Miller Lab


Rowley, A.J., Square, T.A., and Miller, C.T. (2022) Site pleiotropy of a stickleback tooth and fin enhancer (submitted). biorxiv link

Jin, Y., Aguilar-Gomez, D., Brandt, D.Y.C., Square, T.A., Li, J., Liu, Z., Wang, T., Sudmant, P.H., Miller, C.T., and Nielsen, R. (2022) Population genomics of variegated toad-headed lizard Phrynocephalus versicolor and its adaptation to the colorful sand of the Gobi Desert. Genome Biology and Evolution Jun 9;evac076. doi: 10.1093/gbe/evac076. PMID: 35679302.

Stepaniak, M.D., Square, T.A., and Miller, C.T. (2021) Evolved Bmp6 enhancer alleles drive spatial shifts in gene expression during tooth development in sticklebacks. Genetics Dec 10;219(4):iyab151. PMCID: PMC8664583.

Square, T.A., Sundaram, S., Mackey, E.J., and Miller, C.T. (2021) Distinct tooth regeneration systems deploy a conserved battery of genes. Evodevo 12(1): 4. PMCID: PMC7995769.

Hulsey, C.D., Cohen, K.E., Johanson, Z., Karagic, N., Meyer, A., Miller, C.T., Sadier, A., Summers, A.P., and Fraser, G.J. (2020) Grand challenges in comparative tooth biology. Integrative and Comparative Biology 60(3):563-580. PMCID: PMC7821850.

Wucherpfennig J.I., Miller C.T., and Kingsley D.M. (2019) Efficient CRISPR-Cas9 editing of major evolutionary loci in sticklebacks. Evol Ecol Res. 20(1):107-132. PMCID: PMC8664273.

Cleves, P.A., Hart, J.C., Agoglia, R.M., Jimenez, M.T., Erickson, P.A., Gai, L., Miller, C.T. (2018) An intronic enhancer of Bmp6 underlies evolved tooth gain in sticklebacks. PLoS Genet. 14(6):e1007449.

Hart, J.C., Ellis, N.A., Eisen, M.B., Miller, C.T. (2018) Convergent evolution of gene expression in two high-toothed stickleback populations. PLoS Genet. 14(6):e1007443.

Erickson, P.A., Baek, J., Hart, J.C., Cleves, P.A., Miller, C.T. (2018) Genetic Dissection of a Supergene Implicates Tfap2a in Craniofacial Evolution of Threespine Sticklebacks. Genetics. 209(2):591-605.

Hart, J.C., Miller, C.T. (2017) Sequence-Based Mapping and Genome Editing Reveal Mutations in Stickleback Hps5 Cause Oculocutaneous Albinism and the casper Phenotype. G3 (Bethesda).7(9):3123-3131.

Martin, C.H., Erickson, P.A., Miller, C.T. (2017) The genetic architecture of novel trophic specialists: larger effect sizes are associated with exceptional oral jaw diversification in a pupfish adaptive radiation. Mol Ecol. 26(2):624-638.

Askary, A., Smeeton, J., Paul, S., Schindler, S., Braasch, I., Ellis, N.A., Postlethwait, J., Miller, C.T., Crump, J.G. (2016) Ancient origin of lubricated joints in bony vertebrates. Elife. 5. pii: e16415.

Erickson, P.A., Ellis, N.A., and Miller, C.T. (2016) Microinjection for transgenesis and genome editing in threespine sticklebacks. J. Vis. Exp., (111)

Ellis, N.A., Donde, N.N., and Miller, C.T. (2016) Early development and replacement of the stickleback dentition. J. Morphol., 277(8):1072-83.

Ellis, N.A. and Miller, C.T. (2016) Dissection and flat-mounting of the threespine stickleback branchial skeleton. J. Vis. Exp. 111:e54056.

Erickson, P.A., Glazer, A.M., Killingbeck, E.E., Agoglia, R.M., Baek, J., Carsanaro, S.M., Lee, A.M., Cleves, P.A., Schluter D., and Miller, C.T. (2016) Partially repeatable genetic basis of benthic adaptation in threespine sticklebacks. Evolution 70: 887-902.

Ellis, N.A., Glazer, A.M., Donde, N.N., Cleves, P.A., Agoglia, R.M., and Miller, C.T. (2015) Distinct developmental genetic mechanisms underlie convergently evolved tooth gain in sticklebacks. Development 142: 2442-2451.

Glazer, A.M., Killingbeck, E.E., Mitros, T., Rokhsar, D.S., and Miller, C.T. (2015) Genome assembly improvement and mapping convergently evolved skeletal traits in sticklebacks with Genotyping-by-Sequencing. G3 5:1463-1472.

Erickson, P.A., Cleves, P.A., Ellis, N.A., Schwalbach, K.T., Hart, J.C., and Miller, C.T. (2015) A 190 base pair, TGF-β responsive tooth and fin enhancer is required for stickleback Bmp6 expression. Dev. Biol. 401: 310-323.

Cleves, P.A., Ellis, N.A., Jimenez, M.T., Nunez, S.M., Schluter, D., Kingsley, D.M., and Miller, C.T. (2014) Evolved tooth gain in sticklebacks is associated with a cis-regulatory allele of Bmp6. Proc. Nat. Acad. U.S.A. 111: 13912-13917. (Correction in 111: 18090).

Erickson P.A., Glazer A.M., Cleves P.A., Smith A.S., and Miller C.T. (2014) Two developmentally temporal quantitative trait loci underlie convergent evolution of increased branchial bone length in sticklebacks. Proc R Soc B 281:20140822.

Glazer A.M., Cleves P.A., Erickson P.A., Lam A.Y. and Miller C.T. (2014) Parallel developmental genetic features underlie stickleback gill raker evolution. EvoDevo 5:19.

Miller, C.T.*, Glazer, A.M.*, Summers, B.R., Norman, A., Shapiro, M.D., Blackman, B.K., Cole, B., Peichel, C.L., Schluter, D., Kingsley, D.M. (* = co-first authors) (2014) Modular skeletal evolution in sticklebacks is controlled by additive and clustered quantitative trait loci. Genetics 197:405–420.

Jones, F.C., Grabherr, M.G., Chan, Y.F., Russell, P., Mauceli, E., Johnson, J., Swofford, R., Pirun, M., Zody, M.C., White, S., Birney, E., Searle, S., Schmutz, J., Grimwood, J., Dickson, M.C., Myers, R.M., Miller, C.T., Summers, B.R., Knecht, A.K., Brady, S.D., Zhang, H., Pollen, A.A., Howes, T., Amemiya, C., Broad Institute Genome Sequencing Platform and Whole Genome Assembly Team, Lander, E.S., Palma, F., Kerstin Lindblad-Toh, K., and Kingsley, D.M. (2012) The genomic basis of adaptive evolution in threespine sticklebacks. Nature 484:55-61.

Albert, A.Y.K., Sawaya, S., Vines, T.H., Knecht, A., Miller, C.T., Summers, B.R., Balabhadra, S., Kingsley, D.M., and Schluter, D. (2008) The genetics of adaptive shape shift in stickleback: pleiotropy and effect size. Evolution 62:76-85.

Miller, C.T., Beleza, S., Pollen, A.A., Schluter, D., Kittles, R.A., Shriver, M.D., and Kingsley, D.M. (2007) Cis-regulatory changes in Kit ligand expression and parallel evolution of pigmentation in sticklebacks and humans. Cell 131:1179-1189.

Miller, C.T., Swartz, M.E., Khuu, P.A., Walker, M.B., Eberhart, J.K., and Kimmel, C.B. (2007) mef2ca is required in cranial neural crest to effect Endothelin1 signaling in zebrafish. Dev. Biol. 308:144-157.

Kimmel, C.B., Walker, M.B., and Miller, C.T. (2007) Morphing the hyomandibular skeleton in development and evolution. J. Exp. Zoolog. B Mol. Dev. Evol. 308B:609-624.

Walker, M.B., Miller, C.T., Swartz, M.E., Eberhart, J.K., and Kimmel, C.B. (2007) phospholipase C, beta 3 is required for Endothelin1 regulation of pharyngeal arch patterning in zebrafish. Dev. Biol. 304:194-207.

Walker, M.B., Miller, C.T., Coffin Talbot, J., Stock, D.W., and Kimmel, C.B. (2006) Zebrafish furin mutants reveal intricacies in regulating Endothelin1 signaling in craniofacial patterning. Dev. Biol. 295:194-205.

Yan, Y.L., Willoughby, J., Liu, D., Crump, J.G., Wilson, C., Miller, C.T., Singer, A., Kimmel, C., Westerfield, M., and Postlethwait, J.H. (2005) A pair of Sox: distinct and overlapping functions of zebrafish sox9 co-orthologs in craniofacial and pectoral fin development. Development 132:1069-1083.

Miller, C.T., Maves, L. and Kimmel, C.B. (2004) moz regulates Hox expression and pharyngeal segmental identity in zebrafish. Development 131:2443-2461.

Miller, C.T., Yelon, D., Stainier D.Y., and Kimmel, C.B. (2003) Two endothelin1 effectors, hand2 and bapx1, pattern ventral pharyngeal cartilage and the jaw joint. Development 130:1353-1365.

Kimmel, C.B., Ullmann, B., Walker, M., Miller, C.T., and Crump, J.G. (2003) Endothelin 1-mediated regulation of pharyngeal bone development in zebrafish. Development 130:1339-1351.

Yan, Y.L., Miller, C.T., Nissen, R.M., Singer, A., Liu, D., Kirn, A., Draper, B., Willoughby, J., Morcos, P.A., Amsterdam, A., Chung, B.C., Westerfield, M., Haffter, P., Hopkins, N., Kimmel C., and Postlethwait, J.H. (2002) A zebrafish sox9 gene required for cartilage morphogenesis. Development 129:5065-5079.

Kimmel, C.B., Miller, C.T., and Keynes, R.J. (2001) Neural crest patterning and the evolution of the jaw. J. Anat. 199:105-120.

Kimmel, C.B., Miller, C.T., and Moens, C.B. (2001) Specification and morphogenesis of the zebrafish larval head skeleton. Dev. Biol. 233:239-257.

Miller, C.T. and Kimmel, C.B. (2001) Morpholino phenocopies of endothelin 1 (sucker) and other anterior arch class mutations. Genesis 30:186-187.

Miller, C.T., Schilling, T.F., Lee, K.-H., Parker, J., and Kimmel, C.B. (2000) sucker encodes a zebrafish Endothelin-1 required for ventral pharyngeal arch development. Development 127:3815-3828.

Kimmel, C.B., Miller, C.T., Kruze, G., Ullmann, B., BreMiller, R.A., Larison, K.D. and Snyder, H.C. (1998) The shaping of pharyngeal cartilages during early development of the zebrafish. Dev. Biol. 203:245-263.

Miller, C., McDonald, J., and Francis, D. (1996) Evolution of promoter sequences: elements of a canonical promoter for prespore genes of Dictyostelium. J. Mol. Evol. 43:185-193.