Amy Vandergast
Biography
Dr. Amy Vandergast is a Research Geneticist with the Western Ecological Research Center, where she develops and leads a research program in Conservation and Landscape Genetics and Genomics. Broadly, she seeks to understand how natural and human induced landscape and environmental change impact populations, and shape evolutionary potential. Dr. Vandergast's laboratory group approaches genetic research to inform conservation in three focal areas. 1) At the population level, the team estimates important population parameters such as effective migration (or gene flow) and the number of breeding adults (or effective population size), and quantifies the impacts of landscape changes and disturbance on these parameters. This work informs individual species management. 2) Dr. Vandergast's lab also merges genetic data with mapping and modeling tools to inform biodiversity conservation efforts. Specifically, they define evolutionary significant units within species, reveal evolutionary mechanisms responsible for diversification, and identify regions with high genetic diversity for protection. 3) The team develops genetic approaches for species detection, individual mark recapture, and studies ecological associations (such as predator/prey relationships). These techniques often increase monitoring effectiveness and efficiency when replacing or combining with standard field methodologies.
RESEARCH INTERESTS
- Landscape genetics
- Population genetics
- Conservation biology
- Habitat fragmentation
- Terrestrial invertebrate ecology and evolution
- Linkage design and monitoring
EDUCATION
- Ph.D., Environmental Science, Policy & Management: Division of Insect Biology, University of California, Berkeley (2002)
- M.S., Department of Zoology; Ecology, Evolution & Conservation Biology, University of Hawaii, Manoa (1998)
- B.S., Ecology, Behavior and Evolution, University of California, San Diego (1995)
PROFESSIONAL EXPERIENCE
- Geneticist. USGS Western Ecological Research Center, San Diego Field Station (2004-Present)
- Adjunct Research Professor. San Diego State University, Department of Biology (2002-Present)
- Lecturer. San Diego State University, Department of Biology and Cuyamaca College Department of Biology (2002)
Science and Products
Development of Next Generation Techniques of fecal samples collected from nestling cactus wren
Coastal cactus wren populations have declined in southern California over the last three decades. In San Diego County, this decline has been especially noticeable in the Otay area, which in 2014 supported 14 territories on conserved lands. In the past, there were 25-53 active territories reported for this same area, with the highest estimate in 1992. There is also concern the number of active...
Conservation Genetics and Genomics of Rare and Endangered Species
At the population level, Dr. Amy Vandergast and her team estimates important population parameters such as effective migration (or gene flow) and the number of breeding adults (or effective population size), and quantify the impacts of landscape changes and disturbance on these parameters. This work informs individual species management.
Assessing Spatial Patterns in Genetic Diversity Across Species Assemblages
WERC's Dr. Amy Vandergast and colleagues merge genetic data with mapping and modeling tools to inform biodiversity conservation efforts. They define evolutionary significant units within species, reveal evolutionary mechanisms responsible for diversification, and identify regions with high genetic diversity for protection.
Molecular Species Identification
Dr. Amy Vandergast and team develop genetic approaches for species detection, individual mark recapture, and studying ecological associations (such as predator/prey relationships). These techniques often increase monitoring effectiveness and efficiency when replacing or combining with standard field methodologies.
San Diego Field Station
The San Diego Field Station is the site of research on golden eagles, endangered amphibians and reptiles, and more. Click on the "Science" tab for a comprehensive summary of this study site's projects.
Raster data files for “Prioritizing conserved areas threatened by wildfire for monitoring and management."
The data set consists of 12 input data rasters that cover San Diego County, California. These input rasters represent criteria used in a Pareto ranking algorithm in the manuscript. These include three rasters related to fire threats, three rasters related to habitat fragmentation threats, four rasters related to species biodiversity, and two rasters related to genetic biodiversity. (see the...
Genotypes for six rare plant species found in San Diego County in 2016-2017
To understand the genetic structure of six rare plant species (Acanthomintha ilicifolia, Baccharis vanessae, Chloropyron maritimum ssp. maritimus, Deinandra conjugens, Dicranostegia orcuttiana, Monardella viminea), we obtained samples from known occurrences in San Diego County, prepared and sequenced ddRAD genomic libraries, and developed and analyzed a panel of genetic marker
Distribution and Population Genetic Structure of Coastal Cactus Wrens in Southern California
Data presented are 1.) the locations where Coastal Cactus Wren (Campylorhynchus brunneicapillus) genetic samples were collected in southern California, in 2011, 2012, and 2013; 2.) 2012 and 2013 survey results; 3.) the territory locations of all Cactus Wrens detected in 2011, 2012, and 2013 in Orange, Riverside, and San Diego counties; and 4.) dispersal results on
A Century of Landscape Disturbance and Urbanization of the San Francisco Bay Region affects the Present-day Genetic Diversity of the California Ridgway’s Rail (Rallus obsoletus obsoletus).
Fragmentation and loss of natural habitat have important consequences for wild populations and can negatively affect long-term viability and resilience to environmental change. Salt marsh obligate species, such as those that occupy the San Francisco Bay Estuary in western North America, occupy already impaired habitats as result of human development and modifications and are highly susceptible...
Genetic Landscapes GIS Toolbox: Tools to create genetic divergence and diversity landscapes in ArcGIS
A new analysis approach in landscape genetics and phylogeography is the creation of “genetic landscapes” to visualize genetic structure across geographic space. The Genetic Landscapes GIS Toolbox contains four tools to map genetic landscapes and to summarize multiple genetic landscapes as average and variance surfaces in ArcGIS ® (Environmental Science Research Institute, Redlands, CA, USA)....
High-throughput sequencing reveals distinct regional genetic structure among remaining populations of an endangered salt marsh plant in California
Conservation of rare species requires careful consideration to both preserve locally adapted traits and maintain genetic diversity, as species’ ranges fluctuate in response to a changing climate and habitat loss. Salt marsh systems in California have been highly modified and many salt marsh obligate species have undergone range reductions and...
Milano, Elizabeth R.; Mulligan, Margaret R; Rebman, Jon P.; Vandergast, Amy G. Genes in space: What Mojave desert tortoise genetics can tell us about landscape connectivity
Habitat loss and fragmentation in the Mojave Desert have been increasing, which can create barriers to movement and gene flow leading to decreased populations of native species. Disturbance and degradation of Mojave desert tortoise habitat includes linear features (e.g. highways, railways, and a network of dirt roads), urbanized areas, and their...
Dutcher, Kirsten E; Vandergast, Amy G.; Esque, Todd C.; Mitelberg, Anna; Matocq, Marjorie D; Heaton, Jill S.; Nussear, Ken E Development of a genotyping protocol for Mojave desert tortoise scat
Noninvasive fecal genotyping can be a useful tool for population monitoring of elusive species. We tested extraction protocols on scat samples from the threatened Mojave Desert tortoise, Gopherus agassizii, to evaluate whether scat-based mark–recapture and population genetic monitoring studies are feasible.We extracted DNA from G. agassizii scat...
Mitelberg, Anna; Vandergast, Amy G.; Nussear, Ken E; Dutcher, Kirsten E; Esque, Todd Pleistocene glacial cycles drove lineage diversification and fusion in the Yosemite toad (Anaxyrus canorus)
Species endemic to alpine environments can evolve via steep ecological selection gradients between lowland and upland environments. Additionally, many alpine environments have faced repeated glacial episodes over the past two million years, fracturing these endemics into isolated populations. In this “glacial pulse” model of alpine diversification...
Maier, Paul A.; Vandergast, Amy G.; Ostoja, Steven M; Aguilar, Andres; Bohonak, Andrew J.
DNA fingerprinting of Southern Mule Deer (Odocoileus hemionus fuliginatus) in North San Diego County, California (2018-19)
Throughout the western United States, efforts are underway to better understand and preserve migration and movement corridors for mule deer and other big game and to minimize the impacts of development and other land-use change on populations. San Diego County is home to a unique non-migratory subspecies of mule deer, the Southern mule deer (...
Mitelberg, Anna; Smith, Julia G.; Vandergast, Amy G.
Sampling across 20 years (1996–2017) reveals loss of diversity and genetic connectivity in the Coachella Valley fringe-toed lizard (Uma inornata)
The Coachella Valley fringe-toed lizard (Uma inornata) is a federally threatened, aeolian sand dune obligate, endemic to the Coachella Valley, California. Historically, U. inornata is thought to have formed a large interconnected metapopulation across the valley, with local dune habitat and population size fluctuations linked to...
Vandergast, Amy G.; Wood, Dustin A.; Fisher, Mark; Barrows, Cameron W.; Mitelberg, Anna; Smith, Julia G. Distinguishing recent dispersal from historical genetic connectivity in the coastal California gnatcatcher
Habitat loss and fragmentation are primary threats to biodiversity worldwide. We studied the impacts of habitat loss and fragmentation on genetic connectivity and diversity among local aggregations of the California gnatcatcher (Polioptila californica californica) across its U.S. range. With a dataset of 268 individuals genotyped at 19...
Vandergast, Amy G.; Kus, Barbara E.; Preston, Kristine L.; Barr, Kelly R.
Population genomic surveys for six rare plant species in San Diego County, California
San Diego County is a hotspot of biodiversity, situated at the intersection of the Baja peninsula, the California floristic province, and the desert southwest. This hotspot is characterized by a high number of rare and endemic species, which persist alongside a major urban epicenter. San Diego County has implemented a strategic management plan...
Milano, Elizabeth R.; Vandergast, Amy G. Prioritizing conserved areas threatened by wildfire and fragmentation for monitoring and management
In many parts of the world, the combined effects of habitat fragmentation and altered disturbance regimes pose a significant threat to biodiversity. This is particularly true in Mediterranean-type ecosystems (MTEs), which tend to be fire-prone, species rich, and heavily impacted by human land use. Given the spatial complexity of overlapping...
Tracey, Jeff A.; Rochester, Carlton J.; Hathaway, Stacie A.; Preston, Kristine L.; Syphard, Alexandra D.; Vandergast, Amy G.; Diffendorfer, James E.; Franklin, Janet; MacKenzie, Jason B.; Oberbauer, Tomas A.; Tremor, Scott; Winchell, Clark S.; Fisher, Robert N.
Conservation genomics of the Mogollon Narrow-headed gartersnake (Thamnophis rufipunctatus) and Northern Mexican gartersnake (Thamnophis eques megalops)
The ability of populations to persist and adapt to abiotic and biotic changes is reliant on genetic diversity. When connectivity across a species landscape is disrupted, the levels and distribution of genetic diversity can rapidly deteriorate as a result of genetic drift, leading to increased inbreeding and reduced adaptive potential. Therefore,...
Wood, Dustin A.; Emmons, Iain D.; Nowak, Erika M.; Christman, Bruce L.; Holycross, Andrew T.; Vandergast, Amy G.
An evaluation of the efficacy of using environmental DNA (eDNA) to detect giant gartersnakes (Thamnophis gigas)
Detecting populations of rare or cryptic species is essential for their conservation. For species like giant gartersnakes (Thamnophis gigas), conventional survey methods can be expensive and inefficient. These sampling difficulties might be overcome by modern techniques that detect deoxyribonucleic acid (DNA) shed by organisms into the environment...
Halstead, Brian J.; Wood, Dustin A.; Bowen, Lizabeth; Waters, Shannon C.; Vandergast, Amy G.; Ersan, Julia S.; Skalos, Shannon M.; Casazza, Michael L. Tackling an intractable problem: Can greater taxon sampling help resolve relationships within the Stenopelmatoidea (Orthoptera: Ensifera)?
The relationships among and within the families that comprise the orthopteran superfamily Stenopelmatoidea (suborder Ensifera) remain poorly understood. We developed a phylogenetic hypothesis based on Bayesian analysis of two nuclear ribosomal and one mitochondrial gene for 118 individuals (84 de novo and 34 from GenBank). These included...
Vandergast, Amy G.; Weissman, David B; Wood, Dustin; Rentz, David C F; Bazelet, Corinna S; Ueshima, Norihiro
Genetics Study Reveals Good News for the Southern California Population of the California Gnatcatcher
Results of a recent study by WERC scientists are providing helpful information to resource managers as they work to protect important habitat.