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September 2003 - present
September 2003 - present
January 2004 - present
Publications
Publications (83)
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‐throughput sequencing inspired publications heralding the ‘genomics revolution’, with predictions about its fu...
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 origin. More recently, methods that involve genetic pedigree reconstruction to identify relationships between indi...
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-wide sequence data in nonmodel organisms. The salmonids (salmon, trout, and charr) are a taxonomic group with abu...
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 California waterways and reservoirs over the past century, possibly resulting in introgression into wild populations...
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 freshwater resident life history is expressed in the Chubut and Negro rivers of northern Argentinian Patagonia, whereas...
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 salmonid species Oncorhynchus mykiss, and investigated how differences among genetic lineages and environmental va...
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 anadromous steelhead trout ( Oncorhynchus mykiss ) from the Russian River, CA, USA, to elucidate sex‐specific patterns o...
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-allelic genetic markers that utilize a high-throughput genomic amplicon sequencing approach to genotype large numbe...
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 ada...
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) genetic variants occurring in populations of rainbow trout (Oncorhynchus mykiss) independently isolated from ocean a...
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 life‐history traits including whether fish were strays. Otolith natural tags (87Sr/86Sr) and genetic stock identification...
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 traits specific to their timing and presumed divergence being caused by the lack of interbreeding. By looking at...
The expression of anadromy in partially migratory salmonid populations is influenced by sex-specific interactions among an individual’s genotype, condition, and environment, but genotype–phenotype relationships prior to the expression of migratory type are poorly understood. We examined whether juvenile growth and condition differed with respect to...
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Males and females often differ in their fitness optima for shared traits that have a shared genetic basis, leading to sexual conflict. Morphologically differentiated sex chromosomes can resolve this conflict and protect sexually antagonistic variation, but they accumulate deleterious mutations. However, how sexual conflict is resolved in species th...
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 approximately 88 million years ago presents an excellent opportunity for studying the effects of WGD as ∼10–15% of each s...
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 anadromous ecotype of the species Oncorhynchus mykiss. These programs sometimes use nonindigenous broodstock s...
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 deleterious mutations. However, many taxa lack differentiated sex chromosomes, and how sexual conflict is resolv...
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 associated DNA (RAD) libraries, reduced representation libraries (RRL) and RNA sequencing. Recently we have perfor...
Validation of the putative SNPs using the 57K SNP chip data.
Actual sequence coverage and genome mapping information for each of the 61 samples.
The Mokelumne River Hatchery has a long history of importation of steelhead eggs and/or fingerlings from other sources, especially the Nimbus and Feather Fish Hatcheries. The production target for the Mokelumne River Fish Hatchery steelhead program is 250,000 yearlings for release each year, which is rarely, if ever, met due to low numbers of adult...
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 regime to restore historic or desired trait values. Here we examined the potential utility of this approach to rest...
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 technology and analysis. Without question, the resulting genomic data will improve the understanding of regions of th...
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 changes can affect the genetic structure of fish populations, as well as driving adaptive evolution to novel en...
Steelhead (Oncorhynchus mykiss) populations have declined dramatically in many parts of their range in North America, most critically in Southern California, where these anadromous trout are now classified as ‘Endangered’ under the United States Endangered Species Act. The widespread introduction of hatchery rainbow trout, the domesticated freshwat...
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 Gate. This river system is heavily affected by water development, agriculture, and invasive species, and salmon...
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. Adaptation of conditional strategies following a change in the selection regime requires evolution of either the...
Parallel adaptive divergence of migratory and reproductive behavior can occur in multiple populations when similar selection is acting on these traits. Timing of migration, sexual maturity, and reproduction can have major impacts on the dynamics and viability of a population. Life-history variation in steelhead, Oncorhynchus mykiss, including varia...
The extent to which human activities have impacted the genetic characteristics and relationships among populations over time is a long-standing, fundamental question in the field of conservation genetics. While many important insights can be gained through the analysis of historical samples from archival sampling efforts and museum collections, deg...
Rapid adaptation to novel environments may drive changes in genomic regions through natural selection. Such changes may be population-specific or, alternatively, may involve parallel evolution of the same genomic region in multiple populations, if that region contains genes or co-adapted gene complexes affecting the selected trait(s). Both quantita...
Expression of phenotypic plasticity depends on reaction norms adapted to historic selective regimes; anthropogenic changes in these selection regimes necessitate contemporary evolution or extirpation. Adaptation of conditional strategies following a change in the selection regime requires evolution of either the environmentally influenced cue (e.g....
Expression of phenotypic plasticity depends on reaction norms adapted to historic selective regimes; anthropogenic changes in these selection regimes necessitate contemporary evolution or extirpation. Adaptation of conditional strategies following a change in the selection regime requires evolution of either the environmentally influenced cue (e.g....
Understanding life history traits is an important first step in formulating effective conservation and management strategies. The use of artificial propagation and supplementation as such a strategy can have numerous effects on the supplemented natural populations and minimizing life history divergence is crucial in minimizing these effects. Here,...
Background/Question/Methods
Quantifying rapid evolution will give insight into how populations respond to novel anthropogenic perturbations. Understanding how threshold traits respond to selection is particularly important and challenging as they are involved in important ecological processes, including dispersal and migration strategies (stay or...
Background/Question/Methods
Animal migrations are amazing phenomena that connect disparate habitats, exerting large influence over recipient ecosystem dynamics. However, migrations may also make populations more vulnerable to anthropogenic impacts such as blockage of migration corridors. A population’s fate in the face of a novel threat depends o...
We investigated the interaction among genetically identified origin, behavioral tendency to emigrate, and Na ⁺ , K ⁺ ‐ATPase enzyme activity in recently diverged subpopulations of resident (above‐barrier) rainbow trout Oncorhynchus mykiss and steelhead (anadromous rainbow trout) in Scott Creek, California. Genetic assignment tests found that the fr...
Abstract – Differential rates of anadromy between males and females are common in partially migratory salmonid populations, but this pattern is not fully clear for Oncorhynchus mykiss (rainbow trout/steelhead) from the limited but mixed data available. In particular, there are very few data on sex ratios of juvenile and nonanadromous (resident) fis...
Coho salmon (Oncorhynchus kisutch) populations at the southern extent of their range, in the Central California Coast (CCC) ESU, are in steep decline and are ESA-listed as Endangered. In recent years, the species has disappeared from numerous basins and streams, including most tributaries of the Russian River, and fish that remain show a high level...
Rapid adaptation to novel environments may be accompanied by genetic changes in specific genomic regions that contain genes controlling selected traits. Identification of marker loci with greater differentiation between populations than expected by purely neutral genomic processes can localize regions of the genome linked to genes affected by diver...
Background/Question/Methods
The traditional view of species as static units is being reexamined due to increasing evidence that ecological and evolutionary processes may overlap in time. Contemporary evolution can have ecological consequences if selection is shaping the morphologies of trophic traits (e.g. beak depth, gill raker spacing). However;...
When natural populations exchange migrants at a rate proportional to their geographic distance, population genetics theory
leads to the expectation of a pattern of isolation-by-distance (IBD), whereby geographic and genetic distance are correlated.
However, the presence or absence of such patterns in modern populations may not fully reflect the his...
Freshwater-resident coastal rainbow trout Oncorhynchus mykiss irideus and the anadromous form of the subspecies, coastal steelhead (summer and winter runs), are present throughout the lower Klamath River–Trinity River system. Although coastal steelhead and other anadromous salmonids historically migrated into the Upper Klamath Basin (which encompas...
Novel genetic resources now make it possible to directly assess the effects of natural selection on specific regions of the salmonid genome. Natural selection on specific genetic loci will also affect the variation in linked flanking regions through “hitchhiking” effects, causing greater differentiation between populations than would be expected fr...
Molecular polymorphisms have been used in a variety of ways to estimate both effective and local census population sizes in nature. A related approach for estimating the current size of a breeding population, explored here for the first time, is the use of genetic ‘marks’ reconstructed for otherwise unknown parents in paternity or maternity analyse...
*NOAA Southwest Fisheries Science Center, National MarineFisheries Service, 110 Shaffer Road, Santa Cruz, CA 95060,USA, †Department of Ecology and Evolutionary Biology,University of California, Santa Cruz, CA, USA, ‡Department ofApplied Math and Statistics, University of California, SantaCruz, CA, USAReceived 11 March 2009; revision received 30 Apr...
Adaptation to novel habitats and phenotypic plasticity can be counteracting forces in evolution, but both are key characteristics of the life history of steelhead/rainbow trout (Oncorhynchus mykiss). Anadromous steelhead reproduce in freshwater river systems and small coastal streams but grow and mature in the ocean. Resident rainbow trout, either...
We developed nine polymorphic microsatellite markers for the Mexican spadefoot toad, Spea multiplicata. Allele numbers range from five to 12, with observed heterozygosities from 0.48 to 0.87. Because two loci are in linkage disequilibrium, these nine loci provide eight independent markers. Three loci exhibit departure from Hardy-Weinberg equilibriu...
Abstract Steelhead/rainbow trout of the species Oncorhynchus,mykissare found in all of the major drainages of the Central Valley, which includes rivers and streams that drain into both the Sacramento and San Joaquin sub-basins. Most of the tributary rivers in this area have dams or other impoundments,and many,of the resulting reservoirs have been s...
An analysis of population structure and genetic diversity was conducted on samples of Oncorhynchus mykiss (steelhead/rainbow trout) from 33 sites in the Klamath–Trinity River basin. Genotype data from 16 microsatellite loci in
almost 1,700 fish revealed genetic differentiation between most sampled locations. Two pairs of samples from the same sites...
Molecular genetic analysis has long been used to identify species or populations that otherwise may be difficult to distinguish. More than 100 species of rockfish (genus Sebastes) occur worldwide, and more than 50 species may be found in relatively small regions, such as the Monterey Bay or Channel Islands in central and southern California. Many s...
We used genetic data from 7 microsatellite loci to determine the frequency of multiple paternity in clutches of giant Amazon river turtles, Podocnemis expansa, from the Orinoco River in Venezuela. Among hatchlings sampled from 32 clutches, paternity analysis found that a minimum of 10.3% could conclusively be shown to have been sired by more than o...
Harbour seals sometimes breed along inland travel corridors where females become clustered in space and time and males establish underwater acoustic display territories similar to terrestrial arenas known as resource-based leks. Under these conditions, we predicted that higher levels of polygyny would be observed than has been previously reported f...
Giant Amazon river turtles, Podocnemis expansa, are indigenous to the Amazon, Orinoco, and Essequibo River basins, and are distributed across nearly the entire width of the South American continent. Although once common, their large size, high fecundity, and gregarious nesting, made P. expansa especially vulnerable to over-harvesting for eggs and m...
Mating systems within the genus Peromyscus have traditionally been inferred from field observations of spatial relationships of males and females and from laboratory behavioral studies. The majority of species within Peromyscus are assumed to be promiscuous, but rarely have these conclusions been verified with molecular data. Genotypes constructed...
Both the ability to generate DNA data and the variety of analytical methods for conservation genetics are expanding at an ever-increasing pace. Analytical approaches are now possible that were unthinkable even five years ago due to limitations in computational power or the availability of DNA data, and this has vastly expanded the accuracy and type...
Both the ability to generate DNA data and the variety of analytical methods for conservation genetics are expanding at an ever-increasing pace. Analytical approaches are now possible that were unthinkable even five years ago due to limitations in computational power or the availability of DNA data, and this has vastly expanded the accuracy and type...
When females receive no direct benefits from multiple matings, concurrent multiple paternity is often explained by indirect genetic benefits to offspring. To examine such possibilities, we analyzed genetic paternity for 1,272 hatchlings, representing 227 clutches, from a nesting population of painted turtles (Chrysemys picta) on the Mississippi Riv...
Molecular polymorphisms have been used in a variety of ways to estimate both effective and local census population sizes in nature. A related approach for estimating the current size of a breeding population, explored here for the first time, is the use of genetic 'marks' reconstructed for otherwise unknown parents in paternity or maternity analyse...
Most studies of genetic parentage in natural populations have been limited to a single breeding season or reproductive episode and, thus, provide only a snapshot of individuals' mating behaviours. Female turtles can store viable sperm in their reproductive tracts for as long as several years, but the extent to which this capacity is utilized in nat...
As evidenced by the articles in this volume, a recent increase in interest in the mating systems of poikilothermic vertebrates has focused primarily on fishes, a few amphibians, and squamate reptiles. Turtles by contrast have received relatively little attention, yet they display a wide variety of mating behaviors and life-history characteristics t...
The phylogenetic relationships among populations of the fossorial California legless lizard, Anniella pulchra, were examined by sequencing a 990-bp region of the mitochondrial cytochrome b gene. The mitochondrial DNA gene tree was then compared with the geographic distributions of two currently recognized subspecies: A. p. nigra, a melanic form res...
— The phylogenetic relationships among populations of the fossorial California legless lizard, Anniella pulchra, were examined by sequencing a 990-bp region of the mitochondrial cytochrome b gene. The mitochondrial DNA gene tree was then compared with the geographic distributions of two currently recognized subspecies: A. p. nigra, a melanic form r...
This study examines the effects of general-protein-9 (Gp-9) genotype on the body mass of polygyne (multiple-queens per nest) Solenopsis invicta Buren workers and males. We found that Gp-9 genotype was significantly associated with variation in worker mass in field but not laboratory colonies. Moreover, triploid workers with 2 distinguishable genoty...
Sixty-six haplotypes at a locus containing a simple dinucleotide (CA)n microsatellite repeat were isolated by PCR-single-strand conformational polymorphism from populations of the horseshoe crab Limulus polyphemus. These haplotypes were sequenced to assess nucleotide variation directly. Thirty-four distinct sequences (alleles) were identified in a...
