Michael D. Shapiro

Assistant 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 adaptive skeletal evolution, we do not know how many genes are involved, which genes are actually responsible for morphological change, whether alterations to these genes affect coding or regulatory regions, 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.

Genetic architecture of evolutionary change

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

Darwin's pigeons

In The Origin of Species, Charles Darwin enthusiastically promotes the enormous diversity among domesticated 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 ecologically and evolutionarily relevant traits that vary among birds. We are generating novel genetic tools for the pigeon to map the number and location of genes that control variation in craniofacial morphology, pigmentation, feather outgrowth, and other important traits. Recently, we used these tools to better understand genetic structure among breeds, and to show that a shared haplotype of the EphB2 gene underlies head crest development in many pigeon breeds.

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 human 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. 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.
  2. M.D. Shapiro and E.T. Domyan (2013) Quick Guide: Domestic Pigeons. Current Biology 23: R302-303
  3. SA Stringham, EA Mulroy, J Xing, D Record, MW Guernsey, JT Aldenhoven, EJ Osborne, MD Shapiro (2012) Divergence, convergence, and the ancestry of feral populations in the domestic rock pigeon. Current Biology 22:302-308 (Cover article)
  4. TA Castoe, AM Bronikowski, ED Brodie III, SV Edwards, ME Pfrender, MD Shapiro, DD Pollock, WC Warren (2011) A proposal to sequence the genome of a garter snake (Thamnophis sirtalis). Standards in Genomic Sciences 4:257-270
  5. Aldenhoven JT, Miller MA, Showers Corneli P, Shapiro MD (2010) Phylogeography of ninespine sticklebacks (Pungitius pungitius) in North America: glacial refugia and the origins of adaptive traits. Molecular Ecology 19: 4061-4076
  6. Chan YF, Marks ME, Jones FC, Villarreal G Jr, Shapiro MD, Fisher S, Southwick AM, Absher DM, Grimwood J, Schmutz J, Myers RM, Petrov D, Jónsson B, Schluter D, Bell MA, Kingsley DM (2010) Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a Pitx1 enhancer. Science 5963:302-305
  7. Shapiro MD, Summers BR, Balabhadra S, Aldenhoven JT, Miller AL, Cunningham C, Bell MA, Kingsley DM (2009) The genetic architecture of skeletal convergence and sex determination in ninespine sticklebacks. Current Biology 19:1140-45
  8. Ross JA, Urton JR, Boland J, Shapiro MD, Peichel CL (2009) Turnover of sex chromosomes in the stickleback fishes (Gasterosteidae). PLoS Genetics 5:e1000391
  9. Shapiro MD, Shubin NH, Downs JP (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
  10. Shapiro MD, Bell MA, Kingsley DM (2006) Parallel genetic origins of pelvic reduction in vertebrates.  Proc Natl Acad Sci USA 103:13753-13718
  11. Shapiro MD, Marks ME, Peichel CL, Blackman BK, Nereng KS, Jonsson B, Schluter D, Kingsley DM (2004) Genetic and developmental basis of evolutionary pelvic reduction in threespine sticklebacks.  Nature 428:717-723
  12. Colosimo PF, Peichel CL, Nereng K, Blackman BK, Shapiro MD, Schluter D, Kingsley DM (2004) The genetic architecture of parallel armor plate reduction in threespine sticklebacks.  PLoS-Biology 2(5):635-641
  13. Shapiro MD, Hanken J, Rosenthal N (2003) Developmental basis of evolutionary digit loss in the Australian lizard Hemiergis.  J Exp Zool 297B(1):48-56
  14. Shapiro MD (2002) Developmental morphology of limb reduction in Hemiergis (Squamata:  Scincidae): chondrogenesis, osteogenesis, and heterochrony.  Journal of Morphology 254(3):211-231 (Cover article)
  15. Shapiro MD, Carl TF (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)
  16. Xavier-Neto J, Shapiro MD, Houghton L, Rosenthal N (2000) Sequential programs of retinoic acid synthesis in the myocardial and epicardial layers of the developing avian heart. Developmental Biology 219(1):129-141

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Last Updated: 4/26/13