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H. Bradley Shaffer

Director, UCLA La Kretz Center for California Conservation Science

Distinguished Professor, Department of Ecology and Evolutionary Biology

brad.shaffer@ucla.edu

Personal Website

Education

1982 – PhD – University of Chicago – Evolutionary Biology
1976 – BS – University of California, Berkeley – Zoology

Research Interests

Evolutionary biology, ecology and conservation biology of amphibians and reptiles. Recent research projects include comparative phylogeography of amphibians and reptiles in California and the central U.S., systematics of freshwater turtles and tortoises in Australia, California, and the rest of the globe, and conservation genetics of endangered California amphibians and reptiles. Recently, we have focused a great deal of ecological and genetical work on the California tiger salamander, an endangered species native to central California grassland habitat.

Projects

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The 2023 UCLA La Kretz Center Public Lecture

It was an honor to have guest lecturer Dr. Jennifer Norris at the 2023 UCLA La Kretz Center Public Lecture to speak about her work leading California’s 30×30 Initiative and…

Optimizing landscape connectivity to conserve endangered species threatened by disease

This project aims to determine optimal strategies for conserving endangered Yosemite Toads (Anaxyrus canorus). Populations of Yosemite toads (Anaxyrus canorus), endemic to the Sierra Nevada range in California, plummeted in…

From sea to summit: conservation genomics of threatened and alpine California butterflies

La Kretz Postdoc Zachary MacDonald is using a combination of whole-genome sequence data and forward-in-time landscape and environmental modelling to predict how changes to habitat suitability, habitat connectivity, and climatic…

UCLA La Kretz 2021 Annual Lecture

This event celebrates ten years of conservation research, featuring 3 minute lightening talks by each of our 13 past, current, and future La Kretz postdoctoral fellows. The presentations are followed…

California Conservation Genomics Project (CCGP)

The CCGP is funded by the State of California, led by the UCLA/La Kretz Center for California Conservation Science, and includes contributing scientists from all 10 UC campuses.

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 —…

Ecological and environmental impacts of the Woolsey fire

On November 8th, 2018 the Woolsey fire swept across the Santa Monica Mountains. It claimed 96,949 acres of undeveloped land in the mountains, making it the most extensive fire ever…

Biodiversity of native species in Los Angeles

La Kretz Postdoc Joscha Beninde is conducting a comparative landscape genomics study to understand how species survive and thrive in urban environments.

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…

UCLA Grand Challenges | Sustainable LA

The UCLA Grand Challenges (GC) is a multi-year initiative that identifies, incentivizes, and finds solutions for the toughest environmental problems addressing our city, and by extension, our world. La Kretz…

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.

Landscape genomic analyses of four endangered California reptile and amphibian species

The La Kretz Center is partnering with the US Fish and Wildlife Service to generate genomic data to inform species listing decisions under the US Endangered Species Act.

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Publications

Applying stochastic and Bayesian integral projection modeling to amphibian population viability analysis

A.F., Messerman, A.G., Clause, L.N., Gray, M.K., H.B., Rollins, P.C., Trenham, H.B., Shaffer, and C.A., Searcy

Published Work | 2022 | Ecological Applications

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The phylogeny of California, and how it informs setting multispecies conservation priorities

E., Toffelmier, J., Beninde, and H.B., Shaffer

Published Work | 2022 | Journal of Heredity, Volume 113, Issue 6, pg. 597–603

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A brief history of population genetic research in California and an evaluation of its utility for conservation decision-making

J., Beninde, E., Toffelmier, and H.B., Shaffer

Published Work | 2022 | Journal of Heredity, Volume 113, Issue 6, December 2022, Pages 604–614

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Seizing the moment: The opportunity and relevance of the California Conservation Genomics Project to state and federal conservation policy

P.L., Fiedler, B., Erickson, M., Esgro, M., Gold, J.M., Hull, J.M. Norris, B., Shapiro, M., Westphal, E., Toffelmier, and H.B., Shaffer

Published Work | 2022 | Journal of Heredity, Volume 113, Issue 6, Pages 589–596

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Reference genome of the rubber boa, Charina bottae (Serpentes: Boidae)

J.L., Grismer, M., Escalona, C., Miller, E., Beraut, C.W., Fairbairn, M.P.A., Marimuthu, O., Nguyen, E., Toffelmier, I.J., Wang, and H.B., Shaffer

Published Work | 2022 | Journal of Heredity, Volume 113, Issue 6, Pages 641–648

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Reference Genome Assembly of the Big Berry Manzanita (Arctostaphylos glauca)

Y., Huang, M., Escalona, G., Morrison, M.P.A., Marimuthu, O., Nguyen, E., Toffelmier, H.B. Shaffer, and A., Litt

Published Work | 2022 | Journal of Heredity, Volume 113, Issue 2, Pages 188–196

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Reference genome of the Monkeyface Prickleback, Cebidichthys violaceus

D.B., Wright, M., Escalona, M.P.A., Marimuthu, R., Sahasrabudhe, O., Nguyen, S., Sacco, E., Beraut, E., Toffelmier, C., Miller, H.B., Shaffer, G., Bernardi, and D.P., German

Published Work | 2022 | Journal of Heredity

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Reference genome of the Woolly Sculpin, Clinocottus analis

D.B., Wright, M., Escalona, M.P.A., Marimuthu, R., Sahasrabudhe, O., Nguyen, S., Sacco, E., Beraut, E., Toffelmier, C., Miller, H.B., Shaffer, and G., Bernardi

Published Work | 2022 | Journal of Heredity

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Reference genome of the color polymorphic desert annual plant sandblossoms, Linanthus parryae

I.G., Anghel, S.J., Jacobs, M., Escalona, M.P.A., Marimuthu, C.W., Fairbairn, E., Beraut, O., Nguyen, E., Toffelmier, H.B., Shaffer, and F., Zapata

Published Work | 2022 | Journal of Heredity, Volume 113, Issue 6, December 2022, Pages 712–721

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CaliPopGen: A genetic and life history database for the fauna and flora of California

J., Beninde, E.M., Toffelmier, A., Andreas, C., Nishioka, M., Slay, A., Soto, J.P., Bueno, G., Gonzalez, H.V., Pham, M., Posta, J.P., Pace, and H.B., Shaffer

Published Work | 2022 | Scientific Data volume 9, Article number: 380 (2022)

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Reference Genome of the Northwestern Pond Turtle, Actinemys marmorata

B.D., Todd, T.S., Jenkinson, M., Escalona, E., Beraut, O., Nguyen, R., Sahasrabudhe, P.A., Scott, E., Toffelmier, I.J., Wang, and H.B., Shaffer

Published Work | 2022 | Journal of Heredity, Volume 113, Issue 6, pg. 624–631

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Optimizing management of invasions in an uncertain world using dynamic spatial models

K.M., Pepin, A.J., Davis, R.S., Epanchin-Niell, A.M., Gormley, J.L., Moore, T.J., Smyser, H.B., Shaffer, et al.

Published Work | 2022 | Ecological Applications 32( 6)

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Landscape Genomics to Enable Conservation Actions: The California Conservation Genomics Project

H.B., Shaffer, E., Toffelmier, R.B., Corbett-Detig, M., Escalona, B., Erickson, P., Fiedler, M., Gold, R.J., Harrigan, S., Hodges, T.K., Luckau, C., Miller, D.R., Oliveira, K.E., Shaffer, B., Shapiro, V.L., Sork, and I.J., Wang.

Published Work | 2022 | Journal of Heredity, Volume 113, Issue 6, pg. 577–588

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Toxic Relationships and Arms-Race Coevolution Revisited

G.M., Bucciarelli, F., Alsalek, L.B., Kats, D.B., Green, and H.B., Shaffer

Published Work | 2022 | Annual Review of Animal Biosciences Vol. 10:63-80

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The Earth BioGenome Project 2020: Starting the clock

H.A., Lewin et al.

Published Work | 2022 | PNAS. 119 (4)

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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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From poison to promise: the evolution of tetrodotoxin and its potential as a therapeutic

Bucciarelli, G. M., M. Lechner, A. Fontes, L. B. Kats, H. L. Eisthen, and H. B. Shaffer

Published Work | 2021 | Toxins 2021, 13, 517

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A global phylogeny of turtles reveals a burst of climate-associated diversification on continental margins

Thomson, R. C., P. Q. Phillip Spinks, and H. B. Shaffer

Published Work | 2021 | PNAS February 16, 2021 118 (7) e2012215118

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Allele specific expression and gene regulation explain transgressive thermal tolerance in non-native hybrids of the endangered California tiger salamander (Ambystoma californiense)

Cooper, R. D. and H. B. Shaffer

Published Work | 2020 | Molecular Ecology 30:987–1004

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Individual heterozygosity predicts translocation success in threatened desert tortoises

Scott, P. A., L. J. Allison, K. J. Field, R. C. Averill-Murray, and H. B. Shaffer

Published Work | 2020 | Science 370:1086-1089

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Turtles and tortoises are in trouble

Stanford, C. B. (with 51 total coauthors)

Published Work | 2020 | Current Biology 30:R721-735

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

Published Work | 2020 | PeerJ 8:e9248:1-23

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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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Amphibian responses in the aftermath of extreme climate events

Bucciarelli, G.M., Clark, M.A., Delaney, K.S., Riley S.P.D.,Shaffer, H.B., Fisher, R.N., Honeycutt, Rodney L., Kats, Lee B.

Published Work | 2020 | Sci Rep 10, 3409 (2020)

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An empirical pipeline for choosing the optimal clustering threshold in RADseq studies

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

Published Work | 2019 | Molecular Ecology Resources 19:1195-1204

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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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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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Phylogenomics of the adaptive radiation of Triturus newts supports gradual ecological niche expansion towards an incrementally aquatic lifestyle

Wielstra, B., E. McCartney-Melstad, J. W. Arntzen, R. K. Butlin and H. B. Shaffer

Published Work | 2019 | Molecular Phylogenetics and Evolution 133:120-127

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Assessing effects of nonnative crayfish on mosquito survival

Gary M. Bucciarelli, Daniel Suh, Avery Davis Lamb, Dave Roberts, Debra Sharpton, H. Bradley Shaffer, Robert N. Fisher, Lee B. Kats

Published Work | 2019 | Conservation Biology 33:122-131

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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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Urban biodiversity arks

Shaffer, H. B.

Published Work | 2018 | Nature Sustainability 1: 725-727

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Genomewide SNP markers breathe new life into phylogeography and species delimitation for the problematic short-necked turtles (Chelidae: Emydura) of eastern Australia

Georges, A., B. Gruber, G. B. Pauly, D. White, M. J. Young, A. Kilian, X. Zhang, H. B. Shaffer, and P.J. Unmack

Published Work | 2018 | Molecular Ecology 27:5195-5213

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Follow-up ecological studies for cryptic species discoveries: Decrypting the leopard frogs of the eastern U.S.

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

Published Work | 2018 | U.S. PLoS ONE 13(11): e0205805

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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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Molecular phylogeny and divergence of the Map Turtles (Emydidae: Graptemys)

Thomson, R.C., P. Q. Spinks, and H. B. Shaffer

Published Work | 2018 | Molecular Phylogenetics and Evolution 121: 61-70

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Molecular toolkit and guidelines for the management of genetic pollution. Reptile, Amphibian and Fish Conservation Netherlands

Wielstra, B., J.W. Arntzen, R.K. Butlin, J.J.C.W. van Delft, K. Vrieling & H.B. Shaffer

Progress Report | 2018

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Occurrence of Batrachochytrium dendrobatidis in anurans of the Mediterranean region of Baja California, México

Peralta-García, A., Adams, A.J., Galina-Tessaro, P., Briggs, C.J., Valdez-Villavicencio, J.H., Hollingsworth, B.D., Shaffer, H.B., and R.N. Fisher

Published Work | 2018 | Diseases of Aquatic Organisms 127:193-200

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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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Phylogenomic analyses of 539 highly informative loci dates a fully resolved time tree for the major clades of living turtles (Testudines)

Shaffer, H.B., McCartney-Melstad, E., Near, T., Mount, G. G., and P.Q. Spinks

Published Work | 2017 | Molecular Phylogenetics and Evolution, 115: 7-15

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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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