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LEE LAB

Department of Integrative Biology
430 Lincoln Drive, Birge Hall
University of Wisconsin
Madison, WI 53706

Office:  (608) 262-2675 (please email)
Lab:  (608) 262-9225
Email:
 carollee(at)wisc(dot)edu  

 


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. Two postdocs 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:

Balancing selection, particularly temporally fluctuating selection, has been hypothesized to contribute significantly to standing genetic variation, which could facilitate adaptation to novel environments. My study, published in Nature Ecology & Evolution, was the first to find empirical support for this idea, demonstrating that the same SNPs under balancing selection in the native saline range are also under parallel directional selection during recent freshwater invasions by populations of the copepod Eurytemora affinis complex (Stern & Lee 2020). I also used a powerful experimental evolution approach, combined with time-resolved whole-genome sequencing, to investigate the role of genetic architecture in facilitating rapid salinity adaptation. I found a remarkable degree of parallel evolution in over 1000 loci across ten replicate lines exposed to declining salinity in the laboratory, with the same SNPs responding to selection far more than expected given the polygenic nature of salinity tolerance (Stern, Diaz, and Lee, Nature Communications, In Revision). Using simulations, I showed that this degree of parallel evolution was consistent with synergistic epistasis among alleles and balancing selection maintaining genetic variation in the wild.

I have recently obtained my Ph.D. degree from the China Agricultural University with a focus on phylogeography, invasion biology, and genomics. I will joining the Lee Lab as a postdoctoral researcher in August, 2021. My previous projects mainly focused on population genetics of hemipteran insects, such as periodical cicada, spotted lanternfly and sycamore lace bug, to reveal their evolutionary histories including speciation, phylogeography, and invasion history using NGS-based mitogenomic sequencing and genome-wide SNPs (Du et al. 2019, Molecular Biology and Evolution; Du et al. 2021, Evolutionary Applications). My project in 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, especially temperature and salinity change in wild and laboratory populations.

 

Graduate Students:

My research investigates responses of populations of the copepod Eurytemora affinis complex and their associated microbiomes across environmental gradients and invasion events. I am using population genomic analyses to characterize demographic history and identify candidate SNPs and genes under selection in response to temperature and salinity gradients in E. affinis complex populations in the North and Baltic Seas. These candidate loci may provide important information regarding how populations of E. affinis might adapt to current and future climate change. Additionally, I am using both single gene (e.g., 16S rRNA) and metagenomic methods to determine how E. affinis complex-associated microbiomes change in composition and function across independent saline-to-freshwater invasion events. Host-associated microbiomes have been linked to critical host functions, such as digestion, neurological function, and defense against pathogens. Thus, understanding how the microbiome changes across saline-to-freshwater invasion events may also provide critical understanding for how the copepod-microbiome holobiont may respond to current and future salinity and temperature change.

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.  

My research applies theoretical approaches to address fundamental questions in evolutionary biology, especially those pertaining to mechanisms of rapid adaptation to novel environments. I am currently investigating several problems related to recombination rate evolution and the role of epistasis. During periods of rapid environmental change, species must adapt in order to persist in their native range. Often this adaptation requires coordinated evolution of multiple genes. Linkage between these genes can hinder selection unless broken by recombination events. Currently, I am studying the role of recombination and epistasis in adaptive evolution using forward time genetic simulations.

Website: https://nw-anderson.github.io/

For several independent saline to freshwater invasions in the E. 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. In the future, I will analyze the evolutionary dynamics of these same ion transporters across a shorter time-scale, within the genus Eurytemora, using phylogenomic methods. These projects will further our understanding of the patterns of evolution of these critical candidate gene families across multiple hierarchical levels, within the species complex Eurytemora affinis, at longer time scales in the genus, and across the phylum.

 Lab Technician:

I am currently working at Dr. Carol Lee's lab at the Université de Montpellier, in collaboration with French scientists Drs. Catherine Lorin-Nebel and Delphine Bonnet. My current project investigates the genetic mechanisms underlying adaptation to freshwater conditions in populations of the Eurytemora affinis complex. Currently we are using forward genetic cross experiments to determine the effects of specific ion transporter alleles on fitness traits at different salinities. Our ultimate goal is to combine these results with allele frequency data to construct demographic models of "Evolutionary Rescue" for Baltic Sea populations of E. affinis in the face of declining salinity with Climate Change.

Research Assistants:

Alexander Taylor: Culture Czar  

Lydia Larsen: Ordering and Culture Czar

Kelli Marschall: Algal Czar

Ruxuan Qiu: Outgoing Algal Czar  

Ben Wilson

Angelis Puls: Inbred Line Czar

Kirsten Gahan

Samuel Lu

Sarah Fritz

Aaron Kufner:  Molecular Evolution and Evolutionary History of the VHA subunit Gene Families 

Nick Mathers:  Molecular Evolution and Evolutionary History of the NHA and NHE Gene Families  

 

Selected Lab Alumni
Molecular Lab

 

David Stern, Computational Genomics Specialist, Medical Science & Computing (MSC), National Institute of Allergy and Infectious Diseases (NIAID)   

Marijan Posavi, Senior Research Scientist in Genomics, University of Pennsylvania and University of New Mexico 

Davorka Gulisija, Assistant Professor, University of New Mexico   

Greg Gelembiuk, Department of Entomology,  University of Wisconsin - Madison

Suzanne Peyer, McPherson Eye Research Institute, University of Wisconsin

Brian Metzger, Departments of Human Genetics & Ecology and Evolution, University of Chicago

Martin Bontrager, Computational Biologist, Tempus, Inc.

Jane Remfert, Virginia Commonwealth University

Daniel Skelly, Senior Computational Scientist, The Jackson Labs

Kelsey Johnson, Postdoctoral Scientist, University of Minnesota

Wynne Moss, Postdoctoral Scientist, Conservation Science Partners

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

Kevin Fongching Chau, Associate Research Scientist, Hummingbird Bioscience

Taylor Opgenorth, University of Florida College of Veterinary Medicine

Anna Jenstead, Metropolitan Veterinary Center 

Elizabeth Stanford, Veterinary Technician, University of Wisconsin - Madison

Kristin Lee, Data Scientist, Spotify 

Joseph Connolly, University of Idaho  

Sarah Tomke, University of Kentucky

Rachel Minehan, University of Wisconsin

Emma McKeel, The Water Institute, University of Wisconsin - Milwaukee

Cullen Meyer, University of Georgia 

Jinwoo Kim 

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

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


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