing loci in high linkage disequilibrium when analyzing structure and gene flow. Here we re-analyze RAD-seq data from several populations of Arctic charr (Salvelinus alpinus) and document a novel ∼1.2 MB SV at the distal end of LG12. This variant contains 15 protein-coding genes connected to a wide-range of functions including cell adhesion and signal transduction. Interestingly, we studied the frequency of this polymorphism in four disjointed populations of charr-one each from Nunavut, Newfoundland, Eastern Russia, and Scotland-and found evidence of the variant only in Nunavut, Canada, suggesting the polymorphism is novel and recently evolved.

An evaluation of the potential factors affecting lifetime reproductive success in salmonids

Lifetime reproductive success (LRS), the number of offspring produced over an organism's lifetime, is a fundamental component of Darwinian fitness. For taxa such as salmonids with multiple species of conservation concern, understanding the factors affecting LRS is critical for the development and implementation of successful conservation management practices. Here, we reviewed the published literature to synthesize factors affecting LRS in salmonids including significant effects of hatchery rearing, life history, and phenotypic variation, and behavioral and spawning interactions. Additionally, we found that LRS is affected by competitive behavior on the spawning grounds, genetic compatibility, local adaptation, and hybridization. Our review of existing literature revealed limitations of LRS studies, and we emphasize the following areas that warrant further attention in future research: (1) expanding the range of studies assessing LRS across different life-history strategies, specifically accounting for distinct reproductive and migratory phenotypes; (2) broadening the variety of species represented in salmonid fitness studies; (3) constructing multigenerational pedigrees to track long-term fitness effects; (4) conducting LRS studies that investigate the effects of aquatic stressors, such as anthropogenic effects, pathogens, environmental factors in both freshwater and marine environments, and assessing overall body condition, and (5) utilizing appropriate statistical approaches to determine the factors that explain the greatest variation in fitness and providing information regarding biological significance, power limitations, and potential sources of error in salmonid parentage studies. Overall, this review emphasizes that studies of LRS have profoundly advanced scientific understanding of salmonid fitness, but substantial challenges need to be overcome to assist with long-term recovery of these keystone species in aquatic ecosystems.

Population Genomics Training for the Next Generation of Conservation Geneticists: ConGen 2018 Workshop

The increasing availability and complexity of next-generation sequencing (NGS) data sets make ongoing training an essential component of conservation and population genetics research. A workshop entitled “ConGen 2018” was recently held to train researchers in conceptual and practical aspects of NGS data production and analysis for conservation and ecological applications. Sixteen instructors provided helpful lectures, discussions, and hands-on exercises regarding how to plan, produce, and analyze data for many important research questions. Lecture topics ranged from understanding probabilistic (e.g., Bayesian) genotype calling to the detection of local adaptation signatures from genomic, transcriptomic, and epigenomic data. We report on progress in addressing central questions of conservation genomics, advances in NGS data analysis, the potential for genomic tools to assess adaptive capacity, and strategies for training the next generation of conservation genomicists.

Monarch Butterfly Migration as an Integrative Model of Complex Trait Evolution

AbstractUnderstanding the genetic architecture of complex trait adaptation in natural populations requires the continued development of tractable models that explicitly confront organismal and environmental complexity. A decade of high-throughput sequencing-based investigations into the genomic basis of migration points to an integrative framework that incorporates quantitative genetics, evolutionary developmental biology, phenotypic plasticity, and epigenetics to explain migration evolution. In this perspective, I argue that the transcontinental migration of the monarch butterfly (Danaus plexippus) can serve as a compelling system to study the mechanism of evolutionary lability of a complex trait. Monarchs show significant phenotypic and genotypic diversity across their global range, with phenotypic switching that allows for explicit study of evolutionary lability. A developmental approach for elucidating how migratory traits are generated and functionally integrated will be important for understanding the evolution of monarch migration traits. I propose a plasticity threshold model to describe migration lability, and I describe novel functional techniques that will help resolve open questions and model assumptions. I conclude by considering the relationships between adaptive genetic architecture, anthropogenic climate change, and conservation management practice and the timeliness of the monarch migration model to illuminate these connections given the rapid decline of the North American migration.

Environmentally triggered shifts in steelhead migration behavior and consequences for survival in the mid-Columbia River

The majority of Columbia River summer-run steelhead encounter high river temperatures (near or > 20°C) during their spawning migration. While some steelhead pass through the mid-Columbia River in a matter of days, others use tributary habitats as temperature refuges for periods that can last months. Using PIT tag detection data from adult return years 2004-2016, we fit 3-component mixture models to differentiate between "fast", "slow", and "overwintering" migration behaviors in five aggregated population groups. Fast fish migrated straight through the reach on average in ~7-9 days while slow fish delayed their migration for weeks to months, and overwintering fish generally took ~150-250 days. We then fit covariate models to examine what factors contributed to the probability of migration delay during summer months (slow or overwintering behaviors), and to explore how migration delay related to mortality. Finally, to account for the impact of extended residence times in the reach for fish that delayed, we compared patterns in estimated average daily rates of mortality between migration behaviors and across population groups. Results suggest that migration delay was primarily triggered by high river temperatures but temperature thresholds for delay were lowest just before the seasonal peak in river temperatures. While all populations groups demonstrated these general patterns, we documented substantial variability in temperature thresholds and length of average delays across population groups. Although migration delay was related to higher reach mortality, it was also related to lower average daily mortality rates due to the proportional increase in reach passage duration being larger than the associated increase in mortality. Lower daily mortality rates suggest that migration delay could help mitigate the impacts of harsh migration conditions, presumably through the use of thermal refuges, despite prolonged exposure to local fisheries. Future studies tracking individual populations from their migration through reproduction could help illuminate the full extent of the tradeoffs between different migration behaviors.

Growth genes are implicated in the evolutionary divergence of sympatric piscivorous and insectivorous rainbow trout (Oncorhynchus mykiss)

Background

Identifying ecologically significant phenotypic traits and the genomic mechanisms that underly them are crucial steps in understanding traits associated with population divergence. We used genome-wide data to identify genomic regions associated with key traits that distinguish two ecomorphs of rainbow trout (Oncorhynchus mykiss)—insectivores and piscivores—that coexist for the non-breeding portion of the year in Kootenay Lake, southeastern British Columbia. “Gerrards” are large-bodied, rapidly growing piscivores with high metabolic rates that spawn north of Kootenay Lake in the Lardeau River, in contrast to the insectivorous populations that are on average smaller in body size, with lower growth and metabolic rates, mainly forage on aquatic insects, and spawn in tributaries immediately surrounding Kootenay Lake. We used pool-seq data representing ~ 60% of the genome and 80 fish per population to assess the level of genomic divergence between ecomorphs and to identify and interrogate loci that may play functional or selective roles in their divergence.

Results

Genomic divergence was high between sympatric insectivores and piscivores (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$F_{\text{ST}}$$\end{document}FST = 0.188), and in fact higher than between insectivorous populations from Kootenay Lake and the Blackwater River (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$F_{\text{ST}}$$\end{document}FST = 0.159) that are > 500 km apart. A window-based \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$F_{\text{ST}}$$\end{document}FST analysis did not reveal “islands” of genomic differentiation; however, the window with highest \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$F_{\text{ST}}$$\end{document}FST estimate did include a gene associated with insulin secretion. Although we explored the use of the “Local score” approach to identify genomic outlier regions, this method was ultimately not used because simulations revealed a high false discovery rate (~ 20%). Gene ontology (GO) analysis identified several growth processes as enriched in genes occurring in the ~ 200 most divergent genomic windows, indicating many loci of small effect involved in growth and growth-related metabolic processes are associated with the divergence of these ecomorphs.

Conclusion

Our results reveal a high degree of genomic differentiation between piscivorous and insectivorous populations and indicate that the large body piscivorous phenotype is likely not due to one or a few loci of large effect. Rather, the piscivore phenotype may be controlled by several loci of small effect, thus highlighting the power of whole-genome resequencing in identifying genomic regions underlying population-level phenotypic divergences.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-021-01795-9.

Partial migration of a maraena whitefish Coregonus maraena population from the River Elbe, Germany

The maraena whitefish Coregonus maraena is a threatened anadromous species in the North Sea, which in the past was decimated to near extinction. Since the late 1980s, several re-establishment programs have been implemented in rivers draining into the North Sea, but the scientific basis for sustainable conservation measures is often lacking, since little is known about the biology of this species. In this study, otolith microchemistry of fish ranging from 24.6 to 58.4 cm in total length (median 31.3 cm, SD 8.4 cm) was used to characterize the migration behavior of a reintroduced population of maraena whitefish from the River Elbe, Germany. Our analyses revealed the presence of 3 different migration patterns: (1) one-time migration into high-salinity habitat (North Sea) within the first year of life (29.6%), (2) multiple migrations between low- and high-salinity habitats starting in the first year of life (14.8%) and (3) permanent residency within low-salinity habitats, a pattern displayed by the majority (55.6%) of sampled individuals. Not only do these results reveal differential migration behavior, but they also indicate that permanent river residency is common in the River Elbe population of C. maraena. The role of the Elbe as both a feeding and a spawning habitat should thus be considered more explicitly in current conservation measures to support recovery of this species.

The Impacts of Dam Construction and Removal on the Genetics of Recovering Steelhead (Oncorhynchus mykiss) Populations across the Elwha River Watershed

Dam construction and longitudinal river habitat fragmentation disrupt important life histories and movement of aquatic species. This is especially true for Oncorhynchus mykiss that exhibits both migratory (steelhead) and non-migratory (resident rainbow) forms. While the negative effects of dams on salmonids have been extensively documented, few studies have had the opportunity to compare population genetic diversity and structure prior to and following dam removal. Here we examine the impacts of the removal of two dams on the Elwha River on the population genetics of O. mykiss. Genetic data were produced from >1200 samples collected prior to dam removal from both life history forms, and post-dam removal from steelhead. We identified three genetic clusters prior to dam removal primarily explained by isolation due to dams and natural barriers. Following dam removal, genetic structure decreased and admixture increased. Despite large O. mykiss population declines after dam construction, we did not detect shifts in population genetic diversity or allele frequencies of loci putatively involved in migratory phenotypic variation. Steelhead descendants from formerly below and above dammed populations recolonized the river rapidly after dam removal, suggesting that dam construction did not significantly reduce genetic diversity underlying O. mykiss life history strategies. These results have significant evolutionary implications for the conservation of migratory adaptive potential in O. mykiss populations above current anthropogenic barriers.

Steelhead (Oncorhynchus mykiss) lineages and sexes show variable patterns of association of adult migration timing and age-at-maturity traits with two genomic regions

As life history diversity plays a critical role in supporting the resilience of exploited populations, understanding the genetic basis of those life history variations is important for conservation management. However, effective application requires a robust understanding of the strength and universality of genetic associations. Here, we examine genetic variation of single nucleotide polymorphisms in genomic regions previously associated with migration phenology and age-at-maturity in steelhead (Oncorhynchus mykiss) from the Columbia River. We found chromosome 28 markers (GREB1L, ROCK1 genes) explained significant variance in migration timing in both coastal and inland steelhead. However, strength of association was much greater in coastal than inland steelhead (R 2 0.51 vs. 0.08), suggesting that genomic background and challenging inland migration pathways may act to moderate effects of this region. Further, we found that chromosome 25 candidate markers (SIX6 gene) were significantly associated with age and size at first return migration for inland steelhead, and this pattern was mediated by sex in a predictable pattern (males R 2 = 0.139-0.170; females R 2 = 0.096-0.111). While this encourages using these candidate regions in predicting life history characteristics, we suggest that stock-specific associations and haplotype frequencies will be useful in guiding implementation of genetic assays to inform management.

Y-chromosome haplotypes are associated with variation in size and age at maturity in male Chinook salmon

Variation in size and age at maturity is an important component of life history that is influenced by both environmental and genetic factors. In salmonids, large size confers a direct reproductive advantage through increased fecundity and egg quality in females, while larger males gain a reproductive advantage by monopolizing access to females. In addition, variation in size and age at maturity in males can be associated with different reproductive strategies; younger smaller males may gain reproductive success by sneaking among mating pairs. In both sexes, there is a trade-off between older age and increased reproductive success and increased risk of mortality by delaying reproduction. We identified four Y-chromosome haplogroups that showed regional- and population-specific variation in frequency using RADseq data for 21 populations of Alaska Chinook salmon. We then characterized the range-wide distribution of these haplogroups using GT-seq assays. These haplogroups exhibited associations with size at maturity in multiple populations, suggesting that lack of recombination between X and Y-chromosomes has allowed Y-chromosome haplogroups to capture different alleles that influence size at maturity. Ultimately, conservation of life history diversity in Chinook salmon may require conservation of Y-chromosome haplotype diversity.

Whole genome resequencing reveals genomic regions associated with thermal adaptation in redband trout

Adaptation to local environments involves evolution of ecologically important traits and underlying physiological processes. Here, we used low coverage whole-genome resequencing (lcWGR) on individuals to identify genome regions involved in thermal adaptation in wild redband trout Oncorhynchus mykiss gairdneri, a subspecies of rainbow trout that inhabits ecosystems ranging from cold montane forests to high elevation deserts. This study includes allele frequency-based analyses for selective sweeps among populations, followed by multiple association tests for specific sets of phenotypes measured under thermal stress (acute and chronic survival/mortality; high or low cardiac performance groups). Depending on the groups in each set of analyses, sequencing reads covered 43%-75% of the genome at ≥15× and each analysis included millions of SNPs across the genome. In tests for selective sweeps among populations, a total of six chromosomal regions were significant. The further association tests for specific phenotypes revealed that the region on chromosome 4 was consistently the most significant and contains the cerk gene (ceramide kinase). This study provides insight into a potential genetic mechanism of local thermal adaptation and suggests cerk may be an important candidate gene. However, further validation of this cerk gene is necessary to determine if the association with cardiac performance results in a functional role to influence thermal performance when exposed to high water temperatures and hypoxic conditions.

Validation and association of candidate markers for adult migration timing and fitness in Chinook Salmon

Recent studies have begun to elucidate the genetic basis for phenotypic traits in salmonid species, but many questions remain before these candidate genes can be directly incorporated into conservation management. In Chinook Salmon (Oncorhynchus tshawytscha), a region of major effect for migration timing has been discovered that harbors two adjacent candidate genes (greb1L, rock1), but there has been limited work to examine the association between these genes and migratory phenotypes at the individual, compared to the population, level. To provide a more thorough test of individual phenotypic association within lineages of Chinook Salmon, 33 candidate markers were developed across a 220 Kb region on chromosome 28 previously associated with migration timing. Candidate and neutral markers were genotyped in individuals from representative collections that exhibit phenotypic variation in timing of arrival to spawning grounds from each of three lineages of Chinook Salmon. Association tests confirmed the majority of markers on chromosome 28 were significantly associated with arrival timing and the strongest association was consistently observed for markers within the rock1 gene and the intergenic region between greb1L and rock1. Candidate markers alone explained a wide range of phenotypic variation for Lower Columbia and Interior ocean-type lineages (29% and 78%, respectively), but less for the Interior stream-type lineage (5%). Individuals that were heterozygous at markers within or upstream of rock1 had phenotypes that suggested a pattern of dominant inheritance for early arrival across populations. Finally, previously published fitness estimates from the Interior stream-type lineage enabled tests of association with arrival timing and two candidate markers, which revealed that fish with homozygous mature genotypes had slightly higher fitness than fish with premature genotypes, while heterozygous fish were intermediate. Overall, these results provide additional information for individual-level genetic variation associated with arrival timing that may assist with conservation management of this species.

Cis-regulatory differences in isoform expression associate with life history strategy variation in Atlantic salmon

A major goal in biology is to understand how evolution shapes variation in individual life histories. Genome-wide association studies have been successful in uncovering genome regions linked with traits underlying life history variation in a range of species. However, lack of functional studies of the discovered genotype-phenotype associations severely restrains our understanding how alternative life history traits evolved and are mediated at the molecular level. Here, we report a cis-regulatory mechanism whereby expression of alternative isoforms of the transcription co-factor vestigial-like 3 (vgll3) associate with variation in a key life history trait, age at maturity, in Atlantic salmon (Salmo salar). Using a common-garden experiment, we first show that vgll3 genotype associates with puberty timing in one-year-old salmon males. By way of temporal sampling of vgll3 expression in ten tissues across the first year of salmon development, we identify a pubertal transition in vgll3 expression where maturation coincided with a 66% reduction in testicular vgll3 expression. The late maturation allele was not only associated with a tendency to delay puberty, but also with expression of a rare transcript isoform of vgll3 pre-puberty. By comparing absolute vgll3 mRNA copies in heterozygotes we show that the expression difference between the early and late maturity alleles is largely cis-regulatory. We propose a model whereby expression of a rare isoform from the late allele shifts the liability of its carriers towards delaying puberty. These results exemplify the potential importance of regulatory differences as a mechanism for the evolution of life history traits.

Alternative life history strategies are an important source of diversity within populations and promote the maintenance of adaptive capacity and population resilience. However, in many cases the molecular basis of different life history strategies remains elusive. Age at maturity is a key adaptive life history trait in Atlantic salmon and has a relatively simple genetic basis. Using salmon age at maturity as a model, we report a mechanism whereby different transcript isoforms of the key age at maturity gene, vestigial-like 3 (vgll3), associate with variation in the timing of male puberty. Our results show how gene regulatory differences in conjunction with variation in gene transcript structure can encode for complex alternative life histories.

Genomic islands of divergence infer a phenotypic landscape in Pacific lamprey

High rates of dispersal can breakdown coadapted gene complexes. However, concentrated genomic architecture (i.e., genomic islands of divergence) can suppress recombination to allow evolution of local adaptations despite high gene flow. Pacific lamprey (Entosphenus tridentatus) is a highly dispersive anadromous fish. Observed trait diversity and evidence for genetic basis of traits suggests it may be locally adapted. We addressed whether concentrated genomic architecture could influence local adaptation for Pacific lamprey. Using two new whole genome assemblies and genotypes from 7,716 single nucleotide polymorphism (SNP) loci in 518 individuals from across the species range, we identified four genomic islands of divergence (on chromosomes 01, 02, 04, and 22). We determined robust phenotype-by-genotype relationships by testing multiple traits across geographic sites. These trait associations probably explain genomic divergence across the species' range. We genotyped a subset of 302 broadly distributed SNPs in 2,145 individuals for association testing for adult body size, sexual maturity, migration distance and timing, adult swimming ability, and larval growth. Body size traits were strongly associated with SNPs on chromosomes 02 and 04. Moderate associations also implicated SNPs on chromosome 01 as being associated with variation in female maturity. Finally, we used candidate SNPs to extrapolate a heterogeneous spatiotemporal distribution of these predicted phenotypes based on independent data sets of larval and adult collections. These maturity and body size results guide future elucidation of factors driving regional optimization of these traits for fitness. Pacific lamprey is culturally important and imperiled. This research addresses biological uncertainties that challenge restoration efforts.

Distribution of genetic variation underlying adult migration timing in steelhead of the Columbia River basin

Fish migrations are energetically costly, especially when moving between freshwater and saltwater, but are a viable strategy for Pacific salmon and trout (Oncorhynchus spp.) due to the advantageous resources available at various life stages. Anadromous steelhead (O. mykiss) migrate vast distances and exhibit variation for adult migration phenotypes that have a genetic basis at candidate genes known as greb1L and rock1. We examined the distribution of genetic variation at 13 candidate markers spanning greb1L, intergenic, and rock1 regions versus 226 neutral markers for 113 populations (n = 9,471) of steelhead from inland and coastal lineages in the Columbia River. Patterns of population structure with neutral markers reflected genetic similarity by geographic region as demonstrated in previous studies, but candidate markers clustered populations by genetic variation associated with adult migration timing. Mature alleles for late migration had the highest frequency overall in steelhead populations throughout the Columbia River, with only 9 of 113 populations that had a higher frequency of premature alleles for early migration. While a single haplotype block was evident for the coastal lineage, we identified multiple haplotype blocks for the inland lineage. The inland lineage had one haplotype block that corresponded to candidate markers within the greb1L gene and immediately upstream in the intergenic region, and the second block only contained candidate markers from the intergenic region. Haplotype frequencies had similar patterns of geographic distribution as single markers, but there were distinct differences in frequency between the two haplotype blocks for the inland lineage. This may represent multiple recombination events that differed between lineages where phenotypic differences exist between freshwater entry versus arrival timing as indicated by Micheletti et al. (2018a). Redundancy analyses were used to model environmental effects on allelic frequencies of candidate markers, and significant variables were migration distance, temperature, isothermality, and annual precipitation. This study improves our understanding of the spatial distribution of genetic variation underlying adult migration timing in steelhead as well as associated environmental factors and has direct conservation and management implications.

Association of genetic and climatic variability in giant sequoia, Sequoiadendron giganteum, reveals signatures of local adaptation along moisture-related gradients

Uncovering the genetic basis of local adaptation is a major goal of evolutionary biology and conservation science alike. In an era of climate change, an understanding of how environmental factors shape adaptive diversity is crucial to predicting species response and directing management. Here, we investigate patterns of genomic variation in giant sequoia, an iconic and ecologically important tree species, using 1,364 bi-allelic single nucleotide polymorphisms (SNPs). We use an F _ST outlier test and two genotype-environment association methods, latent factor mixed models (LFMMs) and redundancy analysis (RDA), to detect complex signatures of local adaptation. Results indicate 79 genomic regions of potential adaptive importance, with limited overlap between the detection methods. Of the 58 loci detected by LFMM, 51 showed strong correlations to a precipitation-driven composite variable and seven to a temperature-related variable. RDA revealed 24 outlier loci with association to climate variables, all of which showed strongest relationship to summer precipitation. Nine candidate loci were indicated by two methods. After correcting for geographic distance, RDA models using climate predictors accounted for 49% of the explained variance and showed significant correlations between SNPs and climatic factors. Here, we present evidence of local adaptation in giant sequoia along gradients of precipitation and provide a first step toward identifying genomic regions of adaptive significance. The results of this study will provide information to guide management strategies that seek to maximize adaptive potential in the face of climate change.

Network Analysis of Linkage Disequilibrium Reveals Genome Architecture in Chum Salmon

Many studies exclude loci that exhibit linkage disequilibrium (LD); however, high LD can signal reduced recombination around genomic features such as chromosome inversions or sex-determining regions. Chromosome inversions and sex-determining regions are often involved in adaptation, allowing for the inheritance of co-adapted gene complexes and for the resolution of sexually antagonistic selection through sex-specific partitioning of genetic variants. Genomic features such as these can escape detection when loci with LD are removed; in addition, failing to account for these features can introduce bias to analyses. We examined patterns of LD using network analysis to identify an overlapping chromosome inversion and sex-determining region in chum salmon. The signal of the inversion was strong enough to show up as false population substructure when the entire dataset was analyzed, while the effect of the sex-determining region on population structure was only obvious after restricting analysis to the sex chromosome. Understanding the extent and geographic distribution of inversions is now a critically important part of genetic analyses of natural populations. Our results highlight the importance of analyzing and understanding patterns of LD in genomic dataset and the perils of excluding or ignoring loci exhibiting LD. Blindly excluding loci in LD would have prevented detection of the sex-determining region and chromosome inversion while failing to understand the genomic features leading to high-LD could have resulted in false interpretations of population structure.

Opinion: Is gene mapping in wild populations useful for understanding and predicting adaptation to global change?

Changing environmental conditions will inevitably alter selection pressures. Over the long term, populations have to adapt to these altered conditions by evolutionary change to avoid extinction. Quantifying the 'evolutionary potential' of populations to predict whether they will be able to adapt fast enough to forecasted changes is crucial to fully assess the threat for biodiversity posed by climate change. Technological advances in sequencing and high-throughput genotyping have now made genomic studies possible in a wide range of species. Such studies, in theory, allow an unprecedented understanding of the genomics of ecologically relevant traits and thereby a detailed assessment of the population's evolutionary potential. Aimed at a wider audience than only evolutionary geneticists, this paper gives an overview of how gene-mapping studies have contributed to our understanding and prediction of evolutionary adaptations to climate change, identifies potential reasons why their contribution to understanding adaptation to climate change may remain limited, and highlights approaches to study and predict climate change adaptation that may be more promising, at least in the medium term.

Transforming ecology and conservation biology through genome editing

As the conservation challenges increase, new approaches are needed to help combat losses in biodiversity and slow or reverse the decline of threatened species. Genome-editing technology is changing the face of modern biology, facilitating applications that were unimaginable only a decade ago. The technology has the potential to make significant contributions to the fields of evolutionary biology, ecology, and conservation, yet the fear of unintended consequences from designer ecosystems containing engineered organisms has stifled innovation. To overcome this gap in the understanding of what genome editing is and what its capabilities are, more research is needed to translate genome-editing discoveries into tools for ecological research. Emerging and future genome-editing technologies include new clustered regularly interspaced short palindromic repeats (CRISPR) targeted sequencing and nucleic acid detection approaches as well as species genetic barcoding and somatic genome-editing technologies. These genome-editing tools have the potential to transform the environmental sciences by providing new noninvasive methods for monitoring threatened species or for enhancing critical adaptive traits. A pioneering effort by the conservation community is required to apply these technologies to real-world conservation problems.

Conservation and Management of Salmon in the Age of Genomics

Salmon were among the first nonmodel species for which systematic population genetic studies of natural populations were conducted, often to support management and conservation. The genomics revolution has improved our understanding of the evolutionary ecology of salmon in two major ways: (a) Large increases in the numbers of genetic markers (from dozens to 10⁴-10⁶) provide greater power for traditional analyses, such as the delineation of population structure, hybridization, and population assignment, and (b) qualitatively new insights that were not possible with traditional genetic methods can be achieved by leveraging detailed information about the structure and function of the genome. Studies of the first type have been more common to date, largely because it has taken time for the necessary tools to be developed to fully understand the complex salmon genome. We expect that the next decade will witness many new studies that take full advantage of salmonid genomic resources.

No evidence for an association between Clock gene allelic variation and migration timing in a long-distance migratory shorebird (Limosa lapponica baueri)

The gene Clock is a key part of the Core Circadian Oscillator, and the length of the polyglutamine (poly-Q) repeat sequence in Clock (ClkpolyQcds) has been proposed to be associated with the timing of annual cycle events in birds. We tested whether variation in ClkpolyQcds corresponds to variation in migration timing in the bar-tailed godwit (Limosa lapponica baueri), a species in which individuals show strong annual consistency in their migration timing despite the New Zealand population migrating across a 5-week period. We describe allelic variation of the ClkpolyQcds in 135 godwits over-wintering in New Zealand (N.Z.) and investigate whether polymorphism in this region is associated with northward migration timing (chronophenotype) from N.Z. or (for 32 birds tracked by geolocator) after the primary stopover in Asia. Six Clock alleles were detected (Q₇‒Q₁₂) and there was substantial variation between individuals (heterozygosity of 0.79). There was no association between ClkpolyQcds polymorphism and migration timing from N.Z. The length of the shorter Clock allele was related to migration timing from Asia, though this relationship arose largely from just a few northern-breeding birds with longer alleles. Other studies show no consistent associations between ClkpolyQcds and migration timing in birds, although Clock may be associated with breeding latitude in some species (as an adaptation to photoperiodic regime). Apparent relationships with migration timing could reflect latitude-related variation in migration timing, rather than Clock directly affecting migration timing. On current evidence, ClkpolyQcds is not a strong candidate for driving migration timing in migratory birds generally.

Association Mapping Based on a Common-Garden Migration Experiment Reveals Candidate Genes for Migration Tendency in Brown Trout

A better understanding of the environmental and genetic contribution to migratory behavior and the evolution of traits linked to migration is crucial for fish conservation and fisheries management. Up to date, a few genes with unequivocal influence on the adoption of alternative migration strategies have been identified in salmonids. Here, we used a common garden set-up to measure individual migration distances of generally highly polymorphic brown trout Salmo trutta from two populations. Fish from the assumedly resident population showed clearly shorter migration distances than the fish from the assumed migratory population at the ages of 2 and 3 years. By using two alternative analytical pipelines with 22186 and 18264 SNPs obtained through RAD-sequencing, we searched for associations between individual migration distance, and both called genotypes and genotype probabilities. None of the SNPs showed statistically significant individual effects on migration after correction for multiple testing. By choosing a less stringent threshold, defined as an overlap of the top 0.1% SNPs identified by the analytical pipelines, GAPIT and Angsd, we identified eight candidate genes that are potentially linked to individual migration distance. While our results demonstrate large individual and population level differences in migration distances, the detected genetic associations were weak suggesting that migration traits likely have multigenic control.

Fish conservation in the land of steppe and sky: Evolutionarily significant units of threatened salmonid species in Mongolia mirror major river basins

Mongolia's salmonids are suffering extensive population declines; thus, more comprehensive fisheries management and conservation strategies are required. To assist with their development, a better understanding of the genetic structure and diversity of these threatened species would allow a more targeted approach for preserving genetic variation and ultimately improve long-term species recoveries. It is hypothesized that the unfragmented river basins that have persisted across Mongolia provide unobstructed connectivity for resident salmonid species. Thus, genetic structure is expected to be primarily segregated between major river basins. We tested this hypothesis by investigating the population structure for three salmonid genera (Hucho, Brachymystax and Thymallus) using different genetic markers to identify evolutionarily significant units (ESUs) and priority rivers to focus conservation efforts. Fish were assigned to separate ESUs when the combined evidence of mitochondrial and nuclear data indicated genetic isolation. Hucho taimen exhibited a dichotomous population structure forming two ESUs, with five priority rivers. Within the Brachymystax genus, there were three B. lenokESUs and one B. tumensisESU, along with six priority rivers. While B. tumensiswas confirmed to display divergent mtDNA haplotypes, haplotype sharing between these two congeneric species was also identified. For T. baicalensis,only a single ESU was assigned, with five priority rivers identified plus Lake Hovsgol. Additionally, we confirmed that T. nigrescens from Lake Hovsgol is a synonym of T. baicalensis. Across all species, the most prominent pattern was strong differentiation among major river basins with low differentiation and weak patterns of isolation by distance within river basins, which corroborated our hypothesis of high within-basin connectivity across Mongolia. This new genetic information provides authorities the opportunity to distribute resources for management between ESUs while assigning additional protection for the more genetically valuable salmonid rivers so that the greatest adaptive potential within each species can be preserved.

The genetics and epigenetics of animal migration and orientation: birds, butterflies and beyond

Migration is a complex behavioural adaptation for survival that has evolved across the animal kingdom from invertebrates to mammals. In some taxa, closely related migratory species, or even populations of the same species, exhibit different migratory phenotypes, including timing and orientation of migration. In these species, a significant proportion of the phenotypic variance in migratory traits is genetic. In others, the migratory phenotype and direction is triggered by seasonal changes in the environment, suggesting an epigenetic control of their migration. The genes and epigenetic changes underpinning migratory behaviour remain largely unknown. The revolution in (epi)genomics and functional genomic tools holds great promise to rapidly move the field of migration genetics forward. Here, we review our current understanding of the genetic and epigenetic architecture of migratory traits, focusing on two emerging models: the European blackcap and the North American monarch butterfly. We also outline a vision of how technical advances and integrative approaches could be employed to identify and functionally validate candidate genes and cis-regulatory elements on these and other migratory species across both small and broad phylogenetic scales to significantly advance the field of genetics of animal migration.