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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Postdoc Elias Oziolor has joined the lab

Elias will be examining population genomic change through time in Alaskan populations of Pacific herring (among other things). Welcome Elias!

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Reid Brennan has graduated!

Reid Brennan is now Dr. Reid Brennan. He has already moved on from Davis and will soon be starting his postdoc at the University of Vermont in Melissa Pespeni’s lab. Congratulations Reid!

The first two chapters of his thesis work are  published (see below), and the third – which integrates association mapping with genome scans to discover the genetic basis of adaptation to different osmotic environments in killifish – is on its way. Hold onto your seats!

Brennan, R.S., R. Hwang, M. Tse, N.A. Fangue, and A. Whitehead (2016). Local adaptation to osmotic environment in killifish, Fundulus heteroclitus, is supported by divergence in swimming performance but not by differences in excess post-exercise oxygen consumption or aerobic scopeComparative Biochemistry and Physiology, Part A, 196: 11-19. PDF.

Brennan, R.S., F. Galvez, and A. Whitehead (2015). Reciprocal osmotic challenges reveal mechanisms of divergence in phenotypic plasticity in the killifish Fundulus heteroclitusJournal of Experimental Biology, 218: 1212-1222.  PDF.

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Bet Haverim award to Tony!

Ph.D. student Tony Gill was just awarded a research grant from the Bet Haverim Seventh Grade class. Their class is learning about philanthropy, and they decided to pool part of their mitzvah gifts to fund a research project (what a great idea!). They put out a call for proposals, evaluated the applications, and made a funding decision. Tony prepared a proposal on the herring virus story, and it was awarded. Hats off to the Bet Haverim Seventh graders, and congrats to Tony!

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Our abalone in the news!

Our ocean acidification work on red abalone at BML featured on NBC news.

Nice job Sara and Dan!

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Presentation award to Lisa Cohen

Congratulations to Lisa Cohen! – she won a presentation award for “Reassembling 600+ marine transcriptomes: automated pipeline development and evaluation” at yesterday’s MCIP colloquium. Nice job Lisa!!!

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Two new papers just out

Our review article on evolutionary rescue from pollution, with examples from the killifish system:

Whitehead, A., B.W. Clark, M.E. Hahn, and D. Nacci (in press). When evolution is the solution to pollution: Key principles, and lessons from rapid repeated adaptation of killifish (Fundulus heteroclitus) populations. Evolutionary Applications.

Killifish genome release manuscript, with detailed analysis of the nature of genetic variation within a population of this highly heterozygous species:

Reid, N.M., C.E. Jackson, D. Gilbert, P. Minx, M.J. Montague, T.H. Hampton, L.W. Helfrich, B.L. King, D. Nacci, N. Aluru, S.I. Karchner, J.K. Colbourne, M.E. Hahn, J.R. Shaw, M.F. Oleksiak, D.L. Crawford, W.C. Warren, and A. Whitehead (in press). The Atlantic killifish (Fundulus heteroclitus) genome and the landscape of genome variation within a population. Genome Biology & Evolution.

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