Publications
View "My Bibliography" from NCBI
2020 |
Preprint: R. Bruders, M. Sidesinger, M.D. Shapiro. The Almond plumage color pattern is associated with eye pigmentation defects in the domestic pigeon (Columba livia). bioRxiv doi: https://doi.org/10.1101/2020.10.17.339655. |
2020 |
Preprint: J.G. Baldwin-Brown, S.M. Villa, A.I. Vickrey, K.P. Johnson, S.E. Bush, D.H. Clayton, M.D. Shapiro. The assembled and annotated genome of the pigeon louse Columbicola columbae, a model ectoparasite. bioRxiv doi: https://doi.org/10.1101/2020.10.08.330514. |
2020 |
R. Bruders, H. Van Hollebeke, E.J. Osborne, Z. Kronenberg, M. Yandell, M.D. Shapiro. A copy number variant is associated with a spectrum of pigmentation patterns in the rock pigeon (Columba livia). PLoS Genetics 16: e1008274. |
2020 |
G. Pacheco, H. van Grouw, M.D. Shapiro, M.T.P. Gilbert, F. Vieira. Darwin’s Fancy Revised: An Updated Understanding of the Genomic Constitution of Pigeon Breeds. Genome Biology and Evolution, doi: 10.1093/gbe/evaa027. |
2020 |
R.S. Krauss, D.D.W. Cornelison, G. Kardon, M.D. Shapiro, P.L. Koch. Science at Sundance 2020. Science 367: 1188-1191. Link to AAAS blog |
2019 |
E.F. Boer, H.F. Van Hollebeke, S. Park, C.R. Infante, D.B. Menke, M.D. Shapiro. Pigeon foot feathering reveals conserved limb identity networks. Developmental Biology. Link to paper on journal website |
2019 |
S.M. Villa, J.C. Altuna, J.S. Ruff, A.B. Beach, L.I. Mulvey, E.J. Poole, H.E. Campbell, K.P. Johnson, M.D. Shapiro, S.E. Bush, and D.H. Clayton. Reproductive isolation arises as a by-product of rapid local adaptation in a natural population. Proceedings of the National Academy of Sciences of the USA. Link to paper on journal website |
2019 |
M. Webster, L. Chouinard-Thuly, G. Herczeg, J. Kitano, R. Riley, S. Rogers, M.D. Shapiro, T. Shikano, K. Laland. A Four-Questions Perspective on Public Information Use in Sticklebacks (Gasterosteidae). Royal Society Open Science 6: 181735. Link to paper on journal website or download PDF |
2019 |
R.S. Krauss, M.D. Shapiro, P.L. Koch, G. Kardon and D.D.W. Cornelison. Science at Sundance. Science 363: 1270-1274. Link to AAAS blog |
2019 |
S.E. Bush, S.M. Villa, J.C. Altuna, K.P. Johnson, M.D. Shapiro, D.H. Clayton. Host defence triggers rapid adaptive radiation in experimentally evolving parasites. Evolution Letters. Link to paper on journal website |
2018 |
A.I. Vickrey, R. Bruders, Z. Kronenberg, E. Mackey, R.J. Bohlender, E. Maclary, R. Maynez, E.J. Osborne, K.P. Johnson, C.D. Huff, M. Yandell, M.D. Shapiro. Introgression of regulatory alleles and a missense coding mutation drive plumage pattern diversity in the rock pigeon. eLife 7: e34803. Link to paper on journal website or download PDF |
2018 |
C. Holt, M. Campbell, D.A. Keays, N. Edelman, A. Kapusta, E. Maclary, E. Domyan, A. Suh, W.C. Warren, M. Yandell, M.T.P. Gilbert, M.D. Shapiro. Improved genome assembly and annotation for the rock pigeon (Columba livia). G3: Genes | Genomes | Genetics 8: 1391-1398. Link to paper on journal website or download PDF |
2017 |
E.F. Boer, H.F. Van Hollebecke, M.D. Shapiro. Genomic determinants of epidermal appendage patterning and structure in domestic birds. Developmental Biology. doi: 10.1016/j.ydbio.2017.03.022. Link to accepted manuscript (open access) |
2017 |
B.M. Boyd, J.A. Allen, N. Nguyen, A.D. Sweet, T. Warnow, M.D. Shapiro, S. Villa, S. Bush, D. Clayton, K.P. Johnson. Phylogenomics using target-restricted assembly resolves intra-generic relationships of parasitic lice (Phthiraptera: Columbicola). Systematic Biology. doi: 10.1093/sysbio/syx027. PDF |
2016/ 2017 |
E.T. Domyan, M.D. Shapiro. Pigeonetics takes flight: Evolution, development, and genetics of intraspecific variation. Developmental Biology 427: 241-250. Link to Developmental Biology website (open access article) |
2016 |
E.T. Domyan, Z. Kronenberg, C. Infante, A.I. Vickrey, S.A. Stringham, R. Bruders, M.W. Guernsey, S. Park, J. Payne, R. Beckstead, G. Kardon, D.B. Menke, M. Yandell, M.D. Shapiro. Molecular shifts in limb identity underlie development of feathered feet in two domestic avian species. eLife 5:e12115. PDF from eLife website. (If link doesn't work, try here.) |
2015 |
Z. Kronenberg, E.J. Osborne, K. Cone, E. Domyan, M.D. Shapiro, N. Elde, M, Yandell. Wham: Identifying Structural Variants of Biological Consequence. PLoS Computational Biology 11: e1004572. PDF |
2015 |
A.I. Vickrey, E.T. Domyan, M.P. Horvath, M.D. Shapiro. Convergent evolution of head crests in two domesticated columbids is associated with different missense mutations in EphB2. Molecular Biology and Evolution. PDF from Oxford Journals website. (If link doesn't work, try here). PDF of news article by J. Caspermeyer here. |
2015 |
K.L. Cooper, M.D. Shapiro. Preface to the Special Issue on Evolution and Morphological Diversity. Developmental Dynamics 244: 1181-1183. PDF |
2015 |
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. PDF |
2014 |
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 |
2014 |
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. |
2014 |
M.T.P. Gilbert, M.D. Shapiro. Domestication of pigeons. Encyclopedia of Global Archaeology, Springer. PDF of proofs. |
2013 |
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 |
2013 |
M.D. Shapiro, E.T. Domyan. Quick Guide: Domestic pigeons. Current Biology 23: R302-303. PDF |
2013 |
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. |
2012 |
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 |
2011 |
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 |
2010 |
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 |
2010 |
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 |
2009 |
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) |
2009 |
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 |
2008 |
M.D. Shapiro. Major Transitions in Vertebrate History (Book Review). Quarterly Review of Biology 83(3): 306. |
2007 |
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 |
2006 |
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 |
2004 |
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 |
2004 |
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 |
2003 |
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 |
2003 |
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 |
2002 |
M.D. Shapiro. Developmental morphology of limb reduction in Hemiergis (Squamata: Scincidae): chondrogenesis, osteogenesis, and heterochrony. Journal of Morphology 254(3): 211-231. PDF |
2001 |
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 |
2001 |
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. |
2000 |
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 |
1999 |
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 |
1998 |
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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wordle based on common text from titles and abstracts of publications |
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