I am broadly interested in biodiversity and the evolutionary processes that produce this diversity. My research centers on phylogenetic reconstruction, the inferences that can be made using modern systematic techniques, and development of new methods for the analysis of comparative data. Because most species are extinct, relying solely on the extant fauna can lead to spurious inferences about the history of life. Thus, much of my current work is focused on building comprehensive phylogenetic hypotheses of all species in a particular evolutionary lineage. This entails merging paleontological and genomic data in large-scale phylogenetic analyses. Given the detailed historical information in comprehensive evolutionary trees, it is possible to test specific transformational hypotheses and to assess competing models of evolution at different hierarchical scales. Recent work includes phylogenetic studies of whale origins, an examination of the gene duplications that led to the evolution of mammalian milk proteins, and tests for selection on egg-specific proteins that are critical in fertilization.

For graduate training, I participate in the Evolutionary Biology track within the Department of Biology, as well as the Evolution and Ecology Graduate Research Unit.

• Gatesy, J., R. DeSalle, and W. Wheeler. 1993. Alignment-ambiguous nucleotide sites and the exclusion of systematic data. Molecular Phylogenetics and Evolution 2:152-157.
• Gatesy, J., C. Hayashi, R. DeSalle, and E. Vrba. 1994. Rate limits for mispairing and compensatory change: the mitochondrial ribosomal DNA of antelopes. Evolution 48:188-196.
• Gatesy, J., P. O’Grady, and R. Baker. 1999. Corroboration among data sets in simultaneous analysis: Hidden support for phylogenetic relationships among higher level artiodactyl taxa. Cladistics 15:271-313 (cover article).
• Gatesy, J. 2000. Linked branch support and tree stability. Systematic Biology 49:800-807.
• Gatesy, J., and M. O’Leary. 2001. Deciphering whale origins with molecules and fossils. Trends in Ecology and Evolution 16:562-570 (cover article).
• Gatesy, J., C. Matthee, R. DeSalle, and C. Hayashi. 2002. Resolution of a supertree/supermatrix paradox. Systematic Biology 51: 652-664.
• Gatesy, J., G. Amato, M. Norell, R. DeSalle, and C. Hayashi. 2003. Combined support for wholesale taxic atavism in gavialine crocodylians. Systematic Biology 52:403-422 (cover article).

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