Feder Research Group in Evolutionary Dynamics
Our goal is to understand the dynamics of rapidly-evolving populations, especially viruses evolving within their hosts and solid tumors progressing to malignancy. In particular, we are characterizing how spatial organization shapes these evolutionary outcomes, and developing approaches to leverage spatial data to better understand evolutionary histories.
The lab is based in the Department of Genome Sciences at the University of Washington. To learn more about the goals of the lab, please check out the research and publication pages.
The lab accepts graduate students through the Genome Sciences and Molecular and Cellular Biology graduate programs. Prospective graduate students, rotation students and postdoctoral fellows are encouraged to get in touch with Alison.
Population genetics was developed around the idea that adaptive variation is rare, and populations must typically wait for the next beneficial mutation. However, we increasingly realize that in a wide variety of natural populations, including pathogens evolving in their hosts and cancer cells in tumors, many beneficial mutations exist simultaneously (i.e., ones that increase growth rate or allow replication in the presence of drugs) and those mutations can spread in concert. Even though such populations create some of the world's most urgent medical and agricultural problems, our understanding of their evolution is limited by the historical assumptions of population-genetic theory. In the Feder lab, our goal is to understand evolutionary dynamics in this era of abundant genetic variation.
Spatial structure becomes crucially important in the regime where populations rapidly produce beneficial mutations. Structure sets the pace for how beneficial mutations compete and spread. This provides both opportunity and challenge: watching how mutations spread in space allows crucial insights into the degree of parallelism in adaptation, the way that beneficial mutations interact to influence fitness, and the underlying natural history of these populations. However, spatial structure also shapes the adaptive responses themselves. As a result, where beneficial mutations happen to arise may be more important for the ensuing population dynamics than what the mutations are at the molecular scale. When space constrains competition we have an incomplete theoretical understanding of the resulting population dynamics. Despite the growing availability of spatially-resolved genetic data, we need new techniques to draw inferences from spatially and temporally-sampled populations, and corresponding new frameworks to understand the patterns that rapid evolution leaves in time and space.
We combine evolutionary theory and computation with genomic data sampled from clinical and experimental settings to understand the forces that drive rapid adaptation across space. We work across multiple types of spatial organization, considering especially rapid within-host viral evolution and adaptive dynamics in solid tumors. We leverage data collected in time series and with explicit attention to spatial location, and develop new quantitative techniques to analyze data of this form. We characterize the patterns rapid adaptation leaves in space and through time, and in turn, determine how space can and does shape these processes.
- January 2022: Laura Baquero Galvis joins the lab for a rotation. Welcome, Laura!
- December 2021: Funding from the Gilead Research Scholars Program in HIV will support our ongoing work on HIV drug resistance evolution.
- October 2021: Hunter Colegrove joins the lab for a rotation. Welcome, Hunter!
- September 2021: Our paper on multi-drug resistance evolution in HIV is out in eLife (see also the nice highlight in Nature Eco Evo). Lane Warmbrod from the Institute for Public Health Genetics joins the lab for a rotation. Welcome, Lane!
- July 2021: Maya Lewinsohn presents her research on phylodynamic applications in cancer at SMBE 2021. Nice work, Maya!
- June 2021: The lab opens in the Genome Sciences Department at the University of Washington. Elena Romero joins as the lab's first graduate student. Welcome, Elena!
Joining the lab
Postdoctoral fellowsThe Feder Lab at the University of Washington is hiring postdoctoral fellows.
Broadly, the goals of the lab are to understand how spatial structure shapes rapid evolutionary processes, and develop approaches to leverage spatial information to better understand when and how populations will evolve. Within that, we are focusing on two specific research directions:
- Leveraging phylogenetics to understand tumor evolution and progression through time and space.
- Pairing models of viral dynamics and clinical sequencing data to understand the evolution of viral multi-drug resistance evolution in spatially and temporally-heterogeneous environments.
- Develop your own ideas aligned with the direction of the lab.
- Collaborate with other scientists from the lab, the Department of Genome Sciences, the Seattle scientific community and more broadly.
- Mentor students at the graduate, undergraduate and high school level
- Grow your own research program and plan for the next stages of your career.
PhD studentsThe lab accepts graduate students through the Genome Sciences and Molecular and Cellular Biology graduate programs. Prospective graduate students are very welcome to get in touch with questions about the lab, although this is not required to gain admittance to the program. Applications are due Dec 1.
Currently a grad student in GS or MCB interested in a rotation? Feel free to reach out to chat about project ideas!
Undergraduate studentsUndergraduate students with an interest in computational biology, mathematical modeling of biological systems, and/or evolutionary genomics are encouraged to get in touch regarding potential projects. Please send an email explaining why you're interested in the lab's work along with a CV/resume touching on any relevant experience or coursework (esp. programming) to affeder (at) uw.edu.
E-mail: affeder (at) uw.edu
We're located in Foege Hall S103 in the Department of Genome Sciences.
You can find a current and complete list of publications on Google scholar.
Understanding patterns of HIV multi-drug resistance through models of temporal and spatial drug heterogeneity (2021)
[paper in eLife, highlight in Nature Eco Evo]
Alison Feder, Kristin Harper, Chanson Brumme, Pleuni Pennings
The clarifying role of time series data in the population genetics of HIV (2021)
[paper in PLOS Genetics]
Alison Feder, Pleuni Pennings, Dmitri Petrov
Evolutionary dynamics in structured populations under strong population genetic forces (2019)
[paper in G3]
Alison Feder, Pleuni Pennings, Joachim Hermisson*, Dmitri Petrov*
The relationship between haplotype-based FST and haplotype length (2019)
[paper in Genetics, video abstract]
Rohan Mehta, Alison Feder, Simina Boca, Noah Rosenberg
Within-patient HIV mutation frequencies reveal fitness costs of CpG dinucleotides, drastic amino acid changes and G->A mutations (2018)
[paper in PLOS Genetics]
Kristof Theys*, Alison Feder*, Maoz Gelbart*, Marion Hartl, Adi Stern, Pleuni Pennings
High resolution spatio-temporal assessment of SHIV evolution reveals a highly dynamic process within the host (2017)
[paper in PLOS Pathogens, video abstract]
Alison Feder, Christopher Kline, Patricia Polacino, Mackenzie Cottrell, Angela Kashuba, Brandon Keele, Shiu-Lok Hu, Dmitri Petrov, Pleuni Pennings*, Zandrea Ambrose*
More effective drugs lead to harder selective sweeps in the evolution of drug resistance in HIV-1 (2016)
[paper in eLife, video abstract]
Alison Feder, Soo-Yon Rhee, Susan Holmes, Bob Shafer, Dmitri Petrov* and Pleuni Pennings*
The population genetics of drug resistance evolution in natural populations of viral, bacterial and eukaryotic pathogens. (2016)
[paper in Molecular Ecology]
Ben Wilson*, Nandita Garud*, Alison Feder*, Zoe Assaf*, and Pleuni Pennings
Identifying Signatures of Selection in Genetic Time Series (2014)
[paper in Genetics]
Alison Feder*, Sergey Kryazhimskiy*, Joshua Plotkin
LDx: estimation of linkage disequilibrium from high-throughput pooled resequencing data.
[paper in PLOS One, download LDx]
Alison Feder, Dmitri Petrov, Alan Bergland
Natural selection affects multiple aspects of genetic variation at putatively neutral sites across the human genome. [paper in PLOS Genetics]
Kirk Lohmueller, Anders Albrechtsen, Yingrui Li, Su Yeon Kim, Thorfinn Korneliussen, Nicolas Vinckenbosch, Geng Tian, Emilia Huerta-Sanchez, Alison Feder, Niels Grarup, Torben Jorgensen, Tao Jiang, Daniel R. Witte, ... , Rasmus Nielsen
- Video abstract for 'The Relationship Between Haplotype-Based FST and Haplotype Length':
- Video abstract for 'A spatio-temporal assessment of simian/human immunodeficiency virus (SHIV) evolution reveals a highly dynamic process within the host':
Alison Feder (she/her)Principal investigator [CV]
affeder (at) uw.edu
Elena RomeroGenome Sciences PhD student
Elena received her BS in Mathematical and Computational Biology at Harvey Mudd College. She is currently working to quantify patterns of intrapatient HIV recombination in time series data.
You? Learn more about joining the lab.
Maya LewinsohnGenome Sciences & MSTP student
Maya is leading a project in collaboration with the Feder lab to infer modes of tumor growth from cancer phylogenetic data.
Laura Baquero GalvisMCB PhD rotation student
Laura received her BS in Biology at Metropolitan State University of Denver. She is currently a graduate student in the Molecular and Cellular Biology program, and her rotation project involves creating a computational model to understand the spatial heterogeneity of HIV antiretrovirals.
Lane WarmbrodPublic Health Genetics PhD rotation student
Lane received her MS in Experimental Pathology at the University of Texas Medical Branch and MPH in Biosecurity at Saint Louis University. She is currently a PhD student in Public Health Genetics.
Hunter ColegroveGenome Sciences rotation student
Hunter received his BA in Biochemistry from the University of Washington. During his rotation, Hunter developed a pipeline to call SNVs from spatial transcriptomics data.
We organize two journal clubs focused on the evolution and genomics of cancer and HIV.