PEQG – Genes to Genomes https://genestogenomes.org A blog from the Genetics Society of America Thu, 01 Feb 2024 23:34:00 +0000 en-US hourly 1 https://wordpress.org/?v=6.6.2 https://genestogenomes.org/wp-content/uploads/2023/06/cropped-G2G_favicon-32x32.png PEQG – Genes to Genomes https://genestogenomes.org 32 32 TAGC 2024 Early Career Award Winners https://genestogenomes.org/tagc-2024-early-career-award-winners/ Thu, 01 Feb 2024 15:30:01 +0000 https://genestogenomes.org/?p=86655 GSA is pleased to announce the winners of the early career awards presented at The Allied Genetics Conference 2024. These awards are specific to particular TAGC communities and recognize early career scientists’ outstanding work on their respective research organisms. The awardees will present their talks in keynote sessions at TAGC 2024. 

Don’t miss the opportunity to hear these outstanding scientists discuss their work. Access the full conference schedule online.


C. elegans 

Sydney Brenner Award

Sneha Ray 

Fred Hutchinson Cancer Research Center  

The Sydney Brenner Dissertation Thesis Award is presented to a graduate student who has completed an outstanding PhD research project in the area of genetics and genomics of C. elegans.


Drosophila 

Larry Sandler Award

Sherzod Tokamov

University of California, Berkeley

The Larry Sandler Award is presented to outstanding recent graduates who have completed a PhD in an area of Drosophila research. The award serves to honor Dr. Sandler for his many contributions to Drosophila genetics and his exceptional dedication to the training of Drosophila biologists. 


Mammalian 

IMGS President’s Award

Jason Bubier

The Jackson Laboratory for Mammalian Genetics

This new award, the IMGS President’s Award, is presented to an early career scientist in recognition of their exceptional accomplishments in independent research in mammalian genetics. The award celebrates their contributions both to the IMGS and the field of genetics as a whole.


Population, Evolutionary and Quantitative Genetics (PEQG) 

James F. Crow Early Career Researcher Award

Olivia Harringmeyer

Harvard University

The James F. Crow Early Career Researcher Award is presented to students and recent PhDs conducting PEQG research. The award serves to honor Professor James F. Crow and his numerous, impactful contributions to the field of genetics. 


Yeast 

Angelika Amon Award

Xiaoxue Snow Zhou 

New York University

The Angelika Amon Award is presented to an outstanding recent PhD graduate. The award serves to honor Dr. Amon for her many discoveries through the use of yeast genetics, and her exceptional dedication to training and mentorship.


Zebrafish 

International Zebrafish Society Genetics Trainee Award

Mollie Sweeny 

Duke University 

The International Zebrafish Society Genetics Trainee Award recognizes excellence in research, in particular discoveries leading to significant scientific or technological advances through the use of zebrafish genetics.

]]>
New members of the GSA Board of Directors: 2024–2026 https://genestogenomes.org/new-members-of-the-gsa-board-of-directors-2024-2026/ Thu, 14 Dec 2023 18:14:12 +0000 https://genestogenomes.org/?p=86404 We are pleased to announce the election of four new leaders to the GSA Board of Directors: 2024 Vice President/2025 President Brenda Andrews Professor, University of Toronto It’s an honor to continue my association with the Society by serving as Vice President of the Board of Directors. I have broad knowledge of the ongoing activities…]]>

We are pleased to announce the election of four new leaders to the GSA Board of Directors:

2024 Vice President/2025 President

Brenda Andrews

Professor, University of Toronto

It’s an honor to continue my association with the Society by serving as Vice President of the Board of Directors. I have broad knowledge of the ongoing activities of the Society and see more opportunities for expanding the GSA profile internationally, including outreach to scientists in geographic regions underserved by major societies. The current International Seminar Series and this year’s International C. Elegans Conference in Glasgow are great examples of international outreach, and these types of activities should be expanded.

I will prioritize support for early- and mid-career researchers, in recognition of the challenges they face. GSA can help scientists by providing mentorship, training, and increased advocacy efforts whether for funding or communicating the value of basic research. It is important that the next generation of scientists see value in the activities supported by the Society, including our journals, which face challenges in light of the rapidly evolving landscape of academic publishing. Here, we must continue to foster relationships with authors, improving the visibility of their work, and helping to raise the profiles of our journals. All of our work must be considered in the context of GSA’s ongoing commitment to inclusivity. Here, the Society may wish to work with other groups to enable access to genetics and genomics research by young people from under-represented groups. I found that a program I started at the Donnelly Centre that supported visits to labs by local high school classes from less privileged parts of Toronto was very impactful.

Times have changed and so must GSA. I hope to learn from and listen to you as we shape GSA together.

Director

Arun Sethuraman

Associate Professor, San Diego State University

I am honored to be elected to the GSA Board of Directors. I have served as an Associate Editor at G3: Genes|Genomes|Genetics since 2017 and on GSA’s Conference Committee since 2021 as a representative of the population, evolutionary, and quantitative genetics group, and my work includes contributions to a recent training grant submitted to fund early-career and historically excluded geneticists attending TAGC 2024. I look forward to serving the GSA membership in an active Directorial role. As an early-career researcher at a Minority Serving Institution, I see this as an invaluable opportunity for me to be the voice of a largely underrepresented group of researchers in the Society. I am thrilled to have this opportunity to join a dedicated and diverse team of geneticists, editorial board members, and Society staff who are actively working to change the face and representation of our field.

My commitment to serving on GSA’s Board comes with a push to address five key issues that are close to my heart: (1) developing important training resources to actively involve undergraduates in genetics and genomics research as part of GSA’s catalog of activities and conferences; (2) changing how we teach fundamentals of genetics with exclusionary language by organizing a GSA community-wide effort to crowdsource and develop a new teaching paradigm for topics such as transmission, sex determination, polygenic selection, and genome-wide association studies; (3) interfacing with the equity and inclusion and conference committees in continuing to assess GSA’s membership demographic to build actionable items to increase participation of a diverse audience at all GSA conferences and to recruit and train a diverse group of editors, reviewers, and members; (4) actively featuring methods tutorials and blurbs of published work on the Genes to Genomes blog, specifically highlighting the work of early-career researchers, graduate and undergraduate students; and (5) increasing GSA’s representation at undergraduate and minority-focused conferences (e.g. SACNAS meetings, ABRCMS, Beckman Symposia).

Director

Eyleen O’Rourke

Associate Professor, University of Virginia

I bring to this role a strong background in molecular genetics research, having published in reputable journals, and presented my work at national and international conferences. Additionally, my experience as a teacher and mentor has enriched my understanding of the educational needs within our community. I pledge to collaborate with fellow board members and the broader GSA membership to advance our shared goals. I will listen to your feedback, actively seek your input, and work hard to represent your interests. I humbly request your support in this endeavor.

My work will be grounded in three core principles:

  1. Advancing Genetics Research: I believe that supporting and promoting cutting-edge genetics research is core to our society’s mission. I will actively foster collaboration and knowledge sharing among GSA members. I propose initiatives such as promoting the selection of unpublished work for oral presentation at GSA-organized conferences. Additionally, I will advocate for increased research funding and opportunities, catering to the needs of both early-career and established researchers.
  2. Education and Outreach: Genetics should transcend the confines of the laboratory. In an era where the public does not trust lifesaving vaccines, I am committed to enhancing the society’s educational initiatives. I will work on programs that promote genetics literacy and support science education at all levels. By bridging the gap between scientific discoveries and public understanding, we can strengthen our society’s impact.
  3. Diversity and Inclusion: Science works at its best when it reflects the diversity of our broader community. As a first-generation high-school graduate and Latina, I have dedicated the past decade to learn, teach, and champion inclusive research and teaching practices. I have promoted minorities both locally and internationally. I pledge to carry this dedication into GSA, advocating for programs that support underrepresented groups and nations in genetics. I will work diligently to foster an inclusive environment where every voice is not only heard but valued.

Together, we can advance genetics research, education, and inclusivity. Thank you for consideration, and I look forward to the opportunity to serve you.

Director

Jason Stajich

Professor, University of California, Riverside

I am honored to have the opportunity to serve on the Board of Directors of GSA. The Society has enabled many opportunities in my career, and I am eager to contribute back. I first became a GSA member in graduate school and was completely hooked on the community and research after attending my first Fungal Genetics conference. I have served as an Associate Editor at GENETICS since 2018, and previously contributed to conferences by sitting on the Neurospora and Fungal Genetics Policy Committees. I am currently a Professor in the Department of Microbiology and Plant Pathology where I have taught in the fields of Genomics, Microbiology, and Bioinformatics for the past 14 years. I currently serve as Vice Chair of my department and previously have served the campus faculty as Chair of the Academic Senate and as chair of the Graduate Council. I am excited to contribute to the Society’s efforts in building training and mentorship for early career scientists, helping shape the advocacy for science and genetics in funding and policy decisions, and providing perspectives on the community’s needs to advance new research systems and questions.

As a member of the Board, I will continue to champion the value and importance of diverse research systems and diverse research communities to address fundamental understandings of genetics and biology. I am an omnivore of biological research systems and believe there are strengths in a collection of computational and experimental approaches across a variety of organisms. My own draw to science was found in the satisfaction of problem solving, and I will contribute my efforts to the Society as we consider different problems such as the public perception of science, retaining and recruiting a broad representation of individuals to work in our field, or the creativity needed in how societies navigate changes in journal publication strategies. The GSA Journals have been a home for my publications and the conferences and members have been a strong and supportive community for my research and development. If elected, I would dedicate the time and energy to help sustain and grow our society.

]]>
GENETICS welcomes new editor Konrad Lohse https://genestogenomes.org/genetics-welcomes-new-editor-konrad-lohse/ Mon, 11 Sep 2023 14:01:00 +0000 https://genestogenomes.org/?p=86248 A new associate editor is joining GENETICS in population and evolutionary genetics. We’re excited to welcome Konrad Lohse to the editorial team. Konrad LohseAssociate Editor Konrad Lohse is a population geneticist interested in learning about evolution in natural populations from genomic data. After a BSc at the University of St Andrews, he obtained a PhD…]]>

A new associate editor is joining GENETICS in population and evolutionary genetics. We’re excited to welcome Konrad Lohse to the editorial team.

Konrad Lohse headshot

Konrad Lohse
Associate Editor

Konrad Lohse is a population geneticist interested in learning about evolution in natural populations from genomic data. After a BSc at the University of St Andrews, he obtained a PhD at Edinburgh University under the mentorship of Nick Barton and Graham Stone working on inference of population history. Konrad is currently a Senior Lecturer at Edinburgh University, and he leads a research group that combines theoretical work on the coalescent with genomic studies of adaptation, chromosome evolution and speciation in insects (including various species of butterflies and Drosophila). His group has developed a coalescent-based method to scan genomes of recently diverged taxa for barriers to gene-flow.

]]>
GENETICS welcomes new editor Thomas Lenormand https://genestogenomes.org/genetics-welcomes-new-editor-thomas-lenormand/ Wed, 06 Sep 2023 19:00:00 +0000 https://genestogenomes.org/?p=86250 A new associate editor is joining GENETICS in the population and evolutionary genetics section. We’re excited to welcome Thomas Lenormand to the editorial team. Thomas Lenormand Associate Editor Thomas Lenormand is Centre National de la Recherche Scientifique research director at the CEFE laboratory. He is an evolutionary geneticist, combining mathematical theory, statistical developments, laboratory experiments,…]]>

A new associate editor is joining GENETICS in the population and evolutionary genetics section. We’re excited to welcome Thomas Lenormand to the editorial team.

Thomas Lenormand headshot

Thomas Lenormand

Associate Editor

Thomas Lenormand is Centre National de la Recherche Scientifique research director at the CEFE laboratory. He is an evolutionary geneticist, combining mathematical theory, statistical developments, laboratory experiments, and field work. His work covers a wide range of issues at the intersection of evolution, genetics, and ecology. He is mainly interested in adaptation, the evolution of genetic systems (sex, asex, meiosis, recombination, sex chromosomes) and the effect of mutations. He was an editor and an associate editor of several evolutionary biology journals, twice an European Research Council laureate, and a Harvard Radcliffe fellow. He has received several awards, including the Dobzhansky Prize from the Society for the Study of Evolution.

]]>
#PEQG22 GSA Poster Award Winners https://genestogenomes.org/strongpeqg22-gsa-poster-award-winners-strong/ Thu, 07 Jul 2022 15:11:00 +0000 https://genestogenomes.org/?p=80306 Congratulations to all the winners of poster awards at the 2022 Population, Evolutionary, and Quantitative Genetics Conference! Undergraduate Students First Place: Rachel EderArizona State UniversityPoster Title: Understanding the heterogeneity in gene regulatory responses to misfolded protein toxicity Second Place: Doran GoldmanStanford UniversityPoster Title: Effect of inoculation dose on colonization success in gut-derived microbial communities Graduate…]]>

Congratulations to all the winners of poster awards at the 2022 Population, Evolutionary, and Quantitative Genetics Conference!


Undergraduate Students

First Place: Rachel Eder
Arizona State University
Poster Title: Understanding the heterogeneity in gene regulatory responses to misfolded protein toxicity

Second Place: Doran Goldman
Stanford University
Poster Title: Effect of inoculation dose on colonization success in gut-derived microbial communities

Graduate Students

First Place: Elena Romero
University of Washington
Poster Title: High viral load is associated with elevated recombination rate in intra-host HIV populations.

Second Place: Maike Morrison
Stanford University
Poster Title:  FSTruct: An FST-based tool for quantifying ancestry variability

Third Place: Atoosa M Samani
University of Utah
Poster Title: Unravelling the Genetic Architecture of Rolling Behavior in the Domestic Pigeon (Columba livia)

]]>
The 2022 PEQG session chairs offer a delightful blend of breadth and depth https://genestogenomes.org/the-2022-peqg-session-chairs-offer-a-delightful-blend-of-breadth-and-depth/ Tue, 15 Mar 2022 14:53:08 +0000 https://genestogenomes.org/?p=78165 Guest post by C Brandon Ogbunu. 2022 marks the return of the Population, Evolutionary, and Quantitative Genetics (PEQG) Conference, organized by the Genetics Society of America. Part of the meeting’s popularity stems from being one of the few conferences that brings together leading thinkers in subfields of genetics that don’t typically overlap, across a range of…]]>

Guest post by C Brandon Ogbunu.

2022 marks the return of the Population, Evolutionary, and Quantitative Genetics (PEQG) Conference, organized by the Genetics Society of America. Part of the meeting’s popularity stems from being one of the few conferences that brings together leading thinkers in subfields of genetics that don’t typically overlap, across a range of model organisms, united by methods and perspectives.

The meeting, which will take place June 7-10 in Pacific Grove, CA, at Asilomar Conference Grounds, is well-known for its structure: a combination of keynote addresses, awards, and short talks of various kinds. One of the key aspects of this structure is the session chairs: junior scientists who have established themselves as leaders in the various areas of population, evolutionary, and quantitative genetics. During the meeting, they each chair a session full of talks, and give 30-minute talks of their own during the final keynote session. The session chairs provide an opportunity for us to view the present and future of the field.

The 2022 session chairs promise to deliver on this tradition, featuring a tremendous lineup of thinkers who study problems as diverse as speciation genomics in plants to epistasis in human genomic data sets. This specific collection of speakers displays both breadth and depth, and so the chair keynote session promises to excite.

Below I will highlight these session chairs, commenting briefly on why I am personally so excited to hear about their work.

Nancy Chen

Evolutionary biology is, in part, a science that is defined by information from the past, but how do we use it to ask questions about contemporary evolution in natural populations? These are the questions of the “Pop Gen Chen Lab,” run by Nancy Chen. The lab addresses questions and utilizes tools to think about contemporary questions in short-term evolution, and how genetic variation is maintained in contemporary populations. In addition, the Chen lab makes use of the Florida Scrub Jay (a very compelling and well-studied system) to study population decline. The Chen lab has also generated an extremely useful list of resources on issues related to diversity, equity, and inclusion, and continues to be a leading voice on these matters in the population genetics community. 

Lorin Crawford

Though he was raised in southern California, Lorin Crawford will come to PEQG from balmy New England, where his research program is sprawled out between Microsoft Research in Boston and Brown University (in Providence) where he is the RGSS Assistant Professor. It is difficult to fully capture the richness of his research program. He utilizes advanced statistical and machine learning approaches to directly address provocative questions in population genetics. For example, he has pioneered statistical tests that can be used to detect pairwise epistasis between mutations in large genomic data sets. In addition, his work dissects the architecture of complex traits. Lastly, Crawford has recently begun to explore the ethics of genomics evolution. Recent work in this realm has challenged notions that are used to characterize populations, such as “transethnic.”

Rafael Guerrero

From North Carolina comes Rafael Guerrero, an Assistant Professor at North Carolina State University. He runs a program that develops tools that have already transformed our approach to classical questions in population and evolutionary genetics and explores the questions directly relevant to practical problems in biomedicine and bioengineering. In the former sense, Guerrero has done groundbreaking work on chromosome evolution and hybrid incompatibilities in light of speciation genetics, both central and critical questions in evolutionary genetics. In the latter sense, Guerrero’s mastery of theoretical tools has allowed him to explore areas such as the genomics of adverse pregnancy outcomes, and the physiological determinants of epistatic interactions as they manifest in the evolution of antibiotic resistance.

Priya Moorjani

The Genetics Society of America is well-known for its commitment to model systems research and has long championed its importance. But it also recognizes the importance of human genetics and evolutionary biology, not only because we…are humans, but also because human evolution is an amazing problem space for cutting-edge questions in evolutionary and population genetics. Few scientists are doing more exciting work in this area than Priya Moorjani. Moorjani uses statistical and computational approaches to understand the role of genetic variation in human evolution, demography, and mapping disease risk alleles at the University of California, Berkeley. Moorjani has also investigated fundamental questions in primate evolution, such as the proper estimation of mutation rates. Moorjani has mastered the art of transforming a species that we all care about–Homo sapiens–into a model system in evolutionary genetics. 

Rori Rohlfs

As Assistant Professor at San Francisco State University, Rori Rohlfs won’t need to travel especially far to get to Asilomar, but everything with Rori is an intellectual expedition. Rohlfs runs an exciting program that has examined everything from the evolution of gene regulation to critical statistical questions relevant to genomic testing and forensics. Rohlfs has accomplished this while also being a widely recognized teacher and mentor. Lastly, Rohlfs was one of the corresponding authors on an outstanding 2019 study published in GENETICS that analyzed early population genetics literature and identified the many women that were often denied proper credit for their participation.

Daniel Runcie

When I teach evolution, I often discuss a 2018 study that estimated the biomass of living things on earth, organized by different taxa. Though I do not study plants, I often use it to explain that when it comes to life on earth, plant life is the heavyweight champion. Daniel Runcie runs a thrilling research program that attempts to understand how and why plants are so successful, and especially questions related to genetic variation and phenotypic plasticity. The Runcie lab attempts to identify pathways and networks related to how plants respond to a dynamic environment. One of the reasons that plants have been so successful is their ability to respond to change. The Runcie lab uses a host of tools—statistical, network, and ecophysiological—to understand these questions.

Learn more about the #PEQG22 Session Chairs, as well as Invited Speakers, on the conference website. Registration is open now.


C. Brandon Ogbunu

About the author

C. Brandon Ogbunu is Assistant Professor in the Department of Ecology and Evolutionary Biology at Yale University and one of the organizers of the 2022 Population, Evolutionary, and Quantitative Genetics Conference.

]]>
Hybrid (conference) vigor https://genestogenomes.org/hybrid-conference-vigor/ Wed, 15 Sep 2021 09:05:04 +0000 https://genestogenomes.org/?p=76611 Four GSA communities are excited to meet in person in 2022 — and to experiment with hybrid conferences that combine the benefits of online and in-person meetings. After two years of online meetings of all kinds, we are thrilled to return to scientific conversations in person! In 2022, many of us will be together again,…]]>

Four GSA communities are excited to meet in person in 2022 — and to experiment with hybrid conferences that combine the benefits of online and in-person meetings.


After two years of online meetings of all kinds, we are thrilled to return to scientific conversations in person! In 2022, many of us will be together again, enjoying the science—and the company—at our regular in-person conferences with virtual attendance options. #Fungal22 and #PEQG22 will take place at Asilomar in Pacific Grove, California and #Dros22 will be in San Diego, California. #Yeast22 will be held in person at a location to be announced soon. All four organizing committees are working hard on creating can’t-miss programs to reunite and recharge their communities.

A few of the things we have missed most about scientific conferences “in real life” include meeting new colleagues at random, building stronger relationships with old colleagues, having unscheduled but in-depth conversations, discovering amazing talks far outside our specialties, and being able to dedicate focused time to the meeting away from everyday life. The intellectual buzz of several intense days of science at a GSA meeting is an enriching experience that has immediate results: new ideas, new collaborations, new jobs, new friends. 

Of course, we learned a lot from our experiments with online conferences in 2020 and 2021. For example, having the talks recorded ended the ubiquitous fear of missing out on something exciting in a concurrent session. And more people were able to ask questions via chat than was ever possible via a microphone. Most importantly, we learned that the virtual format could be more inclusive, lowering barriers to participation.

So, in 2022, GSA is leading the way in conference innovation  once again, this time with offering virtual attendance options alongside the full in-person conference, including opportunities to present online and access talk recordings, posters, and professional development events. While there is no way for us to completely replicate the in-person experience online, we hope that these select virtual options will translate to new “hybrid vigor” for GSA conferences by opening the experience to remote participants and enhancing the experience for those on site.

This flexibility seems even more critical while we continue to endure the uncertainty and risks of a pandemic. Because we understand that making future travel plans is difficult right now, we are adopting a flexible registration policy that will allow registrants to change from the in-person to virtual options (or vice versa) up until the month before the meeting.

As scientists, we all know that experiments come with costs. In this case, the new format has much higher labor, contractor, equipment, and technology costs than either an in-person or an online-only event. Note that the 2022 conferences are not expected to break even.

The past 18 months of conference experiments have been financially costly for the GSA, but also rewarding. Crucially, we have invested in these trials in order to maintain community connections and scientific contributions in a time of need. Despite the anticipated losses, we consider the virtual attendance option in 2022 to be an important step in learning how to balance the needs of in-person and online participants. We are excited to see what happens and to continue to evolve how scientists meet and exchange ideas.

2021 GSA Executive Committee

Hugo Bellen, President

E. Jane Hubbard, Vice-President

Denise J. Montell, Immediate Past President

Erika L. Matunis, Secretary

Michael Buszczak, Treasurer

Steven Munger, Member at Large

Tracey DePellegrin, GSA Executive Director

]]>
James F. Crow Award talks at TAGC 2020 https://genestogenomes.org/james-f-crow-award-talks-at-tagc-2020/ Fri, 19 Jun 2020 21:03:00 +0000 https://genestogenomes.org/?p=77453 The James F. Crow Early Career Researcher Award recognizes outstanding achievements by students and recent PhDs presenting their work at the Population, Evolutionary, and Quantitative Genetics (PEQG) Conference, which was part of TAGC Online in 2020. The 2020 winner and finalists for this prestigious PEQG award spoke in a high-profile session at the conference. Check…]]>

The James F. Crow Early Career Researcher Award recognizes outstanding achievements by students and recent PhDs presenting their work at the Population, Evolutionary, and Quantitative Genetics (PEQG) Conference, which was part of TAGC Online in 2020. The 2020 winner and finalists for this prestigious PEQG award spoke in a high-profile session at the conference. Check out the recording below!

Winner

Carl Veller, Harvard University 

Finalists

Cara Brand, University of Pennsylvania

Moisés Exposito-Alonso, Stanford University

Pavitra Muralidhar, Harvard University

Yuval Simons, Stanford University

]]>
Katherine Xue studies how the flu evolves inside you https://genestogenomes.org/katherine-xue-studies-how-the-flu-evolves-inside-you/ Thu, 09 Aug 2018 14:00:32 +0000 https://genestogenomes.org/?p=21801 The recipient of the 2018 Crow Award reveals details of flu evolution at the smallest —and largest—scales. For many viral diseases, a vaccine can provide lifelong protection. But for flu, you need a new shot every year. The influenza virus evolves so fast it presents a constantly moving target for both our immune systems and…]]>

The recipient of the 2018 Crow Award reveals details of flu evolution at the smallest —and largest—scales.


For many viral diseases, a vaccine can provide lifelong protection. But for flu, you need a new shot every year. The influenza virus evolves so fast it presents a constantly moving target for both our immune systems and public health authorities, fueling epidemics like the particularly bad season we just endured. With over 30,000 people hospitalized in the United States alone this season, the flu provides a dramatic reminder of the importance of understanding evolutionary dynamics.

Katherine Xue, a graduate student at the University of Washington, is revealing the mechanics of influenza evolution on scales ranging from an individual person up to the entire planet. Xue was awarded the 2018 James F. Crow Award for Early Career Researchers for her doctoral work on the subject after a presentation at the Population, Evolutionary, and Quantitative Genetics Conference in May.

In a special session of talks by Crow Award finalists, Xue spoke about using deep sequencing to examine diversity in flu virus populations.

“Up until recently, we were only able to look at the average genetic identity across the millions or billions of flu viruses in a single infection,” says Xue. “We’ve used deep sequencing to show that within a single infection there are fast evolutionary dynamics that have been invisible to previous technologies.”

Xue approaches clinical topics with the conceptual tools developed by evolutionary and population geneticists. Linking ideas across fields is characteristic of Xue, says her mentor Jesse Bloom (Fred Hutchinson Cancer Research Center / University of Washington), whether it’s between medicine and evolutionary theory or between science and the humanities.

“What makes Katherine stand out is her ability to think about big scientific concepts and connect ideas,” says Bloom. “She’ll see and connect ideas in ways that I can’t.”

Viral cooperation

When Xue first rotated in Bloom’s lab, she was working on a molecular virology project about how a particular viral protein binds to a cell. In the course of examining sequence databases, she noticed the mutation she was studying was often ambiguously annotated.

Inspired by this hint of population diversity, she wondered whether the two viral variants might interact with each other. She was able to establish that the mutation tended to occur alongside the wild type version within a population; the mutation was deleterious to virus reproduction on its own but beneficial when mixed with wild-type. This example of cooperation suggests that interactions between different variants within flu populations can be important factors in virus evolution.

A glimpse of evolution in action

But can evolution be detected within the virus population of a single individual? Xue was drawn to the question of how global flu evolution traces back to the founding infections in which each mutation must first arise.

“I was intrigued because it was hard to imagine how this works,” says Xue. “Flu infections are very short; there’s not a lot of time for a new mutation to reach frequencies large enough to ensure it makes it over to the next infected person.” In the language of population geneticists, flu populations are repeatedly subjected to extreme bottlenecks. But observing such rapid evolution in action is extremely challenging.

Xue and her colleagues in the Bloom lab used a unique approach to get around this problem. They partnered with clinicians Michael Boeckh and Steve Pergam at the Fred Hutchinson Cancer Research Center, who had collected samples from four immunocompromised patients over the course of their months-long flu infections. Deep sequencing these samples gave them an in-depth view of a process that would normally be finished within days in a person with healthy immune defenses.

“I initially had doubts that this project would show us anything interesting or be worth doing,” says Bloom. “But Katherine is very independent and persistent, and she kept going despite my occasional words of discouragement.”

The results were dramatic. Over the span of about two months, there was a substantial amount of flu evolution within each patient. Mutations arose regularly, fluctuated in frequency, and even became fixed in the population in a few cases. They also saw evidence that some of these changes are due to selection. The same mutations would often arise independently and then rise to substantial frequencies in multiple patients, suggesting these particular changes were adaptive.

Remarkably, the mutations that arose repeatedly in different patients were sometimes the same mutations that spread through the global flu population within the next decade. The immunocompromised patients seemed to be microcosms of global evolutionary patterns. “We were astonished,” said Xue.

Most of these recurring mutations affect the part of the flu haemagglutinin protein that is most recognized by the host immune system, so the team hypothesizes that the changes help the flu escape host defenses.

These results raise many questions about how evolutionary dynamics interact across scales. How far do the conclusions generalize? Where and when do natural selection and genetic drift act? How do normal week-long infections generate enough diversity to fuel rapid global evolution? Could understanding these processes translate to better flu season predictions? Xue’s graduate research continues to explore flu evolution with these questions in mind.

Connecting ideas

The scientific big picture is never far from Xue’s mind, it seems. Alongside her thesis research, Xue is pursuing a certificate in science and technology studies, with a capstone project on the history of flu research. “I have really loved being part of the history, philosophy, and sociology of science community here,” she says. “It’s given me a lot of perspective that has been really enriching.”

A few years ago Xue helped start the UW Genomics Salon, which is a group of students and postdocs who take part in freeform discussions about the intersections of science and society. These discussions touch on policy, advocacy, communication, education, representation, law, art, and a host of other topics.

Bloom thinks Xue’s broad interests are yet another reflection of her creativity and ability to link ideas across fields. Before graduate school, she spent a few years working as a science writer for the Harvard Magazine. “She’s an exceptionally good science communicator and very dedicated to creating connections between science and other fields. It’s pretty awesome to have someone like that around!”

[youtube https://youtu.be/fTdaAwqdt0k&w=500&rel=0]

Watch #PEQG18 presentations from all the other  outstanding finalists for the Crow Award here.

]]>
Videos from PEQG18 Keynote and Crow Award sessions https://genestogenomes.org/videos-from-peqg18-keynote-and-crow-award-sessions/ https://genestogenomes.org/videos-from-peqg18-keynote-and-crow-award-sessions/#comments Thu, 28 Jun 2018 14:04:52 +0000 https://genestogenomes.org/?p=19060 Watch presentations from the conference, including talks from Katie Peichel and Jonathan Pritchard. Now that the dust has settled from the whirlwind of the first ever standalone GSA Population, Evolutionary, and Quantitative Genetics Conference (PEQG18), we’re delighted to be able to share the audio and synched slides from the Keynote and Crow Award sessions. We’re…]]>

Watch presentations from the conference, including talks from Katie Peichel and Jonathan Pritchard.


Now that the dust has settled from the whirlwind of the first ever standalone GSA Population, Evolutionary, and Quantitative Genetics Conference (PEQG18), we’re delighted to be able to share the audio and synched slides from the Keynote and Crow Award sessions.

We’re gratified too that attendees got so much of value from the conference. Many have approached GSA staff and the conference organizers with rave reviews of their experience, and, despite the usual growing pains of a new conference, the results from the attendee survey have also been overwhelmingly positive.

We’re excited to incorporate some of the lessons we’ve learned into planning the next PEQG. It will be held April 22–26, 2020 in the metro Washington, DC, area at The Allied Genetics Conference (TAGC20). PEQG will join the C. elegans, Drosophila, mouse, Xenopus, yeast, and zebrafish research communities for a mix of community-specific and cross-community sessions.

Stay tuned for more announcements on the upcoming conference and for several more PEQG18 blog reports in the coming weeks. Enjoy the talks below!

 

PEQG18 Keynotes

Jonathan Pritchard Stanford University/HHMI

Omnigenic Architecture of Human Complex Traits

Catherine Peichel University of Bern

Genetics of Adaptation in Sticklebacks

Trudy Mackay North Carolina State University

Context-Dependent Effects of Alleles Affecting Genetic Variation of Quantitative Traits COMING SOON

Finalists for the 2018 Crow Award for Early Career Researchers

Amy Goldberg UC Berkeley

A mechanistic model of assortative mating in a hybrid population

Emily Josephs UC Davis

Detecting polygenic adaptation in maize

Jeremy Berg Columbia University 

Population genetic models for highly polygenic disease

Katherine Xue University of Washington 

Evolutionary dynamics of influenza across spatiotemporal scales

Alison Feder Stanford University 

Intra-patient evolutionary dynamics of HIV drug resistance evolution in time and space

Emily Moore North Carolina State University 

Genetic variation at a conserved non-coding element contributes to microhabitat-associated behavioral differentiation in Malawi African cichlid fishes

 


Videos

Jonathan Pritchard 

[youtube https://youtu.be/H18k55ruCOY&w=500&rel=0]

Catherine Peichel

[youtube https://youtu.be/QRCcLixjUtc&w=500&rel=0]

Amy Goldberg 

[youtube https://youtu.be/kccUNkF7SgY&w=500&rel=0]

Emily Josephs 

[youtube https://youtu.be/CxQOrK9h6D4&w=500&rel=0]

Jeremy Berg

[youtube https://youtu.be/HqA1H24LPZc&w=500&rel=0]

Katherine Xue

[youtube https://youtu.be/fTdaAwqdt0k&w=500&rel=0]

Alison Feder

[youtube https://youtu.be/ntM0448h2lA&w=500&rel=0]

Emily Moore

[youtube https://youtu.be/aX4_HS0K1kA&w=500&rel=0]

]]>
https://genestogenomes.org/videos-from-peqg18-keynote-and-crow-award-sessions/feed/ 2