Reverse Ecology:
Computational Integration of Genomes, Organisms, and Environments

IGERT faculty


First year students

August Guang
B.S. Mathematics, Harvey Mudd College
I am interested in assembly and phylogenetics algorithms, and the reproducibility and accuracy of their results. Although the number of programs and algorithms for genome assembly and tree reconstruction expands every year, there is often no way to assess their benefits and drawbacks or to compare between specific programs, and the metrics that are out there are not well understood. Eventually I hope to develop methods that will address these issues.

Lillian Hancock
B.S. Biology, Trinity College ‘08
M.S. Biology, University of Rhode Island ‘10
Generally, I am interested in convergent evolution and the genetic and environmental mechanisms underlying adaptation and evolution in plants, ranging from green and red algae to angiosperms. My Master’s research focused on red algal organellar genome evolution as a model for understanding the process by which organisms become obligately parasitic. For my doctorate research, I will be investigating Crassulacean Acid Metabolism (CAM) photosynthesis evolution in the context of two lineages in the Portulacineae, Montiaceae and Anacampserotaceae. Through the phylogenetic resolution of these two clades, we aim to gain an understanding of the genetic and environmental enablers to the CAM syndrome and its evolutionary relationship to intermediate CAM-like phenotypes and succulence.

Emily Hollenbeck
B.A. Biology, University of Pennsylvania
Many species have been observed moving up in elevation as well as latitude in response to warmer climates. I am interested in altitudinal range shifts occurring under current and future climate change. Steep mountains provide a spatially rapid gradient of environmental conditions and community assemblages, which could potentially mean much shorter (and easier) shifts in order for species to reach an ideal climate. However, climate change in many locations is more complex than a simple rise in temperature, and both biotic and abiotic mismatches may impact species’ fitness in a new location. I hope to explore the fitness consequences of range shifts from various angles, including population genetics, local adaptation, and physiological ecology.

Yinghong Lan
B.S. Biosciences, 2012, University of Science and Technology of China, Hefei, China
Horizontal gene transfer is recognized as one of the most important mechanisms in prokaryotic evolution, especially in shaping the structure and function of microbial communities. I’m generally interested in the factors that determine the tendency of genes to be transferred or the barriers against it and the effect of horizontal gene transfer on speciation and metabolic network. My research will focus on analyzing datasets of prokaryotic genomes using bioinformatics approaches with a modularity perspective on metabolic network and studying speciation from a genomic dynamics view.

Second-year students

Christopher Graves
B.S. Biological Sciences, University of Vermont
My interests are in directly testing predictions of evolutionary theory through controlled experimental studies of evolution in microbial populations. Much of our understanding of evolution comes from mathematical inference rather than empirical observation due to the time scale on which most evolutionary processes act. Bacteria and other microbes offer an exciting model system because their short generation time and small genomes allow evolutionary processes to be examined while they occur and enable quantitative predictions based on evolutionary theory to be experimentally tested in the lab.

Elizabeth Makrides
BS Biology, University of North Carolina at Chapel Hill
MS Applied Mathematics, Brown University
I am primarily interested in using dynamical systems techniques to study natural systems. My mathematical research focuses on localized coherent structures and pattern formation. In particular, I am interested in the effects of symmetry breaking terms on the bifurcation structure of the cubic-quintic Swift-Hohenberg equation, which models pattern formation in a variety of contexts, including binary fluid convection, optical systems, reaction-diffusion systems, and spatial structures in ecology.

Victor Schmidt
B.S. Biology, 2006. St. Lawrence University, Canton, NY.
M.S. Marine Biology, 2009. University of North Carolina, Wilmington.
I am interested in the influence community shifts within host microbiomes can have on disease development, pathogen transmission and environmental health. My current research examines the microbiomes associated with a single fish species across a range of environmental conditions, and looks to determine the relative influence of genotype versus environment on microbiome community structure.