Rank and order: evaluating the performance of SNPs for individual assignment in a non-model organism.

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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. With hundreds or thousands of SNPs potentially available, there is interest in comparing and developing methods for evaluating SNPs to create panels of high-throughput assays that are customized for performance, research questions, and resources. Here we use five different methods to rank 43 new SNPs and 71 previously published SNPs for sockeye salmon: F(ST), informativeness (I(n)), average contribution to principal components (LC), and the locus-ranking programs BELS and WHICHLOCI. We then tested the performance of these different ranking methods by creating 48- and 96-SNP panels of the top-ranked loci for each method and used empirical and simulated data to obtain the probability of assigning individuals to the correct population using each panel. All 96-SNP panels performed similarly and better than the 48-SNP panels except for the 96-SNP BELS panel. Among the 48-SNP panels, panels created from F(ST), I(n), and LC ranks performed better than panels formed using the top-ranked loci from the programs BELS and WHICHLOCI. The application of ranking methods to optimize panel performance will become more important as more high-throughput assays become available.

PMID: 23185290 [PubMed – indexed for MEDLINE]

via pubmed: school of aquatic an… http://www.ncbi.nlm.nih.gov/pubmed/23185290?dopt=Abstract

Putative phage hyperparasite in the rickettsial pathogen of abalone, “Candidatus Xenohaliotis californiensis”.

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Putative phage hyperparasite in the rickettsial pathogen of abalone, “Candidatus Xenohaliotis californiensis”.

Microb Ecol. 2012 Nov;64(4):1064-72

Authors: Friedman CS, Crosson LM

Abstract
Studies on the ecology of microbial parasites and their hosts are predicated on understanding the assemblage of and relationship among the species present. Changes in organismal morphology and physiology can have profound effects on host-parasite interactions and associated microbial community structure. The marine rickettsial organism, “Candidatus Xenohaliotis californiensis” (WS-RLO), that causes withering syndrome of abalones has had a consistent morphology based on light and electron microscopy. However, a morphological variant of the WS-RLO has recently been observed infecting red abalone from California. We used light and electron microscopy, in situ hybridization and16S rDNA sequence analysis to compare the WS-RLO and the morphologically distinct RLO variant (RLOv). The WS-RLO forms oblong inclusions within the abalone posterior esophagus (PE) and digestive gland (DG) tissues that contain small rod-shaped bacteria; individual bacteria within the light purple inclusions upon hematoxylin and eosin staining cannot be discerned by light microscopy. Like the WS-RLO, the RLOv forms oblong inclusions in the PE and DG but contain large, pleomorphic bacteria that stain dark navy blue with hematoxylin and eosin. Transmission electron microscopy (TEM) examination revealed that the large pleomorphic bacteria within RLOv inclusions were infected with a spherical to icosahedral-shaped putative phage hyperparasite. TEM also revealed the presence of rod-shaped bacteria along the periphery of the RLOv inclusions that were morphologically indistinguishable from the WS-RLO. Binding of the WS-RLO-specific in situ hybridization probe to the RLOv inclusions demonstrated sequence similarity between these RLOs. In addition, sequence analysis revealed 98.9-99.4 % similarity between 16S rDNA sequences of the WS-RLO and RLOv. Collectively, these data suggest that both of these RLOs infecting California abalone are “Candidatus Xenohaliotis californiensis,” and that the novel variant is infected by a putative phage hyperparasite that induced morphological variation of its RLO host.

PMID: 22729142 [PubMed – indexed for MEDLINE]

via pubmed: school of aquatic an… http://www.ncbi.nlm.nih.gov/pubmed/22729142?dopt=Abstract

Half Baked Extravaganza

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You are invited to the first annual Half Baked Extravaganza!

When
Tuesday May 14, 8:30 AM to 5 PM

Where
Main Auditorium of the Northwest Fisheries Science Center
2725 Montlake Blvd. E. – Seattle, WA

We will start with coffee and donuts at 8:30 and the talks will begin at
9:00 a.m. There are fifteen talks scheduled on a range of subjects and
fisheries. The schedule with titles and speakers is attached. Like previous
half-baked seminars this is meant to be informal and much of what is being
presented is work in progress.

Feel free to pass this on to others you think might be interested in coming!

Parking is very limited at the NWFSC so keep that in mind when deciding how
to get here.

If you have any questions please contact Dan Holland (NWFSC) at (206) 302-1752 or by e-mail.

Sensitivity of salmonid freshwater life history in Western US streams to future climate conditions.

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Sensitivity of salmonid freshwater life history in Western US streams to future climate conditions.

Glob Chang Biol. 2013 May 2;

Authors: Beer WN, Anderson JJ

Abstract
We projected effects of mid-21(st) century climate on the early-life growth of Chinook salmon (Oncorhynchus tshawytscha) and steelhead (O. mykiss) in western United States streams. Air temperature and snowpack trends projected from climate models and observed 20(th) century trends were used to predict future seasonal stream temperatures. Fish growth from winter to summer was projected with temperature-dependent models of egg development and juvenile growth. Based on temperature data from 115 sites, by mid-21(st) century the effects of climate change are projected to be mixed. Fish in warm-region streams that are currently cooled by snowmelt will grow less, and fish in sub-optimally cool streams will grow more. Relative to 20(th) century conditions, by mid-21(st) century juvenile salmonids’ weights are expected to be lower in the Columbia Basin and California Central Valley but unchanged or greater in coastal and mountain streams. Because fish weight affects fish survival, the predicted changes in weight could impact population fitness depending on other factors such as density effects, food quality and quantity changes, habitat alterations, etc. The level of year-to-year variability in stream temperatures is high and our analysis suggests that identifying effects of climate change over the natural variability will be difficult except in a few streams. This article is protected by copyright. All rights reserved.

PMID: 23640715 [PubMed – as supplied by publisher]

via pubmed: school of aquatic an… http://www.ncbi.nlm.nih.gov/pubmed/23640715?dopt=Abstract

Evidence for an Amoeba-Like Infectious Stage of Ichthyophonus sp. and Description of a Circulating Blood Stage: A Probable Mechanism for Dispersal Within the Fish Host

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Evidence for an Amoeba-Like Infectious Stage of Ichthyophonus sp. and Description of a Circulating Blood Stage: A Probable Mechanism for Dispersal Within the Fish Host

Author(s): Richard Kocan , Scott LaPatra , and Paul Hershberger
Source: Journal of Parasitology, 99(2):235-240. 2013.
Published By: American Society of Parasitologists
DOI: http://dx.doi.org/10.1645/GE-3255.1
URL: http://www.bioone.org/doi/full/10.1645/GE-3255.1

Abstract
Small amoeboid cells, believed to be the infectious stage of Ichthyophonus sp., were observed in the bolus (stomach contents) and tunica propria (stomach wall) of Pacific staghorn sculpins and rainbow trout shortly after they ingested Ichthyophonus sp.–infected tissues. By 24–48 hr post-exposure (PE) the parasite morphed from the classically reported multinucleate thick walled schizonts to 2 distinct cell types, i.e., a larger multinucleate amoeboid cell surrounded by a narrow translucent zone and a smaller spherical cell surrounded by a ‘‘halo’’ and resembling a small schizont. Both cell types also appeared in the tunica propria, indicating that they had recently penetrated the columnar epithelium of the stomach. No Ichthyophonus sp. pseudo-hyphae (‘‘germination tubes’’) were observed in the bolus or penetrating the stomach wall. Simultaneously, Ichthyophonus sp. was isolated in vitro from aortic blood, which was consistently positive from 6 to 144 hr PE, then only intermittently for the next 4 wk. Small PAS-positive cells observed in blood cultures grew into colonies consisting of non-septate tubules (pseudo-hyphae) terminating in multinucleated knob-like apices similar to those seen in organ explant cultures. Organ explants were culture positive every day; however, typical Ichthyophonus sp. schizonts were not observed histologically until 20–25 days PE. From 20 to 60 days PE, schizont diameter increased from 25 lm to 82 lm. Based on the
data presented herein, we are confident that we have resolved the life cycle of Ichthyophonus sp. within the piscivorous host.

Opportunistic exploitation: an overlooked pathway to extinction.

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Opportunistic exploitation: an overlooked pathway to extinction.

Trends Ecol Evol. 2013 Apr 4;

Authors: Branch TA, Lobo AS, Purcell SW

Abstract
How can species be exploited economically to extinction? Past single-species hypotheses examining the economic plausibility of exploiting rare species have argued that the escalating value of rarity allows extinction to be profitable. We describe an alternative pathway toward extinction in multispecies exploitation systems, termed ‘opportunistic exploitation’. In this mode, highly valued species that are targeted first by fishing, hunting, and logging become rare, but their populations can decline further through opportunistic exploitation while more common but less desirable species are targeted. Effectively, expanding exploitation to more species subsidizes the eventual extinction of valuable species at low densities. Managers need to recognize conditions that permit opportunistic depletion and pass regulations to protect highly desirable species when exploitation can expand to other species.

PMID: 23562732 [PubMed – as supplied by publisher]

via pubmed: school of aquatic an… http://www.ncbi.nlm.nih.gov/pubmed/23562732?dopt=Abstract

Riding the crimson tide: mobile terrestrial consumers track phenological variation in spawning of an anadromous fish.

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Riding the crimson tide: mobile terrestrial consumers track phenological variation in spawning of an anadromous fish.

Biol Lett. 2013;9(3):20130048

Authors: Schindler DE, Armstrong JB, Bentley KT, Jankowski K, Lisi PJ, Payne LX

Abstract
When resources are spatially and temporally variable, consumers can increase their foraging success by moving to track ephemeral feeding opportunities as these shift across the landscape; the best examples derive from herbivore-plant systems, where grazers migrate to capitalize on the seasonal waves of vegetation growth. We evaluated whether analogous processes occur in watersheds supporting spawning sockeye salmon (Oncorhynchus nerka), asking whether seasonal activities of predators and scavengers shift spatial distributions to capitalize on asynchronous spawning among populations of salmon. Both glaucous-winged gulls and coastal brown bears showed distinct shifts in their spatial distributions over the course of the summer, reflecting the shifting distribution of spawning sockeye salmon, which was associated with variation in water temperature among spawning sites. By tracking the spatial and temporal variation in the phenology of their principal prey, consumers substantially extended their foraging opportunity on a superabundant, yet locally ephemeral, resource. Ecosystem-based fishery management efforts that seek to balance trade-offs between fisheries and ecosystem processes supported by salmon should, therefore, assess the importance of life-history variation, particularly in phenological traits, for maintaining important ecosystem functions, such as providing marine-derived resources for terrestrial predators and scavengers.

PMID: 23554279 [PubMed – in process]

via pubmed: school of aquatic an… http://www.ncbi.nlm.nih.gov/pubmed/23554279?dopt=Abstract