A5033241824- Genetic diversity and population structure
- Fish Ecology and Management Studies
- Genomics and Phylogenetic Studies
- Identification and Quantification in Food
- Isotope Analysis in Ecology
- Pacific and Southeast Asian Studies
- Genetic and phenotypic traits in livestock
- Environmental DNA in Biodiversity Studies
- Coral and Marine Ecosystems Studies
- Marine animal studies overview
- Species Distribution and Climate Change
- Geomagnetism and Paleomagnetism Studies
- Aquatic Invertebrate Ecology and Behavior
- Marine and fisheries research
- Magnetic and Electromagnetic Effects
- Aquaculture disease management and microbiota
- Physiological and biochemical adaptations
- Plant and Fungal Species Descriptions
- Genetics, Bioinformatics, and Biomedical Research
- Mollusks and Parasites Studies
- Ichthyology and Marine Biology
- Research Data Management Practices
- Paleontology and Evolutionary Biology
- Scientific Computing and Data Management
- Evolution and Science Education
University of Hawaii at Hilo
2015-2023
United States Geological Survey
2005-2023
Pacific Island Ecosystems Research Center
2023
Oregon Department of Fish and Wildlife
2007-2022
Oregon State University
2005-2022
University of Hawaii–West Oahu
2022
University of Hawaiʻi at Mānoa
2019
Forest and Rangeland Ecosystem Science Center
2005
University of Wisconsin–Milwaukee
2003
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 Single nucleotide polymorphisms (SNPs) are appealing genetic markers due to several beneficial attributes, but uncertainty remains about how many of these bi‐allelic necessary have sufficient power differentiate populations, a task now generally accomplished with highly polymorphic microsatellite markers. In this study, we tested the utility 37 SNPs and 13 microsatellites for differentiating 29 broadly distributed populations Chinook salmon ( n = 2783). Information content all loci...
Phenotypic variation is critical for the long-term persistence of species and populations. Anthropogenic activities have caused substantial shifts reductions in phenotypic across diverse taxa, but underlying mechanism(s) (i.e., plasticity and/or genetic evolution) consequences (e.g., ability to recover variation) are unclear. Here we investigate widespread dramatic changes adult migration characteristics wild Chinook salmon by dam construction other anthropogenic activities. Strikingly, find...
Phylogeographical analyses conducted in the Pacific Northwestern United States have often revealed concordant patterns of genetic diversity among taxa. These studies demonstrate distinct North/South discontinuities that been attributed to Pleistocene glaciation. We examined phylogeographical red tree voles (Phenacomys longicaudus) western Oregon by analysing mitochondrial control region sequences for 169 individuals from 18 areas across species' range. Cytochrome b were also analysed a...
The field of conservation genetics, when properly implemented, is a constant juggling act integrating molecular ecology, and demography with applied aspects concerning managing declining species or implementing laws policies. This young has grown substantially since the 1980s following development polymerase chain reaction now into genomics era. Our laboratory 'grown up' field, having worked on these issues for over three decades. multidisciplinary approach entails understanding behavior...
Animals use geomagnetic fields for navigational cues, yet the sensory mechanism underlying magnetic perception remains poorly understood. One idea is that are physically transduced by magnetite crystals contained inside specialized receptor cells, but evidence intracellular, biogenic in eukaryotes scant. Certain bacteria produce intracellular compartments, representing most ancient form of biomineralization known and having evolved prior to emergence crown group eukaryotes, raising question...
Abstract The number of greater prairie‐chickens in Wisconsin has decreased by 91% since 1932. current population approximately 1500 birds exists primarily four isolated management areas. In previous studies the populations we documented low levels genetic variation at microsatellite loci and mitochondrial DNA control region. Here investigate changes structure between areas over last 50 years. We estimated harmonic mean effective size ( N e ) years comparing allele frequencies from early...
Abstract: Over the last century, populations of Greater Prairie Chicken ( Tympanuchus cupido ) have declined or gone extinct throughout midwestern North America. In Wisconsin population by 50% from 1951 to 1961 and has remained at low 1500 individuals but fluctuating levels for past 40 years. We examined historic contemporary 1996–1999 prairie chickens in determine whether there was a loss genetic variation following bottleneck. compared microsatellite DNA six loci 1951, n = 47 1996–1999, 87...
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 Managing weak stocks in mixed‐stock fisheries often relies on proxies derived from data‐rich indicator stocks, although there have been limited tests of the appropriateness such proxies. For example, full cohort reconstruction tagged Klamath River fall‐run Chinook Salmon Oncorhynchus tshawytscha northern California enables use detailed models to inform management. Information gained this stock is also used management untagged, threatened Coastal (CCC) stock, where it assumed that a...
The rice coral, Montipora capitata, is widely distributed throughout the Indo-Pacific and comprises one of most important reef-building species in Hawaiian Islands. Here, we describe a de novo assembly its genome based on linked-read sequencing approach developed by 10x Genomics. final draft consisted 27,870 scaffolds with N50 size 186 kb contained fairly complete set (81%) metazoan benchmarking (BUSCO) genes. Based haploid (615 Mb) read k-mer profiles, estimated to fall between 600 700 Mb,...
Understanding seasonal migration and localized persistence of populations is critical for effective species harvest conservation management. Pacific salmon (genus Oncorhynchus) forecasting models predict stock composition, abundance, distribution during annual assessments proposed fisheries impacts. Most models, however, fail to account the influence biophysical factors on year-to-year fluctuations in migratory distributions stock-specific survival. In this study, ocean relative abundance...
Hawaiian plant radiations often result in lineages with exceptionally high species richness and extreme morphological ecological differentiation. However, they typically display low levels of genetic variation, hindering the use classic DNA markers to resolve their evolutionary histories. Here we utilize a phylogenomic approach generate first generally well-resolved phylogenetic hypothesis for evolution Bidens (Asteraceae) adaptive radiation, including refined initial colonization divergence...
Scleractinian corals are a vital component of coral reef ecosystems, and significant cultural economic value worldwide. As anthropogenic natural stressors contributing to global decline reefs, understanding health is critical help preserve these ecosystems. Growth anomaly (GA) disease that has negative impacts on biology, yet our its etiology pathology lacking. In this study we used RNA-seq along with de novo metatranscriptome assembly homology assignment identify genes expressed in three...
Abstract Taro (Colocasia esculenta) is a food staple widely cultivated in the humid tropics of Asia, Africa, Pacific and Caribbean. One greatest threats to taro production Leaf Blight caused by oomycete pathogen Phytophthora colocasiae. Here we describe de novo genome assembly use it analyze sequence data from resistant mapping population. The was assembled linked-read sequences (10x Genomics; ∼60x coverage) gap-filled scaffolded with contigs Oxford Nanopore Technology long-reads linkage map...
Taro, Colocasia esculenta, is one of the world's oldest root crops and particular economic cultural significance in Hawai'i, where historically more than 150 different landraces were grown. We developed a genome-wide set 2400 high-quality single nucleotide polymorphism (SNP) markers from 70 taro accessions Hawaiian, South Pacific, Palauan, mainland Asian origins, with several objectives: 1) uncover phylogenetic relationships between Hawaiian other Pacific landraces, 2) shed light on history...
Abstract: Genome-level data can provide researchers with unprecedented precision to examine the causes and genetic consequences of population declines, which inform conservation management. Here, we present a high-quality, long-read, de novo genome assembly for one world's most endangered bird species, 'Alalā (Corvus hawaiiensis; Hawaiian crow). As only remaining native crow species in Hawai'i, survived solely captive-breeding program from 2002 until 2016, at point long-term reintroduction...
Data analysis tasks at an Ocean Observatory require integrative and domain-specialized use of database, workflow, visualization systems. We describe a platform to support these developed as part the cyberinfrastructure NSF Science Technology Center for Coastal Margin Observation Prediction integrating provenance-aware workflow system, 3D visualization, remote query engine large-scale ocean circulation models. show how disparate tools complement each other give examples real scientific...
The plant genus Bidens (Asteraceae or Compositae; Coreopsidae) is a species-rich and circumglobally distributed taxon. 19 hexaploid species endemic to the Hawaiian Islands are considered an iconic example of adaptive radiation, which many imperiled high conservation concern. Until now, no genomic resources were available for this genus, may serve as model system understanding evolutionary genomics explosive diversification. Here, we present high-quality reference genome Hawai'i Island B....