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Faculty research interests in Molecular Evolutionary Genetics include studies on the evolution of metabolic regulation, alternative splicing, self-incompatibility in plants, phylogeny of vertebrates, Caribbean biogeography, adaptive evolution at the molecular level, statistical methods of analyzing molecular data, human evolution, population genetics of Drosophila pseudoobscura, and the evolutionary genetics of bacteria.

The Institute of Molecular Evolutionary Genetics, directed by Distinguished Professor of Biology Masatoshi Nei, has its home in the department and has garnered international recognition for its leadership in this newly emergent field. About half of the institute's twenty-six faculty members are from the Department of Biology; other departments represented are Anthropology, Entomology, Molecular and Cell Biology, and Computer Science. The institute provides graduate student and postdoctoral support, and sponsors weekly seminars and special conferences. In 1992, the institute hosted an international meeting that was attended by several hundred researchers. The success of that meeting led to the establishment of the Society for Molecular Biology and Evolution (Masatoshi Nei, President-elect), with annual meetings beginning in 1993.

Molecular Evolutionary Genetics is a multidisciplinary science that integrates molecular biology, developmental biology, and population biology. Penn State has a strong reputation in the field of evolutionary genetics through both the Institute of Molecular Evolutionary Genetics and the Molecular Cellular Integrative Biosciences graduate program, many members of which belong to the Department of Biology.