Publications

2017

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