2009
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.
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.
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
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
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.
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
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
Ryan, M. E., J. R. Johnson, and B. M. Fitzpatrick. 2009. Invasive hybrid tiger salamander genotypes impact native amphibians. PNAS 106(27)11167-11121.
2008
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.
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.
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.
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
Searcy, C. A., and H. B. Shaffer. 2008. Calculating biologically accurate mitigation credits: insights from the California tiger salamander. Conservation Biology 22: 997-1005.
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.
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.
2007
Shaffer, HB and RC Thomson. 2007. Delimiting species in recent radiations. Systematic Biology 56(6): 896-906
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.
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.
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.
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.
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.
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.
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.
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.
2006
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.
2005
Trenham, Peter C., and H. Bradley Shaffer. 2005. Amphibian upland habitat use and its consequences for population viability. Ecological Applications 15:1158–1168.
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.
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.
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.
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.
2004
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.
Fitzpatrick, Benjamin M. and H. Bradley Shaffer. 2004. Environment-dependent admixture dynamics in a tiger salamander hybrid zone. Evolution, 58(6):1282-1293.
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.
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.
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.
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.
2003
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.
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.
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.
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.
2002
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.
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.
Sanderson, M.J. and H.B. Shaffer. 2002. Troubleshooting molecular phylogenetic analyses. Annual Reviews of Ecology and Systematics 33:49-72.
2001
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.
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.
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.
2000
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.
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.
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.
Voss, SR, HB Shaffer. 2000. Evolutionary Genetics of Metamorphic Failure Using Wild-Caught vs. Laboratory Axolotls (Ambystoma mexicanum). Molecular Ecology 9:1401-1407.
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.