Michael D. Shapiro

Associate Professor of Biology

Mike Shapiro

A.B. University of California, Berkeley

Ph.D. Harvard University




Michael Shapiro's Lab Page

Michael Shapiro's PubMed Literature Search


What are the genetic and developmental origins of unique traits in natural populations and species of vertebrates? Both evolutionary and medical biologists are interested in the ways that genotypic changes can influence growth and morphology, yet we know remarkably little about the genetic and developmental mechanisms that generate natural morphological diversity. For example, in most cases of evolutionary change, we do not know how many genes are involved, which genes are actually responsible for trait variation, whether alterations to these genes affect coding or regulatory regions, how genes interact in cases of complex traits, or whether the same genes are involved repeatedly in the evolution of similar traits in different populations and species. To address these topics, we combine genetics, developmental biology, and fieldwork to study morphological evolution in natural populations and domesticated species.

Darwin's pigeons

In The Origin of Species, Charles Darwin enthusiastically promotes the enormous diversity among domestic pigeons — generated by thousands of years of artificial selection on a single species by human breeders — as an important proxy for understanding natural selection in wild populations and species. Indeed, he notes that the vast diversity among pigeon breeds within a single species is reminiscent of levels of diversity among multiple genera of other birds. What is the genetic basis of this tremendous variation? Pigeons offer a promising opportunity to study many evolutionarily relevant traits that vary among birds. We are generating new genomic resources for the pigeon to understand the number and location of genes that control variation in craniofacial morphology, pigmentation, feather outgrowth, craniofacial morphology, behavior, and other important traits. Recently, we used these tools to better understand genetic structure among breeds (Stringham et al. 2012), to show that a shared haplotype of the EphB2 gene underlies head crest development in many pigeon breeds (Shapiro et al. 2013), and to dissect interactions among genes (Tyrp1, Slc45a2, Sox10) that control complex color types (Domyan et al. 2014).

Genetic architecture of evolutionary change

Stickleback fish are ideal model organisms for genetic and developmental studies of natural variation because different populations vary dramatically in skeletal structures and other traits. Despite this diversity, populations within a species from throughout the Northern Hemisphere can typically be crossed in the laboratory for genetic mapping experiments. Using an integrative approach that combines comparative genomics, quantitative trait locus mapping, and gene expression studies, we are studying the genetic basis of variation within and among species of sticklebacks. This approach allows us to test whether similar genetic mechanisms underlie similar adaptive phenotypes in different populations and species, a topic of enduring interest to geneticists and evolutionary biologists.

Broader implications

Many aspects of development are highly conserved among vertebrates. Thus, new insights gleaned from our work will illuminate the genetic mechanisms that control tissue growth, morphology, and functional traits in many other organisms, including both normal and abnormal development in human populations. Ultimately, we hope that our studies of variation generated by natural and artificial selection will inform our understanding of the genetic bases of both adaptive evolutionary change and disease.

Shapiro Figure Michael Shapiro Figure Two
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Divergence, convergence, and the ancestry of feral populations in the domestic rock pigeon. Current Biology 22:302-308 (Cover article)


  1. 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. (2014) Epistatic and combinatorial effects of pigmentary gene mutations in the domestic pigeon. Current Biology 24: 459-464
  2. 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. (2014) Additive and clustered quantitative trait loci control anatomically regional skeletal evolution in sticklebacks. Genetics 197: 405-420
  3. M.W. Guernsey, L. Ritscher, M.A. Miller, T. Shoeneberg, M.D. Shapiro. (2013) 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: e74475
  4. 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* (* co-corresponding and senior authors). (2013) Genomic diversity and evolution of the head crest in the rock pigeon. Science. 339: 1063-1067
  5. M.D. Shapiro and E.T. Domyan. (2013) Quick Guide: Domestic Pigeons. Current Biology 23: R302-303
  6. S.A. Stringham, E.A. Mulroy, J. Xing, D. Record, M.W. Guernsey, J.T. Aldenhoven, E.J. Osborne, M.D. Shapiro. (2012) Divergence, convergence, and the ancestry of feral populations in the domestic rock pigeon. Current Biology 22: 302-308 (Cover article)
  7. 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. (2011) A proposal to sequence the genome of a garter snake (Thamnophis sirtalis). Standards in Genomic Sciences 4: 257-270
  8. J.T. Aldenhoven, M.A. Miller, P. Showers Corneli, M.D. Shapiro. (2010) Phylogeography of ninespine sticklebacks (Pungitius pungitius) in North America: glacial refugia and the origins of adaptive traits. Molecular Ecology 19: 4061-4076
  9. 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, D.M. Kingsley. (2010) Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a Pitx1 enhancer. Science 5963: 302-305
  10. M.D. Shapiro, B.R. Summers, S. Balabhadra, J.T. Aldenhoven, A.L. Miller, C. Cunningham, M.A. Bell, D.M. Kingsley. (2009) The genetic architecture of skeletal convergence and sex determination in ninespine sticklebacks. Current Biology 19: 1140-1145
  11. J.A. Ross, J.R. Urton, J. Boland, M.D. Shapiro, C.L. Peichel. (2009) Turnover of sex chromosomes in the stickleback fishes (Gasterosteidae). PLoS Genetics 5: e1000391
  12. M.D. Shapiro, N.H. Shubin, J.P. Downs. (2007) Limb reduction and diversity in reptilian evolution, pp. 225-244. In B.K. Hall (ed.), Fins Into Limbs: Evolution, Development, and Transformation, University of Chicago Press
  13. M.D. Shapiro, M.A. Bell, D.M. Kingsley. (2006) Parallel genetic origins of pelvic reduction in vertebrates. Proc Natl Acad Sci USA 103: 13753-13718
  14. M.D. Shapiro, M.E. Marks, C.L. Peichel, B.K. Blackman, K.S. Nereng, B. Jonsson, D. Schluter, D.M. Kingsley. (2004) Genetic and developmental basis of evolutionary pelvic reduction in threespine sticklebacks.  Nature 428: 717-723
  15. P.F. Colosimo, C.L. Peichel, K. Nereng, B.K. Blackman, M.D. Shapiro, D. Schluter, D.M. Kingsley. (2004) The genetic architecture of parallel armor plate reduction in threespine sticklebacks.  PLoS-Biology 2: 635-641
  16. M.D. Shapiro, J. Hanken, N. Rosenthal. (2003) Developmental basis of evolutionary digit loss in the Australian lizard HemiergisJ Exp Zool 297B: 48-56
  17. M.D. Shapiro. (2002) Developmental morphology of limb reduction in Hemiergis (Squamata:  Scincidae): chondrogenesis, osteogenesis, and heterochrony.  Journal of Morphology 254: 211-231 (Cover article)
  18. M.D. Shapiro, T.F. Carl. (2001) 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. (Cover photo)
  19. J. Xavier-Neto, M.D. Shapiro, L. Houghton, N. Rosenthal. (2000) Sequential programs of retinoic acid synthesis in the myocardial and epicardial layers of the developing avian heart. Developmental Biology 219: 129-141