Publications

Listed in reverse chronological order
  • 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. PDF
  • 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. PDF
  • 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. PDF
  • 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. PDF
  • 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. 2013. 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. PDF
  • 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, www.iucn–tftsg.org/cbftt/. PDF
  • 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. PDF
  • 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. PDF
  • 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. PDF
  • 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. PDF
  • 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. PDF
  • 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. PDF
  • 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, http://www.iucn–tftsg.org/cbftt/.
  • Mautz, W. J. and H. B. Shaffer. 2011. Colonization of Hawaii Island by the Brown Anole (Anolis sagrei). Herpetological Review 42:508-509. PDF
  • 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. PDF
  • 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. PDF
  • 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. PDF
  • 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. PDF
  • 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. PDF
  • 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 PDF
  • 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. PDF
  • 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. PDF
  • 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. PDF
  • 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. PDF
  • 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. PDF
  • 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, http://www.iucn–tftsg.org/cbftt/. PDF
  • Thomson, R. C. and H. B. Shaffer. 2010. Rapid progress on the vertebrate tree of life. BMC Biology 2010, 8:19. PDF
  • 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. PDF
  • 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. PDF
  • 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. PDF
  • 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. PDF
  • 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 PDF
  • Genome 10K Community of Scientists (66 coauthors). 2009. Genome 10K: A proposal to obtain whole-genome sequence for 10,000 vertebrate species. Journal of Heredity 100:659-674. PDF
  • Shaffer, H. B. Turtles (Testudines). 2009. In The Timetree of Life. S. B. Hedges and S. Kumar, Eds. (Oxford University Press, New York), pp. 398-401. PDF
  • Shaffer, H. B. 2009. Modern Reptiles. in M. Ruse and J Travis, eds., Evolution: The first four billion years. Pps 739-742. Harvard University Press, Cambridge.
  • Wang I. J., Savage W. K., and Shaffer H. B. 2009. Landscape genetics and least cost path analysis reveal unexpected migration routes in the California tiger salamander, Ambystoma californiense. Molecular Ecology, 18: 1365-1374 PDF
  • Fitzpatrick, B. M., J. R. Johnson, D. K. Kump, H. B. Shaffer, J. J. Smith, and S. R. Voss. 2009. Rapid fixation of non-native alleles revealed by genome-wide SNP analysis of hybrid tiger salamanders. BMC Evolutionary Biology 9:176 PDF
  • Spinks, P. Q. and H. B. Shaffer. 2009. Conflicting mitochondrial and nuclear phylogenies for the widely disjunct Emys (Testudines: Emydidae) Species Complex, and what they tell us about biogeography and hybridization. Systematic Biology 58:1-20. PDF
  • Spinks, Phillip Q., Robert C. Thomson, Geoff A. Lovely and H. Bradley Shaffer. 2009. Assessing what is needed to resolve a molecular phylogeny: simulations and empirical data from emydid turtles. BMC Evolutionary Biology, 9:56 PDF
  • Spinks, Phillip Q., Robert C. Thomson, and H. Bradley Shaffer. 2009. A reassessment of Cuora cyclornata Blanck, McCord and Le, 2006 (Testudines, Geoemydidae) and a plea for taxonomic stability. Zootaxa 2018: 58–68 PDF
  • Ryan, M. E., J. R. Johnson, and B. M. Fitzpatrick. 2009. Invasive hybrid tiger salamander genotypes impact native amphibians. PNAS 106(27)11167-11121. PDF
  • Near, T. J., P. A. Meylan, and H. B. Shaffer. 2008. Caveats on the use of fossil calibrations for molecular dating: A reply to Parham and Irmis. American Naturalist 171:137-140.PDF
  • Shaffer, H.B., D.E. Starkey, and M.K. Fujita. 2008. Molecular insights into the systematics of the snapping turtles (Chelydridae). In R.J. Brooks, A.C. Steyermark, and M.S. Finkler, eds., Biology of the Snapping Turtle (Chelydra serpentina). pp. 44-49. Johns Hopkins Univ.Press, Baltimore.PDF
  • Wang, I. J. and H. B. Shaffer. 2008. Coloration is a highly labile trait in an aposematic species: A phylogenetic analysis of color evolution in the strikingly polymorphic strawberry poison-dart frog. Evolution 62:2742-2759.PDF
  • Thomson, RC, AM Shedlock, SV Edwards, HB Shaffer. 2008. Developing markers for multilocus phylogenetics in non-model organisms: a test case with turtles. Molecular Phylogenetics and Evolution. 49: 514-525 PDF
  • Searcy, C. A., and H. B. Shaffer. 2008. Calculating biologically accurate mitigation credits: insights from the California tiger salamander. Conservation Biology 22: 997-1005.PDF
  • Gamble, T., P. B. Berendzen, H. B, Shaffer, D. E. Starkey, and A. M. Simons. 2008. Species limits and phylogeography of North American cricket frogs (Acris: Hylidae). Molecular Phylogenetics and Evolution 48:112-125.PDF
  • Ives, I., P. Q. Spinks, and H. B. Shaffer. 2008. Morphological and Genetic Variation in the endangered Sulawesi tortoise Indotestudo forstenii: Evidence of Distinct Lineages? Conservation Genetics 9:709-713.PDF
  • Shaffer, HB and RC Thomson. 2007. Delimiting species in recent radiations. Systematic Biology 56(6): 896-906 PDF
  • Shaffer, H.B., FitzSimmons, N.N., Georges, A., and Rhodin, A.G.J. (Eds.) Defining Turtle Diversity: Proceedings of a Workshop on Genetics, Ethics, and Taxonomy of Freshwater Turtles and Tortoises. Chelonian Research Monographs No. 4, 200 pp. PDF
  • Turtle Taxonomy Working Group [Bickham, J.W., Parham, J.W., Philippen, H.D., Rhodin, A.G.J., Shaffer, H.B., Spinks, P.Q., and van Dijk, P.P.; H.B. Shaffer, lead author]. 2007. Turtle taxonomy: methodology, recommendations, and guidelines. In: Shaffer, H.B., FitzSimmons, N.N., Georges, A., and Rhodin, A.G.J. (Eds.) Defining Turtle Diversity: Proceedings of a Workshop on Genetics, Ethics, and Taxonomy of Freshwater Turtles and Tortoises. Chelonian Research Monographs No. 4, pp. 73-84.PDF
  • Turtle Taxonomy Working Group [Bickham, J.W., Iverson, J.B., Parham, J.W., Philippen, H.D., Rhodin, A.G.J., Shaffer, H.B., Spinks, P.Q., and van Dijk, P.P.; J. W. Parham, lead author]. 2007. An annotated list of modern turtle terminal taxa, with comments on areas of taxonomic instability and recent change. In: Shaffer, H.B., FitzSimmons, N.N., Georges, A., and Rhodin, A.G.J. (Eds.) Defining Turtle Diversity: Proceedings of a Workshop on Genetics, Ethics, and Taxonomy of Freshwater Turtles and Tortoises. Chelonian Research Monographs No. 4, pp. 173-199.PDF
  • Fitzpatrick, B. M. and H.B. Shaffer. 2007. Hybrid vigor between native and introduced salamanders raises new challenges for conservation. Proceedings of the National Academy of Sciences, USA 104:15793-15798.PDF
  • Spinks, P.Q. and H. B. Shaffer. 2007. Conservation phylogenetics of the Asian box turtles (Geoemydidae, Cuora): mitochondrial introgression, numts, and inferences from multiple nuclear loci. Conservation Genetics 8:641-657.PDF
  • Fitzpatrick, B.M. and H.B. Shaffer. 2007. Introduction history and habitat variation explain the landscape genetics of hybrid tiger salamanders. Ecological Applications 17(2):598-608. PDF
  • Davidson, C., Benard, M. F., Shaffer, H. B., Parker, J. M., O’Leary, C., Conlon, J. M., and Rollins-Smith, L. A. 2007. Effects of chytrid and carbaryl exposure on survival, growth and skin peptide defenses in foothill yellow-legged frogs. Environmental Science and Technology 41:1771-1776.PDF
  • Pauly, Gregory B., Oliver Piskurek, and H. Bradley Shaffer. 2007. Phylogeographic concordance in the southeastern United States: the flatwoods salamander, Ambystoma cingulatum, as a test case. Molecular Ecology, 16:415–429. PDF
  • Weisrock, David W., H. Bradley Shaffer, Brian L. Storz, Shonna R. Storz and S. Randal Voss. 2006. Multiple nuclear gene sequences identify phylogenetic species boundaries in the rapidly radiating clade of Mexican ambystomatid salamanders. Molecular Ecology 15: 2489–2503. PDF
  • Trenham, Peter C., and H. Bradley Shaffer. 2005. Amphibian upland habitat use and its consequences for population viability. Ecological Applications 15:1158–1168. PDF
  • Spinks, P.Q. and H.B. Shaffer. 2005. Rangewide molecular analysis of the western pond turtle (Emys marmorata): cryptic variation, isolation by distance, and their conservation implications. Molecular Ecology, 14:2047-2064. PDF
  • Near, T. J., P. A. Meylan and H. B. Shaffer. 2005. Assessing concordance of fossil calibration points in molecular clock studies: an example using turtles. American Naturalist 165:137-146. PDF
  • Krenz, J. G., G.J.P. Naylor, H. B. Shaffer and F. J. Janzen. 2005. Molecular phylogenetics and evolution of turtles. Molecular Phylogenetics and Evolution 37:178-191.PDF
  • Shaffer, H. B. 2005. Ambystoma gracile (Baird, 1859) Northwestern salamander. Pp. 609-611 In Lannoo, M.J. (Ed.), Amphibian declines. The conservation status of United States species. University of California Press, Berkeley, California.
  • Shaffer, H. B. and P. C. Trenham. 2005. Ambystoma californiense (Gray, 1853) California tiger salamander. Pp. 605-608 In Lannoo, M.J. (Ed.), Amphibian declines. The conservation status of United States species. University of California Press, Berkeley, California.
  • Engstrom, T.N., H. B. Shaffer and W. P. McCord. 2004. Multiple data sets, high homoplasy, and the phylogeny of softshell turtles (Testudines: Trionychidae). Systematic Biology 53:693-710. PDF
  • Fitzpatrick, Benjamin M. and H. Bradley Shaffer. 2004. Environment-dependent admixture dynamics in a tiger salamander hybrid zone. Evolution, 58(6):1282-1293. PDF
  • Fujita, Matthew K., Tag N. Engstrom, David E. Starkey, and H. Bradley Shaffer. 2004. Turtle phylogeny: insights from a novel nuclear intron. Molecular Phylogenetics and Evolution. 31:1031-1040. PDF
  • Shaffer, H. Bradley, Gregory B. Pauly, Jeffrey C. Oliver, and Peter C. Trenham. 2004. The molecular phylogenetics of endangerment: cryptic variation and historical phylogeography of the California tiger salamander, Ambystoma californiense. Molecular Ecology 13:3033-3049.PDF
  • Shaffer, H. Bradley, G.M.Fellers, S. Randal Voss, J.C. Oliver, and Gregory B. Pauly. 2004. Species boundaries, phylogeography, and conservation genetics of the red-legged frog (Rana aurora/draytonii) complex. Molecular Ecology 13: 2667-2677.PDF
  • Spinks, Phillip Q., H.Bradley Shaffer, John B. Iverson, and William P. McCord. 2004. Phylogenetic hypotheses for the turtle family Geoemydidae. Molecular Phylogenetics and Evolution. 32:164-182. PDF
  • Riley, S.P.D., H.B. Shaffer, S.R. Voss, and B.M. Fitzpatrick. 2003. Hybridization between a rare, native tiger salamander (Ambystoma californiense) and its introduced congener. Ecological Applications 13(5):1263-1275. PDF
  • Shaffer, H. B. 2003. Mole salamanders (Ambystomatidae). Pp. 355-361 In Hutchins, M., Duellman, W. E., and Schlager, N. (Editors) Grzimek's Animal Life Encyclopedia. Second edition. Volume 6, Amphibians, Gale Group, Farmington Hills, MI.
  • Spinks, P.Q., G.B. Pauly, J.J. Crayon and H.B. Shaffer. 2003. Survival of the western pond turtle (Emys marmorata) in an urban environment. Biological Conservation 113(2):257-267. PDF
  • Starkey, D.E., H.B. Shaffer, R. R. Burke, M.R.J. Forstner, J. B. Iverson, F. J. Janzen, A. G.J. Rhodin, and G. R. Ultsch. 2003. Molecular Systematics, Phylogeography, and the Effects of Pleistocene Glaciation in the Painted Turtle (Chrysemys picta) Complex. Evolution 57(1):119-128. PDF
  • Voss, S. R., K. Prudic, J. Oliver, and H.B. Shaffer. 2003. Candidate gene analysis of metamorphic timing in ambystomatid salamanders. Molecular Ecology 12:1217-1223. PDF
  • Davidson, C., H. B. Shaffer and M. R. Jennings. 2002. Spatial tests of the pesticide drift, habitat destruction, UV-B and climate change hypotheses for California amphibian declines. Conservation Biology 16(6):1588-1601. PDF
  • Engstrom, T.N., H.B Shaffer, and W.P. McCord. 2002. Phylogenetic diversity of endangered and critically endangered southeast Asian softshell turtles (Trionychidae: Chitra). Biological Conservation 104:173-179. PDF
  • Sanderson, M.J. and H.B. Shaffer. 2002. Troubleshooting molecular phylogenetic analyses. Annual Reviews of Ecology and Systematics 33:49-72. PDF
  • Davidson, C., H. B. Shaffer and M. R. Jennings. 2001. Declines of the California red-legged frog: climate, UV-B, habitat, and pesticides hypotheses. Ecological Applications 11:464-479. PDF
  • Iverson, J. B., P. Q. Spinks, H. B. Shaffer, W. P. McCord and I. Das. 2001. Phylogenetic relationships among the Asian tortoises of the genus Indotestudo (Reptilia: Testudines: Testudinidae). Hamadryad 26:271-274. PDF
  • Shaffer, H.B. 2001. Neoteny. Pps. 1304-1305 In: Encyclopedia of Genetics. London: Academic Press.
  • Trenham, P.C., W. D. Koenig and H. B. Shaffer. 2001. Spatially autocorrelated demography and interpond dispersal in the salamander Ambystoma californiense. Ecology 82:3519-3530. PDF
  • McCord, W. P., J. B. Iverson, P. Q. Spinks, and H. B. Shaffer. 2000. A new genus of geoemydid turtle from Asia. Hamadryad 25:20-24. PDF
  • Shaffer, H. B., G. M. Fellers, A. Magee and S. R. Voss. 2000. The genetics of amphibian declines: population substructure and molecular differentiation in the Yosemite Toad, Bufo canorus (Anura, Bufonidae) based on single-strand conformation polymorphism analysis(SSCP) and mitochondrial DNA sequence data. Molecular Ecology 9:245-257. PDF
  • Trenham, P. C., H. B. Shaffer, W. D.Koenig and M. R. Stromberg. 2000. Life history and demographic variation in the California Tiger Salamander (Ambystoma californiense). Copeia 2000:365-377. PDF
  • Voss, SR, HB Shaffer. 2000. Evolutionary Genetics of Metamorphic Failure Using Wild-Caught vs. Laboratory Axolotls (Ambystoma mexicanum). Molecular Ecology 9:1401-1407. PDF
  • Voss, S. R., H. B. Shaffer, J. Taylor, R. Safi, and V. Laudet. 2000. Candidate gene analysis of thyroid hormone receptors in metamorphosing vs. non-metamorphosing salamanders. Heredity 85:107-114. PDF

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