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S.A. Stringham, M.D. Shapiro. Microevolution and the genetic basis of vertebrate diversity: examples from teleost fishes. In K.P. Dial, N.H. Shubin, E.L. Brainerd (eds.), Great Transformations in Vertebrate Evolution. University of Chicago Press, Chicago. (July 2015)


C.T. Miller, A.M. Glazer, B.R. Summers, B.K. Blackman, A.R. Norman, M.D. Shapiro, B.L. Cole, C.L. Peichel, D. Schluter, D.M. Kingsley. Additive and clustered quantitative trait loci control anatomically regional skeletal evolution in sticklebacks. Genetics 197: 405-420. PDF


E.T. Domyan, M.W. Guernsey, Z. Kronenberg, S. Krishnan, R.E. Boissy, A. Vickrey, C. Rodgers, P. Cassidy, S.A. Leachman, J.W. Fondon III, M. Yandell, M.D. Shapiro. Epistatic and combinatorial effects of pigmentary gene mutations in the domestic pigeon. Current Biology 24: 459-464. PDF. PDF of Supplemental Information. Excel file of Table S1.


M.T.P. Gilbert, M.D. Shapiro. Domestication of pigeons. Encyclopedia of Global Archaeology, Springer. PDF of proofs.


M.W. Guernsey, L. Ritscher, M.A. Miller, D.A. Smith, T. Schöneberg, M.D. Shapiro. A Val85Met mutation in Melanocortin-1 receptor is associated with reductions in eumelanic pigmentation and cell surface expression in domestic rock pigeons (Columba livia). PLoS ONE 8(8): e74475. PDF


M.D. Shapiro, E.T. Domyan. Quick Guide: Domestic pigeons. Current Biology 23: R302-303. PDF


M.D. Shapiro*, Z. Kronenberg, C. Li, E.T. Domyan, H. Pan, M. Campbell, H. Tan, C.D. Huff, Haofu Hu, A.I. Vickrey, S.A. Nielsen, S.A. Stringham, Hao Hu, E. Willerslev, M. T. P. Gilbert, M. Yandell, G. Zhang, J. Wang*. Genomic diversity and evolution of the head crest in the rock pigeon. Science 339: 1063-1067. PDF (includes journal cover), Supplementary Materials.


S.A. Stringham, E.A. Mulroy, J. Xing, D. Record, M.W. Guernsey, J.T. Aldenhoven, E.J. Osborne, M.D. Shapiro. Divergence, convergence, and the ancestry of feral populations in the domestic rock pigeon. Current Biology 22: 302-308. PDF (includes journal cover), Supplemental Information file


T.A. Castoe, A.M. Bronikowski, E.D. Brodie III, S.V. Edwards, M.E. Pfrender, M.D. Shapiro, D.D. Pollock, W.C. Warren. A proposal to sequence the genome of a garter snake (Thamnophis sirtalis). Standards in Genomic Sciences 4: 257-270. PDF


J.T. Aldenhoven, M.A. Miller, P. Showers Corneli, and M.D. Shapiro. Phylogeography of ninespine sticklebacks (Pungitius pungitius) in North America: glacial refugia and the origins of adaptive traits. Molecular Ecology 19:4061-4076. PDF, Supporting Information file


Y.F. Chan, M.E. Marks, F.C. Jones, G. Villarreal Jr., M.D. Shapiro, S. Fisher, A.M. Southwick, D.M. Absher, J. Grimwood, J. Schmutz, R.M. Myers, D. Petrov, B. Jónsson, D. Schluter, M.A. Bell, and D.M. Kingsley. Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a Pitx1 enhancer. Science 5963:302-305. PDF


M.D. Shapiro, B.R. Summers, S. Balabhadra, J.T. Aldenhoven, A.L. Miller, C. Cunningham, M.A. Bell, D.M. Kingsley. The genetic architecture of skeletal convergence and sex determination in ninespine sticklebacks. Current Biology 19:1140-1145. PDF, Supplemental Data file (includes linkage map)


J.A. Ross, J.R. Urton, J. Boland, M.D. Shapiro, and C.L. Peichel. Turnover of sex chromosomes in the stickleback fishes (Gasterosteidae). PLoS Genetics 5(2): e1000391. PDF


M.D. Shapiro. Major Transitions in Vertebrate History (Book Review). Quarterly Review of Biology 83(3): 306.


M.D. Shapiro, N.H. Shubin, and J.P. Downs. Limb reduction and diversity in reptilian evolution, pp. 225-244. In B.K. Hall (ed.), Fins into Limbs, University of Chicago Press. PDF


M.D. Shapiro, M.A. Bell, and D.M. Kingsley. Parallel genetic origins of pelvic reduction in vertebrates. Proceedings of the National Academy of Sciences of the USA 103: 13753-13718. PDF


M.D. Shapiro, M.E. Marks, C.L. Peichel, B.K. Blackman, K.S. Nereng, B. Jónsson, D. Schluter, and D.M. Kingsley. Genetic and developmental basis of evolutionary pelvic reduction in threespine sticklebacks. Nature 428: 717-723. PDF Corrigendum in Nature 439: 1014 (2006). PDF


P.F. Colosimo, C.L. Peichel, K. Nereng, B.K. Blackman, M.D. Shapiro, D. Schluter, D.M. Kingsley. The genetic architecture of parallel armor plate reduction in threespine sticklebacks. PLoS Biology 2(5): 635-641. PDF


M.D. Shapiro, J. Hanken, and N. Rosenthal. Developmental basis of evolutionary digit loss in the Australian lizard Hemiergis. Journal of Experimental Zoology (Molecular & Developmental Evolution) 297B: 48-56. PDF


M.D. Shapiro, H. You, N.H. Shubin, Z. Luo, and J.P. Downs. A large ornithomimid pes from the Lower Cretaceous of the Mazongshan Area, Northern Gansu Province, China. Journal of Vertebrate Paleontology 23(3): 695-698. PDF


M.D. Shapiro. Developmental morphology of limb reduction in Hemiergis (Squamata: Scincidae): chondrogenesis, osteogenesis, and heterochrony. Journal of Morphology 254(3): 211-231. PDF


M.D. Shapiro and F.A. Jenkins, Jr. A cynodont from the Upper Triassic of Greenland: tooth replacement and double-rootedness. Bulletin of the Museum of Comparative Zoology 156(1): 49-58. PDF


M.D. Shapiro and T.F. Carl. Novel features of tetrapod limb development in two non-traditional model species: a skink and a direct-developing frog, pp. 337-361. In M. Zelditch (ed.), Beyond Heterochrony: The Evolution of Development. New York: Wiley-Liss.


J. Xavier-Neto, M.D. Shapiro, L. Houghton, and N. Rosenthal. Sequential programs of retinoic acid synthesis in the myocardial and epicardial layers of the developing avian heart. Developmental Biology 219(1): 129-141. PDF


J. Xavier-Neto, C.M. Neville, M.D. Shapiro, L. Houghton, G.F. Wang, W. Nikovits, Jr., F. Stockdale, and N. Rosenthal. A retinoic acid-inducible transgenic marker of sino-atrial development. Development 126(12): 2677-87. PDF


J. Moss, J. Xavier-Neto, M.D. Shapiro, S. Nayeem, P. McCaffery, U. Dräger, and N. Rosenthal. Dynamic patterns of retinoic acid synthesis and response in the developing mammalian heart. Developmental Biology 199(1): 55-71. PDF






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