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San Diego, CA, United States

van Noord J.E.,Southwest Fisheries Science Center
Ichthyological Research | Year: 2013

Myctophids are important components of marine food webs, but little is known about the diets of many species in large stretches of the ocean. To fill this knowledge gap, Myctophum lychnobium, Symbolophorus evermanni, Centrobranchus andreae, Myctophum aurolaternatum, and Myctophum nitidulum were collected off the previously unsampled Mariana Islands in 2007. Myctophum lychnobium predominately consumed pelagic molluscs (28 % by number), amphipods (26 %), and copepods (24 %). Symbolophorus evermanni consumed copepods (53 %) and larval fishes (22 %). Centrobranchus andreae consumed molluscs (90 %). Little dietary overlap occurred among these fishes, and the reliance on molluscs was unusual compared to results from previous studies. © 2012 The Ichthyological Society of Japan. Source

Anderson E.C.,Southwest Fisheries Science Center
Statistical applications in genetics and molecular biology | Year: 2012

Advances in genotyping that allow tens of thousands of individuals to be genotyped at a moderate number of single nucleotide polymorphisms (SNPs) permit parentage inference to be pursued on a very large scale. The intergenerational tagging this capacity allows is revolutionizing the management of cultured organisms (cows, salmon, etc.) and is poised to do the same for scientific studies of natural populations. Currently, however, there are no likelihood-based methods of parentage inference which are implemented in a manner that allows them to quickly handle a very large number of potential parents or parent pairs. Here we introduce an efficient likelihood-based method applicable to the specialized case of cultured organisms in which both parents can be reliably sampled. We develop a Markov chain representation for the cumulative number of Mendelian incompatibilities between an offspring and its putative parents and we exploit it to develop a fast algorithm for simulation-based estimates of statistical confidence in SNP-based assignments of offspring to pairs of parents. The method is implemented in the freely available software SNPPIT. We describe the method in detail, then assess its performance in a large simulation study using known allele frequencies at 96 SNPs from ten hatchery salmon populations. The simulations verify that the method is fast and accurate and that 96 well-chosen SNPs can provide sufficient power to identify the correct pair of parents from amongst millions of candidate pairs. Source

Squires D.,Southwest Fisheries Science Center
Fish and Fisheries | Year: 2010

Buybacks of fishing vessels, licences, access and other rights, and gear, sometimes called decommissioning schemes, have traditionally been a key policy tool to address overcapacity, overexploitation of fish stocks, and distributional issues in fisheries. Two more issues can be added, sustainable use of ecosystems and conservation of biodiversity (i.e. ecological public goods and services) and providing a transition to a more rationalized fishery. This study discusses reasons for buybacks; examines consequences; considers asymmetric information, design of buyback auctions and other design issues; buybacks as a transition to a rationalized industry with strong property rights and governance, financing and transnational fisheries; draws out key lessons from the international experience; and provides an overall evaluation. © 2010 Blackwell Publishing Ltd. Source

Wilson C.,Southwest Fisheries Science Center
Geophysical Research Letters | Year: 2011

The dissipation of surface tidal energy into internal tides plays a critical role in ocean mixing. However, quantifying the spatial distribution of this energy flux, which is required for ocean and climate modeling, has been largely based on modeling efforts and there is a need for validating observations. The summer development of large blooms of chlorophyll along 30N in the E. Pacific is presented as evidence of enhanced tidal mixing. The region near 30 is a "double" critical latitude, with a transformation of internal waves occurring at both diurnal and semidiurnal frequencies. The breakdown at the critical latitude of internal waves generated at Hawaii could provide the physical mechanism to explain these blooms. The blooms develop in a region characterized by a weak summer surface stratification, which is therefore more susceptible to mixing. Copyright 2011 by the American Geophysical Union. Source

MacFarlane R.B.,Southwest Fisheries Science Center
Canadian Journal of Fisheries and Aquatic Sciences | Year: 2010

The greatest rates of energy accumulation and growth in subyearling Chinook salmon (Oncorhynchus tshawytscha) occurred during the first month following ocean entry, supporting the importance of this critical period. Data from an 11-year study in the coastal ocean off California and the San Francisco Estuary revealed that juvenile salmon gained 3.2 kj·day-1 and 0.8 g·day-1, representing 4.3%·day-1 and 5.2% day-1, respectively, relative to estuary exit values. Little gain in energy (0.28 kj·day-1) or size (0.07 g·day-1) occurred in the estuary, indicating that the nursery function typically ascribed to estuaries can be deferred to initial ocean residence. Calculated northern anchovies (Engraulis mordax) equivalents to meet energy gains were one anchovy per day in the estuary (8% body weight·day-1) and about three per day immediately following ocean entry (15% body weight·day-1). Energy content in the estuary was positively related to higher salinity and lower freshwater outflow, whereas in the ocean, cooler temperatures, lower sea level, and greater upwelling resulted in greater gains. These results suggest that greater freshwater flows, warmer sea temperatures, and reduced or delayed upwelling, all of which are indicated by some (but not all) climate models, will likely decrease growth of juvenile Chinook salmon, leading to reduced survival. Source

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