LEE LAB

How can we assess whether populations have the potential to evolve in response to catastrophic environmental change, such as biological invasions, oil spills, or climate change? To what extent are populations constrained from undergoing an evolutionary response? And would independently derived populations show evidence of parallel evolution? Research in the Lee lab currently explores genomic mechanisms underlying physiological adaption underlying catastrophic environmental change, including biological invasions, pollution, and climate change. My lab has used laboratory selection experiments, population genomics, gene expression analyses, quantitative genetics, and comparative physiological studies to document rapid evolutionary responses to environmental change. For example, invasive populations are particularly striking in their capacity to extend their ranges into novel habitats. Analyzing populations that can invade, relative to those that cannot, point to the nature of the native range in shaping the evolutionary potential to undergo habitat shifts. We have examined some key adaptations in response to habitat change across hierarchical levels, from population genomic signatures of selection at ion transporter genes to the molecular evolution of catalytic regions in ion transporters that enable functional evolution during habitat change. We have found the same genomic regions under selection across independent habitat invasions, as well as in selection experiments in the laboratory.  These results are important for understanding how populations will respond to future environmental changes. The Lee Lab welcomes graduate students with a strong background or interest in evolutionary biology or physiological ecology, preferably with experience in laboratory molecular genetics or strong quantitative skills.  The Lee Lab accepts graduate students through the UW Department of Integrative Biology and the UW Graduate Program in Genetics.  Please contact Carol Lee if you are interested in joining the Lee Lab. The Lee Lab is also currently seeking Postdoctoral Researchers to join our dynamic and multi-disciplinary team. One more postdoc will be hired to work in the satellite Lee Lab at the Université de Montpellier in France, where Dr. Lee is an Adjunct Professor.

Lee Lab Members (click on Names or Photos to access personal websites)

Principle Investigator:

Carol Eunmi Lee

 

Postdoctoral Researchers:

I am currently a postdoctoral researcher in Lee Lab at UW-Madison. I obtained my Ph.D. degree in Evolutionary Entomology from China Agricultural University. My research interests lie primarily in genomic adaptive evolution during rapid colonization and invasion. My project in the Lee Lab will apply comparative and population genomic methods, using the copepod Eurytemora affinis species complex as a model system, to explore rapid evolutionary responses to global change. Specifically, my research focuses two main aspects, namely, (1) applying advanced technology to sequence and assemble the chromosome-level reference genomes for different sibling species within the E. affinis complex and performing comparative genomic analyses to resolve the genomic substrates underlying the high adaptive ability of these copepods, and (2) applying laboratory natural selection experiments (Evolve and Resequence) on E. affinis populations to acquire time-series data and identify candidate loci under selection. The goal is to study the epistatic interactions among different loci associated with adaptation to salinity decline and temperature increase, which are predicted consequences of climate change at higher latitudes. Website: https://www.researchgate.net/profile/Zhenyong-Du

Zhenyong Du

I am a postdoctoral researcher in Prof. Lee's group at Université de Montpellier. My research integrates population and quantitative genetics with experimental biology. My work explores how phenotypic and genetic variation is generated, maintained, or eroded through biological evolution. I am particularly interested in phenotypic evolution in the context of new habitat colonization - whether it be contemporary (e.g. biological invasions) or historical (e.g. post-glaciation colonization). I completed my Ph.D. in Paris at the Muséum National d'Histoire Naturelle, CNRS, followed by a postdoc at the Ecological Genetics Research Unit of University of Helsinki and University of Hong Kong. My current project explores the genetic bases of adaptation to varying salinity using the copepod Eurytemora affinis species complex. Specifically, I am quantifying the fitness effects of ion transporter genes involved in response to salinity change. This research will shed light on the genetic mechanisms involved in the adaption to decreasing salinity, a direct consequence of global climate change threatening marine organisms.

Antoine Fraimout

I am currently an NSF postdoctoral research fellow investigating mechanisms of sex determination and the developmental plasticity of sex. My research explores how environmentally sensitive mechanisms of sex determination may evolve in response to changing environments and contribute to species resilience or vulnerability. I completed my PhD at Syracuse University on the function and evolution the internal reproductive environment (i.e., the reproductive tract associated with egg production and transport) in the fruit fly Drosophila melanogaster and extended this research into the communications among cells in the mouse uterus as a postdoctoral research at the University of Vienna. In conjunction with my research on sexual reproduction, and my identity as a queer non-binary scientist, I engage with feminist science and technology studies and queer theory to examine and question meanings of sex and binary sex categories.

Caitlin McDonough-Goldstein

I am a postdoctoral researcher currently based at the "Centre d'écologie fonctionnelle et évolutive" in Montpellier. I am a mathematician with a focus on statistics and stochastic processes, and my work revolves mostly around modeling of population dynamics and detecting signatures of evolutionary forces in data. I obtained my Ph.D. in computational biology from the Institute of Genetics in Cologne and afterwards spent four years at the Laboratoire d'informatique, de robotique et de microélectronique in Montpeller working on evolutionary models in two or more dimensions. Recently, I joined the Lee Lab in order to analyze the evolutionary mechanisms that enables Eurytemora affinis complex populations to repeatedly adapt to environmental change, using statistical methods inspired from mathematical population genetics. I am conducting my research in collaboration with the team members located at the University of Montpellier, as well as with co-advisor Luis-Miguel Chevin.

Johannes Wirtz

 

Graduate Students:

The goal of my research is to gain fundamental insights into the physiological and evolutionary mechanisms of freshwater adaptation by populations of the copepod Eurytemora affinis complex. Previous studies from the Lee Lab have found a set of ion transporter paralogs under parallel selection during freshwater invasions. I aim to understand how expression of these key ion transporters paralogs evolve in situ in invasive freshwater populations relative to their saline ancestors during salinity decline. To achieve this goal, I am performing in situ immunohistochemical staining to quantify evolutionary shifts in localization and in situ expression of ion transporter paralogs between freshwater and saline populations of the E. affinis complex. I am also quantifying evolutionary changes in whole animal protein expression of these ion transporter paralogs. Additionally, I will analyze the genetic association between the candidate ion transporter paralogs and fitness at different salinities. I am currently conducting most of my research in the Lee Lab at the Université de Montpellier in France, co-advised by Dr. Catherine Lorin-Nebel. I will be obtaining two Ph.D.s, from both the University of Wisconsin and Université de Montpellier.

Teresa Popp

Very little research has been conducted to estimate mutation rate µ in non-model systems, particularly for populations with profound ecological importance, such as the copepod Eurytemora. My current goal is to estimate the rate and spectrum of de novo mutations in a Eurytemora affinis complex population using a classical mutation accumulation (MA) experimental design. To achieve this goal, I have collected experimental data for 40 MA lines. I established several replicate MA lines using individual gravid female copepods isolated from an established inbred line maintained in the Lee Lab. After performing further inbreeding for 3-5 generations the lines were then sequenced. I am currently analyzing these data to calculate the mutation rate and mutation spectrum. Such information will allow us to infer the rate at which genetic variation in wild Eurytemora has been established. My results will lay the groundwork for predictions on how genetic variation will change in Eurytemora populations faced with novel selective pressures.

Jacob Fredette-Roman

For several independent saline to freshwater invasions in the Eurytemora affinis species complex, the Lee lab has found signatures of parallel selection acting on many of the same ion transporter paralogs. These include paralogs of Na+/K+-ATPase, Na+/H+ antiporter, carbonic anhydrase, and V-type H+-ATPase. My current research project is focused on reconstructing the evolutionary history and patterns of molecular evolution of these crucial ion transporters across the phylum Arthropoda and across independent saline to freshwater invasions. I am currently focusing on the evolutionary history and molecular evolution of the Na+/H+ antiporter gene family. This gene family is of special interest because paralogs of this gene family show the strongest signatures of selection during habitat invasions.

Patricia Zito

My present research focuses on investigating the evolutionary history and patterns of molecular evolution of the critical ion transporter Na+/K+-ATPase gene family in the copepod Eurytemora affinis species complex. Certain paralogs of this gene family are repeatedly under selection during independent invasions from saline to freshwater habitats. My previous Master's degree research mainly focused on lineage diversity and introgression in zooplankton populations, as well as gene expression in different developmental stages of Daphnia.

Jinhui Wang

 Laboratory Technicians/Lab Managers:

Until 2023 I was the laboratory manager overseeing the operations in the Lee Lab, including copepod culturing, maintenance of equipment, hiring, scheduling, and training of personnel. I also collaborated with lab members on a long term evolution experiment involving the copepod Eurytemora affinis complex. We investigated the impacts of climate change variables (salinity, temperature x salinity) on the evolutionary trajectories of beneficial alleles. Currently, I am exploring patterns of molecular evolution in the Na+,K+,2Cl- cotransporter (NKCC) gene family, which is a major target of selection during salinity transitions. Finally, I have an avid interest in birds and plan to enter a Ph.D. program in the coming years.

Alexander Taylor

Research Assistants:

Joye (Yifei) Zhou: Lab Management, algal culturing, general operations

Brooke Lewis: Ordering Czar, Scheduling, experiment with Postdoc Caitlin McDonough-Goldstein  

Samuel Lu: Algae culture co-Czar, Selection Experiment

Conor Bendett: Protist Specialist, training

Madigan Freng: Algal culture co-Czar

Josh Deruyter: Safety Czar, biocarbonate transporter gene family

 

Selected Lab Alumni (incomplete list)

Marijan Posavi, Martin Bontrager, Greg Gelembiuk, Jane Remfert

 

David Stern (former Postdoc): Associate Bioinformatics Principal Investigator, National Biodefense Analysis and Countermeasures Center (NBACC)

Teresa Popp (Ph.D. degree): Postdoctoral Fellow, Department of Entomology, The Ohio State University, Wooster

Marijan Posavi (Ph.D. degree): Research Assistant Professor and Senior Genome Researcher, Center for Evolutionary and Theoretical Immunology, University of New Mexico

Davorka Gulisija Ph.D. degree): Assistant Professor, Department of Biology, University of New Mexico

Greg Gelembiuk  (Ph.D. degree and Postdoc): Data Analyst, Department of the Independent Police Monitor, City of Madison

Suzanne Peyer (Ph.D. degree): Research Scientist, School of Environmental and Forest Sciences, University of Washington

Brian Metzger  (Research Assistant and Lab Manager): Assistant Professor, Biological Sciences, University of Purdue

Juanita Diaz (MS degree): Teaching Faculty II, Biology Learning Center Coordinator, University of Wisconsin-Madison

Martin Bontrager (Ph.D. degree): Computational Biologist, Tempus, Inc.

Jane Remfert, Center for Environmental Studies, Virginia Commonwealth University

Michael Gerner, Associate Professor, Department of Immunology, University of Washington

Christine Petersen, Fisheries Biologist, BPA, U.S. Department of Energy

Kyle Piller, Professor, Biological Sciences, Southeastern Louisiana University

Brian Eads, Digital Product Development Lead, Bayer Crop Science

Daniel Skelly, Senior Computational Scientist, The Jackson Labs

Kelsey Johnson, Postdoctoral Scientist, University of Minnesota

Wynne Moss, Biologist, USGS Northern Rocky Mountain Science Center

Andrew Tritt, Bioinformatics Data Engineer, Computational Research Division, U.S. Department of Energy

Kevin Fongching Chau, Research Scientist, Hummingbird Bioscience, Singapore

Emily Ruell, Registration Specialist, National Wildlife Research Center (NWRC), US Department of Agriculture  

Taylor Opgenorth, Veterinary Ophthalmology Resident, University of Wisconsin - Madison 

Anna Jenstead, Veterinarian, Metropolitan Veterinary Center

Elizabeth Stanford, Veterinary Technician, University of Wisconsin - Madison

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