S. Shawn McCafferty

Associate Professor of Biology


Phone: 508-286-5642


Ph.D., SUNY Stony Brook, Department of Ecology and Evolution 1992
M.Sc., SUNY Stony Brook, Marine Science Research Center 1982
B.S., North Carolina State University 1979


Main Interests

I am an evolutionary biologist with broad interests in both evolution and ecology. However, my main areas of expertise lie in molecular ecology & evolution and population genomics. I am particularly interested in the role natural selection plays in driving patterns of molecular variation within and among natural populations, and how demographic changes in populations can impact levels of adaptive molecular variation. Though I have worked on a cross section of life, from bacteria to humans, I have to admit to a strong bias towards marine organisms, fish in particular. Below is a brief summary of my research interests.

Other Interests

When not working I try to spend as much time as possible with my family. I train extensively in Aikido and Daito Ryu Aikijujutsu. My other interests include SCUBA diving whenever I can, ocean kayaking, fishing, and generally just being outside enjoying the natural world.


McCafferty, S.S., A. Shorette*, J. Simundza*, and B. Brennessel. 2013. Paucity of genetic variation at a MHC Class I gene in Massachusetts populations of the diamondback terrapin (Malaclemys terrapin): cause for concern or “evolution at a turtle’s pace”? Journal of Herpetology, 47 (2), pp. 222-226.

McCafferty, S.S., A.P. Martin, and E. Bermingham. 2012. Pliocene diversification and phylogeographic pattern in the lower Mesoamerican cichlid Aequidens coeruleopunctatus(Cichlidae).  Int. J. Evol.,  2012, Article ID 780169.

McCafferty, S.S., N. Warren*, C. Wilbur*, and S. Shumway. 2009. Genetic divergence among Massachusetts populations of the vernal pool fairy shrimp Eubranchipus vernalis (Crustacea; Anostraca). Northeast Naturalist 17: 284-305.

Morris, R.L., M.P. Hoffman, R.A. Obar, S.S. McCafferty, I.R. Gibbons, A.D. Leone, J. Cool, E.L. Allgood, A.M. Musante, K.M. Judkins, B.J. Rossetti, A.P. Rawson, and D.R. Burgess. 2006. Analysis of cytoskeletal and motility proteins in the sea urchin genome assembly. Developmental Biology, 300: 219-237.

Sea Urchin Genome Sequencing Consortium. 2006. The Genome of the Sea Urchin Strongylocentrotus purpuratus. Science, 314: 941-952.

McCafferty S, Bermingham E, Quenouille B, Planes S, Hoelzer G, Asoh K. 2002. Historical biogeography and molecular systematics of the Indo-Pacific genus Dascyllus (Teleostei: Pomacentridae). Molecular Ecology, 11:1377-92

Banford HM, Bermingham E, Collette B, and McCafferty S. 1999. Phylogenetic systematics of the Scomberomorus regalis (Teleostei: Scombridae) species group: molecules, morphology and biogeography of Spanish Mackerels. Copeia, 1999(3): 596?613.

Bermingham, E., S. McCafferty and A. Martin. 1997. Fish biogeography and molecular clocks: perspectives from the Panamanian Isthmus. Pp . 113-138. In Kocher, T.D. and C. Stepien (eds). Molecular Systematics of Fishes. Academic Press, NY.

Machado, C. A., E. A. Herre, S. McCafferty and E. Bermingham. 1996. Molecular phylogenies of fig pollinating and non-pollinating wasps and the implications for the origin and evolution of the fig-fig wasp mutualism. Journal of Biogeography 23: 531-542.

Summers, K., L. Dahlstrom, L. A. Weigt, S. McCafferty and E. Bermingham. 1996. Phenotypic and mitochondrial DNA divergence in three species of dart-poison frogs with contrasting parental care behavior. Journal of Heredity, 88: 8-13.

Herre, E. A., C. A Machado, E. Bermingham, J. D. Nason, D. M. Windsor, S. S. McCafferty, W. Van Houten and K. Bachmann. 1996. Molecular phylogenies of figs and their pollinating wasps. Journal of Biogeography 23(4): 521-530.

Futuyma, D. and S. McCafferty. 1990. Phylogeny and the evolution of host plant associations in the leaf beetle genus Ophraella (Coleoptera, Chrysomelidae). Evolution, 44: 1885-1913.

Teaching Interests

Courses I routinely teach:

  • BIO111 Ecology and Evolution & BIO112 Cells and Genes
  • BIO211 Genetics
  • BIO303 Evolution
  • BIO316 Molecular Biology and Genomics
  • BIO318 Tropical Field Biology

Student Projects

There are numerous opportunities for students to work in my lab. If you are interested in working in my lab, or have a particular project you want to pursue, by all means come by. Below is a list of current and past student collaborators and their projects.

Jeffrey Sanborn (’16) – Variation in Toll-Like Receptor 21 Within and Among Killifish (Fundulus heteroclitus) Populations from Southeastern Massachusetts and Northern Maine. (BIO500 Honors Thesis).

Faye Haley (’16) – Molecular Variations in Dopamine Receptor D4 (DRD4) and Serotonin Transporter (SLC6A4) in Atlantic White-Sided Dolphin (Langenorhynchus acutus) and Short-Beaked Common Dolphin (Delphinus delphinus). (BIO499)

Jeffrey M. Paer (’15) – Tracking the movement of 13 clinically significant plasmid-residing antibiotic resistance genes between Wheaton College and the surrounding natural environment. (BIO500 Honors Thesis).

Devon Soucier (’14) – Evidence for Selection in the Toll–Like Receptors in Atlantic killifish Fundulus heteroclitus. (BIO500 Honors Thesis).

Kathryn Svec (’14) – Variation at the TLR4 genomic region in white sided and common dolphins. (BIO399/499)

Kristen Palmer (’13) – Variation at the MHCI and MHCII gene regions in Squalus acanthias: evidence for selection. (BIO500 Honors Research)

Jeremy Golden (’13) – Metagenomic analysis of bacterial communities in the hind gut of the termite Reticulitermes flavipes. (BIO499)

Jessica Smith (’12) – A novel method to detect genomic variation in diamondback terrapins using anchored SINE sequencing. (BIO399)

Samantha Farrel (’11) – Variation at MHC Class 2 Locus in Northwest Atlantic Spiny Dogfish. (BIO499)

Caroline Letourneau (’11) – Use of microsatellites to determine the effective population size of a local population of spotted salamanders (Ambystoma maculatum). (BIO500 Honors Thesis)

Alison Mehlhorn (’11) – Allelic variation of the major histocompatability complex and toll-like receptor gene regions in a grey seal (Halichoerus grypus) population. (BIO500 Honors Thesis)

Chapman Beekman (’10) – Investigating variation in dopamine receptor genes of Atlantic white sided and common dolphins. (BIO500 Honors Thesis)

Jacob Korzun (’10) – Identification of the toll-like receptors in grey seals. (BIO500 Honors Thesis)

Amanda Shorette (’09) – Variation at the Major Histocompatability Complex Class I (MHC I) gene region in local populations of the diamondback terrapin Malaclemys terrapin. (BIO500 Honors Thesis)

Kelly Griffin (’09) – Adaptive molecular variation at immune loci in the grey seal Halichoerus grypus. (BIO399)

Jennifer Carrol (’09) – MHC Class I and II loci in the spotted salamander Ambystioma maculatum.

Laura Fleck (’08) – The identification of the Major Histocompatability Complex (MHC) Class I and Class II genes in diamondback terrapin Malaclemys terrapin. (BIO499)

Mary Ostrander (’08) – Major histocompatability complex (MHC) variation in stranded marine mammals and its correlation with disease. (BIO499)

Ashley Jennings (’07) – Multiple paternity in the spiny dogfish Squalus acanthias. (Bio499)

Erin Allgood (’07) – Genetic variation in the invasive watermilfoil Myriophyllum spicatum. (Bio499)

Robert Borkowski (’06) – The diversity of sulfate reducing bacteria in Boston Harbor: a metagenomic approach. (Bio499)

Roxana Mesias (’06) – Subcloning of the leucine rich extracellular domain of the human toll-like receptor 4 gene into the pET23b expression plasmid. (Bio499)

Liz Jacques (’05) – Finding genetic markers for population genetic analysis of Malaclemys terrapin. (Bio500 Committee Member)

Maris Madeira (’05) – Spatial variation in the introduced asian shore crab Hemigrapsus sanguenensis along the east coast of the U.S. (Bio499)

Chris Wilbur (’05) – Phylogeography of the fairy shrimp Eubranchipus vernalis in Massachusetts vernal pools. (Bio499)

Nick Warren (’04) – Spatial variation in fairy shrimp populations at differing geographic scales. (Bio499)

Research Interests

  • Role of natural selection in driving patterns of molecular diversity.
  • Genes associated with the adaptive and innate immune system as a model for understanding the molecular basis of adaptations in natural populations.
  • Ecological and evolutionary genomics.
  • Application of population genomics and phylogenetics to conservation biology.
  • Ecology and evolution of coral reef organisms.





Mars Center for Science and Technology, Rm 2133