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
Microsatellite genotypes for desert tortoise (Gopherus agassizii) in Ivanpah Valley (2015-2017)
Microsatellite genotypes for desert tortoise (Gopherus agassizii) from scat (2016-2018)
Reduced representation sequencing data for Yosemite Toad (Anaxyrus canorus) populations in the southern Sierra Nevada
Distribution and Population Genetic Structure of Coastal Cactus Wrens in Southern California
Genetic Structure of California Gnatcatcher Populations in Southern California from 2012 through 2013
Genotypes for six rare plant species found in San Diego County in 2016-2017
Data release for persistence of historical population structure in an endangered species despite near-complete biome conversion in Californias San Joaquin Desert
DNA fingerprinting of Southern Mule Deer (Odocoileus hemionus fuliginatus) to determine movement across California State Route 67
Extensive species diversification and marked geographic phylogenetic structure in the Mesoamerican genus Stenopelmatus (Orthoptera: Stenopelmatidae: Stenopelmatinae) revealed by mitochondrial and nuclear 3RAD data
Integrating telemetry data at several scales with spatial capture–recapture to improve density estimates
Generic relationships of New World Jerusalem crickets (Orthoptera: Stenopelmatoidea: Stenopelmatinae), including all known species of Stenopelmatus
Distribution, abundance, and genomic diversity of the endangered antioch dunes evening primrose (Oenothera deltoides subsp. howellii) surveyed in 2019
Using movement to inform conservation corridor design for Mojave desert tortoise
Newly documented population extends geographic range and genetic diversity for the Leaf-toed Gecko (Phyllodactylus nocticolus) into the Transverse Ranges of southern California
High-throughput sequencing reveals distinct regional genetic structure among remaining populations of an endangered salt marsh plant in California
Genes in space: What Mojave desert tortoise genetics can tell us about landscape connectivity
DNA fingerprinting of Southern Mule Deer (Odocoileus hemionus fuliginatus) in North San Diego County, California (2018-19)
Development of a genotyping protocol for Mojave desert tortoise scat
Pleistocene glacial cycles drove lineage diversification and fusion in the Yosemite toad (Anaxyrus canorus)
Sampling across 20 years (1996–2017) reveals loss of diversity and genetic connectivity in the Coachella Valley fringe-toed lizard (Uma inornata)
Science and Products
- Science
- Data
Filter Total Items: 20
Microsatellite genotypes for desert tortoise (Gopherus agassizii) in Ivanpah Valley (2015-2017)
These data show the multilocus genotypes, gender, and midline carapace length (MCL) for desert tortoises (Gopherus agassizii) sampled in the central portion of the Mojave desert tortoise range. This data supports the following publication: Dutcher, K.E., Vandergast, A.G., Esque, T.C., Mitelberg, A., Matocq, M.D., Heaton, J.S. and Nussear, K.E., Genes in space: what Mojave Desert tortoise gMicrosatellite genotypes for desert tortoise (Gopherus agassizii) from scat (2016-2018)
These data show the multilocus genotypes, as well as extraction and sample genotype quality assessments for desert tortoise (Gopherus agassizii) scat samples. These data support the following publication: Mitelberg, A., Vandergast, A.G., Nussear, K.E., Dutcher, K. and Esque, T.C., 2019. Development of a Genotyping Protocol for Mojave Desert Tortoise Scat. Chelonian Conservation and Biology. htReduced representation sequencing data for Yosemite Toad (Anaxyrus canorus) populations in the southern Sierra Nevada
These are DNA sequences isolated using double digest RADseq (NCBI) from Yosemite toads in the central Sierra Nevada of California, and scripts/data necessary to generate genotype files, and reproduce phylogenetic, fastsimcoal, niche overlap, and hybrid zone analyses (Dryad).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 color baGenetic Structure of California Gnatcatcher Populations in Southern California from 2012 through 2013
These data were collected to determine how genetic variation is arrayed across remaining populations of gnatcatchers, allowing inference about individual movement and gene flow patterns among those populations. The work focused on determining the extent to which gnatcatcher aggregations function as an interconnected metapopulation, with aggregations exchanging migrants across a fragmented landscapGenotypes 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 populatioData release for persistence of historical population structure in an endangered species despite near-complete biome conversion in Californias San Joaquin Desert
The recency of large-scale land conversion in Californias San Joaquin Desert raises the probability that the regions numerous endemic species still retain genetic signatures of historical population connectivity. If so, genomic data can serve as a guidance tool for conserving lands that once supported habitat for gene movement. We studied the genetic structuring of the endangered blunt-nosed leopaDNA fingerprinting of Southern Mule Deer (Odocoileus hemionus fuliginatus) to determine movement across California State Route 67
The goal of this project was to primarily assess east-west connectivity across Route 67 and secondarily, north-south connectivity across Scripps Poway Parkway and Poway Road, two highly trafficked roads to the west of Route 67. We collected deer scat piles from both sides of these crossings in spring between March and June of 2015, and again in fall throughout October 2015. Collected pellets were - Publications
Filter Total Items: 78
Extensive 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. VandergastIntegrating telemetry data at several scales with spatial capture–recapture to improve density estimates
Accurate population estimates are essential for monitoring and managing wildlife populations. Mark–recapture sampling methods have regularly been used to estimate population parameters for rare and cryptic species, including the federally listed Mojave desert tortoise (Gopherus agassizii); however, the methods employed are often plagued by violations of statistical assumptions, which have the poteAuthorsCorey I Mitchell, Kevin T. Shoemaker, Todd C. Esque, A. G. Vandergast, Steven J. Hromada, Kirsten E. Dutcher, Jill S. Heaton, Kenneth E. NussearGeneric relationships of New World Jerusalem crickets (Orthoptera: Stenopelmatoidea: Stenopelmatinae), including all known species of Stenopelmatus
The New World Jerusalem crickets currently consist of 4 genera: Stenopelmatus Burmeister, 1838, with 33 named entities; Ammopelmatus Tinkham, 1965, with 2 described species; Viscainopelmatus Tinkham, 1970, with 1 described species, and Stenopelmatopterus Gorochov, 1988, with 3 described species. We redefine the generic boundaries of these 4 genera, synonymize Stenopelmatopterus under StenopelmatusAuthorsDavid B Weissman, Amy G. Vandergast, Hojun Song, Seunggwan Shin, Duane D McKenna, Norihiro UeshimaDistribution, abundance, and genomic diversity of the endangered antioch dunes evening primrose (Oenothera deltoides subsp. howellii) surveyed in 2019
Sand dune ecosystems are highly dynamic landforms found along coastlines and riverine deltas where a supply of sand-sized material is available to be delivered by aquatic and wind environments. These unique ecosystems provide habitat for a variety of endemic and rare plant and animal species. Sand dunes have been affected by human development, sand mining, and shoreline stabilization from invasiveUsing movement to inform conservation corridor design for Mojave desert tortoise
BackgroundPreserving corridors for movement and gene flow among populations can assist in the recovery of threatened and endangered species. As human activity continues to fragment habitats, characterizing natural corridors is important in establishing and maintaining connectivity corridors within the anthropogenic development matrix. The Mojave desert tortoise (Gopherus agassizii) is a threatenedAuthorsSteven J. Hromada, Todd C. Esque, Amy G. Vandergast, Kirsten E. Dutcher, Corey I Mitchell, Miranda E Gray, Tony Chang, Brett G. Dickson, Kenneth E. NussearNewly documented population extends geographic range and genetic diversity for the Leaf-toed Gecko (Phyllodactylus nocticolus) into the Transverse Ranges of southern California
Between 19 – 30 May 2018, one of us [AW] discovered a disjunct population of Peninsula leaf-toed geckos, Phyllodactylus nocticolus (Phyllodactylidae) on the northern edge of the Coachella Valley in the Little San Bernardino Mountains of the Transverse Ranges (Fig. 1a). The previously northernmost location for the species is Tahquitz Canyon, Riverside Co. (MVZ 212205) in the Peninsular Ranges 20 kmAuthorsDustin A. Wood, Alyssa Worrel-Black, Robert Black, Anna Mitelberg, Mark Fisher, Robert N. Fisher, A. G. Vandergast, Cameron W. BarrowsHigh-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 habitat loss with concomitant losses of genetic diversiAuthorsElizabeth R. Milano, Margaret R Mulligan, Jon P. Rebman, Amy G. VandergastGenes 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 associated infrastructure, mining activities, energyAuthorsKirsten E. Dutcher, Amy G. Vandergast, Todd C. Esque, Anna Mitelberg, Marjorie D Matocq, Jill S. Heaton, Ken E NussearDNA 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 (Odocoileus hemionus fuliginatus; herein referred to as “AuthorsAnna Mitelberg, Julia G. Smith, Amy G. VandergastDevelopment 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 samples collected in California and Nevada using sevAuthorsAnna Mitelberg, Amy G. Vandergast, Ken E Nussear, Kirsten E. Dutcher, Todd EsquePleistocene 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, cycles of allopatry and ecologically divergent glAuthorsPaul A. Maier, Amy G. Vandergast, Steven M Ostoja, Andres Aguilar, Andrew J. BohonakSampling 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 stochastic droughts and flooding. Since the 1950s, aeolian habitat inAuthorsAmy G. Vandergast, Dustin A. Wood, Mark Fisher, Cameron W. Barrows, Anna Mitelberg, Julia G. Smith - Web Tools
- News