Amy Vandergast
Dr. Amy Vandergast is a Research Geneticist with the Western Ecological Research Center.
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
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)
Education and Certifications
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)
Science and Products
Developing inter-agency templates for FAIR genetic data archiving
Standardizing, aggregating, analyzing and disseminating global wildlife genetic and genomic data for improved management and advancement of community best practices
Tracking Bats and Coronaviruses
Development of Next Generation Techniques of fecal samples collected from nestling cactus wren
Conservation Genetics and Genomics of Rare and Endangered Species
Assessing Spatial Patterns in Genetic Diversity Across Species Assemblages
Molecular Species Identification
San Diego Field Station
Cactus Wren Invertebrate Diet Derived from Sequencing of Nestling Fecal Samples in San Diego County, California
Assessing Connectivity among Coastal and Interior Cactus Wrens in California using Population Genomics (2021)
Microsatellite Genetic Marker Genotypes from Southern Mule Deer (Odocoileus hemionus fuliginatus) Sampled in San Diego County, California
Capture Data and SNP Genotypes to Evaluate Subspecies Range Boundaries of the Bell’s vireo (Vireo bellii pusillus and V. b. arizonae) (2010-2022)
Microsatellite Genotypes for Coastal Cactus Wrens (Campylorhynchus brunneicapillus) from Southern California, 2009-2019
Microsatellite Loci for Mogollon Narrowheaded Gartersnake (Thamnophis rufipunctatus) and the Northern Mexican Gartersnake (Thamnophis eques megalops) in Arizona and New Mexico (2020-2021)
Raster data files for Prioritizing conserved areas threatened by wildfire for monitoring and management.
Polioptila californica Genotype Data from California, USA and Baja California, Mexico
Growth, Drought Response, and Genomic Structure Data for Whitebark Pine in the Sierra Nevada of California (ver. 2.0, May 2023)
Oenothera deltoides Genotype Data from Contra Costa County, California in 2019
San Francisco Gartersnake (Thamnophis sirtalis tetrataenia) Genomic and Demographic Data from San Mateo County and Northeastern Santa Cruz County Collected Between 2016 - 2018
Coachella Valley Fringe-Toed Lizard (Uma inornata) Capture Data (2017 and 2018)
High inter-population connectivity and occasional gene flow between subspecies improves recovery potential for the endangered Least Bell’s Vireo
Move it or lose it: Predicted effects of culverts and population density on Mojave desert tortoise (Gopherus agassizii) connectivity
Fecal metabarcoding of the endangered Pacific pocket mouse (Perognathus longimembris pacificus) reveals a diverse and forb rich diet that reflects local habitat availability
Linear and landscape disturbances alter Mojave desert tortoise movement behavior
Growth, drought response, and climate-associated genomic structure in whitebark pine in the Sierra Nevada of California
Using landscape genomics to delineate future adaptive potential for climate change in the Yosemite toad (Anaxyrus canorus)
Landscape genetics of a sub-alpine toad: Climate change predicted to induce upward range shifts via asymmetrical migration corridors
Reference genome of the California glossy snake, Arizona elegans occidentalis: A declining California Species of Special Concern
Recent declines in genetic diversity with limited dispersal among coastal cactus wren populations in San Diego County, California
Subspecies differentiation and range-wide genetic structure are driven by climate in the California gnatcatcher, a flagship species for coastal sage scrub conservation
Gene pool boundaries for the Yosemite toad (Anaxyrus canorus) reveal asymmetrical migration within meadow neighborhoods
Extensive species diversification and marked geographic phylogenetic structure in the Mesoamerican genus Stenopelmatus (Orthoptera: Stenopelmatidae: Stenopelmatinae) revealed by mitochondrial and nuclear 3RAD data
Science and Products
- Science
Developing inter-agency templates for FAIR genetic data archiving
Standardized archiving of genetic data is essential for reuse in monitoring biodiversity and data syntheses.Standardizing, aggregating, analyzing and disseminating global wildlife genetic and genomic data for improved management and advancement of community best practices
Global biodiversity is rapidly declining, threatening humans, ecosystems, and the services that society relies upon. Monitoring and understanding the extent of biodiversity declines can support policy decisions. Genetic diversity is the foundation of biodiversity, determining the capacity of populations to adapt to environmental changes and to sustain function and structure in all ecosystems. WhilTracking Bats and Coronaviruses
Below are the USGS 2020 Coronavirus Aid, Relief and Economic Security Act (CARES Act) research projects related to tracking bats and coronaviruses. Select tabs above for related items.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. - Data
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Cactus Wren Invertebrate Diet Derived from Sequencing of Nestling Fecal Samples in San Diego County, California
This dataset contains the invertebrates (identified to Order and Family) present in Cactus Wren nestling fecal samples and found using DNA sequencing (metabarcoding) methods. Nestling fecal samples were collected from one or more handled nestlings per territory collected between April and July of 2015 through 2019 in San Diego, California. The steps to process these data are detailed in the Data QAssessing Connectivity among Coastal and Interior Cactus Wrens in California using Population Genomics (2021)
The Coastal Cactus Wren is a species of high conservation concern in southern California. The goal of this project was to obtain taxonomic resolution of subspecies boundaries between coastal and desert populations of Cactus Wrens. We collected genetic samples from Cactus Wrens at California desert sites and combined this dataset with previously collected samples from coastal populations to resolveMicrosatellite Genetic Marker Genotypes from Southern Mule Deer (Odocoileus hemionus fuliginatus) Sampled in San Diego County, California
Collection of microsatellite genetic data from multiple projects involving southern mule deer (Odocoileus hemionus fuliginatus) in San Diego County, California. Samples were collected 2005-2007, 2010, 2012-2013, 2015, and 2018-2020. These data support the following publication: Mitelberg, A., Smith, J.G., and Vandergast, A.G., 2019, DNA Fingerprinting of Southern mule deer (Odocoileus hemionus fuCapture Data and SNP Genotypes to Evaluate Subspecies Range Boundaries of the Bell’s vireo (Vireo bellii pusillus and V. b. arizonae) (2010-2022)
Genetic samples in the form of a small blood sample were collected from 263 Bell's vireos (Vireo bellii) in drainages throughout southern and central California, Arizona, southern Nevada, and southwestern Utah. We used population genomic techniques to delineate the range limit between the Least Bell's Vireo (V. b. pusillus) and its conspecific geographical neighbor, the Arizona Bell's Vireo (V. bMicrosatellite Genotypes for Coastal Cactus Wrens (Campylorhynchus brunneicapillus) from Southern California, 2009-2019
These data show multilocus genotypes, banding age, and territory for coastal cactus wrens (Campylorhynchus brunneicapillus) sampled in coastal southern California between 2009 and 2019. These data support the following publication: Vandergast, A.G., Kus, B.E., Smith, J.G. and Mitelberg, A., 2022. Recent declines in genetic diversity with limited dispersal among coastal cactus wren populations inMicrosatellite Loci for Mogollon Narrowheaded Gartersnake (Thamnophis rufipunctatus) and the Northern Mexican Gartersnake (Thamnophis eques megalops) in Arizona and New Mexico (2020-2021)
The Mogollon Narrowheaded gartersnake (Thamnophis rufipunctatus) and the Northern Mexican gartersnake (Thamnophis eques megalops) are both listed as Threatened under the Federal Endangered Species Act. Both species have a strong association with aquatic habitats, and these habitats have been highly altered from impoundments, land-use changes, and the introduction and spread of non-native aquatic sRaster 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 PLOS OPolioptila californica Genotype Data from California, USA and Baja California, Mexico
This dataset contains genomic records from 184 California Gnatcatchers (Polioptila californica) collected at 18 sites in southern California (USA), 13 sites in Baja California (Mexico), and 17 sites in Baja California Sur (Mexico). Genomic markers were generated from ddRAD loci (Peterson and others, 2012) and analyzed using the Stacks v2.53 (Catchen and others, 2013) pipeline. The genotypes for alGrowth, Drought Response, and Genomic Structure Data for Whitebark Pine in the Sierra Nevada of California (ver. 2.0, May 2023)
These data represent stem growth from whitebark pine at 27 sites in the Sierra Nevada of California. Values for stem growth were derived from increment cores, processed following standard methods. Samples were also compared against a genomic data collected at the same trees. These data support the following publication: van Mantgem, P.J., Milano, E.R., Dudney, J., Nesmith, J.C.B, Vandergast, A.Oenothera deltoides Genotype Data from Contra Costa County, California in 2019
This dataset contains 212 samples from 8 Oenothera deltoides subsp. howellii occurrences, 3 occurrences of the unknown taxon- clade X, and 3 occurrences of related Oenothera deltoides subsp. cognata. Genomic markers were generated from ddRAD loci (Peterson and others, 2012) and analyzed using the Stacks v2.53 (Catchen and others, 2013) pipeline. The genotypes for all samples are provided in a VCFSan Francisco Gartersnake (Thamnophis sirtalis tetrataenia) Genomic and Demographic Data from San Mateo County and Northeastern Santa Cruz County Collected Between 2016 - 2018
Conversion and fragmentation of wildlife habitat often leads to smaller and isolated populations and can reduce a species' ability to disperse across the landscape. As a consequence, genetic drift can quickly lower genetic variation and increase vulnerability to extirpation. For species of conservation concern, quantification of population size and connectivity can clarify the influence of geneticCoachella Valley Fringe-Toed Lizard (Uma inornata) Capture Data (2017 and 2018)
This dataset includes location, field measurements, and descriptions of 330 Uma inornata sampled for the research study entitled "Sampling Across 20 Years (1996-2017) Reveals Loss of Diversity and Genetic Connectivity in the Coachella Valley Fringe-Toed Lizard (Uma inornata)". Field sampling occurred between March and September of 2017 and between April and June of 2018. Lizards were located by vi - Publications
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High inter-population connectivity and occasional gene flow between subspecies improves recovery potential for the endangered Least Bell’s Vireo
Increasingly, genomic data are being used to supplement field-based ecological studies to help evaluate recovery status and trends in endangered species. We collected genomic data to address two related questions regarding the Least Bell’s Vireo (Vireo bellii), an endangered migratory songbird restricted to southern California riparian habitat for breeding. First, we sought to delineate the rangeAuthorsA. G. Vandergast, Barbara E. Kus, Dustin A. Wood, Anna Mitelberg, Julia G. Smith, Elizabeth R. MilanoMove it or lose it: Predicted effects of culverts and population density on Mojave desert tortoise (Gopherus agassizii) connectivity
Roadways and railways can reduce wildlife movements across landscapes, negatively impacting population connectivity. Connectivity may be improved by structures that allow safe passage across linear barriers, but connectivity could be adversely influenced by low population densities. The Mojave desert tortoise is threatened by habitat loss, fragmentation, and population declines. The tortoise contiAuthorsKirsten E. Dutcher, Kenneth E. Nussear, Jill S. Heaton, Todd C. Esque, A. G. VandergastFecal metabarcoding of the endangered Pacific pocket mouse (Perognathus longimembris pacificus) reveals a diverse and forb rich diet that reflects local habitat availability
Information on diet breadth and preference can assist in understanding links between food resources and population growth and inform habitat restoration for rare herbivores. We assessed the diet of the endangered Pacific pocket mouse using metabarcoding of fecal samples and compared it to plant community composition in long-term study plots in two populations on Marine Corps Base Camp Pendleton, SAuthorsA. G. Vandergast, Cheryl S. Brehme, Deborah D. Iwanowicz, Robert S. Cornman, Devin T. Adsit-Morris, Robert N. FisherLinear and landscape disturbances alter Mojave desert tortoise movement behavior
Introduction: Animal movements are influenced by landscape features; disturbances to the landscape can alter movements, dispersal, and ultimately connectivity among populations. Faster or longer movements adjacent to a localized disturbance or within disturbed areas could indicate reduced habitat quality whereas slower or shorter movements and reduced movements may indicate greater availability ofAuthorsSteven J. Hromada, Todd C. Esque, A. G. Vandergast, K. Kristina Drake, Felicia Chen, Benjamin O Gottsacker, Jordan Andrew Swart, Ken E NussearGrowth, drought response, and climate-associated genomic structure in whitebark pine in the Sierra Nevada of California
Whitebark pine (Pinus albicaulis Engelm.) has experienced rapid population declines and is listed as threatened under the Endangered Species Act in the United States. Whitebark pine in the Sierra Nevada of California represents the southernmost end of the species' distribution and, like other portions of its range, faces threats from an introduced pathogen, native bark beetles, and a rapidly warmiAuthorsPhillip J. van Mantgem, Elizabeth R. Milano, Joan Dudney, Jonathan C.B. Nesmith, Amy G. Vandergast, Harold S.J. ZaldUsing landscape genomics to delineate future adaptive potential for climate change in the Yosemite toad (Anaxyrus canorus)
An essential goal in conservation biology is delineating population units that maximize the probability of species persisting into the future and adapting to future environmental change. However, future-facing conservation concerns are often addressed using retrospective patterns that could be irrelevant. We recommend a novel landscape genomics framework for delineating future “Geminate EvolutionaAuthorsPaul A. Maier, Amy G. Vandergast, Andrew J. BohonakLandscape genetics of a sub-alpine toad: Climate change predicted to induce upward range shifts via asymmetrical migration corridors
Climate change is expected to have a major hydrological impact on the core breeding habitat and migration corridors of many amphibians in the twenty-first century. The Yosemite toad (Anaxyrus canorus) is a species of meadow-specializing amphibian endemic to the high-elevation Sierra Nevada Mountains of California. Despite living entirely on federal lands, it has recently faced severe extirpations,AuthorsPaul A. Maier, A. G. Vandergast, Steven M Ostoja, Andres Aguilar, Andrew J. BohonakReference genome of the California glossy snake, Arizona elegans occidentalis: A declining California Species of Special Concern
The glossy snake (Arizona elegans) is a polytypic species broadly distributed across southwestern North America. The species occupies habitats ranging from California’s coastal chaparral to the shortgrass prairies of Texas and southeastern Nebraska, to the extensive arid scrublands of central México. Three subspecies are currently recognized in California, one of which is afforded state-level protAuthorsDustin A. Wood, Jonathan Q. Richmond, Merly Escalona, Mohan P. A. Marimuthu, Oanh Nguyen, Samuel Sacco, Eric Beraut, Michael F. Westphal, Robert N. Fisher, A. G. Vandergast, Erin Toffelmier, Ian J Wang, H. Bradley ShafferRecent declines in genetic diversity with limited dispersal among coastal cactus wren populations in San Diego County, California
Habitat loss and fragmentation can lead to smaller and more isolated populations and reduce genetic diversity and evolutionary potential. Conservation programs can benefit from including monitoring of genetic factors in fragmented populations to help inform restoration and management. We assessed genetic diversity and structure among four major populations of the Cactus Wren (Campylorhynchus brunnAuthorsA. G. Vandergast, Barbara E. Kus, Julia G. Smith, Anna MitelbergSubspecies differentiation and range-wide genetic structure are driven by climate in the California gnatcatcher, a flagship species for coastal sage scrub conservation
Understanding genetic structure and diversity within species can uncover associations with environmental and geographic attributes that highlight adaptive potential and inform conservation and management. The California gnatcatcher, Polioptila californica, is a small songbird found in desert and coastal scrub habitats from the southern end of Baja California Sur to Ventura County, California. LackAuthorsA. G. Vandergast, Barbara E. Kus, Dustin A. Wood, Elizabeth R Milano, Kristine L. PrestonGene pool boundaries for the Yosemite toad (Anaxyrus canorus) reveal asymmetrical migration within meadow neighborhoods
The Yosemite toad (Anaxyrus [Bufo] canorus) is a federally threatened species of meadow-specializing amphibian endemic to the high-elevation Sierra Nevada Mountains of California. The species is one of the first amphibians to undergo a large demographic collapse that was well-documented, and is reputed to remain in low abundance throughout its range. Recent phylogeographic work has demonstrated thAuthorsPaul A. Maier, A. G. Vandergast, Steven M. Ostoja, Andres Aguilar, Andrew J. BohonakExtensive species diversification and marked geographic phylogenetic structure in the Mesoamerican genus Stenopelmatus (Orthoptera: Stenopelmatidae: Stenopelmatinae) revealed by mitochondrial and nuclear 3RAD data
The Jerusalem cricket subfamily Stenopelmatinae is distributed from south-western Canada through the western half of the United States to as far south as Ecuador. Recently, the generic classification of this subfamily was updated to contain two genera, the western North American Ammopelmatus, and the Mexican, and central and northern South American Stenopelmatus. The taxonomy of the latter genus wAuthorsJorge Gutiérrez-Rodríguez, Alejandro Zaldívar-Riverón, David B Weissman, A. G. Vandergast - Web Tools
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