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Are large-scale flow experiments informing the science and management of freshwater ecosystems?

Are large-scale flow experiments informing the science and management of freshwater ecosystems?
Frontiers in Ecology and the Environment 12: 176–185. http://dx.doi.org/10.1890/130076
Authors: Julian D Olden, Christopher P Konrad, Theodore S Melis, Mark J Kennard, Mary C Freeman, Meryl C Mims, Erin N Bray, Keith B Gido, Nina P Hemphill, David A Lytle, Laura E McMullen, Mark Pyron, Christopher T Robinson, John C Schmidt, and John G Williams. 

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ss3sim: An R Package for Fisheries Stock Assessment Simulation with Stock Synthesis.

ss3sim: An R Package for Fisheries Stock Assessment Simulation with Stock Synthesis.
PLoS One. 2014;9(4):e92725
Authors: Anderson SC, Monnahan CC, Johnson KF, Ono K, Valero JL
Abstract
Simulation testing is an important approach to evaluating fishery stock assessment methods. In the last decade, the fisheries stock assessment modeling framework Stock Synthesis (SS3) has become widely used around the world. However, there lacks a generalized and scriptable framework for SS3 simulation testing. 

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Abalone withering syndrome: distribution, impacts, current diagnostic methods and new findings.

Abalone withering syndrome: distribution, impacts, current diagnostic methods and new findings.
Dis Aquat Organ. 2014 Apr 3;108(3):261-270
Authors: Crosson LM, Wight N, Vanblaricom GR, Kiryu I, Moore JD, Friedman CS
Abstract
Withering syndrome (WS) is a fatal disease of abalone caused by a Rickettsiales-like organism (WS-RLO). The causative agent, ‘Candidatus Xenohaliotis californiensis’, occurs along the eastern Pacific margin of North America in California, USA, and Baja California, Mexico. 

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Validation of a quantitative PCR assay for detection and quantification of ‘Candidatus Xenohaliotis californiensis’.

Validation of a quantitative PCR assay for detection and quantification of ‘Candidatus Xenohaliotis californiensis’.
Dis Aquat Organ. 2014 Apr 3;108(3):251-9
Authors: Friedman CS, Wight N, Crosson LM, White SJ, Strenge RM
Abstract
Withering syndrome (WS), a serious disease affecting abalone Haliotis spp., is caused by infection from an intracellular Rickettsia-like organism (WS-RLO). Diagnosis of the disease currently relies on a combination of histological examination and molecular methods (in situ hybridization, standard PCR, and sequence analysis). 

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Single-nucleotide polymorphisms (SNPs) identified through genotyping-by-sequencing improve genetic stock identification of Chinook salmon (Oncorhynchus tshawytscha) from western Alaska

Title: Single-nucleotide polymorphisms (SNPs) identified through genotyping-by-sequencing improve genetic stock identification of Chinook salmon (Oncorhynchus tshawytscha) from western Alaska
 
Journal: Canadian Journal of Fisheries and Aquatic Sciences
 
Authors: Wesley A. Larson, James E. Seeb, Carita E. Pascal, William D. Templin, Lisa W. Seeb
 
All authors but William D. Templin are from SAFS
 
Link to the paper: http://www.nrcresearchpress.com/doi/abs/10.1139/cjfas-2013-0502#.Uyy5HfldWZN
 
Abstract: Genetic stock identification (GSI), an important tool for fisheries management that relies upon the ability to differentiate stocks of interest, can be difficult when populations are closely related. 

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Reduced disease in black abalone following mass mortality: phage therapy and natural selection.

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Reduced disease in black abalone following mass mortality: phage therapy and natural selection.
Front Microbiol. 2014;5:78
Authors: Friedman CS, Wight N, Crosson LM, Vanblaricom GR, Lafferty KD
Abstract
Black abalone, Haliotis cracherodii, populations along the NE Pacific ocean have declined due to the rickettsial disease withering syndrome (WS). Natural recovery on San Nicolas Island (SNI) of Southern California suggested the development of resistance in island populations. 

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Genotyping by sequencing resolves shallow population structure to inform conservation of Chinook salmon (Oncorhynchus tshawytscha).

Genotyping by sequencing resolves shallow population structure to inform conservation of Chinook salmon (Oncorhynchus tshawytscha).
Evol Appl. 2014 Mar;7(3):355-69
Authors: Larson WA, Seeb LW, Everett MV, Waples RK, Templin WD, Seeb JE
Abstract
Recent advances in population genomics have made it possible to detect previously unidentified structure, obtain more accurate estimates of demographic parameters, and explore adaptive divergence, potentially revolutionizing the way genetic data are used to manage wild populations. 

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Secondary contact and changes in coastal habitat availability influence the nonequilibrium population structure of a salmonid (Oncorhynchus keta).

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Secondary contact and changes in coastal habitat availability influence the nonequilibrium population structure of a salmonid (Oncorhynchus keta).
Mol Ecol. 2013 Dec;22(23):5848-60
Authors: Petrou EL, Hauser L, Waples RS, Seeb JE, Templin WD, Gomez-Uchida D, Seeb LW
Abstract
Numerous empirical studies have reported lack of migration-drift equilibrium in wild populations. Determining the causes of nonequilibrium population structure is challenging because different evolutionary processes acting at a variety of spatiotemporal scales can produce similar patterns. 

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High-throughput sequencing and pathway analysis reveal alteration of the pituitary transcriptome by 17α-ethynylestradiol (EE2) in female coho salmon, Oncorhynchus kisutch.

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High-throughput sequencing and pathway analysis reveal alteration of the pituitary transcriptome by 17α-ethynylestradiol (EE2) in female coho salmon, Oncorhynchus kisutch.
Aquat Toxicol. 2013 Oct 15;142-143:146-63
Authors: Harding LB, Schultz IR, Goetz GW, Luckenbach JA, Young G, Goetz FW, Swanson P
Abstract
Considerable research has been done on the effects of endocrine disrupting chemicals (EDCs) on reproduction and gene expression in the brain, liver and gonads of teleost fish, but information on impacts to the pituitary gland are still limited despite its central role in regulating reproduction. 

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Diversity of movements by individual anadromous coastal cutthroat trout Oncorhynchus clarkii clarkii.

Diversity of movements by individual anadromous coastal cutthroat trout Oncorhynchus clarkii clarkii.
J Fish Biol. 2013 Nov;83(5):1161-82
Authors: Goetz FA, Baker B, Buehrens T, Quinn TP
Abstract
Wild, downstream-migrating cutthroat trout, Oncorhynchus clarkii clarkii, smolts and adults were captured at a weir in Big Beef Creek, Hood Canal, Washington, surgically implanted with acoustic tags and tracked to identify spring and summer movements using stationary receivers in order to test the assumption that the species moves little while in marine waters. 

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