If you would like PDF reprints, please email me (Jen, at j.wernegreen [at ]

Williams, L.E. and J.J. Wernegreen. 2015. Genome evolution in an ancient bacteria-ant symbiosis: Parallel gene loss among Blochmannia spanning the origin of the ant tribe Camponotini, PeerJ, Apr 2;3:e881. doi: 10.7717/peerj.881.

Wernegreen, J.J. 2015. Endosymbiont evolution: Predictions from theory and surprises from genomes. Annals of the New York Academy of Science: The Year in Evolutionary Biology, Dec;1360:16-35.

Yung, C.M., Vereen, M.K., Herbert, A., Davis, K.M., Yang, J., Kantorowska, A., Ward, C.S., Wernegreen, J.J., Johnson, Z.I., and D.E. Hunt. 2015. Thermally adaptive tradeoffs in closely-related marine bacterial strains. Environmental Microbiology, Jul;17(7):2421-9.

Fan Y. and J. J. Wernegreen 2013. Can’t take the heat: high temperature depletes bacterial endosymbionts of ants. Microbial Ecology 66(3):727-33.

Wernegreen J.J. 2013. First impressions in a glowing host-microbe partnership. Cell Host Microbe. 14(2):121-3.

Williams LE, Wernegreen JJ. 2013. Sequence context of indel mutations and their effect on protein evolution in a bacterial endosymbiont. Genome Biology and Evolution 5(3):599-605.

McFall-Ngai M, Hadfield MG, Bosch TC, Carey HV, Domazet-Loso T, Douglas AE, Dubilier N, Eberl G, Fukami T, Gilbert SF, Hentschel U, King N, Kjelleberg S, Knoll AH, Kremer N, Mazmanian SK, Metcalf JL, Nealson K, Pierce NE, Rawls JF, Reid A, Ruby EG, Rumpho M, Sanders JG, Tautz D, Wernegreen JJ. 2013. Animals in a bacterial world, A new imperative for the life sciences. Proceedings of the National Academy of Sciences USA 110(9):3229-36.

Fan Y, Thompson JW, Dubois LG, Moseley MA, Wernegreen JJ. 2013. Proteomic analysis of an unculturable bacterial endosymbiont (Blochmannia) reveals high abundance of chaperonins and biosynthetic enzymes. Journal of Proteome Research 1;12(2):704-18.

Wernegreen JJ. 2012. Strategies of genomic integration within insect-bacterial mutualisms. Biological Bulletin 223(1):112-22.

Wernegreen J.J. 2012. Endosymbiosis.  Current Biology. 22(14):R555-61.

Wernegreen J.J. 2012. Mutualism meltdown in insects: bacteria constrain thermal adaptation. Curr Opin Microbiol. 15 (3):255-62.

Williams L.E. and J.J. Wernegreen 2012. Purifying selection, sequence composition, and context-specific indel mutations shape intraspecific variation in a bacterial endosymbiont. Genome Biology and Evolution 4(1):44-51.

Wernegreen J.J. 2011. Reduced selective constraint in endosymbionts: elevation in radical amino acid replacements occurs genome-wide. PLoS One 6(12):e28905.

Williams, L.E. and J. J. Wernegreen. 2010. Unprecedented loss of ammonia assimilation capability in a urease-encoding bacterial mutualist.  BMC Genomics, Dec. 2;11:687.

Bordenstein, Seth R., C. Brothers, G. Wolfe, M. Bahr, R.L. Minckley, M.E. Clark, J.J. Wernegreen, Sarah R. Bordenstein, W.S. Reznikoff, and J.H. Werren. 2010. Using the Wolbachia bacterial symbiont to teach inquiry-based science: A high school laboratory seriesAmerican Biology Teacher, 72(8).

Wernegreen J.J., and S.N. Kauppinen, P.H. Degnan. 2010.  Slip into something more functional: Selection maintains ancient frameshifts in homopolymeric sequencesMolecular Biology and Evolution. 27(4):833-9.

Wernegreen, J.J., S.N. Kauppinen, S.G. Brady, and P.S. Ward. 2009. One nutritional symbiosis begat another: Phylogenetic evidence that the ant tribe Camponotini acquired Blochmannia by tending sap-feeding insects. BMC Evolutionary Biology. Dec 16;9:292.

Wernegreen, J. J. and D. E. Wheeler.  2009. Remaining flexible in old alliances: Functional plasticity in constrained mutualismsDNA and Cell Biology, 28(8):371-82.

Tamas I.*, J.J. Wernegreen*, B. Nystedt, S.N. Kauppinen, A.C. Darby, L. Gomez-Valero, D. Lundin, A.M. Poole, and S.G.E. Andersson. 2008.  Endosymbiont gene functions impaired and rescued by polymerase infidelity at poly(A) tracts. Proceedings of the National Academy of Science USA 105(39):14934-39.  (*Shared first authorship.)

Paraskevopoulos, C., S.R. Bordenstein, J.J. Wernegreen, J.H. Werren and K. Bourtzis. 2006.  Towards a Wolbachia multilocus sequence typing system: Discrimination of Wolbachia strains present in Drosophila species. Current Microbiology 53(5):388-95.

Bordenstein S.R., M L. Marshall, A.J. Fry, U. Kim, and J.J. Wernegreen. 2006. The tripartite associations between bacteriophage, Wolbachia, and arthropodsPLoS Pathogens 2(5):e43.

Baldo L., S.R. Bordenstein, J.J. Wernegreen, and J.H. Werren. 2006. Widespread recombination throughout Wolbachia genomes. Molecular Biology and Evolution 23(2):437-449.

Casiraghi M., S.R. Bordenstein, L. Baldo, N. Lo, T. Beninati, J.J. Wernegreen, J.H. Werren, and C. Bandi. 2005. Phylogeny of Wolbachia based on gltA, groEL and ftsZ gene sequences: Clustering of arthropod and nematode symbionts in the F supergroup and evidence for further diversity in the Wolbachia tree. Microbiology 151: 4015-22.

Wernegreen, J.J. 2005. For better or worse: Genomic consequences of intracellular mutualism and parasitism. Current Opinions in Genetics and Development 15(6):572-83.

Degnan P.H., A.B. Lazarus, and J.J. Wernegreen. 2005. Genome sequence of Blochmannia pennsylvanicus indicates parallel evolutionary trends among bacterial mutualists of insects. Genome Research 15(8):1023-1033.

Schaber J., C. Rispe, J.J. Wernegreen, A. Buness, F. Delmotte, F.J. Silva, and A. Moya. 2005. Gene expression levels influence amino acid usage and evolutionary rates in endosymbiotic bacteria. Gene 352:109-117.

Herbeck J.T., P.H. Degnan, and J.J. Wernegreen. 2005. Nonhomogeneous model of sequence evolution indicates independent origins of primary endosymbionts within the Enterobacteriales (gamma- Proteobacteria). Molecular Biology and Evolution 22(3):520-532.

Fry A.J. and J.J. Wernegreen. 2005. The roles of positive and negative selection in the molecular evolution of insect endosymbionts. Gene 355:1-10.

Wernegreen J.J., and D.J. Funk. 2004. Mutation exposed: A neutral explanation for extreme base composition of an endosymbiont genome. Journal of Molecular Evolution 59(6):849-858.

Bordenstein S.R., and J.J. Wernegreen. 2004. Bacteriophage flux in endosymbionts (Wolbachia): Infection frequency, lateral transfer, and recombination rates. Molecular Biology and Evolution 21:1981-91.

Degnan P.H., A.B. Lazarus, C.D. Brock, and J.J. Wernegreen. 2004. Host-symbiont stability and fast evolutionary rates in an ant-bacterium association: cospeciation of Camponotus species and their endosymbionts, Candidatus Blochmannia. Systematic Biology 53(1):95-110.

Wernegreen J.J. 2004. Endosymbiosis: Lessons in conflict resolution. PLoS Biology 2(3):E68.

Herbeck, J.T., D.J. Funk, P.H. Degnan, and J.J. Wernegreen. 2003. A conservative test of genetic drift in the endosymbiotic bacterium Buchnera: Slightly deleterious mutations in the chaperonin groEL. Genetics 165:1651-60.

Herbeck, J.T., D. Wall, and J.J. Wernegreen. 2003. Gene expression level influences amino acid usage, but not codon usage, in the tsetse fly endosymbiont Wigglesworthia. Microbiology 149:2585-96.

Wernegreen, J.J., P.H. Degnan, A.B. Lazarus, C. Palacios, and S.R. Bordenstein. 2003. Genome evolution in an insect cell: distinct features of an ant-bacterial partnership. Biological Bulletin 204(2): 221-231.

Wernegreen, J.J. 2002. Genome evolution in bacterial endosymbionts of insects. Nature Reviews Genetics 3(11): 850-61.

Palacios C., and J.J. Wernegreen. 2002. A strong effect of AT mutational bias on amino acid usage in Buchnera is mitigated at high-expression genes. Molecular Biology and Evolution 19(9): 1575-84.

Wernegreen J.J., A.B. Lazarus, and P.H. Degnan 2002. Small genome of Candidatus Blochmannia, the bacterial endosymbiont of Camponotus, implies irreversible specialization to an intracellular lifestyle. Microbiology 148:2551-6.

Tamas I., L. Klasson, B. Canback, A.K. Naslund, A.S. Eriksson, J.J. Wernegreen, J.P. Sandstrom, N.A. Moran, and S.G.E. Andersson. 2002. 50 million years of genomic stasis in endosymbiotic bacteria. Science 296(5577): 2376-9.

Wernegreen, J.J., Richardson, A.O, and N.A. Moran. 2001. Parallel acceleration of evolutionary rates in symbiont genes underlying host nutrition. Molecular Phylogenetics and Evolution 19(3): 479-85.

Wernegreen, J.J. and Moran, N.A. 2001. Vertical transmission of biosynthetic plasmids in aphid endosymbionts (Buchnera). Journal of Bacteriology 183:785-790.

Funk, D.J., J.J. Wernegreen, and N.A. Moran. 2001. Intraspecific variation in symbiont genomes: Bottlenecks and the aphid-Buchnera association. Genetics 157: 477-489.

Wernegreen, J.J. and N.A. Moran. 2000. Decay of mutualistic potential in aphid endosymbionts through silencing of biosynthetic loci: Buchnera of Diuraphis. Proceedings of the Royal Society B 267:1423-1431.

Wernegreen, J.J., Ochman, H., Jones, I.B., and N.A. Moran. 2000. The decoupling of genome size and sequence divergence in a symbiotic bacterium. Journal of Bacteriology 182: 3867-69.

Funk D.J., L. Helbling, J.J. Wernegreen, and N.A. Moran. 2000. Intraspecific phylogenetic congruence among multiple symbiont genomes. Proceedings of the Royal Society B 267:2517-21.

Moran N.A. and J.J. Wernegreen. 2000. Lifestyle evolution in symbiotic bacteria: Insights from genomics. Trends in Ecology and Evolution 15:321-326.

Clark, M.A., N.A. Moran, P. Baumann, and J.J. Wernegreen.  2000. Cospeciation between bacterial endosymbionts (Buchnera) and a recent radiation of aphids (Uroleucon) and pitfalls of testing for phylogenetic congruence. Evolution 54(2): 517-524.

Wernegreen, J.J. and N.A. Moran. 1999. Evidence for genetic drift in endosymbionts (Buchnera): analyses of protein-coding loci.  Molecular Biology and Evolution 16(1): 83-97.

Wernegreen, J.J. and M.A. Riley. 1999. Comparison of the evolutionary dynamics of symbiotic and housekeeping loci: A case for the genetic coherence of rhizobial lineages. Molecular Biology and Evolution 16(1): 98-113.

Wernegreen, J.J., E.E. Harding, and M.A. Riley. 1997. Rhizobium gone native: Unexpected plasmid stability of indigenous Rhizobium leguminosarum. Proceedings of the National Academy of Science USA 94: 5483-5488.


Book Chapters

Wernegreen, J.J.  2007. Genomic signatures of intracellularity: Evolutionary patterns and paces in bacterial mutualists and parasites.  Pp. 196-212 in Bacterial Pathogenomics, M. J. Pallen, K. E. Nelson, and G. M. Preston, Eds. ASM Press, Washington, DC.