Devon E. Pearse
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View article: Recent Adaptation in a Threatened Salmonid Revealed by Museum Genomics
Recent Adaptation in a Threatened Salmonid Revealed by Museum Genomics Open
Steelhead/rainbow trout ( Oncorhynchus mykiss ) is an imperilled salmonid with two main life history strategies: migrate to the ocean or remain in freshwater. Domesticated hatchery forms of this species have been stocked into almost all Ca…
View article: A genome assembly for Lahontan Cutthroat Trout, <i>Oncorhynchus clarkii henshawi</i>
A genome assembly for Lahontan Cutthroat Trout, <i>Oncorhynchus clarkii henshawi</i> Open
Cutthroat trout (Oncorhynchus clarkii) are diverse Pacific salmonids widely distributed throughout western North America. Distinct lineages of cutthroat trout have been defined based on morphology, geography, and genetic differences. Sever…
View article: A Multipurpose Microhaplotype Panel for Genetic Analysis of California Chinook Salmon
A Multipurpose Microhaplotype Panel for Genetic Analysis of California Chinook Salmon Open
Genetic methods have become an essential component of ecological investigation and conservation planning for fish and wildlife. Among these methods is the use of genetic marker data to identify individuals to populations, or stocks, of ori…
View article: The Genomics Revolution in Nonmodel Species: Predictions vs. Reality for Salmonids
The Genomics Revolution in Nonmodel Species: Predictions vs. Reality for Salmonids Open
The increasing feasibility of whole‐genome sequencing has been highly anticipated, promising to transform our understanding of the biology of nonmodel species. Notably, dramatic cost reductions beginning around 2007 with the advent of high…
View article: A multipurpose microhaplotype panel for genetic analysis of California Chinook salmon
A multipurpose microhaplotype panel for genetic analysis of California Chinook salmon Open
Genetic methods have become an essential component of ecological investigation and conservation planning for fish and wildlife. Among these methods is the use of genetic marker data to identify individuals to populations, or stocks, of ori…
View article: Development of a microhaplotype panel for steelhead/rainbow trout (Oncorhynchus mykiss) and application for phylogenetic analysis in California
Development of a microhaplotype panel for steelhead/rainbow trout (Oncorhynchus mykiss) and application for phylogenetic analysis in California Open
Advances in high-throughput sequencing and bioinformatic data processing have prompted a transition in wildlife and fisheries genetics from the use of allozymes, mtDNA, or microsatellites towards markers that are more amenable to genotypin…
View article: Characterization and distribution of a 14-Mb chromosomal inversion in native populations of rainbow trout (<i>Oncorhynchus mykiss</i>)
Characterization and distribution of a 14-Mb chromosomal inversion in native populations of rainbow trout (<i>Oncorhynchus mykiss</i>) Open
Multiple studies in a range of taxa have found links between structural variants and the development of ecologically important traits. Such variants are becoming easier to find due, in large part, to the increase in the amount of genome-wi…
View article: Recent adaptation in an imperiled salmonid revealed by museum genomics
Recent adaptation in an imperiled salmonid revealed by museum genomics Open
Steelhead/rainbow trout ( Oncorhynchus mykiss ) is an imperiled salmonid with two main life history strategies: migrate to the ocean or remain in freshwater. Domesticated hatchery forms of this species have been stocked into almost all Cal…
View article: Ancestry and genetic structure of resident and anadromous rainbow trout (<i>Oncorhynchus mykiss</i>) in <scp>Argentina</scp>
Ancestry and genetic structure of resident and anadromous rainbow trout (<i>Oncorhynchus mykiss</i>) in <span>Argentina</span> Open
Since the first introduction from North America more than a century ago, rainbow trout ( Oncorhynchus mykiss ) have rapidly established self‐sustaining populations in major river basins of Patagonia. Many generations later, only the freshw…
View article: Genetic parentage reveals the (un)natural history of Central Valley hatchery steelhead
Genetic parentage reveals the (un)natural history of Central Valley hatchery steelhead Open
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 sal…
View article: Distinct patterns of inheritance shape life‐history traits in steelhead trout
Distinct patterns of inheritance shape life‐history traits in steelhead trout Open
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 anadromou…
View article: Development of a novel microhaplotype panel for steelhead/rainbow trout (Oncorhynchus mykiss) and application for phylogenetic analysis in California
Development of a novel microhaplotype panel for steelhead/rainbow trout (Oncorhynchus mykiss) and application for phylogenetic analysis in California Open
The rapid advance of high-throughput sequencing has prompted a transition in wildlife and fisheries genetics from using microsatellites toward markers that are more amenable to genotyping by sequencing. Microhaplotypes are novel multi-alle…
View article: Implications of Large-Effect Loci for Conservation: A Review and Case Study with Pacific Salmon
Implications of Large-Effect Loci for Conservation: A Review and Case Study with Pacific Salmon Open
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…
View article: Polygenic Basis and the Role of Genome Duplication in Adaptation to Similar Selective Environments
Polygenic Basis and the Role of Genome Duplication in Adaptation to Similar Selective Environments Open
Genetic changes underlying adaptation vary greatly in terms of complexity and, within the same species, genetic responses to similar selective pressures may or may not be the same. We examine both complex (supergene) and simple (SNP) genet…
View article: Straying and Life History of Adult Steelhead in a Small California Coastal Stream Revealed by Otolith Natural Tags and Genetic Stock Identification
Straying and Life History of Adult Steelhead in a Small California Coastal Stream Revealed by Otolith Natural Tags and Genetic Stock Identification Open
Straying has been difficult to study directly in natural steelhead Oncorhynchus mykiss populations. We analyzed an opportunistic sample of seven adult steelhead from a small basin on the Big Sur coast of California to determine their life …
View article: A complex phenotype in salmon controlled by a simple change in migratory timing
A complex phenotype in salmon controlled by a simple change in migratory timing Open
Unexpectedly simple Chinook salmon are known to return to spawn at two distinct times of the year: spring and fall. Individuals that return during these times have generally been referred to as parts of distinct groups, or ecotypes, with t…
View article: Publisher Correction: Sex-dependent dominance maintains migration supergene in rainbow trout
Publisher Correction: Sex-dependent dominance maintains migration supergene in rainbow trout Open
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
View article: Long-Term Conservation of Ohnologs Through Partial Tetrasomy Following Whole-Genome Duplication in Salmonidae
Long-Term Conservation of Ohnologs Through Partial Tetrasomy Following Whole-Genome Duplication in Salmonidae Open
Whole-genome duplications (WGDs) have occurred repeatedly and broadly throughout the evolutionary history of eukaryotes. However, the effects of WGD on genome function and evolution remain unclear. The salmonid WGD that occurred approximat…
View article: Anadromy Redux? Genetic Analysis to Inform Development of an Indigenous American River Steelhead Broodstock
Anadromy Redux? Genetic Analysis to Inform Development of an Indigenous American River Steelhead Broodstock Open
The construction of dams and water diversions has severely limited access to spawning habitat for anadromous fishes. To mitigate for these impacts, hatchery programs rear and release millions of juvenile salmonids, including steelhead, the…
View article: Sex-dependent dominance maintains migration supergene in rainbow trout
Sex-dependent dominance maintains migration supergene in rainbow trout Open
Traits with different fitness optima in males and females cause sexual conflict when they have a shared genetic basis. Heteromorphic sex chromosomes can resolve this conflict and protect sexually antagonistic polymorphisms but accumulate d…
View article: A New Single Nucleotide Polymorphism Database for Rainbow Trout Generated Through Whole Genome Resequencing
A New Single Nucleotide Polymorphism Database for Rainbow Trout Generated Through Whole Genome Resequencing Open
Single-nucleotide polymorphisms (SNPs) are highly abundant markers, which are broadly distributed in animal genomes. For rainbow trout (Oncorhynchus mykiss), SNP discovery has been previously done through sequencing of restriction-site ass…
View article: Evolutionary restoration potential evaluated through the use of a trait‐linked genetic marker
Evolutionary restoration potential evaluated through the use of a trait‐linked genetic marker Open
Human‐driven evolution can impact the ecological role and conservation value of impacted populations. Most evolutionary restoration approaches focus on manipulating gene flow, but an alternative approach is to manipulate the selection regi…
View article: Saving the spandrels? Adaptive genomic variation in conservation and fisheries management
Saving the spandrels? Adaptive genomic variation in conservation and fisheries management Open
As highlighted by many of the papers in this issue, research on the genomic basis of adaptive phenotypic variation in natural populations has made spectacular progress in the past few years, largely due to the advances in sequencing techno…
View article: Ancestry and adaptive evolution of anadromous, resident, and adfluvial rainbow trout (<i>Oncorhynchus mykiss</i>) in the San Francisco bay area: application of adaptive genomic variation to conservation in a highly impacted landscape
Ancestry and adaptive evolution of anadromous, resident, and adfluvial rainbow trout (<i>Oncorhynchus mykiss</i>) in the San Francisco bay area: application of adaptive genomic variation to conservation in a highly impacted landscape Open
The streams draining of into San Francisco Bay, California, have been impacted by habitat alteration for over 150 years, and roads, dams, water diversions, and other impediments now block the paths of many aquatic migratory species. These …
View article: You Can’t Unscramble an Egg: Population Genetic Structure of <i>Oncorhynchus mykiss</i> in the California Central Valley Inferred from Combined Microsatellite and Single Nucleotide Polymorphism Data
You Can’t Unscramble an Egg: Population Genetic Structure of <i>Oncorhynchus mykiss</i> in the California Central Valley Inferred from Combined Microsatellite and Single Nucleotide Polymorphism Data Open
Steelhead/rainbow trout (Oncorhynchus mykiss) are found in all of the major tributaries of the Sacramento and San Joaquin rivers, which flow through California's Central Valley and enter the ocean through San Francisco Bay and the Golden G…
View article: Shifting Thresholds: Rapid Evolution of Migratory Life Histories in Steelhead/Rainbow Trout,<i>Oncorhynchus mykiss</i>
Shifting Thresholds: Rapid Evolution of Migratory Life Histories in Steelhead/Rainbow Trout,<i>Oncorhynchus mykiss</i> Open
Expression of phenotypic plasticity depends on reaction norms adapted to historic selective regimes; anthropogenic changes in these selection regimes necessitate contemporary evolution or declines in productivity and possibly extinction. A…
View article: You Can't Unscramble an Egg: Population Genetic Structure of in the California Central Valley Inferred from Combined Microsatellite and Single Nucleotide Polymorphism Data
You Can't Unscramble an Egg: Population Genetic Structure of in the California Central Valley Inferred from Combined Microsatellite and Single Nucleotide Polymorphism Data Open
doi: http://dx.doi.org/10.15447/sfews.2015v13iss4art3 Steelhead/rainbow trout (Oncorhynchus mykiss) are found in all of the major tributaries of the Sacramento and San Joaquin rivers, which flow through California’s Central Valley and ente…