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Stephen W. Schaeffer

Stephen W. Schaeffer

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Professor of Biology, Associate Department Head for Graduate Education

Biology Ombudsperson

507A Mueller
University Park, PA 16802
Phone: (814)865-3269
Lab Address: 507A Mueller
Lab Phone: (814)863-1650


  1. Ph.D., University of Georgia, 1985
  2. M.S., West Virginia University, 1980
  3. B.S., West Virginia Wesleyan College, 1978

Postdoc Training

  1. Harvard University, 1985-1988

Research Interests

Molecular Population Genetics and Genomics

My laboratory is interested in the genomic processes that alter gene and chromosomal frequencies in natural populations of plants and animals.

Chromosomal inversions are often detected in humans when individuals present symptoms of genetic diseases. Individuals with two different inversions can have lower fertility because genetic exchange between inverted chromosomes can lead to the formation of sperm or eggs with less or more genetic information. Inversions, however, also can be present in populations at high frequencies with no apparent negative effects on viability or reproduction. My laboratory tests hypotheses about how inversions arise, spread, and are maintained in populations.

Drosophila pseudoobscura is a model system for the study of inversions because its third chromosome is polymorphic for over 30 different gene arrangements in populations. These arrangements were generated through a series of overlapping paracentric inversions. The inversion frequencies vary among populations forming clines or gradients whose major frequency shifts occur with major climatic zones in the southwestern United States. The gene arrangement frequencies cycle with the seasons and show altitudinal clines. Population cage experiments in the laboratory have shown that different gene arrangements are maintained at stable equilibrium frequencies.

We are using next-generation technologies to assay genetic variation of the complete chromosome as well as transcriptional variation. The re-sequencing data will help us to identify inversion breakpoint sequences and improve the D. pseudoobscura genome assembly. The transcriptome data will help us improve the annotation of gene models in D. pseudoobscura. Molecular population genetic analyses of nucleotide polymorphism and gene expression data will test four classes of hypotheses about how a new inversion spreads through a population: (1) indirect effects due to reduced recombination leading to chromosomes free of deleterious mutations or enhancing the linkage of adaptive genes; (2) genetic drift that fixes underdominant arrangements; (3) direct effects of the chromosomal lesion such as alteration of gene structure or expression; or (4) genetic hitchhiking with an adaptive allele. These analyses will test two hypotheses about how inversions are maintained in populations: (1) by overdominance; or (2) as a protected polymorphism. Genes that show differential expression or protein variation may be manipulated in future experiments designed to understand the molecular genetic basis that underpins inversion evolution.

Ecological Genetics

My laboratory also is involved with collaborative projects with Dr. Charles R. Fisher to understand the ecological and genetic factors that shape the communities at cold seeps and hydrothermal vents. Experimental and theoretical approaches in population genetics are being used to determine how much gene flow occurs among cold seep habitats in the Gulf of Mexico. We have examined the ecological forces that shape communities of tubeworms at the East Pacific Rise (EPR). Three species of tubeworms are found along the EPR that colonize the vents in a successional pattern. The laboratory developed an RFLP assay that can distinguish among the three tubeworm species, which cannot be identified to species with morphological examination. This study found that colonization of vents by Tevnia jerichonana facilitates the colonization of Riftia pachyptila and Oasisia alvinae. Future directions will include a study of the genetics of the morphology of hydrothermal vent tubeworms.

Selected Publications

Wallace, A. G., D. Detweiler, and S. W. Schaeffer. 2011. Evolutionary history of the third chromosome gene arrangements of Drosophila pseudoobscura inferred from inversion breakpoints. Mol. Biol. Evol. 28: 2219-2229.

Meisel, R. P., B. B. Hilldorfer, J. L. Koch, S. Lockton, and S. W. Schaeffer. 2010. Adaptive evolution of genes duplicated from the Drosophila pseudoobscura neo-X chromosome. Mol. Biol. Evol. 27: 1963-1978.

Bhutkar, A. J., S. W. Schaeffer, S. Russo, M. Xu, T. F. Smith, and W. J. Gelbart. 2008. Chromosomal rearrangement inferred from comparisons of twelve Drosophila genomes. Genetics 179: 1657-1680.

Schaeffer, S. W. 2008. Selection in heterogeneous environments maintains the gene arrangement polymorphism of D. pseudoobscura. Evolution 62: 3082-3099.

Schaeffer, S. W., et al. 2008. Polytene Chromosomal Maps of 11 Drosophila species: The order of genomic scaffolds inferred from genetic and physical maps. Genetics 179: 1601-1655.

Carney, S. L., J. F. Flores, K. M. Orobona, D. A. Butterfield, C. R. Fisher, and S. W. Schaeffer. 2007. Environmental differences in hemoglobin gene expression in the hydrothermal vent tubeworm, Ridgeia piscesae. Comp. Biochem. and Physiol. Part B 146: 326-337.

Richards, S., Y. Liu, B. R. Bettencourt, P. Hradecky, S. Letovsky, R. Nielsen, K. Thornton, M. A. Todd, R. Chen, R. P. Meisel, O. Couronne, S. Hua, M. A. Smith, H. J. Bussemaker, M. F. V. Batenburg, S. L. Howells, S. E. Scherer, E. Sodergren, B. B. Matthews, M. A. Crosby, A. J. Schroeder, D. Ortiz-Barrientos, C. M. Rives, M. L. Metzker, D. M. Muzny, G. Scott, D. Steffen, D. A. Wheeler, K. C. Worley, P. Havlak, K. J. Durbin, A. Eagan, R. Gill, J. Hume, M. B. Morgan, Y. Huang, L. Waldron, D. Verduzco, K. P. Blankenburg, H. Robertson, I. Dubchak, M. A. F. Noor, W. W. Anderson, K. White, A. G. Clark, S. W. Schaeffer, W. M. Gelbart, G. Weinstock, and R. A. Gibbs. 2005. Comparative genome sequencing of Drosophila pseudoobscura: Chromosomal, gene and cis-element evolution. Genome Research 15: 1-18.

Schaeffer, S. W., P. Goetting-Minesky, M. Kovacevic, J. Peoples, J. L. Graybill, J. M. Miller, K. Kim, J. G. Nelson, and W. Anderson. 2003. Evolutionary genomics of inversions in Drosophila pseudoobscura: Evidence for epistasis. Proc. Natl. Acad. Sci. 100: 8319-8324.