Unmack, P. J., A. Bennin*, E. Habit, P. Victoriano, and J. B. Johnson.  "Impact of ocean barriers and glaciation on phylogeography of the catfish Trichomycterus areolatus (Teleostei: Trichomycteridae) in Chile."  Biological Journal of the Linnean Society.  97 (2009): 876-892. 

Carissa P. Jones and Jerald B. Johnson.  "Phylogeography of the livebearer Xenophallus umbratilis (Teleostei: Poeciliidae): glacial cycles and sea level change predict diversification of a freshwater tropical fish."  Molecular Ecology.  18 (2009): 1640-1653. 

Johnson, J. B. and J. J. Zuniga Vega.  "Differential mortality predicts life history evolution and shapes population demography in the livebearing fish Brachyrhaphis rhabdophora."  Ecology.  90 (2009): 2243-2252. 

Lee, J. B. and J. B. Johnson.  "Biogeography of the livebearing fish Poecilia gillii in Costa Rica: are phylogeographic breaks congruent with fish community boundaries?."  Molecular Ecology.  18 (2009): 4088-4101. 

Johnson, J. B., S. Peat, and B. J. Adams.  "Where's the ecology in molecular ecology?."  Oikos.  118 (2009): 1601-1609. 

Johnson, J. B. and K. A. Crandall.  "Expanding the toolbox for phylogeographic analysis."  Molecular Ecology.  18 (2009): 4137-4139. 

Johnson, J. B., M. Adair, B. J. Adams, D. J. Fairbanks, V. Itamura, D. E. Jeffery, D. Merrell, S. M. Ritter, and R. R. Tolman.  "Evolution education in Utah: a state office of education-university partnership focuses on why evolution matters."  Evolution: Education & Outreach.  2 (2009): 349-358.  <website>

J. J. Zuniga-Vega, D. N. Reznick, J. B. Johnson.  "Habitat predicts reproductive superfetation and body shape in the livebearing fish Poeciliopsis turrubarensis."  Oikos.  116 (2007): 995-1005. 

Johnson, J. B. and M. C. Belk.  "What the status of Utah chub tells us about conserving common, widespread species."  American Fisheries Society.  53 (2007): 165-173. 

Belk, M. C., J. B. Johnson, M. Smith, K. W. Wilson, and D. D. Houston.  "Variation in intrinsic growth rate among populations of leatherside chub (Snyderichthys copei Jordan & Gilbert): adaptation to temperature or length of growing season?."  Ecology of Freshwater Fish.  14 (2005): 177-184. 

Johnson, J. B., T. E. Dowling, and M. C. Belk.  "Neglected taxonomy of rare desert fishes: congruent evidence for two species of leatherside chub."  Systematic Biology.  53:841-854. (2004). 

Johnson, J. B. and K. S. Omland.  "Model selection in ecology and evolution."  Trends in Ecology and Evolution.  19:101-108 (2004). 

Johnson, J. B. and A. L. Basolo.  "Predator exposure alters female mate choice in the green swordtail."  Behavioral Ecology.  Jan. 2003: 14:619-625. 

Johnson, Jerald B.  "Evolution after the flood: phylogeography of the desert fish Utah chub."  Evolution.  Jan. 2002: 56:948-960. 

Ruckelshaus, M. H., P. Levine, J. B. Johnson, and P. M. Kareiva.  "The Pacific salmon wars: what science brings to the challenge of conserving species."  Annual Review of Ecology and Systematics.  Jan. 2002: 33:665-706. 

Johnson, Jerald B.  "Divergent life histories among populations of the fish Brachyrhaphis rhabdophora: detecting putative agens of selection by candidate model analysis."  Oikos.  Jan. 2002: 96:82-91. 

Johnson, Jerald B.  "Adaptive life-history evolution in the livebearing fish Brachyrhaphis rhabdophora: genetic basis for parallel divergence in age and size at maturity and a test of predator-induced phenotypic plasticity."  Evolution.  Jan. 2001: 55:1486-1491. 

Johnson, Jerald B.  "Hierarchical organization of genetic variation in the Costa Rican livebearing fish Brachyrhaphis rhabdophora (Poeciliidae)."  Biological Journal of the Linnean Society.  Jan. 2001: 72:519-527. 

Johnson, J. B. and M. C. Belk.  "Predation environment predicts divergent life-history phenotypes among populations of the livebearing fish Brachyrhaphis rhabdophora."  Oecologia.  Jan. 2001: 126:142-149.