Yoshizawa, M, Aschida, G., and W. R. Jeffery (2012).  Parental genetic effects in a cavefish adaptive behavior explain disparity between nuclear and mitochondrial DNA.  Evolution (in press).

Yoshizawa, M, Goricki, S., Soares, D., and W. R. Jeffery (2010).  Evolution of a behavioral shift mediated by superficial neuromasts helps cavefish find food in darkness. Curr. Biol. 20: 1631-1636.

Jeffery, W.R. (2009). Regressive evolution in Astyanax cavefish. Annual Review of Genetics 43, 25-27

Yamamoto, Y., Byerly, M.S., Jackman, W.R., and W.R. Jeffery (2009). Pleiotropic functions of  embryonic sonic hedgehog expression link jaw and taste bud amplification with eye loss during cavefish evolution. Developmental Biology. 330:200-211 [pdf]

Jeffery, W.R. (2009). Evolution and development in the cavefish Astyanax. Current Topics in Developmental Biology. 86: 191-221 [pdf]

Strickler, A.G. and W.R. Jeffery (2009). Differentially expressed genes identified by cross species microarray in the blind cavefish Astyanax. Integrative Zoology. 4:31-40 [pdf]

Gross, J.B., Protas, M., Conrad, M., Scheid, P.E., Vidal, O., Jeffery, W.R., Browosky, R., and C.J. Tabin (2008). Synteny and candidate gene prediction using an anchored linkage map of Astyanax mexicanus. Proceedings of the National Academy of Sciences of the United States of America. 105, 20106-20111 [pdf]

Jeffery, W.R. (2008). Emerging systems in Evo/Devo: cavefish and mechanisms of microevolution. Evolution & Development 10: 265-272 [pdf]

Yoshizawa, M. and W.R. Jeffery (2008). Shadow response in the blind cavefish Astyanax reveals conservation of a functional pineal eye. Journal of Experimental Biology 211: 292-299 [pdf]

Strickler, A.G., Yamamoto, Y. and W.R. Jeffery (2007). The lens controls cell survival in the retina: evidence from the blind cavefish Astyanax. Developmental Biology 311: 512-523  [pdf]

Menuet, A., Alunni, A., Joly, J-R., Jeffery, W.R., and S. Retaux (2007). Shh overexpression in Astyanax cavefish: multiple consequences on forebrain development and evolution. Development 134: 845-855

Strickler, A.G., Byerly, M.S, and W.R. Jeffery (2007). Lens gene expression analysis reveals downregulation of the anti-apoptotic αA-crystallin during cavefish eye degeneration. Development, Genes, & Evolution 217: 771-782 [pdf]

Alunni, A., Menuet, A., Candal, E., Penigault, J-B., Jeffery, W.R., and S. Retaux (2007). Developmental mechanisms for retinal degeneration in the blind cavefish Astyanax mexicanus. Journal of Comparative Neurology. 505: 221-233 [pdf]

Protas, M.E., Hersey, C., Kochanek, D., Zhou, Y., Wilkens, H., Jeffery, W.R., Zon, L.I., Borowsky, R. and C.J. Tabin (2006). Genetic analysis of cavefish reveals molecular convergence in the evolution of albinism. Nature Genetics 38: 107-111 [pdf]

Espinasa, L., and W.R. Jeffery (2006). Conservation of retinal circadian rhythms during cavefish eye degeneration. Evolution & Development. 8: 16-22

Jeffery, W.R. (2006). Regressive evolution of pigmentation in the cavefish Astyanax. Israel Journal of Evolution and Ecology. 52: 405-422

Jeffery, W.R. (2005). Adaptive evolution of eye degeneration in the Mexican blind cavefish. Journal of Heredity 96: 185-196 [pdf]

Yamamoto, Y., Stock, D.W., and W.R. Jeffery (2004). Hedgehog signalling controls eye degeneration in blind cavefish. Nature 431: 844-847 [pdf]


Auger, H., Sasakura,Y., Joly, J-S., and W. R. Jeffery  (2010).  Regeneration of oral siphon pigment organs in the ascidian Ciona intestinalis.  Develop. Biol..  339: 374-389.

Jeffery, W.R., Chiba, T., Razy-Krajka, F., Deyts, C., Satoh, N. and J-S. Joly (2008). Trunk lateral cells are neural crest-like cells in the ascidian Ciona intestinalis: insights into the ancestry and evolution of the neural crest. Developmental Biology 324, 152-160 [pdf]

Jeffery, W.R. (2007). Chordate ancestry of the neural crest: new insights from ascidians. Seminars in Cell and Developmental Biology 18: 481-491 [pdf]

Jeffery, W. R. (2006). Neural crest-like cells in ascidians: Phylogenetic distribution, relationship to larval complexity, and pigment cell fate. Journal of Experimental Zoology B (Molecular Developmental Evolution) 306B: 470-480 [pdf]

Jeffery, W.R., Strickler, A.G., and Y. Yamamoto (2004). Migratory neural crest-like cells form body pigmentation in a urochordate embryo. Nature 431: 696-699 [pdf]

Jeffery, W.R. (2004). Evolution and development of brain sensory organs in molgulid ascidians. Evolution & Development 6: 170-179

Jeffery, W.R. (2002). Programmed cell death in the ascidian embryo: Modulation by Fox5A and Manx and roles in the evolution of larval development. Mechanisms of Development 118: 111-124