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Endangered Species Conservation

PROJECTS

2022

DNA methylation variation as a mechanism to alleviate inbreeding depression in the island fox (Urocyon littoralis)

Awardee: Stella Yuan, first year Ph.D. student at UCLA, co-advised by Dr. Robert Wayne and Dr. Kirk Lohmueller. Stella is interested in the evolution of small or declining populations and hopes to use genomic and epigenomic tools to further conservation efforts.

2020

“Fishing” out the exomes of the federally endangered tidewater gobies to identify potential genes under selection

Awardee: Benjamin Ha, Ph.D. student in Ecology and Evolutionary Biology in Dr. Dave Jacobs’ lab. Benjamin's general research interests are to understand how anthropogenic factors impact the genetics of marine populations and communities, and how research may be applied to inform marine conservation and policy.

2020

Characterizing interactions between mountain yellow-legged frog and unarmored threespine stickleback fish to assess the potential for their coexistence

Awardee: Samantha Snowden, Master’s student in Ecology and Evolutionary Biology, co-advised by Greg Grether and Debra Shier. Samantha is interested in bridging ecological research and wildlife conservation.

2020

Managing Pond Hydroperiod to Reverse Invasive Tiger Salamander Introgression

Awardee: Robert Cooper, PhD student in the Shaffer and Grether labs. Robert uses genomics to understand the ecological and evolutionary consequences of recent hybridization between the endangered California tiger salamander and a non-native salamander.

2019

Identifying Drivers of Recent Recruitment Failures in California Tiger Salamanders in Santa Barbara County

Awardee: Erin Toffelmier, Ph.D. student in Brad Shaffer’s lab. Erin's research focuses on understanding the drivers of population declines in the Santa Barbara County populations of the California tiger salamander, Ambystoma californiense.

2019

Western Pond Turtle at-risk species assessment

The western pond turtle is California’s only native freshwater turtle. The turtle’s numbers have been declining due to urbanization, limited water availability, and competition or predation from invasive species —…

2018

Science to safeguard species

UC Natural Reserve System research has laid the foundation for conserving species across the state. A prime example: UCLA professor Brad Shaffer’s work on California tiger salamanders was instrumental in…

2017

Influence of Previous Exposure on Seed Preference in the endangered Pacific pocket mouse (Perognathus longimembris pacificus)

Awardee: Brigit Harvey. Brigit is testing whether the critically endangered Pacific pocket mouse can be trained to consume the seeds of invasive species found across the San Diego County landscape to increase their foraging options in the wild.

2016

California Tiger Salamander

Researchers at the La Kretz Center are developing a framework for protecting the genetic integrity of the endangered California tiger salamander from invasive non-natives.

2016

Desert tortoise conservation

At the La Kretz Center, scientists are working toward a win-win between green energy and endangered species conservation in the Mojave Desert.

2016

Landscape genomics of the western spadefoot toad, Spea hammondii, in the Natural Reserve of Orange County, California

Awardee: Kevin Neal. Kevin will be developing a set of genomic tools to use in a pilot study to analyze genetic connectivity of western spadefoot toad populations at the landscape level in Proctor Valley in San Diego County.

2015

Reintroducing Threatened Western Pond Turtles Into Southern California Ecosystems

In addition to developing a recommendation for creating a self-sustaining population of western pond turtles in the wild, we hope that this project will serve as an educational tool for the nearby community.

2013

An Assessment of Endangered, Threatened, and Species of Special Concern in the University of California Natural Reserve System

Students: Jasneet Bains, Mario Colon, Maxwell Montrose, Vanessa Reyes, Warren Tan, Rachel Thompson, Janet Vu Client: The University of California’s Natural Reserve System Advisor: Dr. Brad Shaffer Final Report

Publications

Managing invasive hybrids with pond hydroperiod manipulation in an endangered salamander system

R.D. Cooper, H.B. Shaffer

Published Work | 2023 | Conservation Biology

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Conservation of northwestern and southwestern pond turtles: Threats, population size estimates, and population viability analysis

Manzo, S., E. G. Nicholson, Z. Devereux, R. N. Fisher, C. W. Brown, P. A. Scott, and H. B. Shaffer

Published Work | 2021 | Journal of Fish and Wildlife Management, 12(2):485–501; e1944-687X

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Genomic and ecological data support the elevation of the El Segundo Blue (Euphilotes bernardino/battoides allyni) to species status

D, Rubinoff, T. Longcore, J. R. Dupuis, and K. Osborne

Published Work | 2021 | The Journal of the Lepidopterists' Society

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Historical museum collections and contemporary population studies implicate roads and introduced predatory bullfrogs in the decline of western pond turtles

Nicholson EG, Manzo S, Devereux Z, Morgan TP, Fisher RN, Brown C, Dagit R, Scott PA, Shaffer HB

Published Work | 2020 | PeerJ 8:e9248

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Experimental removal of introduced slider turtles offers new insight into competition with a native, threatened turtle

Lambert, M. R., J. M. McKenzie, R. M. Screen, A. G. Clause, B. J. Johnson, G. G. Mount, H. B. Shaffer, and G. B. Pauly

Published Work | 2019 | PeerJ 7:e7444

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Cache Pilfering in a Granivore Guild: Implications for Reintroduction Management

R. Chock, G. Grether, D. Shier

Published Work | 2019 | The Journal of Wildlife Management 83(7):1607–1616

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Landscape genomic signatures indicate reduced gene flow and forest-associated adaptive divergence in an endangered neotropical turtle

Gallego-Garcia, N., G. Forero-Medina, M. Vargas-Ramirez, S. Caballero, and H. B. Shaffer

Published Work | 2019 | Molecular Ecology 28:2757–2771

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Global Conservation Status of Turtles and Tortoises (Order Testudines)

Rhodin, A. G. J. and 55 co-authors

Published Work | 2018 | Chelonian Conservation and Biology 17:135-161

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Genomic data recover previously undetectable fragmentation effects in an endangered amphibian

McCartney-Melstad, E., J. K. Vu, and H. B. Shaffer

Published Work | 2018 | Molecular Ecology 27:4430-4443

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Population genomic data reveal extreme geographic subdivision and novel conservation actions for the declining foothill yellow-legged frog

McCartney-Melstad, E., M. Gidiş, and H.B. Shaffer

Published Work | 2018 | Heredity 121:112-125

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Genetic structure and environmental niche modeling confirm two evolutionary and conservation units within the western spadefoot (Spea hammondii)

Neal, K. M., B. B. Johnson, and H. B. Shaffer

Published Work | 2018 | Conservation Genetics 19:937-946

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Desert tortoises in the genomic age: population genomics and the landscape

Shaffer HB, McCartney-Melstad E, Ralph P, Bradburd G, Lundgren E, Vu J, Hagerty B, Sandmeier F, Weitzman C, Tracy CR.

Published Work | 2017 |

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Population genetic and field-ecological analyses return similar estimates of dispersal over space and time in an endangered amphibian

Wang, I.J. and H.B. Shaffer

Published Work | 2017 | Evolutionary Applications 10:630-639

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Distribution, identification, landscape setting, and conservation of Rana kauffeldi in the northeastern U.S.

Schlesinger, M.D., J.A. Feinberg, N.H. Nazdrowicz, J.D. Kleopfer, J. Beane, J.F. Bunnell, J. Burger, E. Corey, K. Gipe, J.W. Jaycox, E. Kiviat, J. Kubel, D. Quinn, C. Raithel, S. Wenner, E.L. White, B. Zarate, and H.B. Shaffer

Progress Report | 2017

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Turtles of the World: Annotated Checklist and Atlas of Taxonomy, Synonymy, Distribution, and Conservation Status (8th Ed.)

Turtle Taxonomy Working Group [A. G. J. Rhodin,, J. B. Iverson, R. Bour, U. Fritz, A. Georges, H. B. Shaffer, and P. P. van Dijk]

Published Work | 2017 | Chelonian Research Monographs 7: 292 pp.

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Do ecological niche models accurately identify climatic determinants of species ranges?

C.A. Searcy and H. B. Shaffer

Published Work | 2016 | American Naturalist 187:423-435

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Ecological equivalency as a tool for endangered species management

C. A. Searcy, H. B. Rollins and H. B. Shaffer

Published Work | 2016 | Ecological Applications 26:94-103

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An Urban Reintroduction of Western Pond Turtles in Southern California

A. Whitaker, A. Lee, H. Fuong, D. Matthews, J. Cañas, N. Shahbol, R. Lou

Progress Report | 2015

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Desert Tortoises in the Genomic Age: Population Genetics and the Landscape

H. B. Shaffer, E. McCartney-Melstad, P. Ralph, G. Bradburd, E. Lundgren, J. Vu, B. Hagerty, F. Sandmeier, C. Weitzman, R. Tracy

Progress Report | 2015

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Determinants of size at metamorphosis in an endangered amphibian and their projected effects on population stability

C.A. Searcy, H. Snass, and H. B. Shaffer

Published Work | 2015 | Oikos 124:724-731.

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DISCOVER THE INNOVATIVE
WORK WE ARE DOING ON:

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Earth Month

Endangered Species Conservation

DNA methylation variation as a mechanism to alleviate inbreeding depression in the island fox (Urocyon littoralis)

“Fishing” out the exomes of the federally endangered tidewater gobies to identify potential genes under selection

Characterizing interactions between mountain yellow-legged frog and unarmored threespine stickleback fish to assess the potential for their coexistence

Managing Pond Hydroperiod to Reverse Invasive Tiger Salamander Introgression

Identifying Drivers of Recent Recruitment Failures in California Tiger Salamanders in Santa Barbara County

Western Pond Turtle at-risk species assessment

Science to safeguard species

Influence of Previous Exposure on Seed Preference in the endangered Pacific pocket mouse (Perognathus longimembris pacificus)

California Tiger Salamander

Desert tortoise conservation

Landscape genomics of the western spadefoot toad, Spea hammondii, in the Natural Reserve of Orange County, California

Reintroducing Threatened Western Pond Turtles Into Southern California Ecosystems

An Assessment of Endangered, Threatened, and Species of Special Concern in the University of California Natural Reserve System

Publications

Managing invasive hybrids with pond hydroperiod manipulation in an endangered salamander system

Conservation of northwestern and southwestern pond turtles: Threats, population size estimates, and population viability analysis

Genomic and ecological data support the elevation of the El Segundo Blue (Euphilotes bernardino/battoides allyni) to species status

Historical museum collections and contemporary population studies implicate roads and introduced predatory bullfrogs in the decline of western pond turtles

Experimental removal of introduced slider turtles offers new insight into competition with a native, threatened turtle

Cache Pilfering in a Granivore Guild: Implications for Reintroduction Management

Landscape genomic signatures indicate reduced gene flow and forest-associated adaptive divergence in an endangered neotropical turtle

Global Conservation Status of Turtles and Tortoises (Order Testudines)

Genomic data recover previously undetectable fragmentation effects in an endangered amphibian

Population genomic data reveal extreme geographic subdivision and novel conservation actions for the declining foothill yellow-legged frog

Genetic structure and environmental niche modeling confirm two evolutionary and conservation units within the western spadefoot (Spea hammondii)

Desert tortoises in the genomic age: population genomics and the landscape

Population genetic and field-ecological analyses return similar estimates of dispersal over space and time in an endangered amphibian

Distribution, identification, landscape setting, and conservation of Rana kauffeldi in the northeastern U.S.

Turtles of the World: Annotated Checklist and Atlas of Taxonomy, Synonymy, Distribution, and Conservation Status (8th Ed.)

Do ecological niche models accurately identify climatic determinants of species ranges?

Ecological equivalency as a tool for endangered species management

An Urban Reintroduction of Western Pond Turtles in Southern California

Desert Tortoises in the Genomic Age: Population Genetics and the Landscape

Determinants of size at metamorphosis in an endangered amphibian and their projected effects on population stability