A5061492432- Fish Ecology and Management Studies
- Genetic diversity and population structure
- Genetic and phenotypic traits in livestock
- Environmental DNA in Biodiversity Studies
- Identification and Quantification in Food
- Aquatic Invertebrate Ecology and Behavior
- Hydrology and Sediment Transport Processes
- Geriatric Care and Nursing Homes
- Microbial Community Ecology and Physiology
- Wildlife-Road Interactions and Conservation
- Fish Biology and Ecology Studies
- Aquaculture disease management and microbiota
- Hydrology and Watershed Management Studies
- Animal Behavior and Reproduction
- Molecular Biology Techniques and Applications
- Wildlife Ecology and Conservation
- Forensic and Genetic Research
- Fish biology, ecology, and behavior
Cramer Fish Sciences (United States)
2012-2024
Washington Department of Fish and Wildlife
2009-2013
University of California, Davis
2002
An international multi-laboratory project was conducted to develop a standardized DNA database for Chinook salmon (Oncorhynchus tshawytscha). This in response the needs of Technical Committee Pacific Salmon Commission identify stock composition caught fisheries during their oceanic migrations. Nine genetics laboratories identified 13 microsatellite loci that could be reproducibly assayed each laboratories. To test were reproducible among laboratories, blind tests verify scoring consistency...
Abstract Environmental DNA (eDNA) detection methods can complement traditional biomonitoring to yield new ecological insights in aquatic systems. However, the conceptual and methodological frameworks for eDNA interpretation were developed primarily freshwater environments have not been well established estuaries marine that are by nature dynamic, turbid, hydrologically complex. context species life history critical successful application of methods, challenges associated with subject a...
Recent advances in molecular interrogation techniques now allow unprecedented genomic inference about the role of adaptive genetic divergence wild populations. We used high-throughput genotyping to screen a genome-wide panel 276 single nucleotide polymorphisms (SNPs) for economically and culturally important salmonid Oncorhynchus mykiss. Samples included 805 individuals from 11 anadromous resident populations northwestern United States British Columbia, represented two major lineages...
Environmental DNA (eDNA) is an emerging sampling method that has been used successfully for detection of rare aquatic species. The Identification tools are less stressful target organisms become increasingly important and endangered A decline in abundance the Southern Distinct Population Segment (DPS) North American Green Sturgeon located California's Central Valley led to its listing as Threatened under Federal Endangered Species Act 2006. While visual surveys spawning effective at...
The dynamic Quaternary geology of the Pacific Ring Fire created substantial challenges for biogeography. Fish life history and population genetic variation were shaped by climate change, repeated formation subsidence ice sheets, sea-level volcanism tectonics, isostatic rebound, now human activities. It is widely recognized in Chinook salmon (Oncorhynchus tshawytscha) that parallel evolution phenotypic plasticity have obscured range-wide patterns life-history segregation with evolutionary...
Abstract It is widely recognized that genetic diversity within species shaped by dynamic habitats. The quantitative and molecular patterns observed are the result of demographics, mutation, migration, adaptation. populations rainbow trout Oncorhynchus mykiss in Columbia River basin (including both resident anadromous forms various subspecies) present a special challenge to understanding relative roles those factors. Standardized microsatellite data were compiled for 226 collections (15,658...
Introductions of non-native fish have the potential to cause substantial economic and ecological losses. In western United States, brook trout (Salvelinus fontinalis) are widely established pose a threat persistence bull confluentus), native char listed as threatened under US Endangered Species Act, due competition hybridization. With identified factor limiting recovery ESA-listed in Malheur Watershed eastern Oregon, managers pursuing eradication efforts. Key efforts is reliable monitoring...
Abstract Due to the challenges associated with monitoring in riverine environments, unbiased and precise spawner abundance estimates are often lacking for populations of Pacific salmon Oncorhynchus spp. listed under Federal Endangered Species Act. We investigated genetic approaches estimate 2009 a population Columbia River Chinook Salmon tshawytscha via mark–recapture rarefaction curves. The marks were genotyped carcasses collected from spawning area during first sampling event. second event...
Microsatellites, which have rapidly become the preferred markers in population genetics, reliably assign individual chinook salmon to winter, fall, late-fall, or spring runs Sacramento River California's Central Valley (Banks et al. 2000 . Can. J. Fish. Aquat. Sci. 57:915–927). A substantial proportion of this discriminatory power comes from Ots-2, a simple CA repeat, is expected evolve under stepwise mutation model. We sequenced 300-bp region around locus and typed 668...
Abstract 1. Around the globe, instream infrastructures such as dams, weirs, and culverts associated with roads are wide‐spread continue to be constructed. There is limited documentation of smaller infrastructure because mixed regulation laws related construction, well difficulty in their size frequency waterscapes. 2. We reviewed evidence different methods used quantify environmental ecological responses (positive, negative, or neutral) culverts. 3. Most studies (78% 87) our review evaluated...
Abstract We introduce artemis, a new package for the R statistical programming environment designed to analyze quantitative polymerase chain reaction (qPCR) data from environmental DNA studies. The artemis directly addresses several challenges analyzing eDNA survey data, including censorship of generated by qPCR analysis. performance models is compared with commonly used regression approaches using both simulated and experimental data. demonstrate that in have favorable characteristics...
Abstract Quantifiable measurement of habitat restoration effects on salmonid reproductive performance is limited, although it necessary for evaluating whether population responses follow management actions. We investigated using close‐kin mark‐recapture methods to partition within standard monitoring metrics juvenile emigrants leaving the natal reach. This approach allowed statistical comparison relative capture rates (recruitment) from Chinook Salmon ( Oncorhynchus tshawytscha ) naturally...
Abstract We used pattern recognition algorithms and image processing to identify individual Chinook salmon Oncorhynchus tshawytscha . Using melanophore spot patterns located on the dorsal head region, ranked all database images against each other. coupled this technology with a graphical user interface visually confirm or reject top‐ranked algorithm results tested process 295 juvenile in seven photo sessions over 251‐d period. Juveniles began developing spots, identifiable images, between...
Abstract The goal for using genetic information derived from embryo samples is to gain insight into the reproductive biology of adult white sturgeon, Acipenser transmontanus Richardson. relationship between egg development stages on extraction quality DNA was determined, and subsequent genotype data were used infer contributing spawner numbers. White sturgeon present in extractions all stages; however, pre‐gastrulation stage embryos generally failed amplify sufficient loci analysis. Using...
The Giant Gartersnake (Thamnophis gigas) is a low density visually evasive species with detection probability based on standard field survey methods (e.g., traps, visual census). Habitat loss has resulted in extirpations or serious declines for T. gigas populations throughout the southern two thirds of its historic range. Uncertainty regarding current distribution and occupancy present management challenges species. Enhancing sensitivity through development environmental DNA sampling (eDNA)...
Abstract We compared a length‐at‐date growth model to truss network (morphometric) models for classifying emigrating juvenile (age 0 through age 1) California Central Valley Chinook Salmon Oncorhynchus tshawytscha three genetically identified races at upstream (salmon generally younger and smaller) downstream older larger) monitoring stations. Morphometric including capture date head standard length ratio performed better than the distinguishing assigned fall‐run late juveniles; prediction...
Abstract Stochastic fluctuation in allele frequencies may reflect microevolutionary processes responsible for genetic change, such as small effective population size ( N e ), which is a legitimate concern imperiled populations affected by environmental or anthropogenic factors. In salmonids, recent empirical studies have provided conflicting results regarding the consistency of within‐population variation over time. present study, we surveyed at 14 microsatellite loci two endemic summer...
Delta Smelt have collapsed demographically, but little is known about their current genetic status. We used 12 microsatellite loci to evaluate two measures of the effective population size (Ne) Smelt. Ne a measure that offers predictive power regarding loss diversity in over time, as well short and long-term risks for fitness resulting from low diversity. found too high accurately estimate with data (upper 95% confidence intervals were infinity), lower NeLD (linkage disequilibrium Ne) above...