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1.
Mol Ecol ; 28(13): 3171-3185, 2019 07.
Artigo em Inglês | MEDLINE | ID: mdl-31132186

RESUMO

Surveys of genomic variation have improved our understanding of the relationship between fitness-related phenotypes and their underlying genetic basis. In some cases, single large-effect genes have been found to underlie important traits; however, complex traits are expected to be under polygenic control and elucidation of multiple gene interactions may be required to fully understand the genetic basis of the trait. In this study, we investigated the genetic basis of the ocean- and river-maturing ecotypes in anadromous Pacific lamprey (Entosphenus tridentatus). In Pacific lamprey, the ocean-maturing ecotype is distinguished by advanced maturity of females (e.g., large egg mass) at the onset of freshwater migration relative to immature females of the river-maturing ecotype. We examined a total of 219 adult Pacific lamprey that were collected at-entry to the Klamath River over a 12-month period. Each individual was genotyped at 308 SNPs representing known neutral and adaptive loci and measured at morphological traits, including egg mass as an indicator of ocean- and river-maturing ecotype for females. The two ecotypes did not exhibit genetic structure at 148 neutral loci, indicating that ecotypic diversity exists within a single population. In contrast, we identified the genetic basis of maturation ecotypes in Pacific lamprey as polygenic, involving two unlinked gene regions that have a complex epistatic relationship. Importantly, these gene regions appear to show stronger effects when considered in gene interaction models than if just considered additive, illustrating the importance of considering epistatic effects and gene networks when researching the genetic basis of complex traits in Pacific lamprey and other species.

2.
Evol Appl ; 12(3): 456-469, 2019 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-30828367

RESUMO

While the goal of supplementation programs is to provide positive, population-level effects for species of conservation concern, these programs can also present an inherent fitness risk when captive-born individuals are fully integrated into the natural population. In order to evaluate the long-term effects of a supplementation program and estimate the demographic and phenotypic factors influencing the fitness of a threatened population of Chinook Salmon (Oncorhynchus tshawytscha), we genotyped tissue samples spanning a 19-year period (1998-2016) to generate pedigrees from adult fish returning to Johnson Creek, Idaho, USA. We expanded upon previous estimates of relative reproductive success (RRS) to include grandparentage analyses and used generalized linear models to determine whether origin (hatchery or natural) or phenotypic traits (timing of arrival to spawning grounds, body length, and age) significantly predicted reproductive success (RS) across multiple years. Our results provide evidence that this supplementation program with 100% natural-origin broodstock provided a long-term demographic boost to the population (mean of 4.56 times in the first generation and mean of 2.52 times in the second generation). Overall, when spawning in nature, hatchery-origin fish demonstrated a trend toward lower RS compared to natural-origin fish (p < 0.05). However, when hatchery-origin fish successfully spawned with natural-origin fish, they had similar RS compared to natural by natural crosses (first-generation mean hatchery by natural cross RRS = 1.11 females, 1.13 males; second-generation mean hatchery by natural cross RRS = 1.03 females, 1.08 males). While origin, return year, and body length were significant predictors of fitness for both males and females (p < 0.05), return day was significant for males but not females (p > 0.05). These results indicate that supplementation programs that reduce the potential for genetic adaptation to captivity can be effective at increasing population abundance while limiting long-term fitness effects on wild populations.

3.
Trends Ecol Evol ; 34(7): 641-654, 2019 07.
Artigo em Inglês | MEDLINE | ID: mdl-30904190

RESUMO

Aquatic species represent a vast diversity of metazoans, provide humans with the most abundant animal protein source, and are of increasing conservation concern, yet landscape genomics is dominated by research in terrestrial systems. We provide researchers with a roadmap to plan aquatic landscape genomics projects by aggregating spatial and software resources and offering recommendations from sampling to data production and analyses, while cautioning against analytical pitfalls. Given the unique properties of water, we discuss the importance of considering freshwater system structure and marine abiotic properties when assessing genetic diversity, population connectivity, and signals of natural selection. When possible, genomic datasets should be parsed into neutral, adaptive, and sex-linked datasets to generate the most accurate inferences of eco-evolutionary processes.


Assuntos
Genética Populacional , Genômica , Animais , Clima , Variação Genética , Seleção Genética
4.
Evol Appl ; 11(9): 1686-1699, 2018 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-30344636

RESUMO

Temperature is a master environmental factor that limits the geographical distribution of species, especially in ectotherms. To address challenges in biodiversity conservation under ongoing climate change, it is essential to characterize relevant functional limitations and adaptive genomic content at population and species levels. Here, we present evidence for adaptive divergence in cardiac function and genomic regions in redband trout (Oncorhynchus mykiss gairdneri) populations from desert and montane streams. Cardiac phenotypes of individual fish were measured in the field with a custom-built electrocardiogram apparatus. Maximum heart rate and its rate limiting temperature during acute warming were significantly higher in fish that have evolved in the extreme of a desert climate compared to a montane climate. Association mapping with 526,301 single nucleotide polymorphisms (SNPs) across the genome revealed signatures of thermal selection both within and among ecotypes. Among desert and montane populations, 435 SNPs were identified as putative outliers under natural selection and 20 of these loci showed significant association with average summer water temperatures among populations. Phenotypes for cardiac performance were variable within each ecotype, and 207 genomic regions were strongly associated with either maximum heart rate or rate limiting temperatures among individuals. Annotation of significant loci provided candidate genes that underlie thermal adaptation, including pathways associated with cardiac function (IRX5, CASQ1, CAC1D, and TITIN), neuroendocrine system (GPR17 and NOS), and stress response (SERPH). By integrating comparative physiology and population genomics, results here advance our knowledge on evolutionary processes of thermal adaptation in aquatic ectotherms.

5.
Nat Genet ; 50(11): 1617, 2018 11.
Artigo em Inglês | MEDLINE | ID: mdl-30224652

RESUMO

When published, this article did not initially appear open access. This error has been corrected, and the open access status of the paper is noted in all versions of the paper. Additionally, affiliation 16 denoting equal contribution was missing from author Robb Krumlauf in the PDF originally published. This error has also been corrected.

6.
BMC Evol Biol ; 18(1): 140, 2018 09 15.
Artigo em Inglês | MEDLINE | ID: mdl-30219030

RESUMO

BACKGROUND: Disparity 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. RESULTS: We 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. CONCLUSIONS: This 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.


Assuntos
Migração Animal/fisiologia , Evolução Biológica , Genoma , Oncorhynchus mykiss/genética , Oncorhynchus mykiss/fisiologia , Seleção Genética , Animais , Cromossomos , Variação Genética , Genética Populacional , Geografia , Haplótipos/genética , Funções Verossimilhança , Filogenia , Polimorfismo de Nucleotídeo Único/genética , Análise de Componente Principal
7.
Proc Biol Sci ; 285(1883)2018 07 18.
Artigo em Inglês | MEDLINE | ID: mdl-30051839

RESUMO

A broad portfolio of phenotypic diversity in natural organisms can buffer against exploitation and increase species persistence in disturbed ecosystems. The study of genomic variation that accounts for ecological and evolutionary adaptation can represent a powerful approach to extend understanding of phenotypic variation in nature. Here we present a chromosome-level reference genome assembly for Chinook salmon (Oncorhynchus tshawytscha; 2.36 Gb) that enabled association mapping of life-history variation and phenotypic traits for this species. Whole-genome re-sequencing of populations with distinct life-history traits provided evidence that divergent selection was extensive throughout the genome within and among phylogenetic lineages, indicating that a broad portfolio of phenotypic diversity exists in this species that is related to local adaptation and life-history variation. Association mapping with millions of genome-wide SNPs revealed that a genomic region of major effect on chromosome 28 was associated with phenotypes for premature and mature arrival to spawning grounds and was consistent across three distinct phylogenetic lineages. Our results demonstrate how genomic resources can enlighten the genetic basis of known phenotypes in exploited species and assist in clarifying phenotypic variation that may be difficult to observe in naturally occurring organisms.


Assuntos
Mapeamento Cromossômico , Genoma , Traços de História de Vida , Reprodução/genética , Salmão/genética , Transcriptoma , Animais , Feminino , Variação Genética , Masculino , Polimorfismo de Nucleotídeo Único
9.
Mol Ecol Resour ; 18(4): 825-837, 2018 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-29633534

RESUMO

High-density genome-wide sequencing increases the likelihood of discovering genes of major effect and genomic structural variation in organisms. While there is an increasing availability of reference genomes across broad taxa, the greatest limitation to whole-genome sequencing of multiple individuals continues to be the costs associated with sequencing. To alleviate excessive costs, pooling multiple individuals with similar phenotypes and sequencing the homogenized DNA (Pool-Seq) can achieve high genome coverage, but at the loss of individual genotypes. Although Pool-Seq has been an effective method for association mapping in model organisms, it has not been frequently utilized in natural populations. To extend bioinformatic tools for rapid implementation of Pool-Seq data in nonmodel organisms, we developed a pipeline called PoolParty and illustrate its effectiveness in genetic association mapping. Alignment expectations based on five pooled Chinook salmon (Oncorhynchus tshawytscha) libraries showed that approximately 48% genome coverage per library could be achieved with reasonable sequencing effort. We additionally examined male and female O. tshawytscha libraries to illustrate how Pool-Seq techniques can successfully map known genes associated with functional differences among sexes such as growth hormone 2. Finally, we compared pools of individuals of different spawning ages for each sex to discover novel genes involved with age at maturity in O. tshawytscha such as opsin4 and transmembrane protein19. While not appropriate for every system, Pool-Seq data processed by the PoolParty pipeline is a practical method for identifying genes of major effect in nonmodel organisms when high genome coverage is necessary and cost is a limiting factor.


Assuntos
Estudos de Associação Genética/métodos , Salmão/genética , Animais , Mapeamento Cromossômico/métodos , Biologia Computacional , Feminino , Genoma , Masculino , Alinhamento de Sequência , Análise de Sequência/métodos , Caracteres Sexuais , Software
10.
Mol Ecol ; 27(3): 659-674, 2018 02.
Artigo em Inglês | MEDLINE | ID: mdl-29290103

RESUMO

Heterogeneous and ever-changing thermal environments drive the evolution of populations and species, especially when extreme conditions increase selection pressure for traits influencing fitness. However, projections of biological diversity under scenarios of climate change rarely consider evolutionary adaptive potential of natural species. In this study, we tested for mechanistic evidence of evolutionary thermal adaptation among ecologically divergent redband trout populations (Oncorhynchus mykiss gairdneri) in cardiorespiratory function, cellular response and genomic variation. In a common garden environment, fish from an extreme desert climate had significantly higher critical thermal maximum (p < .05) and broader optimum thermal window for aerobic scope (>3°C) than fish from cooler montane climate. In addition, the desert population had the highest maximum heart rate during warming (20% greater than montane populations), indicating improved capacity to deliver oxygen to internal tissues. In response to acute heat stress, distinct sets of cardiac genes were induced among ecotypes, which helps to explain the differences in cardiorespiratory function. Candidate genomic markers and genes underlying these physiological adaptations were also pinpointed, such as genes involved in stress response and metabolic activity (hsp40, ldh-b and camkk2). These markers were developed into a multivariate model that not only accurately predicted critical thermal maxima, but also evolutionary limit of thermal adaptation in these specific redband trout populations relative to the expected limit for the species. This study demonstrates mechanisms and limitations of an aquatic species to evolve under changing environments that can be incorporated into advanced models to predict ecological consequences of climate change for natural organisms.


Assuntos
Adaptação Fisiológica , Evolução Biológica , Oncorhynchus mykiss/fisiologia , Temperatura Ambiente , Animais , Mudança Climática , Ecossistema , Regulação da Expressão Gênica , Loci Gênicos , Frequência Cardíaca/fisiologia , Oncorhynchus mykiss/genética , Fenótipo , Análise de Componente Principal , Especificidade da Espécie
11.
Nat Genet ; 50(2): 270-277, 2018 02.
Artigo em Inglês | MEDLINE | ID: mdl-29358652

RESUMO

The sea lamprey (Petromyzon marinus) serves as a comparative model for reconstructing vertebrate evolution. To enable more informed analyses, we developed a new assembly of the lamprey germline genome that integrates several complementary data sets. Analysis of this highly contiguous (chromosome-scale) assembly shows that both chromosomal and whole-genome duplications have played significant roles in the evolution of ancestral vertebrate and lamprey genomes, including chromosomes that carry the six lamprey HOX clusters. The assembly also contains several hundred genes that are reproducibly eliminated from somatic cells during early development in lamprey. Comparative analyses show that gnathostome (mouse) homologs of these genes are frequently marked by polycomb repressive complexes (PRCs) in embryonic stem cells, suggesting overlaps in the regulatory logic of somatic DNA elimination and bivalent states that are regulated by early embryonic PRCs. This new assembly will enhance diverse studies that are informed by lampreys' unique biology and evolutionary/comparative perspective.


Assuntos
Reprogramação Celular/genética , Evolução Molecular , Genoma , Células Germinativas/metabolismo , Mutagênese/fisiologia , Petromyzon/genética , Vertebrados/genética , Animais , Montagem e Desmontagem da Cromatina/genética , Vertebrados/classificação
12.
Mol Ecol ; 27(1): 128-145, 2018 01.
Artigo em Inglês | MEDLINE | ID: mdl-29110354

RESUMO

Organisms typically show evidence of adaptation to features within their local environment. However, many species undergo long-distance dispersal or migration across larger geographic regions that consist of highly heterogeneous habitats. Therefore, selection may influence adaptive genetic variation associated with landscape features at residing sites and along migration routes in migratory species. We tested for genomic adaptation to landscape features at natal spawning sites and along migration paths to the ocean of anadromous steelhead trout (Oncorhynchus mykiss) in the Columbia River Basin. Results from multivariate ordination, gene-environment association and outlier analyses using 24,526 single nucleotide polymorphisms (SNPs) provided evidence that adaptive allele frequencies were more commonly associated with landscape features along migration paths than features at natal sites (91.8% vs. 8.2% of adaptive loci, respectively). Among the 45 landscape variables tested, migration distance to the ocean and mean annual precipitation along migration paths were significantly associated with adaptive genetic variation in three distinct genetic groups. Additionally, variables such as minimum migration water temperature and mean migration slope were significant only in inland stocks of steelhead that migrate up to 1,200 km farther than those near the coast, indicating regional differences in migratory selective pressures. This study provides novel approaches for investigating migratory corridors and some of the first evidence that environment along migration paths can lead to substantial divergent selection. Consequently, our approach to understand genetic adaptation to migration conditions can be applied to other migratory species when migration or dispersal paths are generally known.


Assuntos
Adaptação Fisiológica/genética , Migração Animal/fisiologia , Variação Genética , Genoma , Oncorhynchus mykiss/genética , Animais , Meio Ambiente , Loci Gênicos , Genótipo , Geografia , Polimorfismo de Nucleotídeo Único/genética , Análise de Componente Principal , Estados Unidos
13.
Ecol Evol ; 7(23): 10350-10360, 2017 12.
Artigo em Inglês | MEDLINE | ID: mdl-29238560

RESUMO

Coho salmon were extirpated in the mid-20th century from the interior reaches of the Columbia River but were reintroduced with relatively abundant source stocks from the lower Columbia River near the Pacific coast. Reintroduction of Coho salmon to the interior Columbia River (Wenatchee River) using lower river stocks placed selective pressures on the new colonizers due to substantial differences with their original habitat such as migration distance and navigation of six additional hydropower dams. We used restriction site-associated DNA sequencing (RAD-seq) to genotype 5,392 SNPs in reintroduced Coho salmon in the Wenatchee River over four generations to test for signals of temporal structure and adaptive variation. Temporal genetic structure among the three broodlines of reintroduced fish was evident among the initial return years (2000, 2001, and 2002) and their descendants, which indicated levels of reproductive isolation among broodlines. Signals of adaptive variation were detected from multiple outlier tests and identified candidate genes for further study. This study illustrated that genetic variation and structure of reintroduced populations are likely to reflect source stocks for multiple generations but may shift over time once established in nature.

14.
Mol Ecol ; 26(22): 6253-6269, 2017 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-28977721

RESUMO

Adaptive differences across species' ranges can have important implications for population persistence and conservation management decisions. Despite advances in genomic technologies, detecting adaptive variation in natural populations remains challenging. Key challenges in gene-environment association studies involve distinguishing the effects of drift from those of selection and identifying subtle signatures of polygenic adaptation. We used paired-end restriction site-associated DNA sequencing data (6,605 biallelic single nucleotide polymorphisms; SNPs) to examine population structure and test for signatures of adaptation across the geographic range of an iconic Australian endemic freshwater fish species, the Murray cod Maccullochella peelii. Two univariate gene-association methods identified 61 genomic regions associated with climate variation. We also tested for subtle signatures of polygenic adaptation using a multivariate method (redundancy analysis; RDA). The RDA analysis suggested that climate (temperature- and precipitation-related variables) and geography had similar magnitudes of effect in shaping the distribution of SNP genotypes across the sampled range of Murray cod. Although there was poor agreement among the candidate SNPs identified by the univariate methods, the top 5% of SNPs contributing to significant RDA axes included 67% of the SNPs identified by univariate methods. We discuss the potential implications of our findings for the management of Murray cod and other species generally, particularly in relation to informing conservation actions such as translocations to improve evolutionary resilience of natural populations. Our results highlight the value of using a combination of different approaches, including polygenic methods, when testing for signatures of adaptation in landscape genomic studies.


Assuntos
Adaptação Fisiológica/genética , Clima , Peixes/genética , Genética Populacional , Herança Multifatorial , Animais , Austrália , Evolução Biológica , Espécies em Perigo de Extinção , Estudos de Associação Genética , Deriva Genética , Genótipo , Geografia , Polimorfismo de Nucleotídeo Único
15.
Ecol Evol ; 7(20): 8349-8362, 2017 10.
Artigo em Inglês | MEDLINE | ID: mdl-29075454

RESUMO

The species Oncorhynchus mykiss is characterized by a complex life history that presents a significant challenge for population monitoring and conservation management. Many factors contribute to genetic variation in O. mykiss populations, including sympatry among migratory phenotypes, habitat heterogeneity, hatchery introgression, and immigration (stray) rates. The relative influences of these and other factors are contingent on characteristics of the local environment. The Rock Creek subbasin in the middle Columbia River has no history of hatchery supplementation and no dams or artificial barriers. Limited intervention and minimal management have led to a dearth of information regarding the genetic distinctiveness of the extant O. mykiss population in Rock Creek and its tributaries. We used 192 SNP markers and collections sampled over a 5-year period to evaluate the temporal and spatial genetic structures of O. mykiss between upper and lower watersheds of the Rock Creek subbasin. We investigated potential limits to gene flow within the lower watershed where the stream is fragmented by seasonally dry stretches of streambed, and between upper and lower watershed regions. We found minor genetic differentiation within the lower watershed occupied by anadromous steelhead (FST = 0.004), and evidence that immigrant influences were prevalent and ubiquitous. Populations in the upper watershed above partial natural barriers were highly distinct (FST = 0.093) and minimally impacted by apparent introgression. Genetic structure between watersheds paralleled differences in local demographics (e.g., variation in size), migratory restrictions, and habitat discontinuity. The evidence of restricted gene flow between putative remnant resident populations in the upper watershed and the admixed anadromous population in the lower watershed has implications for local steelhead productivity and regional conservation.

16.
Evol Appl ; 10(4): 402-416, 2017 04.
Artigo em Inglês | MEDLINE | ID: mdl-28352299

RESUMO

Invasive species have become widespread in aquatic environments throughout the world, yet there are few studies that have examined genomic variation of multiple introduced species in newly colonized environments. In this study, we contrast genomic variation in two salmonid species (anadromous Chinook Salmon, Oncorhynchus tshawytscha, 11,579 SNPs and resident Brook Charr Salvelinus fontinalis, 13,522 SNPs) with differing invasion success after introduction to new environments in South America relative to populations from their native range in North America. Estimates of genetic diversity were not significantly different between introduced and source populations for either species, indicative of propagule pressure that has been shown to maintain diversity in founding populations relative to their native range. Introduced populations also demonstrated higher connectivity and gene flow than those in their native range. Evidence for candidate loci under divergent selection was observed, but was limited to specific introduced populations and was not widely evident. Patterns of genomic variation were consistent with general dispersal potential of each species and therefore also the notion that life history variation may contribute to both invasion success and subsequent genetic structure of these two salmonids in Patagonia.

17.
Evol Appl ; 9(10): 1285-1300, 2016 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-27877206

RESUMO

Conservation of life history variation is an important consideration for many species with trade-offs in migratory characteristics. Many salmonid species exhibit both resident and migratory strategies that capitalize on benefits in freshwater and marine environments. In this study, we investigated genomic signatures for migratory life history in collections of resident and anadromous Oncorhynchus nerka (Kokanee and Sockeye Salmon, respectively) from two lake systems, using ~2,600 SNPs from restriction-site-associated DNA sequencing (RAD-seq). Differing demographic histories were evident in the two systems where one pair was significantly differentiated (Redfish Lake, FST = 0.091 [95% confidence interval: 0.087 to 0.095]) but the other pair was not (Alturas Lake, FST = -0.007 [-0.008 to -0.006]). Outlier and association analyses identified several candidate markers in each population pair, but there was limited evidence for parallel signatures of genomic variation associated with migration. Despite lack of evidence for consistent markers associated with migratory life history in this species, candidate markers were mapped to functional genes and provide evidence for adaptive genetic variation within each lake system. Life history variation has been maintained in these nearly extirpated populations of O. nerka, and conservation efforts to preserve this diversity are important for long-term resiliency of this species.

18.
Proc Biol Sci ; 283(1843)2016 Nov 30.
Artigo em Inglês | MEDLINE | ID: mdl-27881749

RESUMO

Evolutionary and ecological consequences of hybridization between native and invasive species are notoriously complicated because patterns of selection acting on non-native alleles can vary throughout the genome and across environments. Rapid advances in genomics now make it feasible to assess locus-specific and genome-wide patterns of natural selection acting on invasive introgression within and among natural populations occupying diverse environments. We quantified genome-wide patterns of admixture across multiple independent hybrid zones of native westslope cutthroat trout and invasive rainbow trout, the world's most widely introduced fish, by genotyping 339 individuals from 21 populations using 9380 species-diagnostic loci. A significantly greater proportion of the genome appeared to be under selection favouring native cutthroat trout (rather than rainbow trout), and this pattern was pervasive across the genome (detected on most chromosomes). Furthermore, selection against invasive alleles was consistent across populations and environments, even in those where rainbow trout were predicted to have a selective advantage (warm environments). These data corroborate field studies showing that hybrids between these species have lower fitness than the native taxa, and show that these fitness differences are due to selection favouring many native genes distributed widely throughout the genome.


Assuntos
Alelos , Hibridização Genética , Oncorhynchus/genética , Seleção Genética , Animais , Genótipo , Espécies Introduzidas , Oncorhynchus/classificação
19.
Proc Biol Sci ; 283(1830)2016 05 11.
Artigo em Inglês | MEDLINE | ID: mdl-27170720

RESUMO

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.


Assuntos
Migração Animal/fisiologia , Oncorhynchus mykiss/genética , Animais , Estudo de Associação Genômica Ampla , Análise Multivariada , Oncorhynchus mykiss/fisiologia , Polimorfismo de Nucleotídeo Único , Fatores de Tempo , Washington
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