​​       SUBMITTED OR IN REVIEW​​​

• *Bedford, NL, *Weber, JN, Tong, W, Baier, F, Kam, A, Greenberg, RA, & HE Hoekstra. (In review at Nature Ecology and Evolution). Behavioural mechanisms underlying the evolution of cooperative burrowing in Peromyscus mice. Preprint available at BioRxiv, https://doi.org/10.1101/731984. (*Equal contribution)

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      PUBLISHED OR IN PRESS

• LE Fuess, JN Weber, S den Haan, NC Steinel, KC Shim, DI Bolnick (In Press) Between‐population differences in constitutive and infection‐induced gene expression in threespine stickleback. Molecular Ecology 

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• LE Fuess, S Den Haan, F Ling, JN Weber, NC Steinel, DI Bolnick (2021) Immune gene expression covaries with gut microbiome composition in stickleback. Mbio 12 (3), e00145-21​​​

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• Ling, F, Steinel, N, Weber, JN, Ma, L, Smith, C, Correa, D, Zhu, B, Bolnick, DI, & G Wang. (2020) Host sex and genotype modify the gut microbiome response to helminth infection. The ISME Journal 14 (5), 1141-1153

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• Weber JN, Tong W. (2019) Perspective: Jumping gene gave fish a freshwater start. Science 364: 831–832. DOI: 10.1126/science aax7936

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• Smith CC, Weber JN, Mikheyev AS, Roces F, Bollazzi M, Kellner K, et al. (2019) Landscape genomics of an obligate mutualism: Concordant and discordant population structures between the leafcutter ant Atta texana and its two main fungal symbiont types. Molecular Ecology. DOI: 10.1111/mec.15111

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• Vasconcellos, M.M., Colli, G.R., Weber, J.N., Ortiz, E.O., Rodrigues, M.T., Cannatella, D.C. (2019) Isolation by instability: Historical climate change shapes population structure and genomic divergence of treefrogs in the Neotropical Cerrado savanna. Molecular Ecology 28 (7): 1748–64. DOI: 10.1111/mec.15045.

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• Weber, J.N., Steinel, N.C., Shim, K.C. and D.I. Bolnick. Recent evolution of extreme cestode growth suppression by a vertebrate host. (2017). PNAS 114 (25) 6575-6580.​​ DOI: 10.1073/pnas.1620095114. 

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• Stuart, Y.E., T. Veen, J.N. Weber, C. Thompson, T. Tasneem, N. Ahmed, R. Izen, B. Doggett, D. Hanson, B. Lohman, K. Peichel, A.P. Hendry, and D.I. Bolnick. (2017) Contrasting effects of environment and genetics generate a predictable continuum of parallel evolution. Nature Ecology & Evolution. 1:0158. DOI: 10.1038/s41559-017-0158.

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• Weber, J.N., Kalbe, M., Shim, K.C., Erin, N.I., Steinel, N.C., Ma, L. and D.I. Bolnick. (2017) Resist globally, infect locally: a trans-continental test of adaptation by stickleback and their tapeworm parasite.  American Naturalist 189(1):43-57. DOI: 10.1086/689597.

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• Weber, J.N., Bradburd, G.S., Stuart, Y.E., Stutz, W.E. and D.I. Bolnick. (2017) Partitioning the effects of isolation by distance, environment, and physical barriers on genomic divergence between parapatric threespine stickleback. Evolution 71(2):342-356. DOI: 10.1111/evo.13110.​ ***See companion article "Digest: Sticklebacks do not just go with the flow"

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• Lohman, B.K., Steinel, N.C., J.N. Weber, and D.I. Bolnick. (2017) Gene expression contributes to the recent evolution of host resistance in a model host parasite system. Frontiers in Immunology. 8:1071. DOI: 10.3389/fimmu.2017.01071.

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• ​Lohman, B.K., Weber, J.N. and D.I. Bolnick. (2016) Evaluation of TagSeq, a reliable low-cost alternative for RNAseq. Molecular Ecology Resources. doi: 10.1111/1755-0998.1252               ***Identified as an "exceptional" molecular Advance by the editors in their annual recap.

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• Puritz, J.B., Matz, M.V., Tooen, R.J., Weber, J.N., Bolnick, D.I. and C.E. Bird (2014). Comment: Demystifying the RAD fad.  Molecular Ecology 23: 5937-5942. DOI: 10.1111/mec.12965.

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• Kowalko, J.E., Rohner, N., Rompani, S.B., Peterson, B.K., Linden, T.A., Yoshizawa, M., Kay, E.H., Weber, J.N., Hoekstra, H.E., Jeffery, W.R., Borowsky, R. and C.J. Tabin (2013). Loss of schooling behavior in cavefish through sight-dependent and sight-independent mechanisms. Current Biology 23, 1874-1883. DOI: 10.1016/j.cub.2013.07.056.

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• Weber, J.N., Peterson, B.K. and H.E. Hoekstra (2013). Discrete genetic modules are responsible for complex burrow evolution in Peromyscus mice. Nature 493, 402-405. DOI: 10.1038/nature11816. ***Highly recommended by Faculty of 1000, commentaries in Science, Nature: News & Views, Scientific American, National Geographic and news coverage by the BBC and the New York Times.

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• Peterson, B.K., Weber, J.N., Kay, E.H., Fisher, H.S. and H.E. Hoekstra (2012). Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS One 7, e37135. DOI: 10.1371/journal.pone.0037135. ***Selected by Faculty of 1000 and one of the most viewed "computational biology" papers in PLoS One.

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• Weber, J.N., Peters, M.B., Tsyusko, O.V., Linnen, C.R., Hagen, C., Schable, N.A., Tuberville, T.D., McKee, A.M., Lance, K.L., Fisher, H.S., Dewey, M.J., Hoekstra, H.E. and T.C. Glenn (2010). Five hundred microsatellite loci for Peromyscus. Conservation Genetics 11: 1243-1246. DOI: 10.1007/s10592-009-9941-x.

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• Weber, J.N. and H.E. Hoekstra (2009). The evolution of burrowing behaviour in deer mice (genus Peromyscus). Animal Behaviour 77: 603-609. DOI: 10.1016/j.anbehav.2008.10.031.

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• Steiner, C.C., Weber, J.N. and H.E. Hoekstra (2007). Adaptive variation in beach mice caused by two interacting pigmentation genes. PLoS Biology 5: 1880-1889. DOI: 10.1371/ journal.pbio.0050219. ***Selected by Faculty of 1000.

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• Allen, D.L., Weber, J.N., Sycuro, L.K. and L.A. Leinwand (2005).  Myocyte enhancer factor-2 and serum response factor binding elements regulate fast myosin heavy chain transcription in vivo.  Journal of Biological Chemistry 280: 17126-17134. DOI: 10.1074/jbc.M501207200.​​

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