Dr. Josef Uyeda

Biological Sciences

Dr. Uyeda’s research program focuses on understanding the drivers of long-term evolutionary change and how these are connected to the ecological, environmental and genetic drivers that we study in contemporary populations. The Uyeda lab works to develop novel statistical methods and software for studying such drivers across the tree of life by integrating process-based models and data of evolutionary and ecological change with phylogenetic trees, which serve as a map for the history of life. Such methods are vital for understanding the effects of global change because they give perspective on the capacity for species and lineages to survive changing environmental conditions not just for our lifetimes, but over the several million-year lifespans of species.


Many gaps exist in our knowledge of how evolutionary adaptation scales from short to long timescales, and why some lineages with seemingly equivalent adaptive capacities can show such different dynamics at macroevolutionary timescales, with some going extinct and others rapidly adapting to changing conditions. Understanding the predictors of macroevolutionary adaptive potential that can be measured in populations and species currently experiencing change is an essential goal to managing the long-term survival of biodiversity.

Dr. Uyeda is an Assistant Professor in the Department of Biological Sciences and teach undergraduate Evolutionary Biology and a graduate course on Macroevolution and Phylogenetics. His expertise lies in Phylogenetics, Bayesian modeling, Statistical Quantitative Genetics, and Macroevolutionary models of trait evolution. He has worked in a variety of systems ranging from microbes to plants to vertebrates, but is most familiar with reptiles and amphibians.

Dr. Uyeda received a PhD from Oregon State University in Zoology and was a Postdoctoral Researcher at the University of Idaho’s Institute for Bioinformatics and Evolutionary Studies. He also serves on the council for the Society for Systematic Biology.


Lab Website

Recent Relevant Publications

Mabee, PM, Dahdul, WM, Balhoff, JP, Lapp, H, Manda, P, Uyeda, JC, Vision, TJ and M Westefield. 2018. Phenoscape: Semantic analysis of organismal traits and genes yields insights in evolutionary biology. In: Application of Semantic Technologies in Biodiversity Science, edited by A. Thessen. IOS Press, Berlin.

Uyeda, JC, Zenil-Ferguson, R and MW Pennell. 2018. Rethinking phylogenetic comparative methods. Systematic Biology 67(6):1091-1109.

Zanne, AE, Pearse, WD, Cornwell, WK, McGlinn, DJ, Wright, IJ and JC Uyeda. 2018. Functional biogeography of angiosperms: life at the extremes. New Phytologist (4):1697-1709.

Boucher, FC, Demery, V, Conti, E, Harmon, LJ and JC Uyeda. 2017. A general model for estimating macroevolutionary landscapes. Systematic Biology, 10.1093/sysbio/syx075.

Uyeda, JC, Pennell, MW, Miller, ET, Maia, R and CT McClain. 2017. The evolution of energetic scaling across the vertebrate tree of life. The American Naturalist, 190 (2): 185-199.

Uyeda, JC, Harmon, LJ and CE Blank. 2016. A comprehensive study of cyanobacterial morphological and ecological evolutionary dynamics through deep geologic time preserved in the genomes of modern taxa. PLoS ONE 11(9): e0162539. doi:10.1371/journal.pone.0162539.

Uyeda, JC, and LJ Harmon. 2014. A novel Bayesian method for inferring and interpreting the dynamics of adaptive landscapes from phylogenetic comparative data. Systematic Biology, 63(6):902-918.

Pennell, MW, Harmon, LJ and JC Uyeda. 2013. Is there room for punctuated equilibrium in macroevolution? Trends in Ecology and Evolution, 29(1):23-32.

Jones, AG, Bürger, R, Arnold, SJ, Hohenlohe, PA and JC Uyeda. 2012. The effects of stochastic and episodic movement of the optimum on the evolution of the G-matrix and the response of the mean to selection. Journal of Evolutionary Biology, 25(11):2210-2231.

Uyeda, JC, Hansen TF, Arnold SJ and J Pienaar. 2011. The million-year wait for macroevolutionary bursts. Proceedings of the National Academy of Sciences, 108(38):15908-15913.