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 PhD program. Prospective graduate students, rotation students and postdoctoral fellows are encouraged to get in touch with Alison.

Research


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.

News


Joining the lab


Postdoctoral fellows

The 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:
  1. Leveraging phylogenetics to understand tumor evolution and progression through time and space.
  2. 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.
As a postdoctoral fellow, you will have the opportunity to
  1. Develop your own ideas aligned with the direction of the lab.
  2. Collaborate with other scientists from the lab, the Department of Genome Sciences, the Seattle scientific community and more broadly.
  3. Mentor students at the graduate, undergraduate and high school level
  4. Grow your own research program and plan for the next stages of your career.
Potential postdoctoral fellows are very much encouraged to get in touch. Generally the most useful emails will touch on your background and previous work, how our research interests may intersect, your timeframe for seeking a position and will include a copy of your CV. Informal inquiries very welcome.

PhD students

The lab accepts graduate students through the Genome Sciences graduate program. 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 interested in a rotation? Feel free to reach out to chat about project ideas!


Undergraduate students

Undergraduate 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 to affeder (at) uw.edu.

Contact


E-mail: affeder (at) uw.edu

We're located in Foege Hall S103 in the Department of Genome Sciences.

Publications


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

Media





  • Video abstract for 'More efficient drugs lead to harder sweeps in the evolution of drug resistance in HIV-1':
  • Team


    Alison Feder (she/her)

    Principal investigator [CV]
    affeder (at) uw.edu





    Elena Romero

    Genome 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.


    Lane Warmbrod

    Public 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 Colegrove

    Genome Sciences rotation student

    Hunter received his BA in Biochemistry from the University of Washington. He is currently a PhD student in the Department of Genome Sciences, and is working to understand prostate cancer evolution from spatial transcriptomics data.

    Collaborators


    Maya Lewinsohn

    Genome Sciences & MSTP student

    Maya is leading a project in collaboration with the Feder lab to infer modes of tumor growth from cancer phylogenetic data.



    You? Learn more about joining the lab.