1998
Trenham, P. C., H. B. Shaffer and P. B. Moyle. 1998. Biochemical identification and assessment of population structure of morphologically similar native and invading smelt species (Hypomesus) in the Sacramento-San Joaquin Estuary, California. Transactions of the American Fisheries Society 127;417-424.
Shaffer, H. B., R. N. Fisher and C. Davidson. 1998. The role of natural history collections in documenting species declines. Trends in Ecology and Evolution 13:27-30.
1997
McKnight, M. L. and H. B. Shaffer. 1997. Large, rapidly evolving intergenic spacers in the mitochondrial DNA of the salamander family Ambystomatidae (Amphibia: Caudata). Molecular Biology and Evolution, 14:1167-1176.
Voss, S. R. and H. B. Shaffer. 1997. Adaptive evolution via a major gene effect: Paedomorphosis in the Mexican axolotl. Proceedings of the National Academy of Sciences, USA. 94:14185-14189.
Shaffer, H. B. P. Meylan and M. L. McKnight. 1997. Tests of turtle phylogeny: molecular, morphological and paleontological approaches. Systematic Biology 46:235-268.
Irschick, D. J. and H. B. Shaffer. 1997. The polytypic species revisited: Morphological differentiation among tiger salamanders (Ambystoma tigrinum) (Amphibia: Caudata). Herpetologica, 53:30-49.
Janzen, F. J., S. L. Hoover and H. B. Shaffer. 1997. Molecular phylogeography of the western pond turtle (Clemmys marmorata): Preliminary results. Chelonian Conservation and Biology 2:623-626.
1996
Voss, S. R. and H. B. Shaffer. 1996. What insights into the developmental traits of urodeles does the study of interspecific hybrids provide? International Journal of Developmental Biology, 40: 885-893.
Fisher, R. N. and H. B. Shaffer. 1996. The decline of amphibians in California’s Great Central Valley. Conservation Biology, 10:1387-1397.
Shaffer, H.B. and M. L. McKnight. 1996. The polytypic species revisited: genetic differentiation and molecular phylogenetics of the tiger salamander (Ambystoma tigrinum) (Amphibia: Caudata) complex. Evolution, 50:417-433.
Shaffer, H. B. and S. R. Voss. 1996. Phylogenetic and mechanistic analysis of a developmentally integrated character complex: Alternate life history modes in ambystomatid salamanders. American Zoologist, 36(1):24-35.
1995
Stanley, S., P. B. Moyle and H. B. Shaffer. 1995. Allozyme analysis of Delta Smelt, Hypomesus transpacificus and Longfin Smelt, Spirinchus thaleichthys in the Sacramento-San Joaquin estuary, California. Copeia, 1995:390-396.
1994
Wade, M. J., M. L. McKnight and H. Bradley Shaffer. 1994. The effects of kin-structured colonization and stepping-stone range expansion on nuclear and cytoplasmic gene diversity. Evolution, 48:1114-1120.
Barry, S. J. and H. B. Shaffer. 1994. The status of the California Tiger Salamander (Ambystoma californiense) at Lagunita: A fifty-year update. Journal of Herpetology 28:159-164.
Zhao, E.-M., R. F. Inger, G.-F. Wu, and H. B. Shaffer. 1994. Morphological variation and ecological distribution of co-occurring larval forms of Oreolalax (Anura: Pelobatidae). Amphibia-Reptilia, 15:109-121.
Shaffer, H.B., R.A. Alford, B.D. Woodward, S.J. Richards, R. G. Altig and C. Gascon. 1994. Quantitative sampling of amphibian larvae. Pps 130-141 in W.R. Heyer et al., editors, Measuring and Monitoring Biological Diversity: Standard Methods for Amphibians. Smithsonian Institution Press, Washington, D.C.
Shaffer, H.B. and E. Juterbock. 1994. Night driving. Pps. 163-166 in W.R. Heyer et al., editors, Measuring and Monitoring Biological Diversity: Standard Methods for Amphibians. Smithsonian Institution Press, Washington, D.C.
1993
Shaffer, H. B. 1993. Phylogenetics of model organisms: The laboratory axolotl, Ambystoma mexicanum. Systematic Biology 42:508-522.
Kellogg, E. A. and H. B. Shaffer. 1993. Model organisms in evolutionary studies. Systematic Biology 42:409-414.
Wu, Guan-Fu, Zhao, Er-Mi, Inger, R. F. and H. B. Shaffer. 1993. A new frog of the genus Oreolalax (Pelobatidae) from Sichuan, China. J. Herpetology, 27:410-413.
Lauder, G.V. and H.B. Shaffer. 1993. Design of feeding systems in aquatic vertebrates: Major patterns and their evolutionary interpretations. pps 113-149 in J. Hanken and B.K. Hall, eds. The Skull, vol 3. University of Chicago Press.
1992
Austin, C.C. and H.B. Shaffer. 1992. Short, medium, and long term repeatability of locomotor performance in the tiger salamander Ambystoma californiense. Functional Ecology 6:145-153.
1991
Shaffer, H.B., J.M. Clark, and F. Kraus. 1991. When molecules and morphology clash: A phylogenetic analysis of the North American ambystomatid (Caudata:Ambystomatidae) salamanders. Systematic Zoology 40(3): 284-303.
Shaffer, H.B., C.C. Austin, and R.B. Huey. 1991. The consequences of metamorphosis on salamander (Ambystoma) locomotor performance. Physiological Zoology 64(1): 212-231.
1990
Inger, R.F., E. Zhao, H. Bradley Shaffer, and G. Wu. 1990. Report on a collection of amphibians and reptiles from Sichuan, China. Fieldiana Zoology, #58.