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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Jane is on her way to PRIMO 2019

Ph.D. student Jane Park is on her way to the Pollutant Responses in Marine Organisms (PRIMO) meeting in South Carolina in a few weeks. She will be presenting a talk “Transgenerational impacts of crude oil exposure on genome-wide expression in developing Gulf killifish”

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Sara awarded a fellowship!

Ph.D. student Sara Boles was just awarded the Sonoma County Fish and Wildlife inaugural Al Gerhardt Scholarship! This will help to continue supporting her work on red abalone eco-physiology, genomics, and conservation.

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Tony awarded a grant

It is official! Ph.D. student Tony Gill was awarded a research grant from the SeaDoc Society: EXPLORING THE EFFECTS OF OIL AND GAS PRODUCT EXPOSURE ON PACIFIC HERRING

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Nice article: Figuring out the mysteries of the PWS herring collapse

Here is a nice popular article that was recently published: Boom and Busted: In trying to untangle a mysterious herring collapse from the aftermath of the Exxon Valdez oil spill, scientists in Prince William Sound are revealing just how resilient—and unpredictable—marine ecosystems can be.

This is thorough, well-written, and nicely researched, and interviews a number of our collaborators. This article provides important context for our newly funded work on comparative physiology and population genetic change through time in Alaska herring populations. We are examining genetic change through time, at the whole genome scale, for the Prince William Sound population (DNA samples from 1991 to 2017) which suffered the collapse. We are also sequencing parallel samples from Sitka Sound and Bering Sea populations, that did not suffer a 1990’s collapse, to serve as reference populations. We predict that the nature of genetic change through time in these populations will tell us important information about the causes and consequences of the collapse. We are using PoolSeq to sequence 100 individuals per population per timepoint over this period. We are also sequencing populations from British Columbia, Washington, and California (from 2017 collections) to get a handle on genetic variation across the species range. These out-of-Alaska populations may also be useful for inferring adaptations that coincide with latitude (e.g., temperature), and be used as a reference to track additional types of genetic change through time, for example from fisheries pressure or from changing climate.

We are also performing laboratory experiments to test whether exposure to oil during early life makes herring more prone to disease in later life – these experiments are mentioned in the article.

We are very happy to be collaborating with Paul Hershberger’s group (USGS) and Nat Scholz and John Incardona’s group (NOAA). From the Whitehead lab, Tony Gill (Ph.D. student) and Elias Oziolor (Postdoc) are currently spearheading our portion of this research program. This is starting with sequencing a reference genome and reference transcriptome for Pacific herring, which is currently in the works. Stay tuned!

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