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Evolutionary Genetics and Genomics

Evolutionary genetics and genomics involve study of the evolution of genes, gene families, genetic systems, genomes, and populations and the genetic basis of phenotypic evolution. The approaches include the use of genetic markers in natural populations, computer simulations and experiments with model organisms.
Italics = secondary appointment in EEB, can serve as graduate co-chair only

Regina Baucom

Regina Baucom’s research broadly revolves around the central question “Why and how do some organisms persist and adapt to inhospitable environments?” She works on this topic utilizing species from the morning glory genus, many of which are agricultural weeds. There are three main projects underway in Baucom’s lab: the evolutionary genomics of plant defense and plant weediness, the influence of the mating system on the evolution of herbicide resistance, and the role of the plant metagenome on adaptation.

Liliana Cortés-Ortiz 

Liliana Cortés-Ortiz integrates genetic, cytogenetic, morphological, and behavioral approaches to understand the evolution and diversification of primates and to establish primate conservation strategies. Her current research includes systematic and phylogeographic investigations of Neotropical primates and the study of hybridization in two well-defined sister species of howler monkeys.

Alison Davis Rabosky 

Alison Davis Rabosky uses field and molecular studies to answer questions about the evolution of behavior, the origins of phenotypic novelty, and biodiversity, often within reptiles.  Her research includes the role of color polymorphism in mimicry systems, the evolution of sociality in lizards, the systematics of New World snakes, and the conservation and management of island endemics.

Vincent Denef

Vincent Denef uses metagenomic and metaproteomic approaches to gather an improved understanding of microbial population dynamics and community functioning within ecosystem context. He is particularly interested in the connection between genomic variation and altered ecological behavior, and how short- and long-term environmental change can drive both. While he has been studying these concepts in systems ranging from abandoned mines to the human gastrointestinal tract, he is currently focusing on freshwater systems such as the Laurentian Great Lakes.

Christopher Dick

Christopher Dick is interested in the ecology and evolutionary history of species-rich tropical forests. His research has focused primarily on phylogeny, phylogeography and population genetics of Neotropical trees. He is also eager to collaborate on projects involving temperate forest trees.

Thomas Duda

Thomas Duda investigates the processes associated with ecological diversification. This work includes field and laboratory studies that involve analyses of feeding ecology, phylogenetics and phylogeography, and molecular investigations of the evolution of venoms of members of the predatory, marine gastropod genus Conus.

Meghan Duffy

Meghan Duffy's research focuses on the ecology and evolution of host-parasite interactions. She is especially interested in the intersection of ecology and evolutionary biology, including how rapid evolution affects ecological host-parasite dynamics, and how ecological context influences host-parasite evolution. Her research uses a combination of observational studies of natural populations and communities, manipulative experiments in the lab and field, and mathematical models.

Melissa Duhaime  

Melissa Duhaime focuses on marine microbiology, spanning two themes: (i) ocean plastic-microbe associations and (ii) marine virus (meta)genomics. For the first, she investigates the role of microbes in the fate of marine plastics, and the role of plastics in marine microbial community structure and function in natural (N. Pacific Gyre, North Sea) and engineered (Biosphere2 Ocean) systems. For the second, she uses genomic tools to investigate evolution and ecology of ocean viruses (phages) and their microbial hosts, with particular interest in the role of nutrient limitation on infection dynamics and virus-host evolution.

D. André Green

André Green is broadly interested in how functional complexity emerges across different scales of biological organization, from molecules and cells to organisms and populations. His thesis and present work is focused on understanding the development of phenotypically plastic traits at the molecular scale in order to illuminate general mechanisms that promote or constrain the generation of biodiversity. He is currently working to establish the monarch butterfly as a model to study the molecular genetic ‘design’ of migration and understand how this design influences evolution of the migration strategy.

Timothy James

Timothy James' research addresses mating and recombination in fungi using molecular techniques. He particularly focuses on the evolution of fungal mating incompatibility systems, as well as the evolution of alternatives to traditional sexual reproduction such as heterokaryosis and mitotic recombination. He studies organisms including mushrooms, water molds and pathogens such as the agent of amphibian chytridiomycosis.

L. Lacey Knowles

Lacey Knowles' research interests are in speciation, phylogeography and evolutionary radiations.

Alexey Kondrashov

Alexey Kondrashov uses data on within-population and between-species genetic variation in order to study natural selection at the level of DNA sequences

Hernán López-Fernández

Hernán López-Fernández studies the evolution of freshwater fishes with emphasis on South and Central America, which house the most diverse freshwater fish fauna on earth. The lab often uses the family Cichlidae as a model because it is an iconic subject of study in vertebrate adaptive evolution and the third most diverse family of Neotropical fishes. Research in the lab combines fieldwork, molecular phylogenetics/phylogenomics and comparative methods to integrate ecology, functional morphology, life histories and geography into macroevolutionary analyses of freshwater fish diversification.

Yin-Long Qiu

Yin-Long Qiu's research focuses on the evolution of land plants, evolution of mitochondrial genomes and reconstruction of land plant phylogeny using gene sequences and genomic structural features.

Tom Schmidt

Thomas Schmidt's laboratory is focused on the physiology and ecology of microbes. We routinely develop and apply nucleic acid-based methods to explore and understand patterns of diversity and function of microbial communities, and to guide cultivation efforts. Our research is currently focused on two microbial communities: those found in terrestrial environments and are involved in the flux of greenhouse gases, and microbes that constitute mammalian microbiome. As we develop a better appreciation for the relationship between the structure and function of these microbial communities, we are conducting research to uncover fundamental principles that explain distribution patterns of microbial populations.

Stephen A. Smith

Stephen Smith is interested in phylogenetics, computational molecular evolution, biogeography, and macroevolution. His research includes developing and implementing methods for the construction and analysis of phylogenetic trees. In addition to constructing trees, he also works on methods for examining geographic evolution and large scale evolutionary patterns. He primarily focuses on plant species, though he is interested in addressing these questions across the tree of life.

Priscilla Tucker

Priscilla Tucker studies genetic changes underlying mammalian diversity. She studies the nature of the species boundary through investigations of genetic interactions between hybridizing species. She also conducts comparative molecular studies across species to document patterns of gene evolution. Recent and current research is focused on species in the rodent genus Mus that are related to the laboratory mouse, a premier model for genetic studies.

Benjamin Winger

Ben Winger studies speciation, biogeography, community assembly, and movement ecology (migration and dispersal) in birds. He uses a variety of approaches and data types in his research, including population genetics, genomics, phylogenetics, museum collections and fieldwork.

Patricia Wittkopp

Patricia Wittkopp's research aims to understand the genetic basis of development and evolution, with an emphasis on the molecular mechanisms controlling gene expressions.

Luis Zaman

Luis Zaman’s research takes a deeply interdisciplinary approach to understanding why evolution appears so relentless and creative. His lab uses experimental evolution of two very different model systems: 1) populations of self-replicating computer programs or digital organisms, and 2) microbial communities consisting of bacteria and bacteriophage (viruses that infect bacteria). The common thread running through his broad research interests is understanding the evolution of diversity, complexity, and evolvability, and how the interplay between ecology and (co)evolution drives these phenomena.

Jianzhi Zhang

Jianzhi Zhang's research covers a wide array of questions in molecular and genomic evolution. He uses theoretical, computational, and experimental approaches to address fundamental question in evolutionary genetics, genomics, and systems biology, such as gene duplication, genetic redundancy, expression evolution, and adaptation.