2024
Chaturvedi, S., M. Escalona, M. P. A. Marimuthu, O. Nguyen, N. Chumchim, C. W. Fairbairn, W. Seligmann, C. Miller, H. B. Shaffer, and N. K. Whiteman. 2024. A draft reference genome assembly of California Pipevine Aristolochia californica Torr. Journal of Heredity 115:507-515. https://doi.org/10.1093/jhered/esae023
MacDonald, Z.G., Shaffer, H. B., Sperling, F.A.H. 2024. Impacts of land use and climate change on natural populations: The butterfly perspective. Chapter 8, pages 108 – 131 In: Cork, S., Whiteside, D. (eds.) Case Studies in Eco Health. 5m Publishing, Sheffield, U.K. DOI: 10.52517/9781789183368.008.
Ward, P. S., E. I. Cash, K. Ferger, M. Escalona, R. Sahasrabudhe, C. Miller, E. Toffelmier. C. Fairbairn, W. Seligmann, H. B. Shaffer, and N. D. Tsutsui. 2024. Reference genome of the bicolored carpenter ant, Camponotus vicinus. Journal of Heredity 115:120-129. https://doi.org/10.1093/jhered/esad055
MacDonald, Z. G., T. Gillespie, and H. B. Shaffer. 2024. The highest butterfly in North America. Frontiers in Ecology and the Environment 22:e2707, doi:10.1002/fee.2707
2023
Curti, J. N., 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, and M. R. Buchalski. 2023. A genome assembly of the Yuma myotis bat, Myotis yumanensis. Journal of Heredity 115:139-148 https://doi.org/10.1093/jhered/esad053.
Westeen, E. P., M. Escalona, E. Beraut, M. P. A. Marimuthu, O. Nguyen, R. N. Fisher, E. Toffelmier, H. B. Shaffer, and I. J. Wang. 2023. A reference genome assembly for the continentally-distributed ring-necked snake, Diadophis punctatus. Journal of Heredity 114:690-697. https://doi.org/10.1093/jhered/esad051
Chaturvedi, S., M. Escalona, M. P. A. Marimuthu, O. Nguyen, N. Chumchim, C. W. Fairbairn, W. Seligmann, C. Miller, H. B. Shaffer, and Noah K. Whiteman. 2023. A draft reference genome assembly of the Pipevine Swallowtail butterfly, Battus philenor. Journal of Heredity 114:698-706.
Westeen, E. P., 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, and I. J. Wang. 2023. A genome assembly for the southern Pacific rattlesnake, Crotalus oreganus helleri, in the western rattlesnake species complex. Journal of Heredity 114:681-689.
Cooper, R. D. and H. B. Shaffer. 2023. Managing invasive hybrids using pond hydroperiod in an endangered salamander system. Conservation Biology, e14167 https://doi.org/10.1111/cobi.14167
Beninde, J., T. W. Delaney, G. Gonzalez, and H. B. Shaffer. 2023. Harnessing iNaturalist to quantify hotspots of urban biodiversity: the Los Angeles case study. Frontiers in Ecology and Evolution. 11:983371. doi: 10.3389/fevo.2023.983371
Gallego-Garcia, N., M. Vargas-Ramírez, and H. B. Shaffer. 2023. The importance of cryptic diversity in the conservation of wide-ranging species: The red-footed tortoise Chelonoidis carbonarius in Colombia. Molecular Ecology 32:4531-4545.
Rodgers, T. W., R. E. Lovich, J. A. Walton, D. J. Prince, B. R. Gonzalez, H. B. Shaffer, and K. E. Mock. 2023. Multiplex qPCR assays for detection of 2 imperiled anuran species, Anaxyrus californicus and Spea hammondii, from environmental DNA. Freshwater Science 42:315-322.
Bishop, A. P., 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, and I. J. Wang. 2023. Assembly of the largest squamate reference genome to date: The western fence lizard, Sceloporus occidentalis. Journal of Heredity 114:521-528.
Richmond, J. Q., J. A. McGuire, M. Escalona, M. P.A. Marimuthu, O. Nguyen, S. Sacco, E. Beraut, E. Toffelmier, R. N. Fisher, I. J. Wang, and H. B. Shaffer. 2023. Reference genome of an iconic lizard in western North America, Blainville’s horned lizard Phrynosoma blainvillii. Journal of Heredity 114:410-417. https://doi.org/10.1093/jhered/esad032
Grether, G. F., J. Beninde, E. Beraut, N. Chumchim, M. Escalona, Z. G. MacDonald, C. Miller, R. Sahasrabudhe, A. M. Shedlock, E. Toffelmier, and H. B. Shaffer. 2023. Reference genome for the American rubyspot damselfly, Hetaerina americana. Journal of Heredity 114:385-394. https://doi.org/10.1093/jhered/esad031
Adams, S. A., 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, and R. G. Gillespie. 2023. Reference genome of the long-jawed orb-weaver, Tetragnatha versicolor (Araneae: Tetragnathidae). Journal of Heredity 114:395-403. https://doi.org/10.1093/jhered/esad013.
Wright, D. B., M. Escalona, M. P. A. Marimuthu, R. Sahasrabudhe, O. Nguyen, S. Sacco, E. Beraut, E. Toffelmier, C. Miller, H. B. Shaffer, and G. Bernardi. Reference genome of the Woolly Sculpin, Clinocottus analis. 2023. Journal of Heredity 114:60-67. https://doi.org/10.1093/jhered/esac055.
Wright, D. B., 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. 2023. Reference genome of the Monkeyface Prickleback, Cebidichthys violaceus. Journal of Heredity 114:52-59. https://doi.org/10.1093/jhered/esac054
Hall, L. A., I. J. Wang, M. Escalona, E. Beraut, S. Sacco, R. Sahasrabudhe, O. Nguyen, E. Toffelmier, H. B. Shaffer, and S. R. Beissinger. Reference genome of the Virginia rail, Rallus limicola. Journal of Heredity 2023 114:428-435. https://doi.org/10.1093/jhered/esad026
Hall, L. A., I. J. Wang, M. Escalona, E. Beraut, S. Sacco, R. Sahasrabudhe, O. Nguyen, E. Toffelmier, H. B. Shaffer, and S. R. Beissinger. 2023. Reference genome of the black rail, Laterallus jamaicensis. Journal of Heredity 114: 436-443. https://doi.org/10.1093/jhered/esad025.
van Riemsdijk, I., J. W. Arntzen, G. M. Bucciarelli, E. McCartney-Melstad, M. Rafajlovic, P. A. Scott, E. Toffelmier, H. B. Shaffer, and B. Wielstra. 2023. Two transects reveal remarkable variation in gene flow on opposite ends a European toad hybrid zone. Heredity 131:15-24. preprint at https://www.biorxiv.org/content/10.1101/746073v2).
Beninde, J., J. E. Vendetti, and H. B. Shaffer. 2023. Biodiversity in a box: Non-native invertebrates preferentially find refugia in green space management infrastructure across urban Los Angeles. Biological Invasions 25:2061-2068.
Bentley, B. B., and 44 additional coauthors. 2023. Divergent sensory and immune gene evolution in sea turtles with contrasting demographic and life histories. Proceedings of the National Academy of Sciences, USA, 120 (7): e2201076120.
2022
Messerman, A. F., A. G. Clause, L. N. Gray, M. Krkosˇek,, H. B. Rollins, P. C. Trenham, H. B. Shaffer* and C. A. Searcy*. 2022. Applying stochastic and Bayesian integral projection modeling to amphibian population viability analysis. Ecological Applications pages 1-16, e2783, https://doi.org/10.1002/eap.2783 * = co-senior authors
Grismer, J., P. Scott, E. Toffelmier, B. Hinds, R. Klabacka, G. Stewart, V. White, J. Oaks, and H. B. Shaffer. 2022. Genomic data reveal local endemism in Southern California Rubber Boas (Serpentes: Boidae, Charina) and the critical need for enhanced conservation actions. Molecular Phylogenetics and Evolution 174: 107542, pages 1-17.
Todd, B. D., Jenkinson, T. S., Escalona, M., Beraut, E., Nguyen, O., Sahasrabudhe, R., Scott, P. A., Toffelmier, E., Wang, I. J., and H. B. Shaffer. 2022. Reference genome of the northwestern pond turtle, Actinemys marmorata. Journal of Heredity 113:624-631.
Shaffer, H. B., 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. 2022. Landscape genomics to enable conservation actions: The California Conservation Genomics Project. Journal of Heredity 113:577-588; DOI: 10.1093/jhered/esac020 (Note: Selected as Editor’s Choice, including cover image; based on this article, the Editor in Chief decided to dedicate an entire issue, #6, to the CCGP.)
Bernardi, G., M. DeBiasse, M. Escalona, M. P. A. Marimuthu, O. Nguyen, S. Sacco, E. Beraut, C. Miller, E. Toffelmier, and H. B. Shaffer. 2022. Reference genome of the California Sheephead, Semicossyphus pulcher (Labridae, Perciformes), a keystone fish predator in kelp forest ecosystems. Journal of Heredity 113:649-656.
Wood, D. A., J. Q. Richmond, M. Escalona, M. P. A. Marimuthu, O. Nguyen, S. Sacco, E. Beraut, M. Westphal, R. N. Fisher, A. G. Vandergast, E. Toffelmier, I. J. Wang, and H. B. Shaffer. 2022. Reference genome of the California glossy snake, Arizona elegans occidentalis: A declining California Species of Special Concern. Journal of Heredity 113:632-640.
Toffelmier, E., J. Beninde, and H. B. Shaffer. 2022. The phylogeny of California, and how it informs setting multi-species conservation priorities. Journal of Heredity 113:597-603. doi.org/10.1093/jhered/esac045
Fiedler, P. L., B. Erickson, M. Esgro, M. Gold, J. M. Hull, J. Norris, B. Shapiro, M. Westphal, E. Toffelmier, and H. B. Shaffer. 2022. Seizing the Moment: The opportunity and relevance of the California Conservation Genomics Project to state and federal conservation policy. Journal of Heredity 113:589-596.
Bernardi, G., J. A. Toy, M. Escalona, M. P. A. Marimuthu, R. Sahasrabudhe, O. Nguyen, S. Sacco, E. Beraut, E., Toffelmier, E., C. Miller and H. B. Shaffer. 2022. Reference genome of the Black Surfperch, Embiotoca jacksoni (Embiotocidae, Perciformes), a California kelp forest fish that lacks a pelagic larval stage. Journal of Heredity 113:657-664.
Beninde, J.*, E. Toffelmier*, and H. B. Shaffer. 2022. A brief history of population genetic research in California and an evaluation of its utility for conservation decision-making. Journal of Heredity 113:604-614. * = co-first authors
Anghel, I. G., S. J. Jacobs, M. Escalona, M. P. A. Marimuthu, C. W. Fairbairn, E. Beraut, O. Nguyen, E. Toffelmier, H. B. Shaffer, and F. Zapata. 2022. Reference genome of the color polymorphic desert annual plant Linanthus parryae. Journal of Heredity 113:712-721.
Grismer, J. L., M. Escalona, C. Miller, E. Beraut, C. W. Fairbairn, M. P. A. Marimuthu, O. Nguyen, E. Toffelmier, I. J. Wang, and H. B. Shaffer. 2022. Reference genome of the rubber boa, Charina bottae (Serpentes: Boidae). Journal of Heredity 113:641-648.
Pepin, K. M., A. J. Davis, R. S. Epanchin-Niell, A. M. Gormley, J. L. Moore, T. J. Smyser, H. B. Shaffer, W. L. Kendall, K. Shea, M. C. Runge, and S. McKee. 2022. Optimizing management of invasions in an uncertain world using dynamic spatial models. Ecological Applications, 32(6):1-11, e2628. https://doi.org/10.1002/eap.2628
Beninde, J., E. M. Toffelmier, A. Andreas, C. Nishioka, M. Slay, A. Soto, J. P. Bueno, G. Gonzalez, H. V. Pham, M. Posta, J. L. Pace, and H. B. Shaffer. 2022. CaliPopGen: A genetic and life history database for the fauna and flora of California. Scientific Data, 9(1):1-12. https://doi.org/10.1038/s41597-022-01479-z
Bucciarelli, G. M., F. Alsalek, L. B. Kats, D. B. Green, and H. B. Shaffer. 2022. Toxic relationships and arms-race coevolution revisited. Annual Reviews of Animal Biosciences, 10:63-80. https://doi.org/10.1146/annurev-animal-013120-024716
Lewin, H. A. (plus 84 co-authors). The Earth BioGenome Project 2020: Starting the clock. 2022. Proceedings of the National Academy of Sciences, USA, 119 :1-7 (No. 4 e2115635118) https://doi.org/10.1073/pnas.2115635118
Huang, Y., M. Escalona, G. Morrison, M. P. A. Marimuthu, O. Nguyen, E. Toffelmier, H. B. Shaffer, and A. Litt. 2022. Reference genome assembly of the big berry Manzanita (Arctostaphylos glauca). Journal of Heredity 113:188-196. https://doi.org/10.1093/jhered/esab071
2021
Ferrara, C., (43 additional co-authors), and H. B. Shaffer. 2021. Richard Carl Vogt (1949–2021) and His Contributions to the Behavioral Ecology of Freshwater Turtles. Herpetological Review 52:704-707.
Gallego-García, N. , S. Caballero, and H. B. Shaffer. 2021. Are genomic updates of well-studied species worth the investment for conservation? A case study of the Critically Endangered Magdalena River turtle. Journal of Heredity, 112:575-589.
Manzo, S., E. G. Nicholson, Z. Devereux, R. N. Fisher, C. W. Brown, P. A. Scott, and H. B. Shaffer. 2021. Conservation of northwestern and southwestern pond turtles: Threats, population size estimates, and population viability analysis. Journal of Fish and Wildlife Management, 12(2):485–501; e1944-687X. https://doi.org/10.3996/JFWM-20-094
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]. 2021. Turtles of the World: Annotated Checklist and Atlas of Taxonomy, Synonymy, Distribution, and Conservation Status (9th Ed.). In: Rhodin, A.G.J., Iverson, J.B., van Dijk, P.P., Stanford, C.B., Goode, E.V., Buhlmann, K.A., 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 8:1–472. doi: 10.3854/crm.8.checklist.atlas.v9.2021. (Also listed under books)
Palomar, G., K. Dudek, M. Migalska, J. W. Arntzen, G. F. Ficetola, D. Jelić, E. Jockusch, I. Martínez-Solano, M. Matsunami, M., H. B. Shaffer, J. Vörös, B. Waldman, B. Wielstra, and W. Babik. 2021. Coevolution between MHC class I and antigen-processing genes in salamanders. Molecular Biology and Evolution, doi:10.1093/molbev/msab237.
Bucciarelli, G. M., M. Lechner, A. Fontes, L. B. Kats, H. L. Eisthen, and H. B. Shaffer. 2021. From poison to promise: the evolution of tetrodotoxin and its potential as a therapeutic. Toxins 2021, 13, 517. DOI:10.3390/ toxins13080517
Scott, P. A., L. J. Allison, K. J. Field, R. C. Averill-Murray, and H. B. Shaffer. 2021. Individual heterozygosity predicts translocation success in threatened desert tortoises. Science 10.1126/science.abg3199 (Note: this is a response to a comment on Scott et al. 2020 by P. W. Hedrick, 2021)
Scott, P. A., L. J. Allison, K. J. Field, R. C. Averill-Murray, and H. B. Shaffer. 2021. Response to Comment on “Individual heterozygosity predicts translocation success in threatened desert tortoises.” Science 10.1126/science.abh2633. (Note: this is a response to a comment on Scott et al. 2020 by B. Hansson et al., 2021)
Messerman, A. F., A. G. Clause, S. V. L. Catania, H. B. Shaffer, and C. A. Searcy. 2021. Coexistence within an endangered predator-prey community in California vernal pools. Freshwater Biology 66:1296-1310. DOI: 10.1111/fwb.13717
Lovich, J. E., G. Jefferson, R. Reynolds, P. A. Scott, H. B. Shaffer, S. Puffer, S. Greely, K. Cummings, R. N. Fisher, K. Meyer-Wilkins, D. Gomez, M. Ford, and C. D. Otahal. 2021. Western pond turtles in the Mojave Desert? A review of their past, present, and possible future. Vertebrate Zoology 71:317-334. https://doi.org/10.3897/vz.71.e63987
Everson, K. M., L. N. Gray, A. G. Jones, N. M. Lawrence, M. E. Foley, K. L. Sovacool, J. D. Kratovil, S. Hotaling, P. M. Hime, A. Storfer, G. Parra-Olea, R. Percino-Daniel, X. Aguilar-Miguel, E. M. O’Neill, L. Zambrano, H. B. Shaffer, and D. W. Weisrock. 2021. Geography is more important than life history in the recent diversification of the tiger salamander complex. Proceedings of the National Academy of Sciences, USA, 118: 1-10 (No. 17 e2014719118).
Phelan, R., B. Baumgartner, S. Brand, E. Brister, S. W. Burgiel, R. A. Charo, I. Coche, A. Cofrancesco, J. A. Delborne, O. Edwards, J. P. Fisher, M. Gaywood, D. R. Gordon, G. Howald, M. E. Hunter, P. Kareiva, A. Mankad, M. Marvier, K. Moseby, A. E. Newhouse, B. J. Novak, G. Ohrstrom, S. Olson, M. J. Palmer, S. Palumbi, N. Patterson, Jr., M. Pedrono, F. Pelegri, Y. Rohwer, O. A. Ryder, J. R. Saah, R. M. Scheller, P. J. Seddon, H. B. Shaffer, B. Shapiro, M. Sweeney, M. R. Tercek, D. Thizy, W. Tilt, M. Weber, R. D. Wegrzyn, B. Whitelaw, M. Winkler, J. Wodak, M. Zimring, and P. Robbins. 2021. Intended Consequences Statement. Conservation Science and Practice, 2021;e371. https://doi.org/10.1111/ csp2.371
Ennen, J. R., M. Agha, S. C. Sweat, W. A. Matamoros, J. E. Lovich, J. B. Iverson, A. G. J. Rhodin, R. C. Thomson, H. B. Shaffer, and C. W. Hoagstrom. 2021. A watershed moment: Analysis of sub-basins refocus the geography of turtle conservation across the globe. Biological Conservation 253:108925. https://doi.org/10.1016/j.biocon.2020.108925
Olson, E. O., P. A. Scott, and H. B. Shaffer. 2021. Phylogeographic origin of California slender salamanders (Batrachoseps attenuates) in the Sutter Buttes. Journal of Herpetology 55:38-45.
Cooper, R. D. and H. B. Shaffer. 2021. Allele specific expression and gene regulation explain transgressive thermal tolerance in non-native hybrids of the endangered California tiger salamander (Ambystoma californiense). Molecular Ecology 30:987–1004. Also preprint posted at http://dx.doi.org/10.1101/772020)
Thomson, R. C., P. Q. Spinks, and H. B. Shaffer. 2021. A global phylogeny of turtles reveals a burst of climate-associated diversification on continental margins. Proceedings of the National Academy of Sciences, USA, 118: 1-10 (No. 7 e2012215118)
2020
Neal, K. M., R. N. Fisher, M. J. Mitrovich, and H. B. Shaffer. 2020. Conservation genomics of the threatened western spadefoot, Spea hammondii, in urbanized southern California. Journal of Heredity 111:6130627 https://doi.org/10.1093/jhered/esaa049 (Note: Selected as Editor’s Choice for the issue of release.)
Scott, P. A., L. J. Allison, K. J. Field, R. C. Averill-Murray, and H. B. Shaffer. 2020. Individual heterozygosity predicts translocation success in threatened desert tortoises. Science 370: 1086-1089
Stanford, C. B. (with 51 total coauthors). 2020. Turtles and tortoises are in trouble. Current Biology 30: R721-735.
Nicholson, E. G., S. Manzo, Z. Devereux, T. P. Morgan, R. N. Fisher, C. Brown, R. Dagit, P. A. Scott, and H. B. Shaffer. 2020. Historical museum collections and contemporary population studies implicate roads and introduced predatory bullfrogs in the decline of western pond turtles. PeerJ8:e9248 DOI 10.7717/peerj.9248 (pages 1-23)
Bucciarelli, G. M., M. A. Clark, K. S. Delaney, S. P. D. Riley, H. B. Shaffer, R. N. Fisher, R. L. Honeycutt and L. B. Kats. 2020. Amphibian responses in the aftermath of extreme climate events. Scientific Reports 10:3409. doi.org/10.1038/s41598-020-60122-2
2019
McCartney-Melstad, E., , M. Gidiş, and H. B. Shaffer. 2019. An empirical pipeline for choosing the optimal clustering threshold in RADseq studies. Molecular Ecology Resources 19:1195-1204. DOI: 10.1111/1755-0998.13029
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. 2019. Experimental removal of introduced slider turtles offers new insight into competition with a native, threatened turtle. PeerJ 7:e7444, http://doi.org/10.7717/peerj.7444
Gallego-Garcia, N., G. Forero-Medina, M. Vargas-Ramirez, S. Caballero, and H. B. Shaffer. 2019. Landscape genomic signatures indicate reduced gene flow and forest-associated adaptive divergence in an endangered neotropical turtle. Molecular Ecology 28:2757–2771.
Wielstra, B., E. McCartney-Melstad, J. W. Arntzen, R. K. Butlin and H. B. Shaffer. 2019. Phylogenomics of the adaptive radiation of Triturus newts supports gradual ecological niche expansion towards an incrementally aquatic lifestyle. Molecular Phylogenetics and Evolution 133: 120-127. (also preprint posted at http://biorxiv.org/cgi/content/short/463752v1)
Bucciarelli, G. M., D. Suh, A. D. Lamb, D. Roberts, D. Sharpton, H. B. Shaffer, R. N. Fisher and L. B. Kats. 2019. Assessing effects of non-native crayfish on mosquito survival. Conservation Biology 33:122-131.
2018
Rhodin, A. G. J. and 55 co-authors. 2018. Global Conservation Status of Turtles and Tortoises (Order Testudines). Chelonian Conservation and Biology 17:135-161.
Shaffer, H. B. 2018. Urban biodiversity arks. Nature Sustainability 1: 725-727.
McCartney-Melstad, E., J. K. Vu, and H. B. Shaffer. 2018. Genomic data recover previously undetectable fragmentation effects in an endangered amphibian. Molecular Ecology 27:4430-4443. (also at https://doi.org/10.1101/306340)
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. 2018. Follow-up ecological studies for cryptic species discoveries: Decrypting the leopard frogs of the eastern U.S. PLoS ONE 13(11): e0205805.
Georges, A., B. Gruber, G. B. Pauly, D. White, M. J. Young, A. Kilian, X. Zhang, H. B. Shaffer, and P.J. Unmack. 2018. Genomewide SNP markers breathe new life into phylogeography and species delimitation for the problematic short-necked turtles (Chelidae: Emydura) of eastern Australia. Molecular Ecology 27:5195-5213.
Wielstra, B., J.W. Arntzen, R.K. Butlin, J.J.C.W. van Delft, K. Vrieling & H.B. Shaffer. 2018. Molecular toolkit and guidelines for the management of genetic pollution. Reptile, Amphibian and Fish Conservation Netherlands (RAVON), pages 1-25.
McCartney-Melstad, E., Gidiş, M., and H.B. Shaffer. 2018. Population genomic data reveal extreme geographic subdivision and novel conservation actions for the declining foothill yellow-legged frog. Heredity 121:112-125. Also available as an online preprint at http://www.biorxiv.org/content/early/2017/09/10/186635
Neal, K. M., Johnson, B. B., and H. B. Shaffer. 2018. Genetic structure and environmental niche modeling confirm two evolutionary and conservation units within the western spadefoot (Spea hammondii). Conservation Genetics 19:936-946.
Peralta-García, A., Adams, A.J., Briggs, C.J., Galina-Tessaro, P., Valdez-Villavicencio, J.H., Hollingsworth, B.D., Shaffer, H.B., and R.N. Fisher. 2018. Occurrence of Batrachochytrium dendrobatidis in anurans of the Mediterranean region of Baja California, México. Diseases of Aquatic Organisms 127:193-200.
Thomson, R.C., P. Q. Spinks, and H. B. Shaffer. 2018. Molecular phylogeny and divergence of the Map Turtles (Emydidae: Graptemys). Molecular Phylogenetics and Evolution 121: 61-70.
2017
Bucciarelli, G. M., Shaffer, H. B., Green, D. B., and L. B. Kats. 2017. An amphibian chemical defense phenotype is inducible across life history stages. Nature Scientific Reports 7:8185.
Shaffer, H.B., McCartney-Melstad, E., Near, T., Mount, G. G., and P.Q. Spinks. 2017. Phylogenomic analyses of 539 highly informative loci dates a fully resolved time tree for the major clades of living turtles (Testudines). Molecular Phylogenetics and Evolution, 115: 7-15.
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]. 2017. Turtles of the World: Annotated Checklist and Atlas of Taxonomy, Synonymy, Distribution, and Conservation Status (8th Ed.) Chelonian Research Monographs 7: 292 pp. ISBN: 978-1-5323-5026-9 (online). Link
Wang, I.J. and H.B. Shaffer. 2017. Population genetic and field-ecological analyses return similar estimates of dispersal over space and time in an endangered amphibian. Evolutionary Applications 10:630-639.
2016
Hime, P. M., Hotaling, S.,Grewelle, R. E.,O’Neill, E. M., Voss, S. R.,Shaffer, H. B., and D. W.Weisrock. 2016. The influence of locus number and information content on species delimitation: an empirical test case in an endangered Mexican salamander. Molecular Ecology 25:5959-5974.
Shaffer, H. B. 2016. Evolution and Conservation pp. 220-237 in How Evolution Shapes our Lives, Essays on Biology and Society, J. B. Losos and R. E. Lenski, editors. Princeton University Press.
Wielstra, B., Burke T., Butlin, R.K., Schaap, O., Shaffer, H. B., Vrieling, K., and J. W. Arntzen. 2016. Efficient screening for ‘genetic pollution’ in an anthropogenic crested newt hybrid zone. Conservation Genetics Resources 8:553-560.
Spinks, P.Q., R.C. Thomson, E. McCartney-Melstad, and H. B. Shaffer. 2016. Phylogeny and temporal diversification of the New World pond turtles (Emydidae). Molecular Phylogenetics and Evolution 103:85-97.
McCartney-Melstad, E., G. G. Mount, and H. B. Shaffer. 2016. Exon capture optimization in amphibians with large genomes. Molecular Ecology Resources 16:1084-1094.
Wayne, R. K. and H. B. Shaffer. 2016. Hybridization and endangered species protection in the molecular era. Molecular Ecology 25:280-289.
Bucciarelli, G. M., D. B. Green, H. B. Shaffer, and L. B. Kats. 2016. Individual fluctuations in toxin levels affect breeding site fidelity in a chemically defended amphibian. Proceedings of the Royal Society B 283:1-9.
Searcy, C. A., and H. B. Shaffer. 2016. Do ecological niche models accurately identify climatic determinants of species ranges? American Naturalist 187:423-435.
Wright, A. N., M. W. Schwartz, R. J. Hijmans, and H. Bradley Shaffer. 2016. Advances in climate models from CMIP3 to CMIP5 do not change predictions of future habitat suitability for California reptiles and amphibians. Climatic Change 134:579-591.
Searcy, C. A., H. B. Rollins and H. B. Shaffer. 2016. Ecological equivalency as a tool for endangered species management. Ecological Applications 26:94-103.
2015
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.]. 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. Chelonian Research Monographs 5(8):000e.1–66.
McCartney-Melstad, E. and H. B. Shaffer. 2015. Amphibian molecular ecology and how it has informed conservation. Molecular Ecology 24:5084-5109.
Spinks, P. Q., A. Georges and H. B. Shaffer. 2015. Phylogenetic uncertainty and taxonomic re-revisions: an example from the Australian short-necked turtles (Testudines: Chelidae) Copeia 103:536-540.
Searcy, C. A., H. Snass, and H. B. Shaffer. 2015. Determinants of size at metamorphosis in an endangered amphibian and their projected effects on population stability. Oikos 124:724-731. doi: 10.1111/oik.01775
Rhodin, A. G. J. (and 69 coauthors). 2015. 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. Bulletin of Zoological Nomenclature 72:65-78.
Wright, A. N., R. J. Hijmans, M. W. Schwartz, and H. B. Shaffer. 2015. Multiple sources of uncertainty affect metrics for ranking conservation risk under climate change. Diversity and Distributions 21:111-122.
Shaffer, H. B., M, Gidiş E. McCartney-Melstad, K. M. Neal, H. M. Oyamaguchi, M. Tellez, and E. M. Toffelmier. 2015. Conservation genetics and genomics of amphibians and reptiles. Annual Reviews of Animal Biosciences 3:113-138.
2014
Feinberg, J. A., C. E. Newman, G. J. Watkins-Colwell, M. D. Schlesinger, B. Zarate, B. R. Curry, H. B. Shaffer, and J. Burger. 2014. Cryptic diversity in metropolis: Confirmation of a new leopard frog species (Anura: Ranidae) from New York City and surrounding Atlantic Coast regions. PLoS ONE 9(10): e108213. doi 10.1371/journal.pone.0108213.
Searcy, C. A. and H. B. Shaffer. 2014. Field validation supports novel niche modeling strategies in a cryptic endangered amphibian. Ecography 37:983-992.
Shaffer, H. B. 2014. Field of genes. BOOM: The journal of California 4:133-138.
Spinks, P. Q., R. C. Thomson, M. Gidis, and H. B. Shaffer. 2014. Multilocus phylogeny of the New-World mud turtles (Kinosternidae) supports the traditional classification of the group. Molecular Phylogenetics and Evolution 76:254-260.
Spinks, P. Q., R. C. Thomson, and H. B. Shaffer. 2014. The advantages of going large: genome-wide SNPs clarify the complex population history and systematics of the threatened western pond turtle. Molecular Ecology 23:2228-2241.
Turtle Taxonomy Working Group [P. P. van Dijk, J. B. Iverson, A. G. J. Rhodin, H. B. Shaffer, and R. Bour]. 2014. Turtles of the world, 7th edition: annotated checklist of taxonomy, synonymy, distribution with maps, and conservation status. 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 5(7):000.329–479,doi:10.3854/crm.5.000.checklist.v7.2014.
Warren, D. L., A. N. Wright, S. N. Seifert, and H. B. Shaffer. 2014. Incorporating model complexity and spatial sampling bias into ecological niche models of climate change risks faced by 90 California vertebrate species of concern. Diversity and Distributions 20:334-343.
Searcy, C. A., L. N. Gray, P. C. Trenham and H. B. Shaffer. 2014. Delayed life history effects, multilevel selection, and evolutionary trade-offs in the California tiger salamander. Ecology 95:68-77.
Searcy, C. A., H. B. Rollins and H. B. Shaffer. 2016. Ecological equivalency as a tool for endangered species management. Ecological Applications 26:94-103.
2013
Johnson, J. R., M. E. Ryan, S. J. Micheletti, and H. B. Shaffer. 2013. Short hydroperiod decreases fitness of nonnative salamanders in California. Animal Conservation 16:556-565.
Shaffer, H. B. and M. D. Purugganan. 2013. Genomics in ecology, evolution and systematics. Annual Review of Ecology, Evolution and Systematics 44:1-4.
Shaffer, H. B. 2013. Evolution and Conservation pp. 766-773 in The Princeton Guide to Evolution, J. Losos, Editor In Chief. Princeton University Press.
Polich, R. L, C. A. Searcy and H. B. Shaffer. 2013. Effects of tail-clipping on survivorship and growth of larval salamanders. J. Wildlife Management 77:1420-1425.
Lambert, M. R., S. N. Nielsen, A. N. Wright, R. C. Thomson, and H. B. Shaffer. 2013. Habitat features determine the basking distribution of introduced red-eared sliders and native western pond turtles. Chelonian Conservation and Biology 12:192-199.
Shaffer, H. B. (and 58 coauthors). 2013. The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. Genome Biology 2013, 14:R28 doi:10.1186/gb-2013-14-3-r28.
Spinks, P. Q., R, C. Thomson, G. B. Pauly, C. E. Newman, G. Mount and H. B. Shaffer. 2013. Misleading phylogenetic inferences based on single-exemplar sampling in the turtle genus Pseudemys. Molecular Phylogenetics and Evolution 68:269-281.
Ryan, M. E., J. R. Johnson, B. M. Fitzpatrick, L. J. Lowenstine, A. M. Picco and H. B. Shaffer. 2013. Lethal effects of water quality on threatened California salamanders but not on co-occurring hybrid salamanders. Conservation Biology 27:95-102.
Searcy, C. A., Gabbai-Saldate, E., and H. B Shaffer. 2013. Microhabitat use and migration distance of an endangered grassland amphibian. Biological Conservation 158:80-87.
2012
O’Neil, E. M., R. Schwartz, C. T. Bullock, J. S. Williams, H. B. Shaffer, X. Aguilar-Miguel, G. Parra-Olea, and D. W. Weisrock. 2012. Parallel tagged amplicon sequencing reveals major lineages and phylogenetic structure in the North American tiger salamander (Ambystoma tigrinum) species complex. Molecular Ecology 22:111-129.
Turtle Taxonomy Working Group [P. P. van Dijk, J. B. Iverson, H. B. Shaffer, R. Bour and A. G. J. Rhodin]. 2012. Turtles of the world, 2012 update: annotated checklist of taxonomy, synonymy, distribution, and conservation status. 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, doi:10.3854/crm.5.000.checklist.v5.2012
Voss, S. R., K. D. Kump, J. A. Walker, H. B. Shaffer, and G. J. Voss. 2012. Thyroid hormone responsive QTL and evolution of paedomorphic salamanders. Heredity 109:293-298.
Spinks, P. Q., R. C. Thomson, Y. Zhang, J. Che, Y. Wu, and H. B. Shaffer. 2012. Species boundaries and phylogenetic relationships in the critically endangered Asian box turtle genus Cuora. Molecular Phylogenetics and Evolution 63:656-667.
Newman, C. E., J. A. Feinberg, L. J. Rissler, J. Burger, and H. B. Shaffer. 2012. A new species of leopard frog (Anura: Ranidae) from the urban northeastern US. Molecular Phylogenetics and Evolution 63:445-455.
Spinks, P.Q., R. C. Thomson, B. Hughes, B. Moxley, R. Brown, A. Deismos, and H. B. Shaffer. 2012. Cryptic variation and the tragedy of unrecognized taxa: the case of international trade in the spiny turtle Heosemys spinosa (Testudines: Geoemydidae). Zoological Journal of the Linnean Society 164:811-824.
Pauly, G. B., S. H. Bennett, J. G. Palis and H. B. Shaffer. 2012. Conservation and genetics of the frosted flatwoods salamander (Ambystoma cingulatum) on the Atlantic Coastal Plain. Conservation Genetics 13:1-7.
2011
Searcy, C. A. and H. B. Shaffer. 2011. Determining the migration distance of a vagile vernal pool specialist: How much land is required for conservation of California tiger salamanders? Pages 73-87 in D. G. Alexander and R. A. Schlising (Editors), Research and recovery in vernal pool landscapes. Studies from the Herbarium, Number 16. California State University, Chico, CA.
Turtle TaxonomyWorking Group [P. P. van Dijk, J. B. Iverson, H. B. Shaffer, R. Bour and A. G. J. Rhodin]. 2011. Turtles of the world, 2011 update: annotated checklist of taxonomy, synonymy, distribution, and conservation status. 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. 000.165–000.242, doi:10.3854/crm.5.000.checklist.v4.2011
Mautz, W. J. and H. B. Shaffer. 2011. Colonization of Hawaii Island by the Brown Anole (Anolis sagrei). Herpetological Review 42:508-509.
Caro, T., O. Evans, E. Fitzherbert, T. A. Gardner, K. Howell, R. Drewes and H. B. Shaffer. 2011. Reptiles of Katavi National Park, western Tanzania, are from different biomes. African Journal of Ecology 49:377-382.
Wang, I. J., J. R. Johnson, B. B. Johnson and H. B. Shaffer. 2011. Effective population size is strongly correlated with breeding pond size in the endangered California tiger salamander, Ambystoma californiense. Conservation Genetics 12:911-920.
Georges, A, R-J Spencer, M. Welsh, H. B. Shaffer, R. Walsh and X. Zhang. 2011. Application of the precautionary principle to taxa of uncertain status – the case of the Bellinger River Turtle. Endangered Species Research 14:127-134.
Gidis, M., P. Q. Spinks, E. Çevik, Y. Kaska, and H. B. Shaffer. 2011. Shallow genetic divergence indicates a Congo-Nile riverine connection for the softshell turtle Trionyx triunguis. Conservation Genetics 12:589-594.
Lind, A. J., P. Q. Spinks, G. M. Fellers and H. B. Shaffer. 2011. Rangewide phylogeography and landscape genetics of the western U. S. endemic frog Rana boylii (Ranidae): implications for the conservation of frogs and rivers. Conservation Genetics 12:269-284.
Johnson, J. R., R. C. Thomson, S. J. Micheletti and H. B. Shaffer. 2011. The origin of tiger salamander (Ambystoma tigrinum) populations in California, Oregon and Nevada: introductions or relicts? Conservation Genetics 12:255-370
2010
Spinks, P. Q., R. C. Thomson, A. J. Barley, C. E. Newman and H. B. Shaffer. 2010. Testing avian, squamate, and mammalian nuclear markers for cross amplification in turtles. Conservation Genetics Resources 2: 127-129.
Caro, T. M. and H. B. Shaffer. 2010. Chelonian antipredator strategies: preliminary and comparative data from Tanzanian Pelusios. Chelonian Conservation and Biology 9:302-305.
Thomson, R. C., P. Q. Spinks and H. B. Shaffer. 2010. Distribution and abundance of invasive red-eared sliders (Trachemys scripta elegans) in California’s Sacramento River basin and possible impacts on native western pond turtles (Emys marmorata). Chelonian Conservation and Biology 9:297-302.
Savage, W., A. Fremier, and H. B. Shaffer. 2010. Landscape genetics of alpine Sierra Nevada salamanders reveal extreme population subdivision in space and time. Molecular Ecology 19:3301-3314.
Johnson, J. R., B. B. Johnson and H. B. Shaffer. 2010. Genotype and temperature affect locomotor performance in a tiger salamander hybrid swarm. Functional Ecology 24:1073-1080.
Turtle Taxonomy Working Group [Rhodin, A.G.J., P. P. van Dijk, J. B. Iverson, and H. B.Shaffer]. 2010. Turtles of the world, 2010 update: annotated checklist of taxonomy,synonymy, distribution, and conservation status. In: Rhodin, A.G.J., Pritchard, P.C.H., vanDijk, P.P., Saumure, R.A., Buhlmann, K.A., Iverson, J.B., and Mittermeier, R.A. (Eds.).Conservation Biology of Freshwater Turtl{Spinks, 2003 #1219}{Spinks, 2003 #1219}es andTortoises: A Compilation Project of the IUCN/SSC Tortoise and Freshwater Turtle SpecialistGroup. Chelonian Research Monographs No. 5, pp. 000.85–000.164, doi:10.3854/crm.5.000.checklist.v3.2010
Thomson, R. C. and H. B. Shaffer. 2010. Rapid progress on the vertebrate tree of life. BMC Biology 2010, 8:19.
Fitzpatrick, B. M., J. R. Johnson, D. K. Kump, J. J. Smith, S. R. Voss and H. B. Shaffer. 2010. Rapid spread of invasive genes into a threatened native species. Proceedings of the National Academy of Sciences, USA, 107:3606-3610.
Barley, A. J., P. Q. Spinks, R. C. Thomson and H. Bradley Shaffer. 2010. Fourteen nuclear genes provide phylogenetic resolution for difficult nodes in the turtle tree of life. Molecular Phylogenetics and Evolution 55:1189-1194.
Johnson, J. R., B. M. Fitzpatrick and H. Bradley Shaffer. 2010. Retention of low-fitness genotypes over six decades of admixture between native and introduced tiger salamanders. BMC Evolutionary Biology 2010, 10:147.
Spinks, P. Q., Thomson, R. C. and H. B. Shaffer. 2010. Nuclear gene phylogeography reveals the historical legacy of an ancient inland sea on lineages of the western pond turtle, Emys marmorata in California. Molecular Ecology, 19: 542–556.
Thomson, R. C. and H. B. Shaffer. 2010. Sparse supermatrices for phylogenetic inference:Taxonomy, alignment, rogue taxa, and the phylogeny of living turtles. Systematic Biology 59:42-58