Selected Publications

Ma, L., Jeffery, W. R., Essner, J. J., and J. E. Kowalko (2015). Genome editing using
     TALENs in blind Mexican cavefish. PLoS ONE (In press).

Yoshizawa, M., Robinson, B. G., Duboue, E. R., Masek, P., O’Quin, K. E., Borowsky,
     R. L., Jeffery, W. R., and A. Keene
(2015). Distinct genetic architecture underlies
     the emergence of foraging traits in the Mexican cavefish. BMC-Biology (In press).

Jeffery, W. R. (2015). The tunicate Ciona: a model system for studying the
     relationship between regeneration and aging. Invert. Reprod. Dev. 59: 17-22.

Jeffery, W. R. (2014). Distal regeneration involves the age-dependent activity of
     branchial sac stem cells in the ascidian Ciona intestinalis. Regeneration 1: doi:

Espinasa, L, Bibliowicz, J., Jeffery, W. R., and S. Rétaux (2014). Enhanced prey
     capture skills in Astynanx cavefish larvae are independent from eye loss. EvoDevo
     5: 35. doi:10.1186/2041-9139-5-35

McGaugh, S. E., Gross, J. B., Aken, B., Blin, M., Borowsky, R., Chalopin, D, Hinaux,
     H., Jeffery, W. R., Keene, A., Ma, L., Minx, P., Murphy, D, O’Quin K. E., Rétaux, S.,
     Rohner, N., Searle, S. M. J, Stahl, B, Tabin, C., Volff, J. N., Yoshizawa, M., and
     W. Warren.
(2014). The cavefish genome reveals candidate genes for eye loss.
     Nature Commun. 5: 5307 doi: 10.1002/dneu.22239.

Ma, L., Parkhurst, A., and W. R. Jeffery (2014). The role of a lens survival pathway
     including sox2 and αA-crystallin in the evolution of cavefish eye degeneration.
     EvoDevo 5: 28 doi:10.1186/2041-9139-5-28

Jeffery, W. R. (2014). Closing the wounds: One hundred and twenty five years of
     regenerative biology in the ascidian Ciona intestinalis. Genesis DOI: 10.1002/

Joachim, B. L., Riesch, R., Jeffery, W. R., and I. Schlupp (2014). Pigment cell
     retention in cavernicolous populations of Poecilia mexicana. Bull. Fish Biol. 14:

Yoshizawa, M., Jeffery, W. R., van Netten, S. M, and M. J. McHenry. (2014). The
     sensitivity of lateral line receptors and their role in behavior of Mexican blind
     cavefish (Astyanax mexicanus). J. Exp. Biol 217: 886-895.

Rohner, N., Jarosz, D. F., Taipale, M., Kowalko, J., Yoshizawa, M., Jeffery, W. R.,
     Borowsky, R. L., Lindquist, S., and C. J. Tabin.
(2013). Cryptic variation in
     morphological evolution: HSP90 as a capacitor for the adaptive loss of eyes in
     cavefish. Science 342: 1372-1375.

Bilandžija, H., Ma L, Parkhurst, A., and W. R. Jeffery. (2013). A potential benefit of
     albinism in Astyanax cavefish: Downregulation of the oca2 gene increases
     L-tyrosine and catecholamine levels as an alternative to melanin synthesis. PLoS
     ONE 8 (11): e80823.

Kowalko J. E., Rohner, N., Linden, T. A., Rompani, S. B., Warren, W. C, Borowsky, R.,
     Tabin C. J., Jeffery, W. R., and M. Yoshizawa.
(2013). Convergence in feeding
     posture occurs through different genetic loci in independently evolved cave
     populations of Astyanax mexicanus. Proc. Natl. Acad. Sci. USA 110 (42)

Kowalko, J. E., Rohner, N., Rompani, S. B., Peterson, B. K., Linden, T., Yoshizawa, M.,
     Kay E. H., Hoekstra H. E., Jeffery, W. R., Borowsky, R., and C. J. Tabin.
     Loss of schooling behavior in cavefish through sight-dependent and sight-
     independent mechanisms. Curr Biol. 2013 Oct 7;23(19):1874-83. doi: 10.1016/

Yoshizawa, M., O’ Quin, K. E., and W. R. Jeffery (2013). QTL clustering as a
     mechanism for rapid multi-trait evolution. Commun. Integr. Biol. 6: e24548. doi:

O’ Quin, K. E., Yoshizawa, M., Doshi, P., and W. R. Jeffery (2013). Quantitative
     genetic analysis of retinal degeneration in the blind cavefish. PLoS ONE 8(2):
     e57281. doi:10.1371/journal.pone.0057281.

Hinaux, H., Poulain, J. Da Silva, C., Noirot, C., Jeffery, W. R., Casane, D., and S.
(2013). De novo sequencing of Astyanax mexicanus surface fish and
     Pachon cavefish transcriptomes reveals enrichment of mutations in putative
     cavefish eye genes. PLoS ONE 8(1): e53553. doi:10.1371/journal.pone.0053553.s

Yoshizawa, M., Yamamoto, Y., O’ Quin, K. E., and W. R. Jeffery (2012). Evolution of
     an adaptive behavior and its sensory receptors promotes eye regression in blind
     cavefish. BMC-Biology 10:108 doi:10.1186/1741-7007-10-108.

Jeffery, W. R. (2012). Siphon regeneration capacity is compromised during aging in
     the ascidian Ciona intestinalis. Mech. Ageing Dev. 133: 629-636.

Gallo, N. D., and W. R. Jeffery (2012). Evolution of space dependent growth in the
     teleost Astyanax mexicanus. PLoS ONE 7(8) e41443. Doi:10.1371/journal.pone.

Yoshizawa, M., Ashida, G., and W. R. Jeffery (2012). Parental genetic effects in a
     cavefish adaptive behavior explain disparity in nuclear and mitochondrial DNA.
     Evolution 66: 2975-2982.

Bilandžija, H., Ćetković, H., and W. R. Jeffery (2012). Evolution of albinism in cave
     planthoppers by a convergent defect in the first step of the melanin biosynthesis
     pathway. Evol. Dev. 14: 196-203.

Protas, M. and W. R. Jeffery (2012). Evolution and development of cave animals:
     From fish to crustaceans. WIREs Developmental Biology. 1: 823-845. doi:

Yoshizawa, M., and W. R. Jeffery (2011). Evolutionary tuning of an adaptive behavior
     requires enhancement of the neuromast sensory system. Commun. Integr. Biol.
     4: 89-91.

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. (2010). Pleiotropy and eye degeneration in cavefish. Heredity 105:

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:


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