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  • UC Riverside
  • College of Natural and Agricultural Sciences



Associate Professor of Biology
Office: 2314 Spieth Hall
Laboratory: 2111 Spieth Hall
Phone: (951) 827-7323


Degree: Yale University, 1993
Link to my collaborative website on whale evolution. 

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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 work has focused on building comprehensive phylogenetic hypotheses for particular evolutionary lineages. This entails merging paleontological and genomic data in large-scale phylogenetic analyses. Given the detailed historical information in well-sampled evolutionary trees, it is possible to test specific transformational hypotheses and to assess competing models of evolution at different hierarchical levels. I have focused my work on vertebrate groups with rich fossil diversity (crocodiles, whales, even-toed ungulates, rhinoceroses). Recent work includes phylogenetic studies of cetacean origins, the convergent evolution of river dolphins, the feeding specializations of baleen whales, crocodylian biogeography, adaptive evolution of mammalian milk proteins, brain genes, and reproductive loci, as well as the silencing (pseudogenization) of olfactory genes and dental genes in divergent clades of whales.


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. In addition, I participate in the Evolutionary Biology Joint-Doctoral Program with San Diego State University.

Selected recent publications:

  • R. Meredith, J. Gatesy, J. Cheng and M. Springer. 2011. Pseudogenization of the tooth gene enamelysin (MMP20) in the common ancestor of extant baleen whales. Proceedings of the Royal Society B 278: 993-1002.
  • M. McGowen, S. Montgomery, C. Clark, and J. Gatesy. 2011. Phylogeny and adaptive evolution of the brain-development gene microcephalin (MCPH1) in cetaceans. BMC Evolutionary Biology 11: 98.
  • R. Meredith, E. Hekkala, G. Amato, and J. Gatesy. 2011. A phylogenetic hypothesis for Crocodylus (Crocodylia) based on mitochondrial DNA: Evidence for a trans-Atlantic voyage from Africa to the New World. Molecular Phylogenetics and Evolution 53: 891-906.
  • J. Geisler, M. McGowen, G. Yang, and J. Gatesy. 2011. A supermatrix analysis of genomic, morphological, and paleontological data from crown Cetacea. BMC Evolutionary Biology 11: 112.
  • T. Deméré, M. McGowen, A. Berta, and J. Gatesy. 2009. Morphological and molecular evidence for a stepwise evolutionary transition from teeth to baleen in mysticete whales. Systematic Biology 57: 15-37.
  • M. McGowen, C. Clark, and J. Gatesy. 2008. The vestigial olfactory receptor subgenome of odontocete whales: Phylogenetic congruence between gene tree reconciliation and supermatrix methods. Systematic Biology 57: 574-590.
  • M. O'Leary and J. Gatesy. 2008. Impact of increased character sampling on the phylogeny of Cetartiodactyla (Mammalia): Combined analysis including fossils. Cladistics 24: 397-442.
  • A. de Queiroz and J. Gatesy. 2007. The supermatrix approach to systematics. Trends in Ecology and Evolution 22: 34-41 (cover article).
  • J. Gatesy and R. Baker. 2005. Hidden likelihood support in genomic data: Can forty-five wrongs make a right? Systematic Biology 54: 483-492.
  • J. Gatesy, G. Amato, M. Norell, R. DeSalle, and C. Hayashi. 2003. Combined support for wholesale taxic atavism in gavialine crocodylians. Systematic Biology 52: 402-423 (cover article).
  • J. Gatesy, C. Matthee, R. DeSalle, and C. Hayashi. 2002. Resolution of a supertree/supermatrix paradox. Systematic Biology 51: 652-664.
  • J. Gatesy and M. O'Leary. 2001. Deciphering whale origins with molecules and fossils. Trends in Ecology and Evolution 16: 562-570 (cover article).
  • J. Gatesy, 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).

Last updated 28 November 2011.