Migratory Movements of Pygmy Blue Whales (Balaenoptera musculus brevicauda) between Australia and Indonesia as Revealed by Satellite Telemetry.

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Migratory Movements of Pygmy Blue Whales (Balaenoptera musculus brevicauda) between Australia and Indonesia as Revealed by Satellite Telemetry.

PLoS One. 2014;9(4):e93578

Authors: Double MC, Andrews-Goff V, Jenner KC, Jenner MN, Laverick SM, Branch TA, Gales NJ

Abstract
In Australian waters during the austral summer, pygmy blue whales (Balaenoptera musculus brevicauda) occur predictably in two distinct feeding areas off western and southern Australia. As with other blue whale subspecies, outside the austral summer their distribution and movements are poorly understood. In order to describe the migratory movements of these whales, we present the satellite telemetry derived movements of eleven individuals tagged off western Australia over two years. Whales were tracked from between 8 and 308 days covering an average distance of 3,009±892 km (mean ± se; range: 832 km-14,101 km) at a rate of 21.94±0.74 km per day (0.09 km-455.80 km/day). Whales were tagged during March and April and ultimately migrated northwards post tag deployment with the exception of a single animal which remained in the vicinity of the Perth Canyon/Naturaliste Plateau for its eight day tracking period. The tagged whales travelled relatively near to the Australian coastline (100.0±1.7 km) until reaching a prominent peninsula in the north-west of the state of Western Australia (North West Cape) after which they travelled offshore (238.0±13.9 km). Whales reached the northern terminus of their migration and potential breeding grounds in Indonesian waters by June. One satellite tag relayed intermittent information to describe aspects of the southern migration from Indonesia with the animal departing around September to arrive in the subtropical frontal zone, south of western Australia in December. Throughout their migratory range, these whales are exposed to impacts associated with industry, fishing and vessel traffic. These movements therefore provide a valuable tool to industry when assessing potential interactions with pygmy blue whales and should be considered by conservation managers and regulators when mitigating impacts of development. This is particularly relevant for this species as it continues to recover from past exploitation.

PMID: 24718589 [PubMed – in process]

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Predator avoidance during reproduction: diel movements by spawning sockeye salmon between stream and lake habitats.

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Predator avoidance during reproduction: diel movements by spawning sockeye salmon between stream and lake habitats.

J Anim Ecol. 2014 Apr 5;

Authors: Bentley KT, Schindler DE, Cline TJ, Armstrong JB, Macias D, Ciepiela LR, Hilborn R

Abstract
1. Daily movements of mobile organisms between habitats in response to changing trade-offs between predation risk and foraging gains are well established; however, less in known about whether similar tactics are used during reproduction, a time period when many organisms are particularly vulnerable to predators. 2. We investigated the reproductive behaviour of adult sockeye salmon (Oncorhynchus nerka) and the activity of their principal predator, brown bears (Ursus arctos), on streams in southwestern Alaska. Specifically, we continuously monitored movements of salmon between lake habitat, where salmon are invulnerable to bears, and three small streams, where salmon spawn and are highly vulnerable to bears. We conducted our study across 2 years that offered a distinct contrast in bear activity and predation rates. 3. Diel movements by adult sockeye salmon between stream and lake habitat were observed in 51.3 ± 17.7% [mean ± SD] of individuals among years and sites. Fish that moved tended to hold in the lake for most of the day, and then migrated into spawning streams during the night coincident with when bear activity on streams tended to be lowest. Additionally, cyclic movements between lakes and spawning streams were concentrated earlier in the spawning season. 4. Individuals that exhibited diel movements had longer average reproductive life-spans than those who made only one directed movement into a stream. However, the relative effect was dependent on the timing of bear predation, which varied between years. When predation pressure primarily occurred early in the spawning run (i.e., during the height of the diel movements), movers lived 120 – 310% longer than non-movers. If predation pressure was concentrated later in the spawning run (i.e., when most movements had ceased), movers only lived 10-60% longer. 5. Our results suggest a dynamic trade-off in reproductive strategies of sockeye salmon; adults must be in the stream to reproduce, but must also avoid predation long enough to spawn. Given the inter-annual variation in the timing and intensity of predation pressure, the advantages of a particular movement strategy will likely vary among years. Regardless, movements by salmon allowed individuals to exploit fine-scale habitat heterogeneity during reproduction that appears to be a strategy to reduce predation risk on the spawning grounds. This article is protected by copyright. All rights reserved.

PMID: 24702169 [PubMed – as supplied by publisher]

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Pesticides in urban streams and prespawn mortality of Pacific coho salmon.

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Pesticides in urban streams and prespawn mortality of Pacific coho salmon.

Arch Environ Contam Toxicol. 2013 Oct;65(3):546-54

Authors: King KA, Grue CE, Grassley JM, Hearsey JW

Abstract
The listing of several runs of Pacific salmon as threatened or endangered and associated federal, state, and local efforts to restore/enhance salmon habitat in the Pacific Northwest make it imperative that the factors associated with these population declines are understood. Prespawn mortality (PSM) has been documented in coho salmon (Oncorhynchus kisutch) within urban streams in western Washington since the late 1990s and is characterized by a suite of neurological and respiratory symptoms with mortality occurring shortly thereafter. Mortality rates in returning adults have ranged between 17 and 100%. The cause of PSM is not known, but the presence of pesticide residues within urban streams led to a hypothesis that PSM in coho salmon and pesticides in urban streams were linked. We exposed pairs of “green” (unripe) prespawn male and female coho salmon to a pesticide mixture (“cocktail”) reported in urban streams in western Washington State, USA. Longevity, ripening in female salmon, and brain acetylcholinesterase were not significantly affected by continuous exposure to the maximum reported concentrations of the pesticides. Fertilization, hatching success, and growth of fry were also not affected when green adults were exposed to these concentrations for 96 h. The absence of effects suggests it is unlikely that pesticides within stormwater are singularly responsible for PSM in coho salmon or that they impair the reproductive capability of exposed adults.

PMID: 23744049 [PubMed – indexed for MEDLINE]

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

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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. Here, we introduce ss3sim, an R package that facilitates reproducible, flexible, and rapid end-to-end simulation testing with SS3. ss3sim requires an existing SS3 model configuration along with plain-text control files describing alternative population dynamics, fishery properties, sampling scenarios, and assessment approaches. ss3sim then generates an underlying ‘truth’ from a specified operating model, samples from that truth, modifies and runs an estimation model, and synthesizes the results. The simulations can be run in parallel, reducing runtime, and the source code is free to be modified under an open-source MIT license. ss3sim is designed to explore structural differences between the underlying truth and assumptions of an estimation model, or between multiple estimation model configurations. For example, ss3sim can be used to answer questions about model misspecification, retrospective patterns, and the relative importance of different types of fisheries data. We demonstrate the software with an example, discuss how ss3sim complements other simulation software, and outline specific research questions that ss3sim could address.

PMID: 24699270 [PubMed – in process]

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

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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. However, as infected abalones have been transported to Chile, China, Taiwan, Iceland, Ireland, Israel, Spain, Thailand and Japan, the geographical range of the etiological agent is suspected to be broad, especially where California red abalones Haliotis rufescens are cultured or in areas where native species have been exposed to this species. Susceptibility varies among species, with up to 99% losses of black abalone H. cracherodii in laboratory and field studies in the USA to no losses among the small abalone H. diversicolor supertexta in Thailand. Some populations that have suffered catastrophic losses due to WS have developed resistance to the disease. In addition, a newly identified phage hyperparasite of the WS-RLO may reduce pathogenicity and dampen associated losses. Diagnosis of WS requires the identification of infection with the pathogen (WS-RLO detected via in situ hybridization or histology coupled with PCR and sequence analysis) accompanied by morphological changes that characterize this disease (e.g. pedal and digestive gland atrophy, and digestive gland metaplasia). A quantitative PCR assay was developed and may be useful in quantifying pathogen DNA. Confirmation of infection cannot be done by PCR analysis alone but can be used as a proxy for infection in areas where the agent is established and is recommended for inclusion in health examinations. Avoidance of WS is best accomplished by the establishment of a health history and multiple health examinations prior to movement of animals.

PMID: 24695239 [PubMed – as supplied by publisher]

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

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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). However, these techniques only provide a semi-quantitative assessment of bacterial load. We created a real-time quantitative PCR (qPCR) assay to specifically identify and enumerate bacterial loads of WS-RLO in abalone tissue, fecal, and seawater samples based on 16S rDNA gene copy numbers. The qPCR assay designed to detect DNA of the WS-RLO was validated according to standards set by the World Organisation for Animal Health. Standard curves derived from purified plasmid dilutions were linear across 7 logs of concentration, and efficiencies ranged from 90.2 to 97.4%. The limit of detection was 3 gene copies per reaction. Diagnostic sensitivity was 100% and specificity was 99.8%. The qPCR assay was robust, as evidenced by its high level of repeatability and reproducibility. This study has shown for the first time that WS-RLO DNA can be detected and quantified in abalone tissue, fecal, and seawater samples. The ability to detect and quantify RLO gene copies in a variety of materials will enable us to better understand transmission dynamics in both farmed and natural environments.

PMID: 24695238 [PubMed – in process]

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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. Experimental challenges in one treatment demonstrated that progeny of disease-selected black abalone from SNI survived better than did those from naïve black abalone from Carmel Point in mainland coastal central California. Unexpectedly, the presence of a newly observed bacteriophage infecting the WS rickettsia (WS-RLO) had strong effects on the survival of infected abalone. Specifically, presence of phage-infected RLO (RLOv) reduced the host response to infection, RLO infection loads, and associated mortality. These data suggest that the black abalone: WS-RLO relationship is evolving through dual host mechanisms of resistance to RLO infection in the digestive gland via tolerance to infection in the primary target tissue (the post-esophagus) coupled with reduced pathogenicity of the WS-RLO by phage infection, which effectively reduces the infection load in the primary target tissue by half. Sea surface temperature patterns off southern California, associated with a recent hiatus in global-scale ocean warming, do not appear to be a sufficient explanation for survival patterns in SNI black abalone. These data highlight the potential for natural recovery of abalone populations over time and that further understanding of mechanisms governing host-parasite relationships will better enable us to manage declining populations.

PMID: 24672512 [PubMed]

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

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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. Here, we identified 10 944 single-nucleotide polymorphisms using restriction-site-associated DNA (RAD) sequencing to explore population structure, demography, and adaptive divergence in five populations of Chinook salmon (Oncorhynchus tshawytscha) from western Alaska. Patterns of population structure were similar to those of past studies, but our ability to assign individuals back to their region of origin was greatly improved (>90% accuracy for all populations). We also calculated effective size with and without removing physically linked loci identified from a linkage map, a novel method for nonmodel organisms. Estimates of effective size were generally above 1000 and were biased downward when physically linked loci were not removed. Outlier tests based on genetic differentiation identified 733 loci and three genomic regions under putative selection. These markers and genomic regions are excellent candidates for future research and can be used to create high-resolution panels for genetic monitoring and population assignment. This work demonstrates the utility of genomic data to inform conservation in highly exploited species with shallow population structure.

PMID: 24665338 [PubMed]

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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. Studies of contemporary populations in northern latitudes suggest that nonequilibrium population structure is probably caused by recent colonization of the region after the last Pleistocene ice age ended ~13,000 years ago. The chum salmon’s (Oncorhynchus keta) range was fragmented by dramatic environmental changes during the Pleistocene. We investigated the population structure of chum salmon on the North Alaska Peninsula (NAP) and, using both empirical data and simulations, evaluated the effects of colonization timing and founder population heterogeneity on patterns of genetic differentiation. We screened 161 single nucleotide polymorphisms and found evidence of nonequilibrium population structure when the slope of the isolation-by-distance relationship was examined at incremental spatial scales. In addition, simulations suggested that this pattern closely matched models of recent colonization of the NAP by secondary contact. Our results agree with geological and archaeological data indicating that the NAP was a dynamic landscape that may have been more recently colonized than during the last deglaciation because of dramatic changes in coastal hydrology over the last several thousand years.

PMID: 24118255 [PubMed – indexed for MEDLINE]

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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. The aim of this study was to further our understanding of the potential effects of natural and synthetic estrogens on the brain-pituitary-gonad axis in fish by determining the effects of 17α-ethynylestradiol (EE2) on the pituitary transcriptome. We exposed sub-adult coho salmon (Oncorhynchus kisutch) to 0 or 12 ng EE2/L for up to 6 weeks and effects on the pituitary transcriptome of females were assessed using high-throughput Illumina(®) sequencing, RNA-Seq and pathway analysis. After 1 or 6 weeks, 218 and 670 contiguous sequences (contigs) respectively, were differentially expressed in pituitaries of EE2-exposed fish relative to control. Two of the most highly up- and down-regulated contigs were luteinizing hormone β subunit (241-fold and 395-fold at 1 and 6 weeks, respectively) and follicle-stimulating hormone β subunit (-3.4-fold at 6 weeks). Additional contigs related to gonadotropin synthesis and release were differentially expressed in EE2-exposed fish relative to controls. These included contigs involved in gonadotropin releasing hormone (GNRH) and transforming growth factor-β signaling. There was an over-representation of significantly affected contigs in 33 and 18 canonical pathways at 1 and 6 weeks, respectively, including circadian rhythm signaling, calcium signaling, peroxisome proliferator-activated receptor (PPAR) signaling, PPARα/retinoid x receptor α activation, and netrin signaling. Network analysis identified potential interactions between genes involved in circadian rhythm and GNRH signaling, suggesting possible effects of EE2 on timing of reproductive events.

PMID: 24007788 [PubMed – indexed for MEDLINE]

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