A mobile sex-determining region, male-specific haplotypes and rearing environment influence age at maturity in Chinook salmon

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

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

A single generation in the wild increases fitness for descendants of hatchery-origin Chinook salmon (Oncorhynchus tshawytscha)

Reintroduction is an important tool for the recovery of imperiled species. For threatened Pacific salmonids (Oncorhynchus spp.) species, hatchery-origin (HOR) individuals from a nearby source are often used to reestablish populations in vacant, historically occupied habitat. However, this approach is challenged by the relatively low reproductive success that HOR Pacific salmonids experience when they spawn in the wild, relative to their natural-origin (NOR) counterparts. In this study, we used genetic parentage analysis to compare the reproductive success of three groups of adult Chinook salmon (Oncorhynchus tshawytscha) reintroduced above Cougar Dam on the South Fork McKenzie River, Oregon: HOR Chinook salmon from an integrated stock; first-generation, wild-born descendants (hereafter F 1s) of Chinook salmon produced at the same hatchery; and NOR Chinook salmon that are presumed to have been produced below the dam, on the mainstem McKenzie River, or elsewhere and volitionally entered a trap below Cougar Dam. We found that F 1s produced nearly as many adult offspring as NORs, and 1.8-fold more adult offspring than HORs. This result suggests that, for the South Fork McKenzie reintroduction program, a single generation in the wild increases fitness for the descendants of HOR Chinook salmon. Although these results are encouraging, care must be taken before extrapolating our results to other systems.

Rapid turnover and evolution of sex-determining regions in Sebastes rockfishes

Nature has evolved a wealth of sex determination (SD) mechanisms, driven by both genetic and environmental factors. Recent studies of SD in fishes have shown that not all taxa fit the classic paradigm of sex chromosome evolution and diverse SD methods can be found even among closely related species. Here, we apply a suite of genomic approaches to investigate sex-biased genomic variation in eight species of Sebastes rockfish found in the northeast Pacific Ocean. Using recently assembled chromosome-level rockfish genomes, we leverage published sequence data to identify disparate sex chromosomes and sex-biased loci in five species. We identify two putative male sex chromosomes in S. diaconus, a single putative sex chromosome in the sibling species S. carnatus and S. chrysomelas, and an unplaced sex determining contig in the sibling species S. miniatus and S. crocotulus. Our study provides evidence for disparate means of sex determination within a recently diverged set of species and sheds light on the diverse origins of sex determination mechanisms present in the animal kingdom.

Reproductive success of jack and full-size males in a wild coho salmon population

Despite the wealth of research on Pacific salmon Oncorhynchus spp. life histories there is limited understanding of the lifetime reproductive success of males that spend less time at sea and mature at a smaller size (jacks) than full-size males. Over half of returning male spawners can be jacks in some populations, so it is crucial to understand their contribution to population productivity. We quantified adult-to-adult reproductive success (RS) of jacks and their relative reproductive success (RRS) compared to full-size males in a wild population of coho salmon in the Auke Creek watershed, Juneau, Alaska. We used genetic data from nearly all individuals (approx. 8000) returning to spawn over a decade (2009-2019) to conduct parentage analysis and calculate individual RS. The average adult-to-adult RS of jacks (mean = 0.7 and s.e. = 0.1) was less than that of full-size males (mean = 1.1 and s.e. = 0.1). Jack RRS was consistently below 1.0 but ranged widely (0.23 to 0.96). Despite their lower average success, jacks contributed substantially to the population by siring 23% of the total returning adult offspring (1033 of 4456) produced between 2009 and 2015. Our results imply that jacks can affect evolutionary and population dynamics, and are relevant to the conservation and management of Pacific salmon.

Implications of Large-Effect Loci for Conservation: A Review and Case Study with Pacific Salmon

The increasing feasibility of assembling large genomic datasets for non-model species presents both opportunities and challenges for applied conservation and management. A popular theme in recent studies is the search for large-effect loci that explain substantial portions of phenotypic variance for a key trait(s). If such loci can be linked to adaptations, 2 important questions arise: 1) Should information from these loci be used to reconfigure conservation units (CUs), even if this conflicts with overall patterns of genetic differentiation? 2) How should this information be used in viability assessments of populations and larger CUs? In this review, we address these questions in the context of recent studies of Chinook salmon and steelhead (anadromous form of rainbow trout) that show strong associations between adult migration timing and specific alleles in one small genomic region. Based on the polygenic paradigm (most traits are controlled by many genes of small effect) and genetic data available at the time showing that early-migrating populations are most closely related to nearby late-migrating populations, adult migration differences in Pacific salmon and steelhead were considered to reflect diversity within CUs rather than separate CUs. Recent data, however, suggest that specific alleles are required for early migration, and that these alleles are lost in populations where conditions do not support early-migrating phenotypes. Contrasting determinations under the US Endangered Species Act and the State of California's equivalent legislation illustrate the complexities of incorporating genomics data into CU configuration decisions. Regardless how CUs are defined, viability assessments should consider that 1) early-migrating phenotypes experience disproportionate risks across large geographic areas, so it becomes important to identify early-migrating populations that can serve as reliable sources for these valuable genetic resources; and 2) genetic architecture, especially the existence of large-effect loci, can affect evolutionary potential and adaptability.

Some thoughts about the words we use for thinking about sex chromosome evolution

Sex chromosomes are familiar to most biologists since they first learned about genetics. However, research over the past 100 years has revealed that different organisms have evolved sex-determining systems independently. The differences in the ages of systems, and in how they evolved, both affect whether sex chromosomes have evolved. However, the diversity means that the terminology used tends to emphasize either the similarities or the differences, sometimes causing misunderstandings. In this article, I discuss some concepts where special care is needed with terminology. The following four terms regularly create problems: ‘sex chromosome’, ‘master sex-determining gene’, ‘evolutionary strata’ and ‘genetic degeneration’. There is no generally correct or wrong use of these words, but efforts are necessary to make clear how they are to be understood in specific situations. I briefly outline some widely accepted ideas about sex chromosomes, and then discuss these ‘problem terms’, highlighting some examples where careful use of the words helps bring to light current uncertainties and interesting questions for future work.

This article is part of the theme issue ‘Sex determination and sex chromosome evolution in land plants’.

The pink salmon genome: Uncovering the genomic consequences of a two-year life cycle

Pink salmon (Oncorhynchus gorbuscha) adults are the smallest of the five Pacific salmon native to the western Pacific Ocean. Pink salmon are also the most abundant of these species and account for a large proportion of the commercial value of the salmon fishery worldwide. A two-year life history of pink salmon generates temporally isolated populations that spawn either in even-years or odd-years. To uncover the influence of this genetic isolation, reference genome assemblies were generated for each year-class and whole genome re-sequencing data was collected from salmon of both year-classes. The salmon were sampled from six Canadian rivers and one Japanese river. At multiple centromeres we identified peaks of Fst between year-classes that were millions of base-pairs long. The largest Fst peak was also associated with a million base-pair chromosomal polymorphism found in the odd-year genome near a centromere. These Fst peaks may be the result of a centromere drive or a combination of reduced recombination and genetic drift, and they could influence speciation. Other regions of the genome influenced by odd-year and even-year temporal isolation and tentatively under selection were mostly associated with genes related to immune function, organ development/maintenance, and behaviour.

A potential role for restricted intertactical heritability in preventing intralocus conflict

Intralocus sexual conflict, which arises when the same trait has different fitness optima in males and females, reduces population growth rates. Recently, evolutionary biologists have recognized that intralocus conflict can occur between morphs or reproductive tactics within a sex and that intralocus tactical conflict might constrain tactical dimorphism and population growth rates just as intralocus sexual conflict constrains sexual dimorphism and population growth rates. However, research has only recently focused on sexual and tactical intralocus conflict simultaneously, and there is no formal theory connecting the two. We present a graphical model of how tactical and sexual conflict over the same trait could constrain both sexual and tactical dimorphisms. We then use Coho salmon (Oncorhynchus kisutch), an important species currently protected under the Endangered Species Act, to investigate the possibility of simultaneous sexual and tactical conflict. Larger Coho males gain access to females through fighting while smaller males are favored through sneaking tactics, and female reproductive success is positively correlated with length. We tested for antagonistic selection on length at maturity among sexes and tactics and then used parent-offspring regression to calculate sex- and tactic-specific heritabilities to determine whether and where intralocus conflict exists. Selection on length varied in intensity and form among tactics and years. Length was heritable between dams and daughters (h 2 ± 95% CI = 0.361 ± 0.252) and between fighter males and their fighter sons (0.867 ± 0.312), but no other heritabilities differed significantly from zero. The lack of intertactical heritabilities in this system, combined with similar selection on length among tactics, suggests the absence of intralocus conflict between sexes and among tactics, allowing for the evolution of sexual and tactical dimorphisms. Our results suggest that Coho salmon populations are unlikely to be constrained by intralocus conflict or artificial selection on male tactic.

How did the guppy Y chromosome evolve?

The sex chromosome pairs of many species do not undergo genetic recombination, unlike the autosomes. It has been proposed that the suppressed recombination results from natural selection favouring close linkage between sex-determining genes and mutations on this chromosome with advantages in one sex, but disadvantages in the other (these are called sexually antagonistic mutations). No example of such selection leading to suppressed recombination has been described, but populations of the guppy display sexually antagonistic mutations (affecting male coloration), and would be expected to evolve suppressed recombination. In extant close relatives of the guppy, the Y chromosomes have suppressed recombination, and have lost all the genes present on the X (this is called genetic degeneration). However, the guppy Y occasionally recombines with its X, despite carrying sexually antagonistic mutations. We describe evidence that a new Y evolved recently in the guppy, from an X chromosome like that in these relatives, replacing the old, degenerated Y, and explaining why the guppy pair still recombine. The male coloration factors probably arose after the new Y evolved, and have already evolved expression that is confined to males, a different way to avoid the conflict between the sexes.

We report new findings concerning the long-studied the guppy XY pair, which has remained somewhat mystifying. We show that it can be understood as a case of a recent sex chromosome turnover event in which an older, highly degenerated Y chromosome was lost, and creation of a new sex chromosome from the ancestral X. This chromosome acquired a male-determining factor, possibly by a mutation in (or a duplication of) a previously X-linked gene, or (less likely) by movement of an ancestral Y-linked maleness factor onto the X. We relate the findings to theoretical models of such events, and argue that the proposed change was free from factors thought to impede such turnovers. The change resulted in the intriguing situation where the X chromosome is old and the Y is much younger, and we discuss some other species where a similar change seems likely to have occurred.

Heterogeneous genetic basis of age at maturity in salmonid fishes

Understanding the genetic basis of repeated evolution of the same phenotype across taxa is a fundamental aim in evolutionary biology and has applications in conservation and management. However, the extent to which interspecific life-history trait polymorphisms share evolutionary pathways remains underexplored. Here, we address this gap by studying the genetic basis of a key life-history trait, age at maturity, in four species of Pacific salmonids (genus Oncorhynchus) that exhibit intra- and interspecific variation in this trait-Chinook Salmon, Coho Salmon, Sockeye Salmon, and Steelhead Trout. We tested for associations in all four species between age at maturity and two genome regions, six6 and vgll3, that are strongly associated with the same trait in Atlantic Salmon (Salmo salar). We also conducted a genome-wide association analysis in Steelhead to assess whether additional regions were associated with this trait. We found the genetic basis of age at maturity to be heterogeneous across salmonid species. Significant associations between six6 and age at maturity were observed in two of the four species, Sockeye and Steelhead, with the association in Steelhead being particularly strong in both sexes (p = 4.46 × 10^-9 after adjusting for genomic inflation). However, no significant associations were detected between age at maturity and the vgll3 genome region in any of the species, despite its strong association with the same trait in Atlantic Salmon. We discuss possible explanations for the heterogeneous nature of the genetic architecture of this key life-history trait, as well as the implications of our findings for conservation and management.