Human recreation influences activity of a large carnivore in an urban landscape, Biological Conservation

E.C., Bolas, A.D., Pingatore, M., Mathur, D.T., Blumstein, J.A., Sikich, J.A., Smith, J.F., Benson, S.P.D., Riley, & R.V., Blakey

Published Work 2025 | Biological Conservation (Vol. 301)

Local adaptation and phenotypic plasticity drive leaf trait variation in the California endemic toyon (Heteromeles arbutifolia).

L. G., Thomas & R., Prunier

Published Work 2024 | American Journal of Botany (Vol. 111:11)

Patterns of a sexually selected trait are not predictable across urban and non-urban populations of a songbird, the dark-eyed junco

E.S., Diamant, M., Kang, & P.J.,Yeh

Published Work 2024 | Urban Ecosystems (Vol 28)

A novel genetic strategy to enable rapid detection of rare non-native alleles

R.D., Cooper, T.K., Luckau, E., Toffelmier, D.G., Cook, S. Martinelli, M.H., Fawcett & H.B., Shaffer

Published Work 2024 | Scientific Report (Vol. 14)

Hazardous wildfire smoke events can alter dawn soundscapes in dry forests of central and eastern Washington, United States

O.V., Sanderfoot, M.W., Tingley, S.B., Bassing, J.K., Vaughan, N.A., June, & B., Gardner

Published Work 2024 | Global Ecology and Conservation (Vol. 54)

A genome assembly for the Chryxus Arctic (Oeneis chryxus), the highest butterfly in North America

Z.G., MacDonald, S., Schoville, M., Escalona, M.P.A., Marimuthu, O., Nguyen, N., Chumchim, C.W., Fairbairn, W., Seligmann, E., Toffelmier, T., Gillespie, & H.B., Shaffer

Published Work 2024 | Journal of Heredity

Wildfire smoke impacts the body condition and capture rates of birds in California

A., Nihei, O.V.,Sanderfoot, K., LaBarbera, M.W. Tingley

Published Work 2024 | Ornithology

Assessing the potential for successful translocation and co-management of two endangered aquatic species

S.K., Snowden, D.M., Shier, K.M., Stemp, G.F., Grether

Published Work 2024 | Animal Conservation

Phylogenomics of the North American Desert Radiation Linanthus (Polemoniaceae) Reveals Mixed Trait Lability and No Single Geographic Mode of Speciation

I.G., Anghel, L.L., Smith, I.H., Lichter-Marck, & F. Zapata

Published Work 2024 | BioRxiv

How and why do species break a developmental trade-off? Elucidating the association of trichomes and stomata across species

A.S., Baird, C.D., Medeiros, M.A., Caringella, J., Bowers, M., Hii, J., Liang, J., Matsuda, K., Pisipati, C., Pohl, B., Simon, S., Tagaryan, T.N., Buckley, L., Sack

Published Work 2024 | Botany

Trait variation in patchy landscapes: Morphology of spotted salamanders (Ambystoma maculatum) varies more within ponds than between ponds

E.T., Green, A.I., Dell, J.A., Crawford, E.G., Biro, D.R. Daversa

Published Work 2024 | PLOS ONE

Comparing fear responses of two lizard species across habitats varying in human impact

B.J., Putman, M.A., Rensel, B.A., Schlinger, S., French, D.T., Blumstein, G.B., Pauly

Published Work 2024 | Journal of Urban Ecology

A Fast, Reproducible, High-throughput Variant Calling Workflow for Population Genomics

C.D., Mirchandani, A.J., Shultz, G.W.C., Thomas, S.J., Smith, M., Baylis, B., Arnold, R., Corbett-Detig, E., Enbody, and T.B. Sackton

Published Work 2023 | Molecular Biology and Evolution

Woody Plant–Soil Relationships in Interstitial Spaces Have Implications for Future Forests Within and Beyond Urban Areas

G.A. Mejía, P.M., Groffman, M.L., Avolio, A.R., Bratt, J., Cavender-Bares, N.H., Grijseels, S.J., Hall, J., Heffernan, S.E., Hobbie, S.B., Lerman, J.L., Morse, D.L., Narango, C., Neill, J. Padullés Cubino, T.L.E., Trammell

Published Work 2023 | Ecosystems

Environmental DNA metabarcoding reveals distinct fish assemblages supported by seagrass (Zostera marina and Zostera pacifica) beds in different geographic settings in Southern California

T. Waters, Z. Gold, A. Obaza, R.F. Ambrose, R.A. Eagle

Published Work 2023 | PLoS ONE

Predicting plant species climate niches on the basis of mechanistic traits

C.D. Medeiros, C. Henry, S. Trueba, I. Anghel, S.D.D. de Leon Guerrero, A. Pivovaroff, L.R. Fletcher, G.P. John, J.A. Lutz, R.M. Alonzo, L. Sack

Published Work 2023 | Functional Ecology, Volume 37, Issue 11

A reference genome assembly for the continentally distributed ring-necked snake, Diadophis punctatus

E.P. Westeen, M. Escalona, E. Beraut, M.P.A. Marimuthu, O. Nguyen, R.N. Fisher, E. Toffelmier, H.B. Shaffer, I.J. Wang

Published Work 2023 | Journal of Heredity, Volume 114, Issue 6

A genome assembly of the Yuma myotis bat, Myotis yumanensis

J.N. Curti, D. Fraser, M. Escalona, C.W. Fairbairn, S. Sacco, R. Sahasrabudhe, O. Nguyen, W. Seligmann, P.H. Sudmant, E. Toffelmier, , J.M. Vazquez, R. Wayne, H.B. Shaffer, M.R. Buchalski

Published Work 2023 | Journal of Heredity

Pathogenic Leptospira are widespread in the urban wildlife of southern California

S.K., Helman, A.F.N., Tokuyama, R.O., Mummah, N.E., Stone, M.W., Gamble, C.E., Snedden, B., Borremans, A.C.R., Gomez, C., Cox, J., Nussbaum, I., Tweedt, D.A., Haake, R.L., Galloway, J., Monzón, S.P.D., Riley, J.A., Sikich, J., Brown, A., Friscia, J.W., Sahl, D.M., Wagner, J.W., Lynch, K.C., Prager, J.O., Lloyd-Smith

Published Work 2023 | Scientific Reports

Urban birds become less fearful following COVID-19 reopenings

E.S. Diamant, I. MacGregor-Fors, D.T. Blumstein and P.J. Yeh

Published Work 2023 | Proceedings of the Royal Society B, Volume 290, Issue 2005

Rethinking local seed sourcing for the restorationof a foundational grass species in California

M.P. Nolan, J.C. Luong, J.M. Valliere, S.J. Mazer, C.M. D'Antonio

Published Work 2023 | Restoration Ecology, Volume 31, Issue 8

Genome-wide markers show continental structuring and mitonuclear discordance in the forest tent caterpillar (Malacosoma disstria Hübner) (Lepidoptera: Lasiocampidae)

A.D. Roe, Z.G. MacDonald, K.L. Snape, F.A.H. Sperling

Published Work 2023 | The Canadian Entomologist

Quantifying uncertainty in inferences of landscape genetic resistance due to choice of individual-based genetic distance metric

J. Beninde, J. Wittische, A.C. Frantz

Published Work 2023 | Molecular Ecological Resources

Quantifying uncertainty in inferences of landscape genetic resistance due to choice of individual-based genetic distance metric

J., Beninde, J., Wittische, & A.C., Frantz

Published Work 2023 | Molecular Ecology

A draft reference genome assembly of the Pipevine Swallowtail butterfly, Battus philenor hirsuta 

S. Chaturvedi, M. Escalona, M.P.A. Marimuthu, O. Nguyen, N. Chumchim, C.W. Fairbairn, W. Seligmann, C. Miller, H.B. Shaffer, N.K. Whiteman

Published Work 2023 | Journal of Heredity, Volume 114, Issue 6

A genome assembly for the southern Pacific rattlesnake, Crotalus oreganus helleri, in the western rattlesnake species complex

E.P. Westeen, M. Escalona, M.L. Holding, E. Beraut, C. Fairbairn, M.P.A. Marimuthu, O. Nguyen, R. Perri, R.N. Fisher, E. Toffelmier, H.B. Shaffer, I.J. Wang

Published Work 2023 | Journal of Heredity, Volume 114, Issue 6

Multiplex qPCR assays for detection of 2 imperiled anuran species, Anaxyrus californicus and Spea hammondii, from environmental DNA

T.W. Rodgers, R.E. Lovich, J.A. Walton, D.J. Prince, B.R. Gonzalez, H.B. Shaffer, K.E. Mock

Published Work 2023 | Freshwater Science, Volume 42

The importance of cryptic diversity in the conservation of wide-ranging species: The red-footed tortoise Chelonoidis carbonarius in Colombia

N. Gallego-Garcia, M. Vargas-Ramírez, H.B. Shaffer

Published Work 2023 | Molecular Ecology, Volume 32, Issue 16

Assembly of the largest squamate reference genome to date: The western fence lizard, Sceloporus occidentalis

A.P. Bishop, E.P. Westeen, M.L. Yuan, M. Escalona, E. Beraut, C. Fairbairn, M.P.A Marimuthu, O. Nguyen, N. Chumchim, E. Toffelmier, R.N. Fisher, H.B. Shaffer, I.J. Wang

Published Work 2023 | Journal of Heredity, Volume 114, Issue 5

Harnessing iNaturalist to quantify hotspots of urban biodiversity: the Los Angeles case study

J. Beninde, T.W. Delaney, G. Gonzalez, H.B. Shaffer

Published Work 2023 | Frontiers in Ecology and Evolution

Phenotypic plasticity in the anthropause: does reduced human activity impact novel nesting behaviour in an urban bird?

S.A. Bressler, E.S. Diamant, C. Cen, P.J. Yeh

Published Work 2023 | Animal Behaviour, Volume 203

Reference genome for the American rubyspot damselfly, Hetaerina americana

G.F. Grether, J. Beninde, E. Beraut, N. Chumchim, M. Escalona, Z.G. MacDonald, C. Miller, R. Sahasrabudhe, A.M. Shedlock, E. Toffelmier, H.B. Shaffer

Published Work 2023 | Journal of Heredity, Volume 114, Issue 4

Reference genome of an iconic lizard in western North America, Blainville’s horned lizard Phrynosoma blainvillii

J.Q. Richmond, J.A. McGuire, M. Escalona, M.P.A. Marimuthu, O. Nguyen, S. Sacco, E. Beraut, E. Toffelmier, R.N. Fisher, I.J. Wang, H.B. Shaffer

Published Work 2023 | Journal of Heredity, Volume 114, Issue 4

Reference genome of the black rail, Laterallus jamaicensis 

L.A. Hall, I.J. Wang, M. Escalona, E. Beraut, S. Sacco, R. Sahasrabudhe, O. Nguyen, E. Toffelmier, H.B. Shaffer, S.R. Beissinger

Published Work 2023 | Journal of Heredity, Volume 114, Issue 4

Reference genome of the Virginia rail, Rallus limicola 

L.A. Hall, I.J. Wang, M. Escalona, E. Beraut, S. Sacco, R. Sahasrabudhe, O. Nguyen, E. Toffelmier, H.B. Shaffer, S.R. Beissinger

Published Work 2023 | Journal of Heredity, Volume 114, Issue 4

Two transects reveal remarkable variation in gene flow on opposite ends of a European toad hybrid zone

I. van Riemsdijk, J.W. Arntzen, G.M. Bucciarelli, E. McCartney-Melstad, M. Rafajlovic, P.A. Scott, E. Toffelmier, H.B. Shaffer, B. Wielstra

Published Work 2023 | Heredity, Volume 131

Biodiversity in a box: three non-native invertebrates preferentially find refugia in green space management infrastructure across urban Los Angeles

J. Beninde, J.E. Vendetti, H.B. Shaffer

Published Work 2023 | Biological Invasions

Reference genome of the long-jawed orb-weaver, Tetragnatha versicolor (Araneae: Tetragnathidae)

S.A. Adams, N.R. Graham, A.J. Holmquist, M.M. Sheffer, E.C. Steigerwald, R. Sahasrabudhe, O. Nguyen, E. Beraut, C. Fairbairn, S. Sacco, W. Seligmann, M. Escalona, H.B. Shaffer, E. Toffelmier, R.G. Gillespie

Published Work 2023 | Journal of Heredity, Volume 114, Issue 4

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

R.D. Cooper, H.B. Shaffer

Published Work 2023 | Conservation Biology

Archived DNA reveals marine heatwave-associated shifts in fish assemblages

Z. Gold, R.P. Kelly, A.O. Shelton, A.R. Thompson, K.D. Goodwin, R. Gallego, K.M. Parsons, L.R. Thompson, D. Kacev, P.H. Barber

Published Work 2023 | Environmental DNA

Editorial: Global urban biodiversity and the importance of scale

D.T. Blumstein, M. Alberti, J. Beninde, R.V. Blakey, J.R. Burger, D.S. Cooper, C.A. Niesner, C.J. Schell, M. Soga, K. Uchida

Published Work 2023 | Frontiers in Conservation Science

Divergent sensory and immune gene evolution in sea turtles with contrasting demographic and life histories

B.P. Bentley, T. Carrasco-Valenzuela, E.K.S. Ramos, H. Pawar, L.S. Arantes, A. Alexander, S.M. Banerjee, P. Masterson, M. Kuhlwilm, M. Pippel, J. Mountcastle, B. Haase, M. Uliano-Silva, G. Formenti, K. Howe, W. Chow, A. Tracey, Y. Sims, S. Pelan, J. Wood, K. Yetsko, J.R. Perrault, K. Stewart, S.R. Benson, Y. Levy, E.V. Todd, H.B. Shaffer, P. Scott, B.T. Henen, R.W. Murphy, D.W. Mohr, A.F. Scott, D.J. Duffy, N.J. Gemmell, A. Suh, S. Winkler, F. Thibaud-Nissen, M.F. Nery, T. Marques-Bonet, A. Antunes, Y. Tikochinski, P.H. Dutton, O. Fedrigo, E.W. Myers, E.D. Jarvis, C.J. Mazzoni, L.M. Komoroske

Published Work 2023 | PNAS, Volume 120, Issue 7

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

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

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

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

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

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

Feedback loops between 3D vegetation structure and ecological functions of animals

N., Russo, A., Davies, R., Blakey, E., Ordway, and T., Smith.

Published Work 2022 | Authorea

Vehicular traffic effects on elk and white-tailed deer behavior near wildlife underpasses

M., Nojoumi, A.P., Clevenger, D.T., Blumstein, and E.S., Abelson

Published Work 2022 | PLOS ONE 17(11)

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

Host association, environment, and geography underlie genomic differentiation in a major forest pest

Zachary G. MacDonald, Kyle L. Snape, Amanda D. Roe, Felix A. H. Sperling

Published Work 2022 | Evolutionary Applications, 15(11)1749-1765

Mountain lions avoid burned areas and increase risky behavior after wildfire in a fragmented urban landscape

Rachel V. Blakey, Jeff A. Sikich, Daniel T. Blumstein, Seth P.D. Riley

Published Work 2022 | Current Biology

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

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

Reference genome assembly of the sunburst anemone, Anthopleura sola

B.H., Cornwell, E., Beraut, C., Fairbairn, O., Nguyen, M.P.A., Marimuthu, M., Escalona, and E., Toffelmier.

Published Work 2022 | Journal of Heredity, Volume 113, Issue 6, Pages 699–705

Host Identity Matters—Up to a Point: The Community Context of Batrachochytrium dendrobatidis Transmission

D.R., Daversa, J., Bosch, A., Manica, T.W.J., Garner, and A., Fenton

Published Work 2022 | The American Naturalist, 200:4, pg 584-597

Phenological and physiological advantages of invasive annuals are strengthened by nitrogen enrichment

Justin M. Valliere,Rhay G. Flores,Branden J. Cason,Mayra J. Hernández

Published Work 2022 | Functional Ecology

Soil Microbial Community Composition and Tolerance to Contaminants in an Urban Brownfield Site

Mejia, M.P., Rojas, C.A., Curd, E. et al.

Published Work 2022 | Microbial Ecology

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)

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

SLOSS-based inferences in a fragmented landscape depend on fragment area and species–area slope

J., Liu, Z.G., MacDonald, X., Si, L., Wu, D., Zeng, G., Hu, P., Ding, and M., Yu

Published Work 2022 | Journal of Biogeography, Volume 49, Issue 6, p. 1075-1085

A natural experiment identifies an impending ecological trap for a neotropical amphibian in response to extreme weather events

M.A., Clark, W.M., Ota, S.J., Smith, B.K., Muramoto, S., Ngo, G.E., Chan, M.A., Kenyon, M.C., Sturtevant, M.G., Diamond, G.M., Bucciarelli, and L.B., Kats.

Published Work 2022 | Ecology and Evolution volume 12, Issue 4

An Overview of Modern Applications of Negative Binomial Modeling in Ecology and Biodiversity

S., Jakub, R.V., Blakey, and F.K.C., Hui

Published Work 2022 | Diversity 14, no. 5: 320

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)

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

UCLA La Kretz Center 2021 Annual Report

Shaffer, H.B. and G.B. Bucciarelli

Annual Report 2022

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

The Earth BioGenome Project 2020: Starting the clock

H.A., Lewin et al.

Published Work 2022 | PNAS. 119 (4)

Niche partitioning in an assemblage of granivorous rodents, and the challenge of community-level conservation

R.Y., Chock, D.M., Shier, and G.F., Grether

Published Work 2022 | Oecologia volume 198, pages 553–565 (2022)

A generalist nematode destabilizes plant competition: no evidence for direct effects, but strong evidence for indirect effects on rhizobia abundance

Catella, Samantha A., Castilleja Fallon Olmsted, Shaniya H. Markalanda, Connor J. McFadden, Corlett W. Wood, and Sara E. Kuebbing

Published Work 2021 | New Phytologist(2021)

Wildlife Affordances of Urban Infrastructure: A Framework to Understand Human-Wildlife Space Use

Niesner, C.A., Blakey, R.V., Blumstein, D.T., Abelson, E.S.

Published Work 2021 | Front. Conserv. Sci.

Bats and Fire: a global review

Loeb, S.C., Blakey, R. V.

Published Work 2021 | Fire Ecol. 17

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

Limited refugia and high velocity range-shifts predicted for bat communities in drought-risk areas of the Northern Hemisphere

Piccioli Cappelli, M., Blakey, R. V., Taylor, D., Flanders, J., Badeen, T., Butts, S., Frick, W.F., Rebelo, H.

Published Work 2021 | Glob. Ecol. Conserv. 28, e01608

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

Distinguishing effects of area per se and isolation from the sample-area effect for true islands and habitat fragments

MacDonald, Z.G., Deane, D.C., Lamb, C.T., He, F., Acorn, J.H., Nielsen, S.E.

Published Work 2021 | Ecography. 44(7), 1051-1066

Genome-Wide Variation in DNA Methylation Predicts Variation in Leaf Traits in an Ecosystem-Foundational Oak Species

Browne L, MacDonald B, Fitz-Gibbon S, Wright JW, Sork VL

Published Work 2021 | Forests

Bats partition activity in space and time in a large, heterogeneous landscape

Beilke, E.A., Blakey, R. V., O’Keefe, J.M.

Published Work 2021 | Ecol. Evol. 11, 6513–6526

SARS-CoV-2: Cross-scale Insights from Ecology and Evolution

Snedden, C.E., Makanani, S.K., Schwartz, S.T., Gamble, A., Blakey, R. V., Borremans, B., Helman, S.K., Espericueta, L., Valencia, A., Endo, A., Alfaro, M.E., Lloyd-Smith, J.O.

Published Work 2021 | Trends Microbiol. 29, 593–605

UCLA La Kretz Center 2020 Annual Report

Shaffer, H.B. and G.B. Bucciarelli

Annual Report 2021

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

Urban biodiversity and the importance of scale

Uchida, K., Blakey, R. V., Burger, J.R., Cooper, D.S., Niesner, C.A., Blumstein, D.T.

Published Work 2021 | TREE 36, 123–131

Northern Goshawk (Accipiter gentilis) Home Ranges, Movements, and Forays Revealed by GPS-Tracking

Blakey, R. V., Siegel, R. B., Webb, E. B., Dillingham, C. P., Johnson, M., & Kesler, D. C.

Published Work 2020 | Journal of Raptor Research, 54(4):388-401

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

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

Opinion: Urban Biodiversity and the Importance of Scale

Uchida, K., Blakey, R. V., Burger, J. R., Cooper, D. S., Niesner, C. A., & Blumstein, D. T.

Published Work 2020 | Trends in Ecology & Evolution Volume 36(2):123-131

Turtles and tortoises are in trouble

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

Published Work 2020 | Current Biology 30:R721-735

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

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

La Kretz Center 2019 Annual Report

Annual Report 2020

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)

Weather underground: Subsurface hydrologic processes mediate tree vulnerability to extreme climatic drought

McLaughlin, Blair C., Rachel Blakey, Andrew P. Weitz, Xue Feng, Brittni J. Brown, David D. Ackerly, Todd E. Dawson, and Sally E. Thompson

Published Work 2020 | Global change biology 26(5):3091-3107

Spatial variation in introgression along a toad hybrid zone in France

I. Van Riemsdijk, J.W. Arntzen, G.M. Bucciarelli, E. McCartney-Melstad, M. Rafajlovic, P.A. Scott, E. Toffelmier, H.B. Shaffer, B. Wielstra

Published Work 2020 | Heredity, Volume 131

Multi-scale habitat selection by Northern Goshawks (Accipiter gentilis) in a fire-prone forest

Blakey, Rachel V., Rodney B. Siegel, Elisabeth B. Webb, Colin P. Dillingham, Matthew Johnson, and Dylan C. Kesler

Published Work 2020 | Biological Conservation 241:108348

Beyond the landscape: Resistance modelling infers physical and behavioural gene flow barriers to a mobile carnivore across a metropolitan area

Kimmig, Sophia E., Joscha Beninde, Miriam Brandt, Anna Schleimer, Stephanie Kramer‐Schadt, Heribert Hofer, Konstantin Börner et al

Published Work 2019 | Molecular ecology 29(3):466-484

Adaptational lag to temperature in valley oak (Quercus lobata) can be mitigated by genome-informed assisted gene flow

Luke Browne, Jessica W. Wright, Sorel Fitz-Gibbon,Paul F. Gugger, and Victoria L. Sork

Published Work 2019 | PNAS December 10, 2019 116 (50) 25179-25185

Right-Censored Mixed Poisson Count Models with Detection Times

Hwang, Wen-Han, Rachel V. Blakey, and Jakub Stoklosa

Published Work 2019 | Journal of Agricultural, Biological and Environmental Statistics 25(1):112-132

Survival and competing mortality risks of mountain lions in a major metropolitan area

J. Benson, J. Sikich, S. Riley

Published Work 2019 | Biological Conservation

Conserving ecological roles of top predators in isolated mountains

Benson, J. F., P. J. Mahoney, T. W. Vickers, J. A. Sikich, P. Beier, S. P. D. Riley, H. B. Ernest, and W. M. Boyce

Published Work 2019 | Ecological Applications 00(00):e02029

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

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

Plant functional traits predict the drought response of native California plant species

Pezner, AK, Pivovaroff AL, Sun W, Sharifi MR, Rundel PW, Seibt U.

Published Work 2019 | International Journal of Plant Science

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

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

The Effect of Ecophysiological Traits on Live Fuel Moisture Content

Alexandria L. Pivovaroff, Nathan Emery, M. Rasoul Sharifi, Marti Witter, Jon E. Keeley and Philip W. Rundel

Published Work 2019 | Fire 2019, 2(2), 28

Invasive annuals respond more negatively to drought than native species

Justin M. Valliere, Evelin B. Escobedo, Gary M. Bucciarelli, M. Rasoul Sharifi and Philip W. Rundel

Published Work 2019 | New Phytologist

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

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

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

Urban biodiversity arks

Shaffer, H. B.

Published Work 2018 | Nature Sustainability 1: 725-727

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

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

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

Repeated mowing to restore remnant native grasslands invaded by nonnative annual grasses: upsides and downsides above and below ground

Justin M. Valliere, Susan Balch, Carole Bell, Carlos Contreras, Bridget E. Hilbig

Published Work 2018 | Restoration Ecology

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

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

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

The effect of newt toxin on an invasive snail

Ota, W.M., Olsen, B., Bucciarelli, G.M. et al.

Published Work 2018 | Hydrobiologia (2018) 817: 341

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

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

La Kretz Center 2017 Annual Report

Annual Report 2018

Urban Nature Gardens at the Natural History Museum of Los Angeles County attract “wildlife spectacle” of insect pollinators

E. Hartop, E. Long, C. Bornstein, L. Gonzalez, B. Brown

Published Work 2018 | Zoosymposia 12: 029–050 (2018)

An amphibian chemical defense phenotype is inducible across life history stages

Bucciarelli, G. M., Shaffer, H. B., Green, D. B., & Kats, L. B.

Published Work 2017 | Scientific Reports, 7(1), 8185

Noxious newts and their natural enemies: Experimental effects of tetrodotoxin exposure on trematode parasites and aquatic macroinvertebrates

Calhoun, D.M., Bucciarelli, G.M., Kats, L.B, Zimmer, R.K., & Johnson, P.T.J.

Published Work 2017 | Toxicon. 137: 120-127

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

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

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 |

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

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.

La Kretz Center 2016 Annual Report

Annual Report 2017

High N, dry: Experimental nitrogen deposition exacerbates native shrub loss and nonnative plant invasion during extreme drought

Justin M. Valliere, Irina C. Irvine, Louis Santiago, Edith B. Allen

Published Work 2017 | Global Change Biology

Testing the ‘microbubble effect’ using the Cavitron technique to measure xylem water extraction curves

Pivovaroff AL, Burlett R, Lavigne B, Cochard H, Santiago LS, Delzon S.

Published Work 2016 | AoB PLANTS 8: plw011

Interactions between demography, genetics, and landscape connectivity increase extinction probability for a small population of large carnivores in a major metropolitan area

JF Benson, PJ Mahoney, JA Sikich, LEK Serieys, JP Pollinge , HB Ernest, SPD Riley

Published Work 2016 | Proc. R. Soc. B 283 : 20160957

Efficient screening for ‘genetic pollution’ in an anthropogenic crested newt hybrid zone

B. Wielstra, T. Burke, R.K. Butlin, O. Schaap, H.B. Shaffer, K. Vrieling, and J. W. Arntzen

Published Work 2016 | Conservation Genetics Resources 8:553-560

Individual and Population Level Resource Selection Patterns of Mountain Lions Preying on Mule Deer along an Urban-Wildland Gradient

J. Benson, J. Sikich, S. Riley

Published Work 2016 | PLOS ONE

Phylogeny and temporal diversification of the New World pond turtles (Emydidae)

P.Q. Spinks, R.C. Thomson, E. McCartney-Melstad, and H. B. Shaffer

Published Work 2016 | Molecular Phylogenetics and Evolution 103:85-97

Individual fluctuations in toxin levels affect breeding site fidelity in a chemically defended amphibian

GM Bucciarelli, DB Green, HB Shaffer, LB Kats

Published Work 2016 | Proc. R. Soc. B 283 : 20160468

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

Exon capture optimization in amphibians with large genomes

E. McCartney-Melstad, G. G. Mount, and H. B. Shaffer

Published Work 2016 | Molecular Ecology Resources 16:1084-1094

Hybridization and endangered species protection in the molecular era

R.K. Wayne and H. B. Shaffer

Published Work 2016 | Molecular Ecology 25:280-289

Advances in climate models from CMIP3 to CMIP5 do not change predictions of future habitat suitability for California reptiles and amphibians

A. N. Wright, M. W. Schwartz, R. J. Hijmans, and H. Bradley Shaffer

Published Work 2016 | Climatic Change 134:579-591

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

La Kretz Center 2015 Annual Report

Annual Report 2015

Amphibian molecular ecology and how it has informed conservation

E. McCartney-Melstad and H. B. Shaffer

Published Work 2015 | Molecular Ecology 24:5084-5109

Phylogenetic uncertainty and taxonomic re-revisions: an example from the Australian short-necked turtles (Testudines: Chelidae)

P.Q. Spinks, A. Georges and H. B. Shaffer

Published Work 2015 | Copeia 103:536-540

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

Turtles and tortoises of the world during the rise and global spread of humanity: first checklist and review of extinct Pleistocene and Holocene chelonians. In: Rhodin, A.G.J., Pritchard, P.C.H., van Dijk, P.P., Sau- mure, R.A., Buhlmann, K.A., Iverson, J.B., and Mittermeier, R.A. (Eds.). Conservation Biology of Freshwater Turtles and Tortoises: A Compilation Project of the IUCN/SSC Tortoise and Freshwater Turtle Specialist Group

Turtle Extinctions Working Group [Rhodin, A.G.J., Thomson, S., Georgalis, G., Karl, H.-V., Danilov, I.G., Takahashi, A., De La Fuente, M.S., Bourque, J.R., Delfino M., Bour, R., Iverson, J.B, Shaffer, H. B., and Van Dijk, P.P.].

Published Work 2015 | Conservation Biology of Freshwater Turtles and Tortoises: A Compilation Project of the IUCN/SSC Tortoise and Freshwater Turtle Specialist Group. Chelonian Research Monographs 5(8):000e.1–66

Comment on Spracklandus Hoser, 2009 (Reptilia, Serpentes, ELAPIDAE): request for confirmation of the availability of the generic name and for the nomenclatural validation of the journal in which it was published

Rhodin, A. G. J. (and 69 coauthors)

Published Work 2015 | Bulletin of Zoological Nomenclature 72:65-78

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

Conservation genetics and genomics of amphibians and reptiles

H. B. Shaffer, M, Gidiş E. McCartney-Melstad, K. M. Neal, H. M. Oyamaguchi, M. Tellez, and E. M. Toffelmier

Published Work 2015 | Annual Reviews of Animal Biosciences 3:113-138

A test of fundamental questions in mimicry theory using long-term datasets

EC Long, KF Edwards, AM Shapiro

Published Work 2015 | Biological Journal of the Linnean Society, 116(3)

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.

Multiple sources of uncertainty affect metrics for ranking conservation risk under climate change

A. N. Wright, R. J. Hijmans, M. W. Schwartz, and H. B. Shaffer

Published Work 2015 | Diversity and Distributions 21:111-122

La Kretz Center 2014 Annual Report

Annual Report 2014

Cryptic diversity in metropolis: Confirmation of a new leopard frog species (Anura: Ranidae) from New York City and surrounding Atlantic Coast regions

J. A. Feinberg, C. E. Newman, G. J. Watkins-Colwell, M. D. Schlesinger, B. Zarate, B. R. Curry, H. B. Shaffer, and J. Burger.

Published Work 2014 | PLoS ONE 9(10): e108213.

Field of genes

H. B. Shaffer

Published Work 2014 | BOOM: The journal of California 4:133-138

Turtles of the world, 7th edition: annotated checklist of taxonomy, synonymy, distribution with maps, and conservation status

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

Published Work 2014 | Chelonian Research Monographs 5(7):000.329–479

Multilocus phylogeny of the New-World mud turtles (Kinosternidae) supports the traditional classification of the group

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

Published Work 2014 | Molecular Phylogenetics and Evolution 76:254-260

Field validation supports novel niche modeling strategies in a cryptic endangered amphibian

C. A. Searcy and H. B. Shaffer

Published Work 2014 | Ecography 37:983-992

The advantages of going large: genome-wide SNPs clarify the complex population history and systematics of the threatened western pond turtle

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

Published Work 2014 | Molecular Ecology 23:2228-2241

Incorporating model complexity and spatial sampling bias into ecological niche models of climate change risks faced by 90 California vertebrate species of concern

D. L. Warren, A. N. Wright, S. N. Seifert, and H. B. Shaffer

Published Work 2014 | Diversity and Distributions 20:334-343

Delayed life history effects, multilevel selection, and evolutionary trade-offs in the California tiger salamander

C. A. Searcy, L. N. Gray, P. C. Trenham and H. B. Shaffer

Published Work 2014 | Ecology 95:68-77

Genomics in ecology, evolution and systematics

H. B. Shaffer and M. D. Purugganan

Published Work 2013 | Annual Review of Ecology, Evolution and Systematics 44:1-4

Effects of tail-clipping on survivorship and growth of larval salamanders

R.L. Polich, C. A. Searcy and H. B. Shaffer

Published Work 2013 | J. Wildlife Management 77:1420-1425

Misleading phylogenetic inferences based on single-exemplar sampling in the turtle genus Pseudemys

P. Q. Spinks, R, C. Thomson, G. B. Pauly, C. E. Newman, G. Mount and H. B. Shaffer

Published Work 2013 | Molecular Phylogenetics and Evolution 68:269-281

The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage

H. B. Shaffer (and 58 coauthors)

Published Work 2013 | Genome Biology 2013, 14:R28

Short hydroperiod decreases fitness of nonnative salamanders in California

J. R. Johnson, M. E. Ryan, S. J. Micheletti, and H. B. Shaffer

Published Work 2013 | Animal Conservation 16:556-565

Evolution and Conservation

H. B. Shaffer

Published Work 2013 | pp. 766-773 in The Princeton Guide to Evolution, J. Losos, Editor In Chief. Princeton University Press

Habitat features determine the basking distribution of introduced red-eared sliders and native western pond turtles

M. R. Lambert, S. N. Nielsen, A. N. Wright, R. C. Thomson, and H. B. Shaffer

Published Work 2013 | Chelonian Conservation and Biology 12:192-199

Lethal effects of water quality on threatened California salamanders but not on co-occurring hybrid salamanders

M. E. Ryan, J. R. Johnson, B. M. Fitzpatrick, L. J. Lowenstine, A. M. Picco and H. B. Shaffer

Published Work 2013 | Conservation Biology 27:95-102

Microhabitat use and migration distance of an endangered grassland amphibian

C. A. Searcy, Gabbai-Saldate, E., and H. B Shaffer

Published Work 2013 | Biological Conservation 158:80-87

Turtles of the world, 2012 update: annotated checklist of taxonomy, synonymy, distribution, and conservation status

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

Published Work 2012 | In: Rhodin, A.G.J., Pritchard, P.C.H., van Dijk, P.P., Saumure, R.A., Buhlmann, K.A., Iverson, J.B., and Mittermeier, R.A. (Eds.). Conservation Biology of Freshwater Turtles and Tortoises: A Compilation Project of the IUCN/SSC Tortoise and Freshwater Turtle Specialist Group. Chelonian Research Monographs No. 5, pp. 000.243–000.328

Parallel tagged amplicon sequencing reveals major lineages and phylogenetic structure in the North American tiger salamander (Ambystoma tigrinum) species complex

E. M. O’Neil, R. Schwartz, C. T. Bullock, J. S. Williams, H. B. Shaffer, X. Aguilar-Miguel, G. Parra-Olea, and D. W. Weisrock

Published Work 2012 | Molecular Ecology 22:111-129

La Kretz Center 2011 Annual Report

Annual Report 2011

La Kretz Center 2018 Annual Report

Annual Report