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162 posts in Publications

Rank and Order: Evaluating the Performance of SNPs for Individual Assignment in a Non-Model Organism.

Rank and Order: Evaluating the Performance of SNPs for Individual Assignment in a Non-Model Organism.
PLoS One. 2012;7(11):e49018
Authors: Storer CG, Pascal CE, Roberts SB, Templin WD, Seeb LW, Seeb JE
Abstract
Single nucleotide polymorphisms (SNPs) are valuable tools for ecological and evolutionary studies. In non-model species, the use of SNPs has been limited by the number of markers available. However, new technologies and decreasing technology costs have facilitated the discovery of a constantly increasing number of SNPs. 

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Coexistence and origin of trophic ecotypes of pygmy whitefish, Prosopium coulterii, in a south-western Alaskan lake

Coexistence and origin of trophic ecotypes of pygmy whitefish, Prosopium coulterii, in a south-western Alaskan lake
Journal of Evolutionary Biology, doi: 10.1111/jeb.12011
Authors: C. P. Gowell*†, T. P. Quinn† & E. B. Taylor‡
*Department of Biology, University of Puget Sound, Tacoma, WA, USA
†School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
‡Department of Zoology, Biodiversity Research Centre and Beaty Biodiversity Museum, University of British Columbia, Vancouver, BC, Canada
Abstract
Ecologically, morphologically and genetically distinct populations within single taxa often coexist in postglacial lakes and have provided important model systems with which to investigate ecological and evolutionary processes such as niche partitioning and ecological speciation. 

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Can interbreeding of wild and artificially propagated animals be prevented by using broodstock selected for a divergent life history?

Can interbreeding of wild and artificially propagated animals be prevented by using broodstock selected for a divergent life history?
Evol Appl. 2012 Nov;5(7):705-19
Authors: Seamons TR, Hauser L, Naish KA, Quinn TP
Abstract
TWO STRATEGIES HAVE BEEN PROPOSED TO AVOID NEGATIVE GENETIC EFFECTS OF ARTIFICIALLY PROPAGATED INDIVIDUALS ON WILD POPULATIONS: (i) integration of wild and captive populations to minimize domestication selection and (ii) segregation of released individuals from the wild population to minimize interbreeding. 

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Impacts of ocean acidification on marine seafood.

Impacts of ocean acidification on marine seafood.
Trends Ecol Evol. 2012 Nov 1;
Authors: Branch TA, Dejoseph BM, Ray LJ, Wagner CA
Abstract
Ocean acidification is a series of chemical reactions due to increased CO(2) emissions. The resulting lower pH impairs the senses of reef fishes and reduces their survival, and might similarly impact commercially targeted fishes that produce most of the seafood eaten by humans. 

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Elevated pCO2 causes developmental delay in early larval Pacific oysters

The paper, “Elevated pCO2 causes developmental delay in early larval Pacific oysters, Crassostrea gigas“, is included in an upcoming special issue on ocean acidification in the journal Marine Biology.  I did the research  in Emily Carrington’s lab in Friday Harbor during the summer of 2011 with the help of researcher Michael “Moose” O’Donnell.  Other co-authors and contributors are SAFS professors Carolyn Friedman and Steven Roberts.   

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Trade-offs in the design of fishery closures: management of silky shark bycatch in the eastern Pacific Ocean tuna fishery.

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Trade-offs in the design of fishery closures: management of silky shark bycatch in the eastern Pacific Ocean tuna fishery.
Conserv Biol. 2009 Jun;23(3):626-35
Authors: Watson JT, Essington TE, Lennert-Cody CE, Hall MA
Abstract
Bycatch–the incidental catch of nontarget species–is a principal concern in marine conservation and fisheries management. In the eastern Pacific Ocean tuna fishery, a large fraction of nonmammal bycatch is captured by purse-seine gear when nets are deployed around floating objects. 

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Synchronous Cycling of Ichthyophoniasis with Chinook Salmon Density Revealed during the Annual Yukon River Spawning Migration

Synchronous Cycling of Ichthyophoniasis with Chinook Salmon Density Revealed during the Annual Yukon River Spawning Migration
Transactions of the American Fisheries Society, Volume 141, Issue 3, 2012
May 4, 2012
by Stanley Zuray, Richard Kocan & Paul Hershberger
Abstract
Populations of Chinook salmon Oncorhynchus tshawytscha in the Yukon River declined by more than 57% between 2003 and 2010, probably the result of a combination of anthropogenic and environmental factors. 

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Pattern and process of biotic homogenization in the New Pangaea.

Pattern and process of biotic homogenization in the New Pangaea.
Proc Biol Sci. 2012 Oct 10;
Authors: Baiser B, Olden JD, Record S, Lockwood JL, McKinney ML
Abstract
Human activities have reorganized the earth’s biota resulting in spatially disparate locales becoming more or less similar in species composition over time through the processes of biotic homogenization and biotic differentiation, respectively. Despite mounting evidence suggesting that this process may be widespread in both aquatic and terrestrial systems, past studies have predominantly focused on single taxonomic groups at a single spatial scale. 

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FISH441 Class Research Published

In this month’s issue of the Journal of Shellfish Research, results from a research project carried out in the lab section of FISH441: Integrative Environmental Physiology was published. David Metzger and Paul Pratt (now both SAFS alum) are primary authors on the paper entitled: Characterizing the Effects of Heavy Metal and Vibrio Exposure on Hsp70 Expression in Crassostrea gigas Gill Tissue. 

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Characterizing short read sequencing for gene discovery and RNA-Seq analysis in Crassostrea gigas.

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Characterizing short read sequencing for gene discovery and RNA-Seq analysis in Crassostrea gigas.
Comp Biochem Physiol Part D Genomics Proteomics. 2012 Jun;7(2):94-9
Authors: Gavery MR, Roberts SB
Abstract
Advances in DNA sequencing technology have provided opportunities to produce new transcriptomic resources for species that lack completely sequenced genomes. However, there are limited examples that rely solely on ultra-short read sequencing technologies (e.g. 

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