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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

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WERC Banded CACW

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...
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Ecosystems, Fisheries Program, Wildlife Program, Eastern Ecological Science Center
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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...
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WERC lizard

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.
By
Ecosystems, Wildlife Program, Western Ecological Research Center (WERC)
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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.
Learn More
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Desert Tortoise WERC

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.
By
Ecosystems, Energy & Wildlife, Wildlife Program, Western Ecological Research Center (WERC)
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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.
Learn More
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Plant extraction wells WERC

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.
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Ecosystems, Wildlife Program, Western Ecological Research Center (WERC)
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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.
Learn More

San 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 genetic
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Western Ecological Research Center (WERC)

Microsatellite 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. ht
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Western Ecological Research Center (WERC)

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 ba
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Western Ecological Research Center (WERC)

Genetic 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 landscap
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Western Ecological Research Center (WERC)

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 populatio
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Western Ecological Research Center (WERC)

Data 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 leopa
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Western Ecological Research Center (WERC)

DNA 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
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Western Ecological Research Center (WERC)
Filter Total Items: 64

Integrating 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 pote
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Ecosystems, Western Ecological Research Center (WERC)

Combining genetic and demographic monitoring better informs conservation of an endangered urban snake

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 genetic
By
Ecosystems, Western Ecological Research Center (WERC)

Generic 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 Stenopelmatus
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Ecosystems, Western Ecological Research Center (WERC)

Distribution, 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 invasive
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Ecosystems, Western Ecological Research Center (WERC)

Using 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 threatened
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Ecosystems, Western Ecological Research Center (WERC)

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 habitat loss with concomitant losses of genetic diversi
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Ecosystems, Western Ecological Research Center (WERC)

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 associated infrastructure, mining activities, energy
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Ecosystems, Western Ecological Research Center (WERC)

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 (Odocoileus hemionus fuliginatus; herein referred to as “
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Ecosystems, Western Ecological Research Center (WERC)

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 samples collected in California and Nevada using sev
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Ecosystems, Western Ecological Research Center (WERC)

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, cycles of allopatry and ecologically divergent gl
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Ecosystems, Western Ecological Research Center (WERC)

Sampling across 20 years (1996–2017) reveals loss of diversity and genetic connectivity in the Coachella Valley fringe-toed lizard (<i>Uma inornata</i>)

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 in
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Ecosystems, Western Ecological Research Center (WERC)

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 microsatellite loci, we analyzed genetic structure across the
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Ecosystems, Western Ecological Research Center (WERC)

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).

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Western Ecological Research Center (WERC)
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You've Heard a Bird Sing, But Have You Heard a Jerusalem Cricket's Drum?

You’ve probably heard a bird singing to find a mate, or even a frog. But have you ever heard a Jerusalem cricket’s drum?

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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.

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