A5056939192- Environmental DNA in Biodiversity Studies
- Microbial Community Ecology and Physiology
- Genetic diversity and population structure
- Genomics and Phylogenetic Studies
- Species Distribution and Climate Change
- Protist diversity and phylogeny
- Identification and Quantification in Food
- Genetic and phenotypic traits in livestock
- Avian ecology and behavior
- Theoretical and Computational Physics
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Complex Network Analysis Techniques
- Evolution and Genetic Dynamics
- Plant Taxonomy and Phylogenetics
- Stochastic processes and statistical mechanics
- Herpesvirus Infections and Treatments
- Neural Networks and Applications
- Bacteriophages and microbial interactions
- Animal Behavior and Reproduction
- Animal Ecology and Behavior Studies
- Platelet Disorders and Treatments
- Statistical Mechanics and Entropy
- Ecology and Vegetation Dynamics Studies
Colorado State University
2019-2025
University of California, Los Angeles
2018-2021
University of California Division of Agriculture and Natural Resources
2021
University of Massachusetts Amherst
1995-1996
Abstract Environmental DNA (eDNA) metabarcoding is a promising method to monitor species and community diversity that rapid, affordable non‐invasive. The longstanding needs of the eDNA are modular informatics tools, comprehensive customizable reference databases, flexibility across high‐throughput sequencing platforms, fast multilocus metabarcode processing accurate taxonomic assignment. Improvements in bioinformatics tools make addressing each these demands within single toolkit reality....
Knowledge of mutation rates is crucial for calibrating population genetics models demographic history in units years. However, remain challenging to estimate because the need identify extremely rare events. We estimated nuclear rate wolves by identifying de novo mutations a pedigree seven wolves. Putative were discovered whole-genome sequencing and verified Sanger parents offspring. Using stringent filters an false negative remaining observable genome, we obtain ∼4.5 × 10-9 per base pair...
Environmental DNA (eDNA) metabarcoding is a powerful tool that can enhance marine ecosystem/biodiversity monitoring programs. Here we outline five important steps managers and researchers should consider when developing eDNA program: (1) select genes primers to target taxa; (2) assemble or develop comprehensive barcode reference databases; (3) apply rigorous site occupancy based decontamination pipelines; (4) conduct pilot studies define spatial temporal variance of eDNA; (5) archive...
Ecosystems globally are under threat from ongoing anthropogenic environmental change. Effective conservation management requires more thorough biodiversity surveys that can reveal system-level patterns and be applied rapidly across space time. Using modern ecological models community science, we integrate DNA Earth observations to produce a time snapshot of regional provide multi-scalar community-level characterization. We collected 278 samples in spring 2017 coastal, shrub, lowland forest...
Climate change is leading to habitat shifts that threaten species persistence throughout California's unique ecosystems. Baseline biodiversity data would provide opportunities for habitats be managed under short-term and long-term environmental change. Aiming data, the UC Conservation Genomics Consortium launched California Environmental DNA (CALeDNA) program a citizen community science biomonitoring initiative uses (eDNA, shed from organisms such as fur, feces, spores, pollen or leaves)....
The invaded cluster algorithm, a method for simulating phase transitions, is described in detail. Theoretical, albeit nonrigorous, justification of the presented and algorithm applied to Potts models two three dimensions. shown be useful both first-order continuous transitions evidently provides an efficient way distinguish between these possibilities. dynamic properties are studied. Numerical evidence suggests that has no critical slowing Ising models. \textcopyright{} 1996 American...
A new cluster algorithm based on invasion percolation is described. The samples the critical point of a spin system without priori knowledge temperature and provides an efficient way to determine other observables in region. method illustrated for two- three-dimensional Ising models. equilibrates configurations much faster than closely related Swendsen-Wang algorithm.
Understanding the geographic linkages among populations across annual cycle is an essential component for understanding ecology and evolution of migratory species facilitating their effective conservation. While genetic markers have been widely applied to describe connections, rapid development new sequencing methods, such as low-coverage whole genome (lcWGS), provides opportunities improved estimates connectivity. Here, we use lcWGS identify fine-scale population structure in a widespread...
Bird migration has fascinated natural historians and scientists for centuries. While the timing of is known to vary by species, population, sex, individual, identifying cause this variation can be challenging. Here we investigate factors underlying migratory in a long-distance bird, Common Yellowthroat (Geothlypas trichas), using population genomic approach. We begin creating map genetic across geographic space (a "genoscape") lcWGS from breeding range. then utilize assays assign 249...
Domesticated animals have been culturally and economically important throughout history. Many of their ancestral lineages are extinct or genetically endangered following hybridization with domesticated relatives. Consequently, they understudied compared to the domestic plants. The pigeon Columba livia, which was pivotal in Darwin's studies, has maintained outsized cultural significance. Its role as a model organism spans fields behavior, genetics, evolution. Domestic pigeons hybridized...
Abstract Global change is leading to habitat shifts that threaten species persistence throughout California’s unique ecosystems. Baseline biodiversity data provide opportunities for ecosystems be managed community complexity and connectivity. In 2017, the University of California Conservation Genomics Consortium launched Environmental DNA (CALeDNA) program, a science initiative monitoring through environmental (eDNA)—DNA shed from organisms fur, mucus, spores, pollen, etc. Community...
Abstract Unique ecosystems globally are under threat from ongoing anthropogenic environmental change. Effective conservation management requires more thorough biodiversity surveys that can reveal system-level patterns and be applied rapidly across space time. We offer a way to use DNA, community science remote sensing together as methods reduce the discrepancy between magnitude of change historical approaches measure it. Taking advantages modern ecological models, we integrate DNA Earth...
Summary Samples from species of high conservation concern are often low in total genomic DNA. Whole Genome Sequencing (WGS) can provide many insights that be used to aid conservation, but current methods for working with quality and input samples cost prohibitive population level analyses. Thus, there is an urgent need a cost-effective method preparing WGS libraries DNA samples. To bridge the gap between sampling techniques commonly genetics yield powerful tool WGS, we developed LI-Seq, more...
Abstract 1. Environmental DNA (eDNA) metabarcoding is a promising method to monitor species and community diversity that rapid, affordable, non-invasive. Longstanding needs of the eDNA are modular informatics tools, comprehensive customizable reference databases, flexibility across high-throughput sequencing platforms, fast multilocus metabarcode processing, accurate taxonomic assignment. As bioinformatics tools continue improve, addressing each these demands within single toolkit becoming...
Understanding the geographic linkages among populations across annual cycle is an essential component for understanding ecology and evolution of migratory species facilitating their effective conservation. While genetic markers have been widely applied to describe connections, rapid development new sequencing methods, such as low-coverage whole genome (lcWGS), provides opportunities improved estimates connectivity. Here, we use lcWGS identify fine-scale population structure in a widespread...
Renewable energy production and development will drastically affect how we meet global demands, while simultaneously reducing the impact of climate change. Although possible effects renewable (mainly from solar- wind-energy facilities) on wildlife have been explored, knowledge gaps still exist, collecting data remains (when negative interactions occur) at installations can act as a first step regarding study species communities interacting with facilities. In case avian species, samples be...
Abstract: Environmental DNA (eDNA) metabarcoding is emerging as a biomonitoring tool available to the citizen science community that promises augment or replace photographic observation. However, eDNA results and observations have rarely been compared document their individual combined power. Here, we use multilocus metabarcoding, method deployed by CALeDNA Program, inventory evaluate biodiversity variation along Pillar Point headland near Half Moon Bay, California. We describe in presence...
Abstract Samples from avian species of high conservation concern are often low in total genomic DNA (gDNA). Feathers collected more frequently than blood, yet they contain gDNA which can present challenges using them for genomics. Whole Genome Sequencing (WGS) provide many insights that be used to aid conservation, but current methods working with feathers cost prohibitive population level analyses. Thus, there is a need cost-effective method preparing WGS libraries feathers. To bridge the...