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Journal Article
Rose, KA, Fiechter J, Curchitser EN, Hedstrom K, Bernal M, Creekmore S, Haynie A, Ito S, Lluch-Cota S, Megrey BA, Edwards CA, Checkley D, Koslow T, McClatchie S, Werner F, MacCall A, Agostini V.  2015.  Demonstration of a fully-coupled end-to-end model for small pelagic fish using sardine and anchovy in the California Current. Progress in Oceanography. 138:348-380.   10.1016/j.pocean.2015.01.012   AbstractWebsite

We describe and document an end-to-end model of anchovy and sardine population dynamics in the California Current as a proof of principle that such coupled models can be developed and implemented. The end-to-end model is 3-dimensional, time-varying, and multispecies, and consists of four coupled sub-models: hydrodynamics, Eulerian nutrient-phytoplankton-zooplankton (NPZ), an individual-based full life cycle anchovy and sardine submodel, and an agent-based fishing fleet submodel. A predator roughly mimicking albacore was included as individuals that consumed anchovy and sardine. All submodels were coded within the ROMS open-source community model, and used the same resolution spatial grid and were all solved simultaneously to allow for possible feedbacks among the submodels. We used a super-individual approach and solved the coupled models on a distributed memory parallel computer, both of which created challenging but resolvable bookkeeping challenges. The anchovy and sardine growth, mortality, reproduction, and movement, and the fishing fleet submodel, were each calibrated using simplified grids before being inserted into the full end-to-end model. An historical simulation of 1959-2008 was performed, and the latter 45 years analyzed. Sea surface height (SSH) and sea surface temperature (SST) for the historical simulation showed strong horizontal gradients and multi-year scale temporal oscillations related to various climate indices (PDO, NPGO), and both showed responses to ENSO variability. Simulated total phytoplankton was lower during strong El Nino events and higher for the strong 1999 La Nina event. The three zooplankton groups generally corresponded to the spatial and temporal variation in simulated total phytoplankton. Simulated biomasses of anchovy and sardine were within the historical range of observed biomasses but predicted biomasses showed much less inter-annual variation. Anomalies of annual biomasses of anchovy and sardine showed a switch in the mid-1990s from anchovy to sardine dominance. Simulated averaged weights- and lengths-at-age did not vary much across decades, and movement patterns showed anchovy located close to the coast while sardine were more dispersed and farther offshore. Albacore predation on anchovy and sardine was concentrated near the coast in two pockets near the Monterey Bay area and equatorward of Cape Mendocino. Predation mortality from fishing boats was concentrated where sardine age-1 and older individuals were located close to one of the five ports. We demonstrated that it is feasible to perform multi-decadal simulations of a fully-coupled end-to-end model, and that this can be done for a model that follows individual fish and boats on the same 3-dimensional grid as the hydrodynamics. Our focus here was on proof of principle and our results showed that we solved the major technical, bookkeeping, and computational issues. We discuss the next steps to increase computational speed and to include important biological differences between anchovy and sardine. In a companion paper (Fiechter et al., 2015), we further analyze the historical simulation in the context of the various hypotheses that have been proposed to explain the sardine and anchovy cycles. (C) 2015 Elsevier Ltd. All rights reserved.

Checkley, DM, Uye S, Dagg MJ, Mullin MM, Omori M, Onbe T, Zhu MY.  1992.  Diel variation of the zooplankton and its environment at neritic stations in the Inland Sea of Japan and the north-west Gulf of Mexico. Journal of Plankton Research. 14:1-40.   10.1093/plankt/14.1.1   AbstractWebsite

Diel variations in the zooplankton and its environment were investigated at two, contrasting neritic stations. The first (BG-1), in the Inland Sea of Japan, was mixed and eutrophic, while the second (GM-1), in the north-west Gulf of Mexico, was stratified and oligotrophic. Intensive studies were conducted at each station in late summer for 2-3 days. Dissolved nutrients and the particulate matter were evenly distributed in time and space at BG-1, but were variable, and often maximal at depth in a nepheloid layer, at GM-1. For each station, approximately 20 categories of zooplankton were enumerated in samples collected with a plankton pump and retained on approximately 100-mu-m mesh filters, In general, the zooplankton at BG-1 exhibited little diel variation in abundance and distribution. By contrast, most types of zooplankton at GM-1 performed diel vertical migrations, though primarily within the lower half of the water column between the thermocline and nepheloid layer. Significantly, similar taxa and stages did not always behave similarly in these two, differing environments, nor did the zooplankton at GM-1 tend to aggregate at the depths of maximal particle abundance or primary productivity. We suggest that studies of diel variation of the distribution and abundance of the zooplankton often require more intense sampling, in time and space, in environments which are stratified rather than mixed.

Dagg, MJ, Jackson GA, Checkley DM.  2014.  The distribution and vertical flux of fecal pellets from large zooplankton in Monterey bay and coastal California. Deep-Sea Research Part I-Oceanographic Research Papers. 94:72-86.   10.1016/j.dsr.2014.09.001   AbstractWebsite

We sampled zooplankton and fecal pellets in the upper 200 m of Monterey Bay and nearby coastal regions in California, USA. On several occasions, we observed high concentrations of large pellets that appeared to be produced during night-time by dielly migrating euphausiids. High concentrations of pellets were found in near-surface waters only when euphausiids co-occurred with high concentrations of large (> 10 mu m) phytoplankton. Peak concentrations of pellets at mid-depth (100 or 150 m) during the day were consistent with the calculated sinking speeds of pellets produced near the surface at night. At these high flux locations (HI group), pellet concentrations declined below mid-depth. In contrast, at locations where the phytoplankton assemblage was dominated by small phytoplankton cells (< 10 mu m), pellet production and flux were low (LO group) whether or not euphausiid populations were high. Protozooplankton concentrations did not affect this pattern. We concluded that the day and night differences in pellet concentration and flux in the HI profiles were mostly due to sinking of dielly-pulsed inputs in the surface layer, and that small zooplankton (Oithona, Oncaea), heterotrophic dinoflagellates, and bacterial activity probably caused some pellet degradation or consumption below 100 m. We estimated that consumption of sinking pellets by large copepods was insignificant. High fluxes of pellets were episodic because they required both high concentrations of large phytoplankton and large stocks of euphausiids. Under these conditions, flux events overwhelmed retention mechanisms, resulting in large exports of organic matter from the upper 200 m. (C) 2014 The Authors. Published by Elsevier Ltd.

Hoss, DE, Checkley Jr. DM, Settle LR.  1989.  Diurnal buoyancy changes in larval Atlantic menhaden (Brevoortia tyrannus). Journal du Conseil International pour l'Exploration de la Mer. 191:105-111. Abstract
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Asch, RG, Checkley Jr DM.  2013.  Dynamic height: A key variable for identifying the spawning habitat of small pelagic fishes. Deep Sea Research Part I: Oceanographic Research Papers. 71:79-91.   10.1016/j.dsr.2012.08.006   AbstractWebsite

Small pelagic fishes off southern California exhibit interannual variations in the regions they occupy. An enhanced understanding of these fluctuations could improve fisheries management and predictions of fish's responses to climate change. We investigated dynamic height as a variable for identifying the spawning habitat of northern anchovy (Engraulis mordax), Pacific sardine (Sardinops sagax), and jack mackerel (Trachurus symmetricus). During cruises between 1998 and 2004, dynamic height was calculated from temperature and salinity profiles, while fish egg concentration was measured with obliquely towed bongo nets and the Continuous, Underway Fish Egg Sampler. Dynamic height ranged between 68 and 108 cm, with values increasing offshore. The greatest probability of encountering anchovy, sardine, and jack mackerel eggs occurred at dynamic heights of 79–83 cm, 84–89 cm, and 89–99 cm, respectively. Four mechanisms were proposed to explain how dynamic height affects egg distribution: (1) dynamic height is a proxy for upper water column temperature and salinity, which are known to influence spawning habitat. (2) Low dynamic heights are indicative of coastal upwelling, which increases primary and secondary productivity. (3) Egg concentration is greater at dynamic heights coincident with geostrophic currents that transport larvae to favorable habitats. (4) Eddies delineated by dynamic height contours retain eggs in productive habitats. To evaluate these mechanisms, a generalized linear model was constructed using dynamic height, temperature, salinity, chlorophyll, zooplankton volume, geostrophic currents, and eddies as independent variables. Dynamic height explained more variance than any other variable in models of sardine and anchovy spawning habitat. Together temperature, salinity, and chlorophyll accounted for 80–95% of the dynamic height effect, emphasizing the importance of the first two mechanisms. However, dynamic height remained statistically significant in the models of anchovy and jack mackerel spawning habitat after considering the effects of all other variables. Dynamic height shows promise as an ecological indicator of spawning habitat, because it integrates the effects of multiple oceanic variables, can be remotely sensed, and is predicted by ocean circulation models.