Migration traits are presumed to be complex and to involve interaction among multiple genes. We used both univariate analyses and a multivariate random forest (RF) machine learning algorithm to conduct association mapping of 15 239 single nucleotide polymorphisms (SNPs) for adult migration-timing phenotype in steelhead (Oncorhynchus mykiss). Our study focused on a model natural population of steelhead that exhibits two distinct migration-timing life histories with high levels of admixture in nature. Neutral divergence was limited between fish exhibiting summer-and winter-run migration owing to high levels of interbreeding, but a univariate mixed linear model found three SNPs from a major effect gene to be significantly associated with migration timing ( p , 0.000005) that explained 46% of trait variation. Alignment to the annotated Salmo salar genome provided evidence that all three SNPs localize within a 46 kb region overlapping GREB1-like (an oestrogen target gene) on chromosome Ssa03. Additionally, multivariate analyses with RF identified that these three SNPs plus 15 additional SNPs explained up to 60% of trait variation. These candidate SNPs may provide the ability to predict adult migration timing of steelhead to facilitate conservation management of this species, and this study demonstrates the benefit of multivariate analyses for association studies.

Landscape features can significantly influence genetic and life history diversity of rainbow/steelhead trout, Oncorhynchus mykiss . In this study, heterozygosity of 21 populations of O. mykiss from the Pacific Northwest, USA, was significantly negatively correlated with features such as elevation (P = 0.0023), upstream distance (P = 0.0129), and precipitation (P = 0.0331), and positively correlated with temperature (P = 0.0123). Mantel tests of isolation by distance were significant for anadromous populations (P = 0.007) but not for resident collections (P = 0.061), and suggested that fluvial distance was not the only significant physical variable that influenced genetic structure of life history types. Principal components interpolated to the drainage indicated that high-elevation sites were primarily occupied by the resident form, and high gradients and barriers act to limit anadromous distribution to lower elevation sites. These patterns of O. mykiss life history diversity provide insight regarding the interaction, distribution, and limitations of resident and anadromous forms of the species within this region.

BackgroundDisparity in the timing of biological events occurs across a variety of systems, yet the understanding of genetic basis underlying diverse phenologies remains limited. Variation in maturation timing occurs in steelhead trout, which has been associated with greb1L, an oestrogen target gene. Previous techniques that identified this gene only accounted for about 0.5–2.0% of the genome and solely investigated coastal populations, leaving uncertainty on the genetic basis of this trait and its prevalence across a larger geographic scale.ResultsWe used a three-tiered approach to interrogate the genomic basis of complex phenology in anadromous steelhead. First, fine scale mapping with 5.3 million SNPs from resequencing data covering 68% of the genome confirmed a 309-kb region consisting of four genes on chromosome 28, including greb1L, to be the genomic region of major effect for maturation timing. Second, broad-scale characterization of candidate greb1L genotypes across 59 populations revealed unexpected patterns in maturation phenology for inland fish migrating long distances relative to those in coastal streams. Finally, genotypes from 890 PIT-tag tracked steelhead determined associations with early versus late arrival to spawning grounds that were previously unknown.ConclusionsThis study clarifies the genetic bases for disparity in phenology observed in steelhead, determining an unanticipated trait association with premature versus mature arrival to spawning grounds and identifying multiple candidate genes potentially contributing to this variation from a single genomic region of major effect. This illustrates how dense genome mapping and detailed phenotypic characterization can clarify genotype to phenotype associations across geographic ranges of species.Electronic supplementary materialThe online version of this article (10.1186/s12862-018-1255-5) contains supplementary material, which is available to authorized users.

Anadromous fishes represent an important ecosystem linkage between marine and inland aquatic and terrestrial habitats. These fishes carry organic matter and marine‐derived nutrient (MDN) subsidies across a vast landscape, often with profound influences on recipient ecosystem food web structure and function. In the Columbia River basin, century‐long declines in the abundance of anadromous fish populations have focused attention on potential mitigation efforts to address MDN deficits. In this study, we evaluate components of the stream food web response (periphyton, macroinvertebrate, and fish) to pasteurized salmon carcass analog (SCA) treatments in 15 streams across the Columbia River basin. Periphyton standing crop, macroinvertebrate density, and salmonid fish growth rates and stomach fullness measures increased following the addition of SCA. We found no significant change in dissolved nutrient concentrations after treatment, suggesting that biological demand exceeded supply. Nitrogen stable isotope signatures confirmed trophic transfer from SCA to lower trophic levels but were noticeably weak in fish tissue samples despite our marked growth and stomach fullness measures. These data indicate that SCA has the potential to increase the productivity of nutrient‐limited freshwater ecosystems and may provide a nutrient mitigation tool in ecosystems where MDNs are severely limited or unavailable.