34 Works

Data from: Population differentiation determined from putative neutral and divergent adaptive genetic markers in Eulachon (Thaleichthys pacificus, Osmeridae), an anadromous Pacific smelt.

John R. Candy, Nathan R. Campbell, Terry D. Beacham, Matthew H. Grinnell, Shawn R. Narum & Wesley A. Larson
Twelve eulachon (Thaleichthys pacificus, Osmeridae) populations ranging from Cook Inlet, Alaska and along the west coast of North America to the Columbia River were examined by restriction-site-associated DNA (RAD) sequencing to elucidate patterns of neutral and adaptive variation in this high geneflow species. A total of 4104 single-nucleotide polymorphisms (SNPs) were discovered across the genome, with 193 putatively adaptive SNPs as determined by FST outlier tests. Estimates of population structure in eulachon with the putatively...

Data from: Climate variables explain neutral and adaptive variation within salmonid metapopulations: the importance of replication in landscape genetics

Brian Hand, Ryan Kovach, Clint C. Muhlfeld, Alisa A. Wade, Diane Whited, Shawn Narum, Andrew Matala, Mike Ackerman, Brittany Garner, John Kimball, Jack Stanford, Gordon Luikart, Brian K. Hand, Diane C. Whited, Brittany A. Garner, Jack A. Stanford, John S. Kimball, Shawn R. Narum & Andrew P. Matala
Understanding how environmental variation influences population genetic structure is important for conservation management because it can reveal how human stressors influence population connectivity, genetic diversity, and persistence. We used riverscape genetics modeling to assess whether climatic and habitat variables were related to neutral and adaptive patterns of genetic differentiation (population specific and pairwise FST) within five metapopulations (79 populations, 4,583 individuals) of steelhead trout (Oncorhynchus mykiss) in the Columbia River Basin, USA. Using 151 putatively...

Data from: Genomic variation underlying complex life history traits revealed by genome sequencing in Chinook salmon

Shawn R. Narum, Alex Di Genova, Steven J. Micheletti, Alejandro Mass & Alejandro Maass
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...

Data from: Development and evaluation of 200 novel SNP assays for population genetic studies of westslope cutthroat trout and genetic identification of related taxa

Nathan R. Campbell, Stephen J. Amish, Victoria L. Pritchard, K. M. McKelvey, Michael K. Young, Michael K. Schwartz, John C. Garza, Gordon Luikart & Shawn R. Narum
DNA sequence data were collected and screened for single nucleotide polymorphisms (SNPs) in westslope cutthroat trout (Oncorhynchus clarki lewisi) and also for substitutions that could be used to genetically discriminate rainbow trout (O. mykiss) and cutthroat trout, as well as several cutthroat trout subspecies. In total, 260 expressed sequence tag-derived loci were sequenced and allelic discrimination genotyping assays developed from 217 of the variable sites. Another 50 putative SNPs in westslope cutthroat trout were identified...

Data from: Physiological and genomic signatures of evolutionary thermal adaptation in redband trout from extreme climates

Zhongqi Chen, Anthony P. Farrell, Amanda Matala, Nicholas Hoffman & Shawn R. Narum
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...

Data from: Genotyping SNPs and inferring ploidy by amplicon sequencing for polyploid, ploidy-variable organisms

Thomas Delomas, Stuart Willis, Blaine Parker, Donella Miller, Paul Anders, Andrea Schreier & Shawn Narum
Whole genome duplication is hypothesized to have played a critical role in the evolution of several major organism groups, including vertebrates, and while many lineages have rediploidized, some retain polyploid genomes. Additionally, variation in ploidy can occur naturally or be artificially induced within select plant and animal species. Modern genetic techniques have not been widely applied to polyploid or ploidy-variable species, in part due to the difficulty of obtaining genotype data from polyploids. In this...

Data from: Maintaining a wild phenotype in a conservation hatchery program for Chinook salmon: the effect of managed breeding on early male maturation

Donald A. Larsen, Deborah L. Harstad, Abby E. Fuhrman, Curtis M. Knudsen, Steven L. Schroder, William J. Bosch, Peter F. Galbreath, David E. Fast & Brian R. Beckman
In many salmonid species, age and size of maturation is plastic and influenced by the interaction between genetic and environmental factors. Hatchery reared salmon often mature at an earlier age and smaller size than wild fish. Modern salmon conservation efforts have focused on managing the level of gene flow between hatchery and natural origin fish to minimize potential genotypic and phenotypic change. In salmonids, maturation probability is dependent on exceeding a genetically set threshold in...

Data from: Genomic region associated with run-timing has similar haplotypes and phenotypic effects across three lineages of Chinook salmon

Stuart Willis
Conserving life history variation is a stated goal of many management programs, but the most effective means by which to accomplish this are often far from clear. Early, premature migrating and late, mature migrating forms of Chinook salmon face unequal pressure from natural and anthropogenic forces. These forces may result in the diminishment of migration variation in some stocks because migration timing is known to be highly heritable. Genomic regions of chromosome 28 are known...

Data from: Use of genotyping-by-sequencing data to develop a high-throughput and multi-functional SNP panel for conservation applications in Pacific lamprey

Jon E. Hess, Nathan R. Campbell, Margaret F. Docker, Cyndi Baker, Aaron Jackson, Ralph Lampman, Brian McIlraith, Mary L. Moser, David P. Statler, William P. Young, Andrew J. Wildbill & Shawn R. Narum
Next generation sequencing data can be mined for highly informative single nucleotide polymorphisms (SNPs) to develop high-throughput genomic assays for non-model organisms. However, choosing a set of SNPs to address a variety of objectives can be difficult because SNPs are often not equally informative. We developed an optimal combination of 96 high-throughput SNP assays from a total of 4,439 SNPs identified in a previous study of Pacific lamprey (Entosphenus tridentatus), and used them to address...

Data from: Supportive breeding boosts natural population abundance with minimal negative impacts on fitness of a wild population of Chinook salmon

Maureen A. Hess, Craig D. Rabe, Jason L. Vogel, Jeff J. Stephenson, Doug D. Nelson & Shawn R. Narum
While supportive breeding programs strive to minimize negative genetic impacts to populations, case studies have found evidence for reduced fitness of artificially produced individuals when they reproduce in the wild. Pedigrees of two complete generations were tracked with molecular markers to investigate differences in reproductive success (RS) of wild and hatchery-reared Chinook salmon spawning in the natural environment to address questions regarding the demographic and genetic impacts of supplementation to a natural population. Results show...

Data from: Adaptive genetic variation distinguishes Chilean blue mussels (Mytilus chilensis) from different marine environments

Cristian Araneda, Maria A. Larrain, Benjamin Hecht & Shawn Narum
Chilean mussel populations have been thought to be panmictic with limited genetic structure. Genotyping-by-sequencing approaches have enabled investigation of genome-wide variation that may better distinguish populations that have evolved in different environments. We investigated neutral and adaptive genetic variation in Mytilus from six locations in southern Chile with 1,240 SNP obtained with RAD-seq. Differentiation among locations with 891 neutral SNPs was low (FST = 0.005). Higher differentiation was obtained with a panel of 58 putative...

Data from: Environmental adaptation in Chinook salmon (Oncorhynchus tshawytscha) throughout their North American range

Benjamin Charles Hecht, Andrew P. Matala, Jon E. Hess & Shawn R. Narum
Landscape genomics is a rapidly growing field with recent advances in both genotyping efficiency and statistical analyses that provide insight towards local adaptation of populations under varying environmental and selective pressure. Chinook salmon (Oncorhynchus tshawytscha) are a broadly distributed Pacific salmon species, occupying a diversity of habitats throughout the northeastern Pacific with pronounced variation in environmental and climate features but little is understood regarding local adaptation in this species. We used a multivariate method, redundancy...

Data from: Signatures of polygenic adaptation associated with climate across the range of a threatened fish species with high genetic connectivity

Katherine A. Harrisson, Stephen J. Amish, Alexandra Pavlova, Shawn R. Narum, Marina Telonis-Scott, Meaghan L. Rourke, Jarod Lyon, Zeb Tonkin, Dean M. Gilligan, Brett A. Ingram, Mark Lintermans, Han Ming Gan, Christopher M. Austin, Gordon Luikart & Paul Sunnucks
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 (6605 biallelic single nucleotide polymorphisms; SNPs) to examine population structure and test for signatures of adaptation...

Data from: Utility of pooled sequencing for association mapping in non-model organisms

Steven J. Micheletti & Shawn R. Narum
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...

Heterogeneous genetic basis of age at maturity in salmonid fishes

Charles Waters, Anthony Clemento, Tutku Aykanat, John Garza, Kerry-Ann Naish, Shawn Narum & Craig Primmer
Understanding the genetic basis of repeated evolution of the same phenotype across taxa is a fundamental aim in evolutionary biology and has applications to conservation and management. However, the extent to which interspecific life-history trait polymorphisms share evolutionary pathways remains under-explored. We address this gap by studying the genetic basis of a key life-history trait, age at maturity, in four species of Pacific salmon (genus Oncorhynchus) that exhibit intra- and interspecific variation in this trait...

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

Jon E. Hess, Joseph S. Zendt, Amanda R. Matala & Shawn R. Narum
Migration traits are presumed to be complex and to involve interaction among multiple genes, thus we employed both univariate analyses and 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...

Data from: Discovery and characterization of novel genetic markers for use in the management of Lahontan cutthroat trout (Oncorhynchus clarkii henshawi)

Victoria L. Pritchard, Nathan R. Campbell, Shawn R. Narum, Mary M. Peacock & John Carlos Garza
The Lahontan cutthroat trout (Oncorhynchus clarkii henshawi) is threatened by habitat destruction, over-harvest and hybridization with nonnative trout. Currently, three Geographic Management Units (GMUs) are recognized within the taxon. Here, we describe a suite of 68 single-nucleotide polymorphism (SNP) genetic markers for use in the study and management of Lahontan cutthroat trout and a closely related subspecies, the Paiute cutthroat trout (O. c. seleneris). These include markers variable within the two subspecies (n = 35),...

Data from: Thermal adaptation and acclimation of ectotherms from differing aquatic climates

Shawn R. Narum, Nathan R. Campbell, Kevin A. Meyer, Michael R. Miller & Ronald W. Hardy
To elucidate the mechanisms of thermal adaptation and acclimation in ectothermic aquatic organisms from differing climates, we used a common-garden experiment for thermal stress to investigate the heat shock response of redband trout (Oncorhynchus mykiss gairdneri) from desert and montane populations. Evidence for adaptation was observed as expression of heat shock genes in fish from the desert population was more similar to control (unstressed) fish and significantly different (P ≤ 0.05) from those from the...

Chromosome 28 genotypes and phenotypes for all samples used in the analyses, full panel of 298 genotypes, and R script for R-squared values

Ilana Koch & Shawn Narum
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...

Data from: Landscape features along migratory routes influence adaptive genomic variation in anadromous steelhead (Oncorhynchus mykiss)

Steven J. Micheletti, Amanda R. Matala, Andrew P. Matala & Shawn R. Narum
Organisms typically show evidence of adaptation to features within their local environment. However, many species undergo long-distance dispersal or migration across larger geographical 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...

The Pacific lamprey genomic divergence, association mapping, temporal Willamette Falls, spatial rangewide datasets

Jon Hess, Jeramiah Smith, Nataliya Timoshevskaya, Cyndi Baker, Christopher Caudill, David Graves, Matthew Keefer, Andrew Kinziger, Mary Moser, Laurie Porter, Greg Silver, Steven Whitlock & Shawn Narum
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...

Data from: Mechanisms of thermal adaptation and evolutionary potential of conspecific populations to changing environments

Zhongqi Chen, Anthony P. Farrell, Amanda Matala & Shawn R. Narum
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,...

Chinook salmon environmental data and allele frequency matrix

Yara Alshwairikh, Rebekah Horn, Travis Seaborn, Shawn Narum, Lisette Waits, William Swain, Steve Stephens-Cardenas, Jenny Olsson & Shayla Kroeze
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 to the conditions at spawning sites on driving selection is still unknown. In this study, we performed genome-environment associations (GEA) to...

Data from: Relative contributions of neutral and non-neutral genetic differentiation to inform conservation of steelhead trout across highly variable landscapes

Andrew P. Matala, Michael W. Ackerman, Matthew R. Campbell & Shawn R. Narum
Mounting evidence of climatic effects on riverine environments, and adaptive responses of fishes has elicited growing conservation concerns. Measures to rectify population declines include assessment of local extinction risk, population ecology, viability, and genetic differentiation. While conservation planning has been largely informed by neutral genetic structure, there has been a dearth of critical information regarding the role of non-neutral or functional genetic variation. We evaluated genetic variation among steelhead trout of the Columbia River Basin,...

Data from: Population genomics of Pacific lamprey: adaptive variation in a highly dispersive species

Jon E. Hess, Nathan R. Campbell, David A. Close, Margaret F. Docker & Shawn R. Narum
Unlike most anadromous fishes that have evolved strict homing behaviour, Pacific lamprey (Entosphenus tridentatus) seem to lack philopatry as evidenced by minimal population structure across the species range. Yet unexplained findings of within-region population genetic heterogeneity coupled with the morphological and behavioural diversity described for the species suggest that adaptive genetic variation underlying fitness traits may be responsible. We employed restriction site–associated DNA sequencing to genotype 4439 quality filtered single nucleotide polymorphism (SNP) loci for...

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