Weisrock, D., Shaffer, H., Storz, B., , & . (2006). Multiple nuclear gene sequences identify phylogenetic species boundaries in the rapidly radiating clade of Mexican ambystomatid salamanders. Molecular Ecology, 15(9), 2489-503. https://doi.org/10.1111/j.1365-294X.2006.02961.x

Fitzpatrick, B., , Kump, D., Smith, J., , & Shaffer, H. (2010). Rapid spread of invasive genes into a threatened native species. Proceedings of the National Academy of Sciences of the United States of America, 107(8), 3606-10. https://doi.org/10.1073/pnas.0911802107 (Original work published 2010)

Fitzpatrick, B., , Kump, D., Shaffer, H., Smith, J., & . (2009). Rapid fixation of non-native alleles revealed by genome-wide SNP analysis of hybrid tiger salamanders. BMC Evolutionary Biology, 9, 176. https://doi.org/10.1186/1471-2148-9-176 (Original work published 2009)

, Kump, D., Walker, J., Shaffer, H., & Voss, G. (2012). Thyroid hormone responsive QTL and the evolution of paedomorphic salamanders. Heredity, 109(5), 293-8. https://doi.org/10.1038/hdy.2012.41

O’Neill, E., Schwartz, R., Bullock, C., Williams, J., Shaffer, H., Aguilar-Miguel, X., … Weisrock, D. (2013). Parallel tagged amplicon sequencing reveals major lineages and phylogenetic structure in the North American tiger salamander (Ambystoma tigrinum) species complex. Molecular Ecology, 22(1), 111-29. https://doi.org/10.1111/mec.12049

Shaffer, H., Fellers, G., , Oliver, J., & Pauly, G. (2004). Species boundaries, phylogeography and conservation genetics of the red-legged frog (Rana aurora/draytonii) complex. Molecular Ecology, 13(9), 2667-77. https://doi.org/10.1111/j.1365-294X.2004.02285.x

, Prudic, K., Oliver, J., & Shaffer, H. (2003). Candidate gene analysis of metamorphic timing in ambystomatid salamanders. Molecular Ecology, 12(5), 1217-23. https://doi.org/10.1046/j.1365-294x.2003.01806.x

, Shaffer, H., Taylor, J., Safi, R., & . (2000). Candidate gene analysis of thyroid hormone receptors in metamorphosing vs. nonmetamorphosing salamanders. Heredity, 85 ( Pt 2), 107-14. https://doi.org/10.1046/j.1365-2540.2000.00714.x

, & Shaffer, H. (2000). Evolutionary genetics of metamorphic failure using wild-caught vs. laboratory axolotls (Ambystoma mexicanum). Molecular Ecology, 9(9), 1401-7. https://doi.org/10.1046/j.1365-294x.2000.01025.x

Shaffer, H., Fellers, G., Magee, A., & . (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(3), 245-57. https://doi.org/10.1046/j.1365-294x.2000.00835.x