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Feder Research Group in Evolutionary Dynamics

Our goal is to understand the dynamics of rapidly-evolving populations, especially viruses and bacteria 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.

Research

Evolutionary processes operating inside our bodies are responsible for a range of adverse disease outcomes, including drug resistance, immune escape, invasion of new tissue or cell types, and cancer initiation and progression. A greater understanding of the forces driving this evolution can inform therapeutic interventions, and diagnostic and preventative measures.

While the study of these populations is important for reasons related to human health, these populations also represent important systems for the study of evolution more broadly. Large population sizes, high mutation rates and strong selective pressures mean that these populations have the capacity to evolve rapidly. Because these populations can often also be sampled longitudinally, this gives us a rare opportunity to watch evolution in real time. Furthermore, because we can observe this evolution unfolding in parallel in multiple independent hosts, we have power to understand the generalizability of these processes. Despite the importance of rapid evolutionary processes, population genetics largely historically considered adaptation as a rare event, so quantitative understanding of these data can provide the substrate for new advances in evolutionary theory.


A key focus of the lab is in understanding the ways that the intra-host environment shapes evolutionary outcomes of these populations. Humans are not Eppendorf tubes - we’re heterogeneous and spatially structured across multiple levels of biological organization. These environments mediate biotic interactions within and between intra-host populations, shape population demography, and impose heterogeneous challenges for growth. With new opportunities to make spatially-explicit population measurements, we are now poised to develop new insights into how intra-host spatial structure drives disease outcomes.

Some of the interests of the lab include:
To address these questions, we use a combination of genomic analysis from clinically and experimentally-derived sources, evolutionary and population genetic modeling, and phylogenetics.

Here's a 15 minute video about some of the lab's interests that was up to date in January 2023:


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 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 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 (esp. programming) 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.
Detecting branching rate heterogeneity in multifurcating trees with applications in lineage tracing data (2024)
[paper on bioRxiv]

Yingnan Gao, Alison Feder

Elevated HIV viral load is associated with higher recombination rate in vivo (2024)
[paper in Molecular Biology & Evolution,
OUP press release]

Elena Romero, Alison Feder

Brain tropism acquisition: the spatial dynamics and evolution of a measles virus collective infectious unit that drove lethal subacute sclerosing panencephalitis (2023) [paper in PLOS Pathogens, Press: Mayo news, Fred Hutch Spotlight Article]

Iris Yousaf*, Will Hannon*, Ryan Donohue, Christian Pfaller, Kalpana Yadav, Ryan Didkan, Sanjay Tyagi, Declan Schroeder, Wun-Ju Shieh, Paul Rota, Alison Feder, Roberto Cattaneo
State-dependent evolutionary models reveal modes of solid tumor growth (2023)
[paper in Nature Ecology & Evolution, News & Views, This Week in Evolution (TWiEVO), This Week in Mathematical Oncology]
Maya Lewinsohn, Trevor Bedford, Nicola Müller*, Alison Feder*
Understanding patterns of HIV multi-drug resistance through models of temporal and spatial drug heterogeneity (2021)
[paper in eLife, highlight in Nature Ecol 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. Her work focuses on how HIV's intra-host demography impacts evolutionary forces like recombination and selection.

    Hunter Colegrove

    Genome Sciences PhD student

    Hunter received his BA in Biochemistry from the University of Washington. Hunter is developing models of cellular competition among epithelial cells.

    Yingnan Gao

    Postdoctoral Scholar

    Yingnan received his Ph.D. in Ecology and Evolutionary Biology at University of Virginia. He is currently working on identifying spatial and phylogenetic patterns in tumor through single-cell sequencing data.

    Alex Robertson

    MCB PhD Student (joint with Ben Kerr)

    Alex received his BS in Global Disease Biology from UC Davis and his MPH in Epidemiology of Microbial Diseases from the Yale School of Public Health. Alex is interested in how intra-cellular interactions (i.e., among viruses, plasmids) affect evolutionary change at the population level, particularly with respect to drug resistance.

    Tongqiu (Iris) Jia

    Genome Sciences PhD Student

    Iris received her BS in Bioinformatics at UC San Diego and MPH in Epidemiology at University of Washington. She is current investigating the dynamics and selection of intra-host Pseudomonas populations.

    Sam Hart

    Postdoctoral Scholar (joint with Kelley Harris)

    Sam received his PhD in Molecular and Cellular Biology from the University of Washington and his BS in Zoology from the University of Vermont. Sam is interested in mutation rate/spectra evolution within and between tumors.

    Yirui Chen

    Undergraduate researcher

    Yirui is an undergraduate at UW majoring in applied and computational math sciences and molecular biology. She is studying selection and recombination in intra-host Pseudomonas aeruginosa evolution.

    Linh Tran

    Postdoctoral Scholar

    Linh received her PhD in Genetics from the University of Arizona and her BA in Chemistry from Bryn Mawr College. She is interested in building and validating methods for inferring evolutionary parameters from cancer genomic data.

    Karl Young

    Genome Sciences Rotation Student

    Karl got his BA in Biology from Reed College in Portland, Oregon. In the past he's studied single-cell resolved host/virus interactions in brain tissue infected with rabies, with the additional goal of engineering viruses for reconstructing synaptic networks. During his rotation, Karl is developing computational tools to design lineage tracing experiments.

    Megan Taylor

    Genome Sciences Rotation Student

    Megan studied MCD Biology (B.S.) at the University of Washington. During her rotation, Megan is working to evaluate how epistasis and mutational availability affect HIV's adaptation to broadly neutralizing antibodies.
    You? Learn more about joining the lab.


    Alumni

    Allie Kreitman

    MSTP Rotation Student

    Nashwa Ahmed

    MCB PhD Rotation Student

    Maya Lewinsohn

    Collaborator/Lab friend

    Dylan Clark

    Undergraduate researcher (2022 - 2024)

    Laura Baquero Galvis

    MCB PhD rotation student (Winter 2022)

    Lane Warmbrod

    Public Health Genetics PhD rotation student (Fall 2021)

    Journal Clubs

    We organize two journal clubs focused on the evolution and genomics of cancer and HIV.
    All are welcome to join.