Amy R. McCune

Professor Emerita


I am an evolutionary biologist who specializes in investigating the history of life through the study of living and fossil fishes. Research in my lab is always evolutionary in focus and, over the years, my students and I have studied a variety of fishes, from ancient forms like lungfishes, bichir, sturgeon, bowfin, gar and their fossil relatives, to a variety of living teleost fishes, including zebrafish and relatives, swordtails, needlefishes and halfbeaks, cichlids, and pupfishes. Our lab uses methods of paleobiology, phylogenetics, genetics and morphology as is necessary to answer the particular questions we are pursuing.

At Cornell, I teach in a variety of courses, including The Vertebrates (BioEE 2740), Biology of Fishes lecture and lab (BioEE 476), Introductory Evolutionary Biology and Diversity (BioEE 1780), Macroevolution (BioEE 4640) and give guest lectures in many other courses. 

Research Focus

We study two broad questions in evolutionary biology: why are some groups so diverse and how do morphological novelties evolve? To explore these questions, we work primarily on fishes, both living and fossil. Recent and ongoing projects on diversification have focused on the ecological, morphological, and genotypic aspects of divergence between closely related species (e.g., Tanganyikan cichlids; Australian skinks) within a phylogenetic framework.

Our lab is currently pursuing the study of the evolution of morphological novelty in vertebrates. Of particular interest is how the lungs of basal bony vertebrates (Osteichthyes) have been modified to function as swimbladders (respiratory or hydrostatic) in more derived ray-fin fishes (Actinopterygii). We are using Micro-CT imaging in a broadly comparative study of bony vertebrates to study the evolution of these air-filled organs (lungs, swimbladders) in a phylogenetic framework. Comparative studies of gene expression to decipher the underlying genetic basis of this important evolutionary transformation are in progress as well.

Past projects on evolutionary novelty have addressed the effects of diet on the jaw and body morphology of cichlids; the ontogeny and phylogeny of jaw morphology in needlefishes and their allies; the development and evolution of pigmentation in zebrafish and morphological variability within zebrafish.



  • Funk, E., E. Birol, and A.R. McCune.  2021. Does the bowfin gas bladder represent an intermediate stage during the lung-to-gas bladder evolutionary transition?  J. Morphology 282:600–611. DOI: 10.1002/jmor.21330
  • Funk, E., C. Breen, N. Kurpios, and A. R. McCune. 2020. Changes in Nkx2.1, Sox2, Bmp4 and Bmp16 expression underlying the lung-to-gas bladder evolutionary transition in ray-finned fishes.  Evolution and Development 22 (5): 384-402.
  • Funk, E. E. Lencer, and A.R. McCune. 2020. Dorsal-ventral inversion in the air-filled organ (lungs, gas bladder) of vertebrates: RNA-sequencing of laser capture micro-dissected embryonic tissue. J. Experimental Zoology, Part B- Molecular and Developmental Evolution 334 (6): 325-338.
  • Lencer, E. S., M. Riccio and A. R. McCune. 2016. Changes in growth rates of oral jaw elements produce evolutionary novelty in bahamian pupfish. Journal of Morphology 277:935-47.
  • Longo, S. J., M. Riccio, and A. R. McCune. 2013. Homology of lungs and gas bladders: insights from arterial vasculature. Journal of Morphology 274:687-703.
  • Cass, A. N., M. D. Servetnick, and A. R. McCune. 2013. Expression of a lung developmental cassette in the adult and developing zebrafish swimbladder. Evolution and Development 15(2):119-132.
  • Wagner, C. E., A. R. McCune, and I. J. Lovette. 2012. Recent speciation in sympatric Tanganyikan cichlid colour-morphs. Molecular Ecology 21:3283-3292.
  • McCune, A. R. and J. C. Schimenti. 2012. Using Genetic Networks and Homology to Understand the Evolution of Phenotypic Traits. Current Genomics 13(1):74-84.
  • Rabosky, D. and A. R. McCune. 2010. Reinventing species selection with molecular phylogenies.  Trends in Ecology and Evolutionary Biology 25(2):68-74.
  • Wagner, C. E. and A. R. McCune. 2009. Contrasting patterns of spatial genetic structure in sympatric rock-dwelling cichlid fishes.  Evolution 63(5):1312-1326.
  • McCune, A. R. 2004. Diversity and speciation of semionotid fishes in Mesozoic rift lakes.  In: Adaptive Speciation, U. Dieckman, M. Doebli, and J. A. J. Metz (eds.).  Cambridge University Press pp. 362-379.
  • McCune, A. R. and R. L. Carlson. 2004. Twenty ways to lose your bladder: Common natural mutants in zebrafish and widespread convergence of swim bladder loss among teleost fishes.  Evolution and Development 6(4):246-259.
  • McClure, M. and A. R. McCune. 2003. Evidence for developmental linkage of pigment patterns with body size and shape in Danios (Teleostei:  Cyprinidae).  Evolution 57(8):1863-1875.
  • McCune, A. R., R. C. Fuller, A. A. Aquilina, R. M. Dawley, J. M. Fadool, D. Houle, J. Travis, and A. S. Kondrashov. 2002. A low genomic number of recessive lethals in natural populations of bluefin killifish and zebrafish.  Science 296:2398-2401.
  • McCune, A. R. and N. R. Lovejoy. 1998. The relative rate of sympatric and allopatric speciation in fishes: Tests using DNA sequence divergence between sister species and among clades.  In: Endless Forms: Species and Speciation, D. Howard and S. Berloccher (eds.).  Oxford University Press pp. 172-185.
  • McCune, A. R. 1996. Biogeographic and stratigraphic evidence for rapid speciation in semionotid fishes.  Paleobiology 22(1):34-48.
  • Normark, B. B., A. R. McCune, and R. G. Harrison. 1991. Phylogenetic relationships of neopterygian fishes inferred from mitochondrial DNA sequences.  Molecular Biology and Evolution 8:819-834.
  • McCune, A. R. 1990. Morphological anomalies in the Semionotus complex: Relaxed selection during colonization of an expanding lake.  Evolution 44(1):71-85.