Microbial Evolution and Ecology
In the Van Dyken Lab at the University of Miami, we are interested in illuminating general principles of complex systems. Complex systems are composed of large numbers of components that interact to produce emergent, macroscopic, collective behavior. Examples include gene regulatory and metabolic networks within cells, cells within multicellular aggregates, individuals in societies, and species in ecological communities and ecosystems. While these systems extend over 12 orders of magnitude in size, the work in our lab operates on the premise that common mathematical and physical principles unite these disparate phenomena, allowing us to explore conceptual connections between fields as diverse as molecular biology, biochemistry, physiology, economics, social sciences, and ecosystem ecology. In general, we are interested in understanding how processes at one scale generate phenomena at higher scales, and in how evolution acts to tune lower-level processes to generate order at higher levels.
We address these abstract questions through the lens of microbial evolution and ecology. We formulate mathematical models and computer simulations of microbes which we then test using high-throughput laboratory experiments in the model unicellular eukaryote, Saccharomyces cerevisiae (i.e., "Budding" or "Brewer's" yeast). Our experiments combine genetic engineering with molecular, cellular and physiological assays, competition experiments (e.g., Evolutionary Games), and long-term experimental evolution.
We are affiliated with the Institute of Theoretical and Mathematical Ecology, the Complexity Initiative, and the Evolutionary Behavior and Brain Sciences group at the University of Miami.
We address these abstract questions through the lens of microbial evolution and ecology. We formulate mathematical models and computer simulations of microbes which we then test using high-throughput laboratory experiments in the model unicellular eukaryote, Saccharomyces cerevisiae (i.e., "Budding" or "Brewer's" yeast). Our experiments combine genetic engineering with molecular, cellular and physiological assays, competition experiments (e.g., Evolutionary Games), and long-term experimental evolution.
We are affiliated with the Institute of Theoretical and Mathematical Ecology, the Complexity Initiative, and the Evolutionary Behavior and Brain Sciences group at the University of Miami.
Publications
Check out my Googlescholar page.
Van Dyken, J. D. Competitive mode strongly influences the probability of evolutionary rescue from a wave of biological invasion. Submitted.
Van Dyken, J. D. Adaptive dynamics of microbial gene expression allocation. In revision.
Van Dyken, J. D. and Zhang, B. Greater (or less) than the sum of its parts: Total carrying capacity in a spatially distributed, n-patch population with weak and strong diffusion. In revision.
Xu, S. and Van Dyken, J.D.* 2017. Microbial expansion-collision dynamics promote cooperation and coexistence on surfaces. Evolution 72: 153-169. *Corresponding author.
Zhang, B., Kula, A., Mack, K.M.L., Zhai, L., Ryce, A., Ni, W-M., DeAngelis, D., Van Dyken, J.D.* 2017. Carrying capacity in a heterogeneous environment with habitat connectivity. Ecology Letters 20 (9), 1118-1128 *Corresponding author.
Van Dyken, J.D. 2017. Propagation and control of gene expression noise with non-linear translation kinetics. Journal of Theoretical Biology 430, 185-194
Van Dyken, J.D 2017. Noise slows the rate of Michaelis-Menten reactions. Journal of Theoretical Biology 430, 21-31 DOI: https://doi.org/10.1016/j.jtbi.2017.06.039
Van Dyken, J.D 2016. Fitness costs of noise in biochemical reaction networks and the evolutionary limits of cellular robustness. bioRxiv, p.068510
Frenkel, E., MacDonald, M., Van Dyken, J.D, Koshaleva, K., Lang, G., Desai, M.M. 2015. Crowded growth leads to the spontaneous evolution of semistable coexistence in laboratory yeast populations. Proceedings of the National Academy of Sciences 112: 11306-11311.
Van Dyken, J.D 2014. “Altruism.” In Oxford Bibliographies in Evolutionary Biology, Ed. Jonathan Losos. New York: Oxford University Press.
Smith, J., J. D. Van Dyken, and G. Velicer. 2014. Nonadaptive processes can create the appearance of facultative cheating in microbes. Evolution 68: 816-826.
Van Dyken, J.D., Mueller, M. I., Mack, K.M.L, and Desai, M.M. 2013. Spatial population expansion promotes the evolution of cooperation in an experimental Prisoner’s Dilemma. Current Biology 23: 919-923.
Van Dyken, J.D, and M. J. Wade. 2012. Origins of altruism diversity II: Runaway altruism co-evolution via reciprocal niche-construction. Evolution 66: 2498-2513.
Van Dyken, J.D, and M. J. Wade. 2012. Origins of altruism diversity I: The diversity of altruistic strategies and their evolutionary responses to local competition. Evolution 66: 2484-2497.
Van Dyken, J.D, and M. J. Wade. 2012. Detecting the molecular signature of social conflict: Theory and a test with bacterial quorum sensing genes. The American Naturalist 179: 436-450.
M.C. Whitlock and Van Dyken, J.D.. 2011. Altruism in viscous populations revisited: Competition and altruism do not exactly cancel even in the island model. Evolutionary Ecology Research 13: 747-752.
Van Dyken, J.D T. Linksvayer, and M. J. Wade. 2011. Kin selection-mutation balance: The evolutionary origin, maintenance and consequences of social cheating. The American Naturalist 177:288-300.
Smith, J., J. D. Van Dyken, P. Zee. 2010. A generalization of Hamilton’s rule for the evolution of microbial cooperation. Science 328: 1700-1703.
Van Dyken, J.D 2010. The components of kin competition. 2010. Evolution 64: 2840-2855.
Van Dyken, J.D and M. J. Wade. 2010. The genetic signature of conditional expression. Genetics 184:557-570.
Snell-Rood EC, Van Dyken JD, Cruickshank TE, Wade MJ, Moczek AP 2010. Toward a population genetic framework of developmental evolution: costs, limits, and consequences of phenotypic plasticity. Bioessays 32: 71-81.
Wade, M. J., D. S. Wilson, C. Goodnight, D. Taylor, Y. Bar-Yam, M. A. de Aguiar, B. Stacey, J. Werfel, G. A. Hoelzer, E. D. Brodie, 3rd, P. Fields, F. Breden, T. A. Linksvayer, J. A. Fletcher, P. J. Richerson, J. D. Bever, J. D. Van Dyken, and P. Zee. 2010. Multilevel and kin selection in a connected world. Nature 463:E8-9.
Demuth, J. P., D. W. Drury, M. L. Peters, J. D. Van Dyken, N. K. Priest, M. J. Wade. 2007. Genome-wide survey of Tribolium castaneum microsatellites and description of 509 polymorphic markers. Mol. Ecol. Notes 7: 1189-1195.
Book Reviews:
Van Dyken , J.D. 2017. Review of "Budding Yeast: A Laboratory Manual". The Quarterly Review of Biology. In press.
Van Dyken, J.D. 2014. Review of "Rapidly Evolving Genes and Genetic Systems". The Quarterly Review of Biology 89: 270.
Van Dyken, J. D. Competitive mode strongly influences the probability of evolutionary rescue from a wave of biological invasion. Submitted.
Van Dyken, J. D. Adaptive dynamics of microbial gene expression allocation. In revision.
Van Dyken, J. D. and Zhang, B. Greater (or less) than the sum of its parts: Total carrying capacity in a spatially distributed, n-patch population with weak and strong diffusion. In revision.
Xu, S. and Van Dyken, J.D.* 2017. Microbial expansion-collision dynamics promote cooperation and coexistence on surfaces. Evolution 72: 153-169. *Corresponding author.
Zhang, B., Kula, A., Mack, K.M.L., Zhai, L., Ryce, A., Ni, W-M., DeAngelis, D., Van Dyken, J.D.* 2017. Carrying capacity in a heterogeneous environment with habitat connectivity. Ecology Letters 20 (9), 1118-1128 *Corresponding author.
Van Dyken, J.D. 2017. Propagation and control of gene expression noise with non-linear translation kinetics. Journal of Theoretical Biology 430, 185-194
Van Dyken, J.D 2017. Noise slows the rate of Michaelis-Menten reactions. Journal of Theoretical Biology 430, 21-31 DOI: https://doi.org/10.1016/j.jtbi.2017.06.039
Van Dyken, J.D 2016. Fitness costs of noise in biochemical reaction networks and the evolutionary limits of cellular robustness. bioRxiv, p.068510
Frenkel, E., MacDonald, M., Van Dyken, J.D, Koshaleva, K., Lang, G., Desai, M.M. 2015. Crowded growth leads to the spontaneous evolution of semistable coexistence in laboratory yeast populations. Proceedings of the National Academy of Sciences 112: 11306-11311.
Van Dyken, J.D 2014. “Altruism.” In Oxford Bibliographies in Evolutionary Biology, Ed. Jonathan Losos. New York: Oxford University Press.
Smith, J., J. D. Van Dyken, and G. Velicer. 2014. Nonadaptive processes can create the appearance of facultative cheating in microbes. Evolution 68: 816-826.
Van Dyken, J.D., Mueller, M. I., Mack, K.M.L, and Desai, M.M. 2013. Spatial population expansion promotes the evolution of cooperation in an experimental Prisoner’s Dilemma. Current Biology 23: 919-923.
Van Dyken, J.D, and M. J. Wade. 2012. Origins of altruism diversity II: Runaway altruism co-evolution via reciprocal niche-construction. Evolution 66: 2498-2513.
Van Dyken, J.D, and M. J. Wade. 2012. Origins of altruism diversity I: The diversity of altruistic strategies and their evolutionary responses to local competition. Evolution 66: 2484-2497.
Van Dyken, J.D, and M. J. Wade. 2012. Detecting the molecular signature of social conflict: Theory and a test with bacterial quorum sensing genes. The American Naturalist 179: 436-450.
M.C. Whitlock and Van Dyken, J.D.. 2011. Altruism in viscous populations revisited: Competition and altruism do not exactly cancel even in the island model. Evolutionary Ecology Research 13: 747-752.
Van Dyken, J.D T. Linksvayer, and M. J. Wade. 2011. Kin selection-mutation balance: The evolutionary origin, maintenance and consequences of social cheating. The American Naturalist 177:288-300.
Smith, J., J. D. Van Dyken, P. Zee. 2010. A generalization of Hamilton’s rule for the evolution of microbial cooperation. Science 328: 1700-1703.
Van Dyken, J.D 2010. The components of kin competition. 2010. Evolution 64: 2840-2855.
Van Dyken, J.D and M. J. Wade. 2010. The genetic signature of conditional expression. Genetics 184:557-570.
Snell-Rood EC, Van Dyken JD, Cruickshank TE, Wade MJ, Moczek AP 2010. Toward a population genetic framework of developmental evolution: costs, limits, and consequences of phenotypic plasticity. Bioessays 32: 71-81.
Wade, M. J., D. S. Wilson, C. Goodnight, D. Taylor, Y. Bar-Yam, M. A. de Aguiar, B. Stacey, J. Werfel, G. A. Hoelzer, E. D. Brodie, 3rd, P. Fields, F. Breden, T. A. Linksvayer, J. A. Fletcher, P. J. Richerson, J. D. Bever, J. D. Van Dyken, and P. Zee. 2010. Multilevel and kin selection in a connected world. Nature 463:E8-9.
Demuth, J. P., D. W. Drury, M. L. Peters, J. D. Van Dyken, N. K. Priest, M. J. Wade. 2007. Genome-wide survey of Tribolium castaneum microsatellites and description of 509 polymorphic markers. Mol. Ecol. Notes 7: 1189-1195.
Book Reviews:
Van Dyken , J.D. 2017. Review of "Budding Yeast: A Laboratory Manual". The Quarterly Review of Biology. In press.
Van Dyken, J.D. 2014. Review of "Rapidly Evolving Genes and Genetic Systems". The Quarterly Review of Biology 89: 270.