Jaenike, J. 2011. Population genetics of beneficial heritable symbionts. TREE (Opinion article), in press.

Fishman, L. and J. Jaenike. 2011. Selfish elements and genetic conflict. Princeton Guide to Evolution. In press.

Unckless, R.L. 2011. A DNA virus of Drosophila. PloS ONE, in press.

Unckless, R. L. and J. Jaenike. 2011. Maintenance of a male-killing Wolbachia in Drosophila innubila by male-killing dependent and male-killing independent mechanisms. Evolution, in press.

Dyer, K. A., C. Burke, and J. Jaenike. 2011. Wolbachia-mediated persistence of mtDNA from a potentially extinct species. Molecular Ecology 20: 2805-2817.

Jaenike, J. and T. Brekke. 2011. Defensive endosymbionts: a cryptic trophic level in community ecology. Ecology Letters 14: 150-155.

Jaenike, J., R. L. Unckless, S. N. Cockburn, L. M. Boelio, and S. J. Perlman. 2010. Adaptive evolution via symbiosis: recent spread of a defensive symbiont in Drosophila. Science 329: 212-215.

Jaenike, J., J. Stahlhut, L. Boelio, and R. Unckless. 2010. Association between Wolbachia and Spiroplasma within Drosophila neotestacea: an emerging symbiotic mutualism? Molecular Ecology 19: 414-425.

Stahlhut, J., C. Desjardins, M. Clark, L. Baldo, J. Russell, J. Werren, and J. Jaenke. 2010. The mushroom habitat as an ecological arena for global exchange of Wolbachia. Molecular Ecology 19: 1940-1952.

Unckless, R.L.and J.K. Herren. 2009. Population genetics of sexually antagonistic mitochondrial mutants under inbreeding. Journal of Theoretical Biology (In press).

Jaenike, J. 2009. Coupled population dynamics of endosymbionts within and between hosts. Oikos 118: 353-362.

Unckless, R.L., L.M. Boelio, J.K. Herren and J. Jaenike. 2009. Wolbachia as populations within individual insects: causes and consequences of density variation in natural populations. Proceedings of the Royal Society of London B 276: 2805-2811.

Jaenike, J. and K.A. Dyer. 2008. No resistance to male-killing Wolbachia after thousands of years of infection. Journal of Evolutionary Biology 21: 1570-1577.

Jaenike, J. 2008. X chromosome drive. Current Biology 18: R508-R511.

Jaenike, J. 2007. Spontaneous emergence of a new Wolbachia phenotype. Evolution, 61(9), :2244-2252

Jaenike, J. 2007. Fighting back against male killers. Trends Ecol. Evol. 22:167-169

Jaenike, J., K. A. Dyer, C. Cornish, and M. S. Minhas. 2006. Asymmetrical reinforcement and Wolbachia infection in Drosophila. PLoS Biol. Oct;4(10):e325

Dyer, K. A. and J. Jaenike. 2005. Evolutionary dynamics of a spatially structured host-parasite association: Drosophila innubila and male-killing Wolbachia. Evolution 59: 1518-1528

Dyer, K. A., M. Minhas, and J. Jaenike. 2005. Expression and modulation of embryonic male-killing in Drosophila innubila: opportunities for multi-level selection. Evolution 59: 838-848.

Shoemaker, D. D., K. A. Dyer, M. Ahrens, K. McAbee, and J. Jaenike. 2004. Molecular evolutionary effects of Wolbachia infections: decreased diversity but increased substitution rate in host mtDNA. Genetics 168: 2049-2058.

Dyer, K. A. and J. Jaenike. 2004. Evolutionarily stable infection by a male-killing endosymbiont in Drosophila innubila: molecular evidence from the host and parasite genomes. Genetics 168: 1443-1445

Dombeck, I. and J. Jaenike. 2004. Ecological genetics of abdominal pigmentation in Drosophila falleni. Evolution 58: 587-596

Perlman, S. J. and J. Jaenike. 2003. Infection success in novel hosts: an experimental phylogenetic study of Drosophila parasitic nematodes. Evolution 57: 544-557.