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 markers to assess...
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 subset of Cactus Wrens...
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)....
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, J.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 Inundation, vegetation, and sediment effects on litter decomposition in Pacific Coast tidal marshes
The cycling and sequestration of carbon are important ecosystem functions of estuarine wetlands that may be affected by climate change. We conducted experiments across a latitudinal and climate gradient of tidal marshes in the northeast Pacific to evaluate the effects of climate- and vegetation-related factors on litter decomposition. We...
Janousek, Christopher; Buffington, Kevin J.; Guntenspergen, Glenn R.; Thorne, Karen M.; Dugger, Bruce D.; Takekawa, John Y. Decomposition of plant litter in Pacific coast tidal marshes, 2014-2015
Decomposition of plant matter is one of the key processes affecting carbon cycling and storage in tidal wetlands. In this study, we evaluated the effects of factors related to climate change (temperature, inundation) and vegetation composition on rates of litter decay in seven tidal marsh sites along the Pacific coast. In 2014 we conducted...
Janousek, Christopher; Buffington, Kevin J.; Guntenspergen, Glenn R.; Thorne, Karen M.; Dugger, Bruce D.; Takekawa, John Y.
Incorporating genetic sampling in long-term monitoring and adaptive management in the San Diego County Management Strategic Plan Area, Southern California
Habitat and species conservation plans usually rely on monitoring to assess progress towards conservation goals. Southern California, USA, is a hotspot of biodiversity and home to many federally endangered and threatened species. Here, several regional multi-species conservation plans have been implemented to balance development and conservation...
Vandergast, Amy G. Persistence of historical population structure in an endangered species despite near-complete biome conversion in California's San Joaquin Desert
Genomic responses to habitat conversion can be rapid, providing wildlife managers with time-limited opportunities to enact recovery efforts that use population connectivity information that reflects predisturbance landscapes. Despite near-complete biome conversion, such opportunities may still exist for the endemic fauna and flora of California's...
Richmond, Jonathan Q.; Wood, Dustin A.; Westphal, Michael F.; Vandergast, Amy G.; Leache, Adam D.; Saslaw, Lawrence; Butterfield, H. Scott; Fisher, Robert N. Are coastal managers ready for climate change? A case study from estuaries along the Pacific coast of the United States
A key challenge for coastal resource managers is to plan and implement climate change adaptation strategies inlight of uncertainties and competing management priorities. In 2014, we held six workshops across estuaries along the Pacific coast of North America with over 150 participants to evaluate resource managers' perceived level of understanding...
Thorne, Karen M.; Elliott-Fisk, Deborah L.; Freeman, Chase; Bui, Thuy-Vy D.; Powelson, Katherine; Janousek, Christopher; Buffington, Kevin J.; Takekawa, John Y. Using science to inform management and improve biological conservation in the Desert Renewable Energy Conservation Plan
The Mojave and Colorado deserts of southern California have been viewed as vast wilderness since early exploration and, until recently, were considered the most untrammeled among western landscapes in the contiguous lower 48 states (United States Department of Agriculture 1893; Leu et al. 2008). However, the factors that define desert wilderness—...
Esque, Todd C.; Fesnock, Amy; Brian Croft; Chen, Felicia; Vandergast, Amy G.
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.