Postdoc in Evolutionary/Population Genomics – available immediately

Location: Whitehead lab, University of California Davis; remote work options will be considered.

Background Info: Our research group studies evolutionary change in human-altered environments. We seek applicants for a Postdoctoral Research Associate to study population genetic change through space and time in Pacific herring. The causes of the collapse of the Prince William Sound (PWS) Pacific herring stock are controversial, and the reasons for the lack of recovery remain a mystery. We hypothesize that interactions between the 1989 Exxon Valdez oil spill and a subsequent viral epidemic were influential. We have collected whole genome sequences from ~1,300 individual fish from across Alaska and across time (four times spanning three decades), and throughout the rest of their range, to explore genomic change associated with the collapse and the period since; with these data we seek to explore and test hypotheses about the causes and consequences of the collapse, and test hypotheses about the genetic basis of parallel local adaptation. This huge population genomics dataset is ready for the right candidate to make rapid progress. Data are collected, and curated; we have a filtered variant data set where summary population genetics statistics have been estimated. Collaborations are in place with scientists in academia and with State and Federal agencies. The ideal candidate has experience in population genetics, statistical genetics, and computational biology. We are especially interested in candidates with a passion for open science and for connecting their work to decision makers, the public, and the broader conservation biology and evolutionary biology communities. There is funding for one year, with possibility of extension. We are open to the candidate working remotely. Our group is committed to creating a safe, inclusive, diverse, optimistic, and equitable work environment.

Responsibilities: Contribution to analysis strategy, code development, data analysis and interpretation, review of relevant literature, preparation of project reports and manuscripts for publication in peer-reviewed journals, presentation at professional conferences.

Minimum qualifications: PhD in genetics, population biology, evolution, genome science, data science, or another relevant field.

Preferred qualifications: Preference will be given to applicants with 1) expertise in population genomics and computational biology; 2) strong communication and organizational skills; 3) can code in R and python and have an interest in transparent and reproducible science; and 4) strong publication records, or the potential for developing one. Our team believes in and values the power of diversity; candidates from groups that have historically been underrepresented in science are strongly encouraged to apply.

Salary: Commensurate with qualifications and experience.

Application: Interested candidates should submit:

  • a one‐page cover letter,
  • your CV, and
  • names and contact information of at least three references familiar with your work.

Please submit materials to Andrew Whitehead (awhitehead@ucdavis.edu) with “Popgen Postdoc” in the subject. Applications will be reviewed as they arrive, interviews will be over Zoom, and the position will remain open until filled. The position is available immediately, with preferred start dates between late spring and early summer 2021.

Email any questions to Andrew Whitehead (awhitehead@ucdavis.edu

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Origin story: Genomic and physiological mechanisms underlying skin plasticity during water to air transition in an amphibious fish

Dong, Y., T.S. Blanchard, A. Noll, P. Vasquez, J. Schmitz, S.P. Kelly, P.A. Wright, and A. Whitehead (2021). Genomic and physiological mechanisms underlying skin plasticity during water to air transition in an amphibious fishJournal of Experimental Biology.

Here is the origin story underlying the events and the science that led to this manuscript, which was a truly collaborative effort between multiple research labs including senior and junior scientists that spanned four nations. This all started with two co-incident serendipitous events. First, I (Andrew Whitehead) was invited to give a seminar talk at McMaster University (Ontario, Canada) by Graham Scott. Learning that I was going to be in the area, Pat Wright at the nearby University of Guelph (my alma mater) graciously invited me to give a seminar talk there too, and to meet with her research group. It was while meeting with Pat’s group that I learned of the mangrove rivulus and it’s extraordinary physiology: the only vertebrate self-fertilizing hermaphrodite (can create isogenic lines), amphibious, can live out of water for months, etc… I’ve always admired Pat’s research and had been keen to work with her; her group is world-renown for their experimental animal physiology work. And she was keen to see what our genomics tools could reveal about the inner workings of this extraordinary creature. So a tentative plan was hatched: Tessa Blanchard, a Masters student in Pat’s lab at the time, was doing some air-exposure experiments, and she would save us some tissues for transcriptomics. Serendipitous event number two: my colleague and my scientific hero George Somero had dropped me a line: A former postdoc of his, Yun-Wei Dong, now a professor in China, was seeking a home for his sabbatical, where he sought to build some skills and experience in transcriptomics. I had never met Yun-Wei, but a recommendation from George was good enough for me. Yun-Wei arrived in Davis about the same time that Tessa was sending us tissue samples – the team was shaping up. Yun-Wei dove head-first into making RNA-seq libraries under the guidance of lab manager Jen Roach, and we soon had a data set which provided the foundation for Yun-Wei’s quick mastery of bioinformatics skills; skills he eventually returned to China with, and embedded them within his own exciting research program, passing them on to his own students and colleagues. The data also provided a training opportunity for Picasso Vasquez, a talented undergraduate student in my lab, who ended up constructing the detailed GitHub repository that supports the transparency and reproducibility of this work. The RNA-seq data, coupled with Tessa’s physiology data, were lifting the hood on the amazing amphibious abilities of these fish, and we wanted to know more, particularly at the level of skin structure. Pat recommended her colleague Scott Kelly at nearby York University – like Pat, a core member of Canada’s cabal of famous comparative animal physiologists, and an expert in electron microscopy specializing in epithelial transport. After hearing about the experiment, and seeing some data, he was hooked. The team was growing. Tessa sent him tissues. Scott’s images were beautiful, and the discoveries were expanding. Of course more answers lead to more questions, so the team was to grow yet again. We wanted to get a sense of which proteins may have evolved in the ancestors of mangrove rivulus to support their unusual physiological abilities. The first person who came to mind was Wes Warren, an expert in comparative genomics – he and I had worked together on a study of comparative protein evolution including our Fundulus killifish. Wes was keen but too busy at the time, so recommended his close colleague Juergen Schmitz in Germany. I had never met Juergen, but a quick look at his outstanding record of research and a recommendation from Wes was all that was needed for me to try to convince Juergen to join our team. After a quick look at the data, Juergen and his student Angela Noll were on board – I was thrilled. What had started as a chance visit with Pat’s group and a tip from George Somero had grown into a collaborative integrative interdisciplinary research endeavor that wrapped around the world (though conference calls between California, Ontario, Germany, and China were challenging). I feel very fortunate to work with this outstanding group of individuals: they are all wonderful human beings, and badass scientists. It has solidified research collaborations and friendships that wrap around the globe. And it has been a stepping stone for several junior folks: Tessa is now a Ph.D. student in Trish Schulte’s lab a UBC, Picasso is a programmer in Titus Brown’s lab at UC Davis and is destined for graduate school, and Angela is a postdoctoral researcher at the German Primate Center. I am reminded that science is a product of teams of people, and serendipity plays a large role in how those teams come to be. The science that emerges is a product of good will, enthusiasm, creativity, hard work, and good communication. You never know when a chance event leads to a whole new research direction, which leads to a whole new group of friends and colleagues spread across the globe. And I am reminded that the work is nucleated by this extraordinary creature mangrove rivulus: ““There is a grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.” (Charles Darwin)

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Sara Boles is now officially Dr. Sara Boles!

Congratulations Sara on completing your Ph.D. in Pharmacology & Toxicology at UC Davis! Sara is now off to start postdoctoral research with Jackson Gross at Bodega Marine Laboratory. Some of Sara’s work was recently published in PNAS, and stay tuned for a couple more very cool upcoming papers on the interactive effects between ocean acidification, temperature, and diet, on developing red abalone; work with important implications for abalone conservation and sustainable aquaculture in the face of climate change. I’m seriously proud of this amazing scholar.

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Jane Park is now officially Dr. Jane Park!

Congratulations Jane on completing your Ph.D. in Genetics from UC Davis! Jane is now off to start her prestigious California Council on Science & Technology (CCST) Science Fellowship in Sacramento. Keep your eyes open for some very cool upcoming papers on the trans-generational impacts of oil exposures on killifish development, physiology, and transcriptome.

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A word on # BlackLivesMatter and Environmental Pollution

Though #BlackLivesMatter focuses on police racism and brutality, and that is where our attention needs to be, recent events bring to mind research in my chosen profession (Environmental Toxicology) clearly showing that pollution disproportionately kills African Americans

The evidence isn’t hard to follow…

There exist stark racial inequities in exposure to environmental pollution in the USA

Exposure to environmental pollution impairs health, e.g., cardiovascular & respiratory illness, diabetes, and birth defects.

African Americans suffer significantly more from cardiovascular & respiratory illness, diabetes, etc. than other ethnic groups in the USA.

Of relevance to other contemporary crises, these health disparities help explain why African Americans have increased risk of death from COVID-19

As argued by many, Environmental Justice and Social Justice are indeed intrinsically interconnected.

By working to tackle environmental pollution, we can relieve the pressure of yet another knee that has been pressing on the necks of African Americans for generations.

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First [self-quarantine] lab meeting of the quarter

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Health Plan for the New Coronavirus Outbreak – from the Lenski Lab

This is a good guide for those running or working in research labs (most points relevant for any workplace, in fact):

https://telliamedrevisited.wordpress.com/2020/02/29/the-lenski-lab-health-plan-for-the-new-coronavirus-outbreak/

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Andrew’s Talk at Evolution 2019 on YouTube

YouTube Video

Title: Evolutionary rescue from extreme chemical pollution enabled by recent adaptive introgression of highly advantageous haplotypes

Presenter: Andrew Whitehead

Co-authors: Elias Oziolor, Noah Reid, Sivan Yair, Kristin Lee, Jeffrey Miller, Sarah Guberman VerPloeg, Peter Bruns, Joseph Shaw, Cole Matson

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Postdoctoral Research Associate Position in Quantitative Genetics and Conservation Genetics

Location: UC Davis.

Background Info: A research team led by Andrew Whitehead and Nann Fangue seeks applicants for a postdoctoral research associate. A recently funded series of projects seeks to characterize the potential of an endangered fish (Delta smelt) to acclimate or adapt to a changing climate. Experiments will leverage the outstanding rearing and experimental facilities available through the UC Davis Fish Conservation and Culture Laboratory (FCCL), which harbors a refuge population of Delta smelt. The successful candidate will use quantitative genetic breeding designs and statistical approaches to estimate additive genetic variation for thermal resilience and for thermal resilience plasticity. The candidate will have the opportunity to interact extensively as part of a larger interdisciplinary and collaborative team of evolutionary geneticists and ecophysiologists. More on the Whitehead lab, Fangue lab, and FCCL can be found at:

The ideal candidate has experience in quantitative genetics, statistical genetics, and computational biology. Also preferred is experience in animal physiology. We are especially interested in candidates with a passion for open science and for connecting their work to decision makers, the public, and the broader conservation biology and evolutionary biology communities.

Responsibilities: Design of breeding strategy, data collection, code development, data analysis and interpretation, review of relevant literature, preparation of project reports and manuscripts for publication in peer-reviewed journals, presentation at professional conferences and State Agency meetings.

Minimum qualifications: PhD in genetics, population biology, genome science, conservation genetics, data science, or another relevant field.

Preferred qualifications: Preference will be given to applicants with 1) expertise in quantitative genetics, statistical genetics, population genetics, or conservation genetics, and physiology; 2) strong communication and organizational skills; 3) can code in C++, and in R and/or python and have an interest in transparent and reproducible science; and 4) strong publication records, or the potential for developing one. Our team believes in and values the power of diversity, thus applicants from historically underrepresented groups are strongly encouraged to apply.

Salary: Commensurate with qualifications and experience.

Application: Interested candidates should submit:

  • a one‐page cover letter,
  • your CV, and
  • names and contact information of at least three references familiar with your work.

Please submit materials to Andrew Whitehead (awhitehead@ucdavis.edu) with “QuantGen Postdoc” in the subject. Applications will be reviewed as they arrive, and the position will remain open until filled.

Email any questions to Andrew Whitehead (awhitehead@ucdavis.edu)  

The positions will remain open until filled with preferred start dates between September 2019 and January 2020.

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Elias’ paper out in Science

Today our paper on the genomic basis of pollution adaptation in Gulf killifish was published in Science. See Twitter thread about the work. On the lab website: find links to press coverage, a podcast, and an audio/visual narration of the paper.

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