Genome-wide profiling of DNA methylation and gene expression in Crassostrea gigas male gametes.

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Genome-wide profiling of DNA methylation and gene expression in Crassostrea gigas male gametes.

Front Physiol. 2014;5:224

Authors: Olson CE, Roberts SB

Abstract
DNA methylation patterns and functions are variable across invertebrate taxa. In order to provide a better understanding of DNA methylation in the Pacific oyster (Crassostrea gigas), we characterized the genome-wide DNA methylation profile in male gamete cells using whole-genome bisulfite sequencing. RNA-Seq analysis was performed to examine the relationship between DNA methylation and transcript expression. Methylation status of over 7.6 million CpG dinucleotides was described with a majority of methylated regions occurring among intragenic regions. Overall, 15% of the CpG dinucleotides were determined to be methylated and the mitochondrial genome lacked DNA methylation. Integrative analysis of DNA methylation and RNA-Seq data revealed a positive association between methylation status, both in gene bodies and putative promoter regions, and expression. This study provides a comprehensive characterization of the distribution of DNA methylation in the oyster male gamete tissue and suggests that DNA methylation is involved in gene regulatory activity.

PMID: 24987376 [PubMed]

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Estimating Historical Eastern North Pacific Blue Whale Catches Using Spatial Calling Patterns.

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Estimating Historical Eastern North Pacific Blue Whale Catches Using Spatial Calling Patterns.

PLoS One. 2014;9(6):e98974

Authors: Monnahan CC, Branch TA, Stafford KM, Ivashchenko YV, Oleson EM

Abstract
Blue whales (Balaenoptera musculus) were exploited extensively around the world and remain endangered. In the North Pacific their population structure is unclear and current status unknown, with the exception of a well-studied eastern North Pacific (ENP) population. Despite existing abundance estimates for the ENP population, it is difficult to estimate pre-exploitation abundance levels and gauge their recovery because historical catches of the ENP population are difficult to separate from catches of other populations in the North Pacific. We collated previously unreported Soviet catches and combined these with known catches to form the most current estimates of North Pacific blue whale catches. We split these conflated catches using recorded acoustic calls from throughout the North Pacific, the knowledge that the ENP population produces a different call than blue whales in the western North Pacific (WNP). The catches were split by estimating spatiotemporal occurrence of blue whales with generalized additive models fitted to acoustic call patterns, which predict the probability a catch belonged to the ENP population based on the proportion of calls of each population recorded by latitude, longitude, and month. When applied to the conflated historical catches, which totaled 9,773, we estimate that ENP blue whale catches totaled 3,411 (95% range 2,593 to 4,114) from 1905-1971, and amounted to 35% (95% range 27% to 42%) of all catches in the North Pacific. Thus most catches in the North Pacific were for WNP blue whales, totaling 6,362 (95% range 5,659 to 7,180). The uncertainty in the acoustic data influence the results substantially more than uncertainty in catch locations and dates, but the results are fairly insensitive to the ecological assumptions made in the analysis. The results of this study provide information for future studies investigating the recovery of these populations and the impact of continuing and future sources of anthropogenic mortality.

PMID: 24892427 [PubMed – as supplied by publisher]

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Rearing in natural and recovering tidal wetlands enhances growth and life-history diversity of Columbia Estuary tributary coho salmon Oncorhynchus kisutch population.

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Rearing in natural and recovering tidal wetlands enhances growth and life-history diversity of Columbia Estuary tributary coho salmon Oncorhynchus kisutch population.

J Fish Biol. 2014 May 28;

Authors: Craig BE, Simenstad CA, Bottom DL

Abstract
This study provides evidence of the importance of tributary tidal wetlands to local coho salmon Oncorhynchus kisutch populations and life-history diversity. Sub-yearling and, to a lesser extent, yearling O. kisutch life histories utilized various estuary habitats within the Grays River, a tidal freshwater tributary of the Columbia Estuary, including restoring emergent wetlands and natural forested wetlands. Migration timing data, size distributions, estuary residence and scale patterns suggest a predominance of sub-yearling migrant life histories, including several that involve extended periods of estuary rearing. Estuarine-rearing sub-yearling O. kisutch exhibited the greatest overall growth rates; the highest growth rates were seen in fish that utilized restoring emergent wetlands. These results contrast with studies conducted in the main-stem Columbia Estuary, which captured few O. kisutch, of which nearly all were hatchery-origin yearling smolts. Restoration and preservation of peripheral and tributary wetland habitats, such as those in the Grays River, could play an important role in the recovery of natural O. kisutch populations in the Columbia River and elsewhere.

PMID: 24890886 [PubMed – as supplied by publisher]

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Brain acetylcholinesterase activity in shiner perch (Cymatogaster aggregata) and juvenile chinook salmon (Oncorhynchus tshawytscha) after application of carbaryl to control burrowing shrimp within Willapa Bay, Washington.

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Brain acetylcholinesterase activity in shiner perch (Cymatogaster aggregata) and juvenile chinook salmon (Oncorhynchus tshawytscha) after application of carbaryl to control burrowing shrimp within Willapa Bay, Washington.

Arch Environ Contam Toxicol. 2013 Nov;65(4):779-89

Authors: Troiano AT, King KA, Grue CE, Grassley JM, Ekblad CJ

Abstract
Carbaryl has been applied in Willapa Bay, Washington, for five decades to control burrowing shrimp (Neotrypaea californiensis and Upogebia pugettensis) on commercial oyster (Crassostrea gigas) beds. Concerns about effects on nontarget species, including fishes, have led to restrictions in use despite a lack of data on in situ exposure. We measured brain acetylcholinesterase (AChE) activity in adult Shiner perch (Cymatogaster aggregata) and juvenile Chinook salmon (Oncorhynchus tshawytscha) after operational applications. We hypothesized that exposure in Shiner perch would be greater than in juvenile Chinook salmon because of their greater site fidelity and benthic foraging. However, Shiner perch exhibited no statistically significant AChE inhibition. Enzyme activity was statistically decreased (≤14 %) in juvenile Chinook salmon after a second spray event; however, inhibition was less than that associated with overt effects and was similar to controls by 48 h after the spray. Diet analyses confirmed that Shiner perch were primarily feeding on benthic invertebrates and that juvenile Chinook salmon were feeding primarily within the water column. Composition of Shiner perch diets and amount of food consumed varied little among channels and time periods; however, Shiner perch on beds consumed more food 6 h after application than those at other time points and locations. There were no consistent differences in the diets of juvenile Chinook salmon within channels among time periods. Results suggest (1) that carbaryl applications pose little hazard to fish in the bay having habitat and dietary preferences similar to those of Shiner perch and juvenile Chinook salmon and (2) that quantification of direct exposure in the field is essential to adequately assess risk.

PMID: 24042340 [PubMed – indexed for MEDLINE]

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Gyrodactylid ectoparasites in a population of rainbow trout (Oncorhynchus mykiss).

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Gyrodactylid ectoparasites in a population of rainbow trout (Oncorhynchus mykiss).

J Am Assoc Lab Anim Sci. 2014 Jan;53(1):92-7

Authors: Garcia RL, Hansen AG, Chan MM, Sanders GE

Abstract
A colony of rainbow trout (Oncorhynchus mykiss) in a decentralized aquatic animal facility was noted to have an increase in morbidity and mortality (from 4 or 5 fish each month to 3 or 4 fish daily) approximately 2 wk after experimental procedures began. The primary clinical signs were erratic swimming behavior and ‘flashing’ of fish against surfaces within housing enclosures. Moribund and normal rainbow trout were presented alive for diagnostic evaluation; samples of water from housing enclosures were provided for water quality assessment. The trout were determined to be infected with gyrodactylids, a common monogenean ectoparasite of the skin and gills in both marine and freshwater fish. This case report describes the diagnosis, pathology, and treatment of gyrodactylids and husbandry modifications associated with the resolution of this clinical aquatic-animal case.

PMID: 24411786 [PubMed – indexed for MEDLINE]

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Spatial Scaling of Non-Native Fish Richness across the United States.

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Spatial Scaling of Non-Native Fish Richness across the United States.

PLoS One. 2014;9(5):e97727

Authors: Guo Q, Olden JD

Abstract
A major goal and challenge of invasion ecology is to describe and interpret spatial and temporal patterns of species invasions. Here, we examined fish invasion patterns at four spatially structured and hierarchically nested scales across the contiguous United States (i.e., from large to small: region, basin, watershed, and sub-watershed). All spatial relationships in both richness and fraction between species groups (e.g., natives vs. exotics) were positive at large scales. However, contrary to predictions using null/neutral models, the patterns at small scales were hump-shaped (unimodal), not simply negative. The fractions of both domestic (introduced among watersheds within the USA) and foreign (introduced from abroad) exotics increased with area across scales but decreased within each scale. The foreign exotics exhibited the highest dominance (lowest evenness) and spatial variation in distribution, followed by domestic exotics and natives, although on average natives still occupy larger areas than domestic and foreign exotics. The results provide new insight into patterns and mechanisms of fish species invasions at multiple spatial scales in the United States.

PMID: 24844226 [PubMed – in process]

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Quantitative PCR analysis used to characterize physiological changes in brain tissue of senescent sockeye salmon.

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Quantitative PCR analysis used to characterize physiological changes in brain tissue of senescent sockeye salmon.

Biogerontology. 2013 Oct;14(5):483-90

Authors: Storer CS, Quinn TP, Roberts SB

Abstract
Senescence varies considerably among fishes, and understanding the evolutionary basis for this diversity has become an important area of study. For rapidly senescing species such as Pacific salmon, senescence is a complex process as these fish are initiating anorexia while migrating to natal spawning grounds, and die within days of reproduction. To better understand senescence in Pacific salmon we examined expression patterns for a suite of genes in brain tissue of pre-senescent and senescent sockeye salmon. Interestingly, a significant increase in expression of genes involved in telomere repair and immune activity was observed in senescent salmon. These data provide insight into physiological changes in salmon undergoing senescence and the factors contributing to variation in observed senescence rates among individuals and populations.

PMID: 23948798 [PubMed – indexed for MEDLINE]

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Patterns of ecosystem metabolism in the Tonle Sap Lake, Cambodia with links to capture fisheries.

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Patterns of ecosystem metabolism in the Tonle Sap Lake, Cambodia with links to capture fisheries.

PLoS One. 2013;8(8):e71395

Authors: Holtgrieve GW, Arias ME, Irvine KN, Lamberts D, Ward EJ, Kummu M, Koponen J, Sarkkula J, Richey JE

Abstract
The Tonle Sap Lake in Cambodia is a dynamic flood-pulsed ecosystem that annually increases its surface area from roughly 2,500 km(2) to over 12,500 km(2) driven by seasonal flooding from the Mekong River. This flooding is thought to structure many of the critical ecological processes, including aquatic primary and secondary productivity. The lake also has a large fishery that supports the livelihoods of nearly 2 million people. We used a state-space oxygen mass balance model and continuous dissolved oxygen measurements from four locations to provide the first estimates of gross primary productivity (GPP) and ecosystem respiration (ER) for the Tonle Sap. GPP averaged 4.1±2.3 g O2 m(-3) d(-1) with minimal differences among sites. There was a negative correlation between monthly GPP and lake level (r = 0.45) and positive correlation with turbidity (r = 0.65). ER averaged 24.9±20.0 g O2 m(-3) d(-1) but had greater than six-fold variation among sites and minimal seasonal change. Repeated hypoxia was observed at most sampling sites along with persistent net heterotrophy (GPP<ER), indicating significant bacterial metabolism of organic matter that is likely incorporated into the larger food web. Using our measurements of GPP, we calibrated a hydrodynamic-productivity model and predicted aquatic net primary production (aNPP) of 2.0±0.2 g C m(-2) d(-1) (2.4±0.2 million tonnes C y(-1)). Considering a range of plausible values for the total fisheries catch, we estimate that fisheries harvest is an equivalent of 7-69% of total aNPP, which is substantially larger than global average for marine and freshwater systems. This is likely due to relatively efficient carbon transfer through the food web and support of fish production from terrestrial NPP. These analyses are an important first-step in quantifying the resource pathways that support this important ecosystem.

PMID: 23967203 [PubMed – indexed for MEDLINE]

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Detection and mapping of QTL for temperature tolerance and body size in Chinook salmon (Oncorhynchus tshawytscha) using genotyping by sequencing.

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Detection and mapping of QTL for temperature tolerance and body size in Chinook salmon (Oncorhynchus tshawytscha) using genotyping by sequencing.

Evol Appl. 2014 Apr;7(4):480-92

Authors: Everett MV, Seeb JE

Abstract
Understanding how organisms interact with their environments is increasingly important for conservation efforts in many species, especially in light of highly anticipated climate changes. One method for understanding this relationship is to use genetic maps and QTL mapping to detect genomic regions linked to phenotypic traits of importance for adaptation. We used high-throughput genotyping by sequencing (GBS) to both detect and map thousands of SNPs in haploid Chinook salmon (Oncorhynchus tshawytscha). We next applied this map to detect QTL related to temperature tolerance and body size in families of diploid Chinook salmon. Using these techniques, we mapped 3534 SNPs in 34 linkage groups which is consistent with the haploid chromosome number for Chinook salmon. We successfully detected three QTL for temperature tolerance and one QTL for body size at the experiment-wide level, as well as additional QTL significant at the chromosome-wide level. The use of haploids coupled with GBS provides a robust pathway to rapidly develop genomic resources in nonmodel organisms; these QTL represent preliminary progress toward linking traits of conservation interest to regions in the Chinook salmon genome.

PMID: 24822082 [PubMed]

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Parallel signatures of selection in temporally-isolated lineages of pink salmon.

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Parallel signatures of selection in temporally-isolated lineages of pink salmon.

Mol Ecol. 2014 Apr 25;

Authors: Seeb LW, Waples RK, Limborg MT, Warheit KI, Pascal CE, Seeb JE

Abstract
Studying the effect of similar environments on diverse genetic backgrounds has long been a goal of evolutionary biologists with studies typically relying on experimental approaches. Pink salmon, a highly-abundant and widely-ranging salmonid, provide a naturally-occurring opportunity to study the effects of similar environments on divergent genetic backgrounds due to a strict two-year semelparous life-history. The species is composed of two reproductively-isolated lineages with overlapping ranges that share the same spawning and rearing environments in alternate years. We used restriction site-associated DNA (RAD) sequencing to discover and genotype approximately 8,000 SNP loci in three population pairs of even- and odd-year pink salmon along a latitudinal gradient in North America. We found greater differentiation within the odd-year than the even-year lineage and greater differentiation in the southern pair from Puget Sound than in the northern Alaskan population pairs. We identified 15 SNPs reflecting signatures of parallel selection using both a differentiation-based method (BAYESCAN) and an environmental correlation method (BAYENV). These SNPs represent genomic regions that may be particularly informative in understanding adaptive evolution in pink salmon and exploring how differing genetic backgrounds within a species respond to selection from the same natural environment. This article is protected by copyright. All rights reserved.

PMID: 24762204 [PubMed – as supplied by publisher]

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