A5085346609- Genetic diversity and population structure
- Fish Ecology and Management Studies
- Genetic and phenotypic traits in livestock
- Animal Behavior and Reproduction
- Amphibian and Reptile Biology
- Environmental DNA in Biodiversity Studies
- Fish Biology and Ecology Studies
- Turtle Biology and Conservation
- Identification and Quantification in Food
- Marine and fisheries research
- Genomics and Phylogenetic Studies
- Wildlife Ecology and Conservation
- Cephalopods and Marine Biology
- Animal Ecology and Behavior Studies
- Plant and animal studies
- Species Distribution and Climate Change
- Reproductive biology and impacts on aquatic species
- Evolution and Genetic Dynamics
- Marine animal studies overview
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Genetics, Bioinformatics, and Biomedical Research
- Avian ecology and behavior
- Protist diversity and phylogeny
- Genetic Mapping and Diversity in Plants and Animals
- Parasite Biology and Host Interactions
NOAA National Marine Fisheries Service Southwest Fisheries Science Center
2015-2025
University of California, Santa Cruz
2014-2024
NOAA National Marine Fisheries Service
2014-2024
National Oceanic and Atmospheric Administration
2012-2024
Simon Fraser University
2015
University of California, Berkeley
2015
NOAA National Marine Fisheries Service Northwest Fisheries Science Center
2015
Brigham Young University
2004-2005
University of Georgia
1997-2002
Abstract Males and females often differ in their fitness optima for shared traits that have a genetic basis, leading to sexual conflict. Morphologically differentiated sex chromosomes can resolve this conflict protect sexually antagonistic variation, but they accumulate deleterious mutations. However, how is resolved species lack largely unknown. Here we present chromosome-anchored genome assembly rainbow trout ( Oncorhynchus mykiss ) characterize 55-Mb double-inversion supergene mediates...
As evidenced by the articles in this volume, a recent increase interest mating systems of poikilothermic vertebrates has focused primarily on fishes, few amphibians, and squamate reptiles. Turtles contrast have received relatively little attention, yet they display wide variety behaviors life-history characteristics that make them excellent candidates for addressing several aspects genetic parentage should contribute to broader understanding animal reproductive strategies. Here we focus...
Sixty-six haplotypes at a locus containing simple dinucleotide (CA)n microsatellite repeat were isolated by PCR-single-strand conformational polymorphism from populations of the horseshoe crab Limulus polyphemus. These sequenced to assess nucleotide variation directly. Thirty-four distinct sequences (alleles) identified in region 570 bp long that included motif. In itself, CA-number varied integer values 5 11 across alleles, except (CA)8 class was not observed. Differences among alleles due...
Rapid adaptation to novel environments may drive changes in genomic regions through natural selection. Such be population-specific or, alternatively, involve parallel evolution of the same region multiple populations, if that contains genes or co-adapted gene complexes affecting selected trait(s). Both quantitative and population genetic approaches have identified associations between specific anadromous (steelhead) resident (rainbow trout) life-history strategies Oncorhynchus mykiss. Here,...
Differentiation between ecotypes is usually presumed to be complex and polygenic. Seasonal patterns of life history in salmon are used categorize them into ecotypes, which often considered "distinct" animals. Using whole-genome sequencing tribal fishery sampling Chinook salmon, we show that a single, small genomic region nearly perfectly associated with spawning migration timing but not adiposity or sexual maturity, traits long perceived as central ecotypes. Distinct does prevent...
Adaptation to novel habitats and phenotypic plasticity can be counteracting forces in evolution, but both are key characteristics of the life history steelhead/rainbow trout (Oncorhynchus mykiss). Anadromous steelhead reproduce freshwater river systems small coastal streams grow mature ocean. Resident rainbow trout, either sympatric with or isolated above barrier dams waterfalls, represent an alternative life-history form that lives entirely freshwater. We analyzed population genetic data...
Abstract Understanding life history traits is an important first step in formulating effective conservation and management strategies. The use of artificial propagation supplementation as such a strategy can have numerous effects on the supplemented natural populations minimizing divergence crucial these effects. Here, we single nucleotide polymorphism ( SNP ) genotypes for large‐scale parentage analysis pedigree reconstruction hatchery population steelhead, anadromous form rainbow trout....
Abstract The streams draining of into San Francisco Bay, California, have been impacted by habitat alteration for over 150 years, and roads, dams, water diversions, other impediments now block the paths many aquatic migratory species. These changes can affect genetic structure fish populations, as well driving adaptive evolution to novel environmental conditions. Here, we determine evolutionary relationships Bay Area steelhead/rainbow trout ( Oncorhynchus mykiss ) populations show that (i)...
Abstract Giant Amazon river turtles, Podocnemis expansa, are indigenous to the Amazon, Orinoco, and Essequibo River basins, distributed across nearly entire width of South American continent. Although once common, their large size, high fecundity, gregarious nesting, made P. expansa especially vulnerable over‐harvesting for eggs meat. Populations have been severely reduced or extirpated in many areas throughout its range, species is now regulated under Appendix II Convention on International...
As highlighted by many of the papers in this issue, research on genomic basis adaptive phenotypic variation natural populations has made spectacular progress past few years, largely due to advances sequencing technology and analysis. Without question, resulting data will improve understanding regions genome under selection extend knowledge genetic evolution. What is far less clear, but been focus active discussion, how such information can or should transfer into conservation practice...
Expression of phenotypic plasticity depends on reaction norms adapted to historic selective regimes; anthropogenic changes in these selection regimes necessitate contemporary evolution or declines productivity and possibly extinction. Adaptation conditional strategies following a change the regime requires either environmentally influenced cue (e.g., size-at-age) state size threshold) at which an individual switches between alternative tactics. Using population steelhead (Oncorhynchus...
Single-nucleotide polymorphisms (SNPs) are highly abundant markers, which 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 performed high coverage whole genome resequencing with 61 unrelated samples, representing a wide range steelhead populations, 49 new samples added to 12...
Abstract 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 protect sexually antagonistic polymorphisms but accumulate deleterious mutations. However, many taxa lack differentiated chromosomes, how is resolved these species largely unknown. Here we present chromosome-anchored genome assembly for rainbow trout ( Oncorhynchus mykiss ) characterize 56 Mb double-inversion supergene...
Genetic methods have become an essential component of ecological investigation and conservation planning for fish wildlife. Among these is the use genetic marker data to identify individuals populations, or stocks, origin. More recently, that involve pedigree reconstruction relationships between within populations also common. We present, here, a novel set multi-allelic microhaplotype markers Chinook salmon which provide unprecedented resolution population discrimination relationship...
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 mixed data available. In particular, there very few on sex ratios juvenile nonanadromous (resident) fish to help assess composition various life stages life‐history types. We used a recently developed Y‐chromosome genetic marker ratio stream‐dwelling (i.e.,...
Abstract Novel genetic resources now make it possible to directly assess the effects of natural selection on specific regions salmonid genome. Natural loci will also affect variation in linked flanking through “hitchhiking” effects, causing greater differentiation between populations than would be expected from purely neutral processes. Here we identify candidate genomic for differential two closely related steelhead–rainbow trout Oncorhynchus mykiss separated last century following...
Abstract 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 steelhead (anadromous trout) Scott Creek, California. Genetic assignment tests found that frequency anadromous origin fish varied by sampling location within watershed. Individuals immediately below barriers assigned both above‐barrier (37%) (63%)...