Geffrey Stopper, Ph.D.

Geffrey F. Stopper, Ph.D.

Associate Professor

Area of Specialization: Evolutionary Biology, Developmental Evolution, Molecular Evolution, Genomics­­

Degrees and Certifications

    The Rothberg Institute for Childhood Diseases, Guilford, CT
    Post-Doctoral Research Scientist in Molecular Biology and Bioinformatics
    April 2007 to August 2008

    Yale University, New Haven, CT
    Ph.D. in Ecology & Evolutionary Biology.
    May 2007

    Yale University, New Haven, CT
    M.S. in Ecology & Evolutionary Biology
    May 2003

    Hartwick College, Oneonta, NY
    B.A. in Biology, Minor in Music
    May 2000

    Affiliations: Society for Integrative and Comparative Biology, Beta Beta Beta Biology Honor Society, Council on Undergraduate Research

Teaching Responsibilities

    • BICC 103 The Human Community and Scientific Discovery
    • BI 111/113 Concepts in Biology I Lecture, Laboratory, & Discussion
    • BI 112/114 Concepts in Biology II Lecture, Laboratory, & Discussion
    • BI 201/203 Organisms to Populations Lecture & Laboratory
    • BI 225/226 Evolutionary Analysis Lecture & Laboratory
    • BI 221 Genetics Laboratory
    • BI 299 Topics in Evolution
    • BI 390 Supervised Research
    • BI 399 Senior Seminar

Research Interests & Grants

    Dr. Stopper has broad research interests, but his research tends to focus on topics that fall within the field of evolutionary biology.

    Developmental Evolution of Tetrapod Limbs
    The main thread of Dr. Stopper’s research is in developmental evolutionary biology, specifically focusing on how changes in genes and the interactions between genes and gene products result in evolutionary change in the development of morphology. Currently Dr. Stopper most often approaches these questions within the context of the evolutionary transition from fin to limb, and the subsequent radiation into the diverse limb morphologies found in land animals. This means that work in his lab usually involves organismal biology in the form of raising animals and performing manipulations to developing embryos or larvae and observing the consequences of those manipulations. It also involves molecular work in the form of DNA & RNA isolation, PCR, RTPCR, and other related technologies.

    Cleared and stained Ambystoma mexicanum limbs. Stopper Lab
    Cleared and stained forelimbs of the Axolotl salamander Ambystoma mexicanum. The image includes a normal 4-fingered limb and three limbs with reduced digit numbers resulting from exposure to cyclopamine to block signaling of the limb morphogen protein, Sonic hedgehog (Stopper and Wagner, 2007).

    Evolution in the Domestication of the Yeast Saccharomyces cerevisiae
    Dr. Stopper is also pursuing research questions related to the domestication and evolution of the yeast used in breadmaking, winemaking, and beer brewing – Saccharomyces cerevisiae. The domestication of this species appears to have involved many phenotypic changes from the wild ancestors, and has resulted in a great diversification to different types, not unlike the diversification to the regional and varied types found in more familiar domesticated species like cats, dogs, and agricultural animals. This research is carried out in collaboration with Sacred Heart’s Dr. Kirk Bartholomew. We are currently investigating 1) the relationships of domesticated yeast strains to better understand their historical pattern of domestication and 2) the phenotypic changes that occurred during yeast domestication and diversification, and the molecular changes underlying these phenotypic changes.

    Stopper Lab Fermenting Beer Flasks
    Fermenting flasks of beer during yeast selection experiments.

Honors, Awards & Fellowships

    • Hartwick College Outstanding Young Alumnus Award (2009)
    • The Company of Biologists “Development” Traveling Fellowship (2004)
    • Society for Integrative and Comparative Biology Grant in Aid of Research (2003)
    • NIH, Yale University Developmental Biology Training Grant, Ruth L. Kirschstein National Research Service Award (2000-2003)

Publications and Presentations

    View More Publications


    Stopper GF, Lazowski A. In Press. Mathematics in Conservation: The Case of the Endangered Florida Panther. National Center for Case Study Teaching in Science, University at Buffalo, State University of New York.

    Lazowski A, Stopper GF. 2013. A case study in elementary statistics: the Florida panther population. PRIMUS: Problems, Resources, and Issues in Mathematics Undergraduate Studies 23(3):247-256.

    Thomas R, Gohlke JM, Stopper GF, Parham FM, Portier CJ. 2009. Choosing the right path: enhancement of biologically relevant sets of genes or proteins using pathway structure. Genome Biol 10, R44.

    Kohlsdorf T, Cummings MP, Lynch VJ, Stopper GF, Takahashi K, Wagner GP. 2008. A Molecular Footprint of Limb Loss: Sequence Variation of the Autopodial Identity Gene Hoxa-13. J Mol Evol 67(6):581-593.

    Stopper GF, Wagner GP. 2007. Inhibition of Sonic hedgehog signaling leads to posterior digit loss in Ambystoma mexicanum: Parallels to natural digit reduction in urodeles. Dev Dyn 236(1):321-331.

    Stopper GF, Wagner GP. 2005. Of chicken wings and frog legs: A smorgasbord of evolutionary variation in mechanisms of tetrapod limb development. Dev Biol 288(1):21-39.

    Lynch VJ, Roth JJ, Takahashi K, Dunn CW, Nonaka DF, Stopper GF, Wagner GP. 2004. Adaptive evolution of HoxA-11 and HoxA-13 at the origin of the uterus in mammals. Proc R Soc Lond B Biol Sci 271(1554):2201-2207.

    Stopper GF, Hecker L, Franssen RA, Sessions SK. 2002. How trematodes cause limb deformities in amphibians. J Exp Zool 294(3):252-263.

    Sessions SK, Franssen A, Horner V, Hecker L, Stopper G. 2001. Update on deformed amphibian research at Hartwick College. In: Adams MS, ed. Indicators of Catskill Ecosystem Health. Purple Mountain Press, Fleischmanns, New York. p 99-116.


    Society for Integrative and Comparative Biology Annual Meeting. Charlestons, SC. January 2012
    Stopper GF, Grzyb A, Perlee B, Swift S, Engel A, Hartman B. “Sonic hedgehog’s negative autoregulatory properties in salamander limb development.” Poster presentation.

    Western Connecticut State University. Danbury, CT. April 2006
    Stopper GF. “Hedgehog function in the evolution of amphibian limb development.” 50 minute seminar.

    Hartwick College βββ (Biology Honors Society) Induction Ceremony. Oneonta, NY. April 2005.
    Stopper GF. “Evolution of Tetrapod Limb Development.” 30 minute Keynote Address.

    Macquarie University. Sydney, Australia. October 2004.
    Stopper GF. “Hedgehog function in the patterning of urodele limbs and other osteichthyan paired appendages.” 30 minute presentation to the lab of Dr. Jean M.P. Joss.

    8th International Conference on Limb Development and Regeneration. Dundee, Scotland. July 2004.
    Stopper GF, Wagner GP, Joss JMP. “Hedgehog function in the patterning of urodele limbs and other osteichthyan paired appendages.” 15 minute talk for evolution of limb development session.

    Yale Department of Ecology & Evolutionary Biology Graduate Student Seminar. Yale University, New Haven, CT. April 2003.
    Stopper GF. “Early Stages of Supernumerary Limb Development in Trematode Infected Frogs.” 50 minute talk in a weekly seminar series given by graduate students and post-docs.

Stopper lab picture for faculty profile

Contact Information

Office Location & Hours

  • Location: Academic Bldg SC 217A

    Academic Bldg SC 217A
    College of Arts and Sciences
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