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Davison, PC, Checkley DM, Koslow JA, Barlow J.  2013.  Carbon export mediated by mesopelagic fishes in the northeast Pacific Ocean. Progress in Oceanography. 116:14-30.   10.1016/j.pocean.2013.05.013   AbstractWebsite

The role of fishes in the global carbon cycle is poorly known and often neglected. We show that the biomass of mesopelagic fishes off the continental USA west to longitude 141 degrees W is positively related to annual net primary productivity, and averages 17 g m(-2). We estimate the export of carbon out of the epipelagic ocean mediated by mesopelagic fishes ("fish-mediated export"; FME) with individual-based metabolic modeling using the catch from 77 mesopelagic trawls distributed over the study area. FME was 15-17% (22-24 mg C m(-2) d(-1)) of the total carbon exported in the study area (144 mg C m(-2) d(-1)), as estimated from satellite data. FME varies spatially in both magnitude and relative importance. Although the magnitude of FME increases with increasing total export, the ratio of FME to total export decreases. FME exceeds 40% of the total carbon export in the oligotrophic North Pacific Subtropical Gyre, but forms <10% of the total export in the most productive waters of the California Current. Because the daytime residence depth of these fishes is below the depths where most remineralization of sinking particles occurs, FME is approximately equal to the passive transport at a depth of 400 m. The active transport of carbon by mesopelagic fishes and zooplankton is similar in magnitude to the gap between estimates of carbon export obtained with sediment traps and by other methods. FME should be considered in models of the global carbon cycle. (C) 2013 Elsevier Ltd. All rights reserved.

Angel, MV, Checkley Jr. DM, Heany SI.  1985.  Chapter One: Plankton migrations. Introduction. Contributions in marine science volume 27 supplement. ( Rankin M, Wohlschlag DE, Eds.).:43-44., Port Aransas, TX: Port Aransas Marine Laboratory, University of Texas Marine Science Institute Abstract
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Jones, WA, Checkley DM.  2017.  Classification of otoliths of fishes common in the Santa Barbara Basin based on morphology and chemical composition. Canadian Journal of Fisheries and Aquatic Sciences. 74:1195-1207.   10.1139/cjfas-2015-0566   AbstractWebsite

Morphological and chemical features of fish otoliths are used to distinguish between populations and stocks. We hypothesized that these features can also be used to distinguish between fishes of different taxonomic groups common in and near the Santa Barbara Basin, including mesopelagic, pelagic, and demersal fish. Sagittal otoliths obtained from 905 fish representing six taxonomic groups were imaged, and 12 geometric and 59 elliptic Fourier morphometric features were extracted. A subset of 143 otoliths was also analyzed for Li, Na, Mg, K, Mn, Sr, and Ba. We used chemical composition in addition to morphology because the latter may be altered between otolith formation and analysis. Two sets of classifiers were made: one using only morphometric features and one using both morphometric and element features. Random forest analysis was generally superior to discriminant function analysis. Highest classification success, evaluated using cross-validation and otoliths of masked identity, was achieved with multiple feature types. The ten strongest discriminatory features of all available feature types were used in the final classification models. Our method is applicable to the classification of otoliths recovered from guts, feces, middens, and sediments as well to classify other biological objects.

Checkley, D.  2009.  Climate change and small pelagic fish. :1onlineresource(xvii,372p.)ill.,maps.., Cambridge, UK ; New York: Cambridge University Press,   10.1017/CBO9780511596681   Abstract
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Politikos, DV, Curchitser EN, Rose KA, Checkley DM, Fiechter J.  2018.  Climate variability and sardine recruitment in the California Current: A mechanistic analysis of an ecosystem model. Fisheries Oceanography. 27:602-622.   10.1111/fog.12381   AbstractWebsite

Recruitment varies substantially in small pelagic fish populations. Understanding of the mechanisms linking environment to recruitment is essential for the effective management of fisheries resources. In this study, we used a fully coupled end-to-end ecosystem model to study the effect of climate variability on sardine recruitment in the California Current System during 1965-2006. Ocean variability was represented by ROMS hydrodynamic and NEMURO biogeochemical models, and sardine population dynamics was simulated through a full life cycle individual-based model. Model analysis was designed to elucidate how changes in abiotic and biotic conditions may impact the spawning habitats, early life stage survival, and ultimately recruitment of sardine. Our findings revealed the importance of spatial processes to shape early life stages dynamics. Shifts in spawning habitats were dictated by the spatial variations in temperature and the behavioral movement of adults. Additionally, the spatial match of eggs with warmer temperatures and larvae with their prey influenced their survival. The northward shifts in spawning locations and the accomplishment of good recruitment in warmer years agreed with existing knowledge. Egg production and survival during egg and yolk-sac larval stages were key factors to drive the long-term variations in recruitment. Finally, our analysis provided a quantitative assessment of climate impact on year-to-year variation in sardine recruitment by integrating multiple hypotheses.

Checkley, DM, Asch RG, Rykaczewski RR.  2017.  Climate, anchovy, and sardine. Annual Review of Marine Sciences, Vol 9. 9:469-493., Palo Alto: Annual Reviews   10.1146/annurev-marine-122414-033819   Abstract

Anchovy and sardine populated productive ocean regions over hundreds of thousands of years under a naturally varying climate, and are now subject to climate change of equal or greater magnitude occurring over decades to centuries. We hypothesize that anchovy and sardine populations are limited in size by the supply of nitrogen from outside their habitats originating from upwelling, mixing, and rivers. Projections of the responses of anchovy and sardine to climate change rely on a range of model types and consideration of the effects of climate on lower trophic levels, the effects of fishing on higher trophic levels, and the traits of these two types of fish. Distribution, phenology, nutrient supply, plankton composition and production, habitat compression, fishing, and acclimation and adaptation may be affected by ocean warming, acidification, deoxygenation, and altered hydrology. Observations of populations and evaluation of model skill are essential to resolve the effects of climate change on these fish.

Lindegren, M, Checkley DM, Rouyer T, MacCall AD, Stenseth NC.  2013.  Climate, fishing, and fluctuations of sardine and anchovy in the California Current. Proceedings of the National Academy of Sciences.   10.1073/pnas.1305733110   AbstractWebsite

Since the days of Elton, population cycles have challenged ecologists and resource managers. Although the underlying mechanisms remain debated, theory holds that both density-dependent and density-independent processes shape the dynamics. One striking example is the large-scale fluctuations of sardine and anchovy observed across the major upwelling areas of the world. Despite a long history of research, the causes of these fluctuations remain unresolved and heavily debated, with significant implications for fisheries management. We here model the underlying causes of these fluctuations, using the California Current Ecosystem as a case study, and show that the dynamics, accurately reproduced since A.D. 1661 onward, are explained by interacting density-dependent processes (i.e., through species-specific life-history traits) and climate forcing. Furthermore, we demonstrate how fishing modifies the dynamics and show that the sardine collapse of the 1950s was largely unavoidable given poor recruitment conditions. Our approach provides unique insight into the origin of sardine‚Äďanchovy fluctuations and a knowledge base for sustainable fisheries management in the California Current Ecosystem and beyond.

Lindegren, M, Checkley DM, Koslow JA, Goericke R, Ohman MD.  2018.  Climate-mediated changes in marine ecosystem regulation during El Nino. Global Change Biology. 24:796-809.   10.1111/gcb.13993   AbstractWebsite

The degree to which ecosystems are regulated through bottom-up, top-down, or direct physical processes represents a long-standing issue in ecology, with important consequences for resource management and conservation. In marine ecosystems, the role of bottom-up and top-down forcing has been shown to vary over spatio-temporal scales, often linked to highly variable and heterogeneously distributed environmental conditions. Ecosystem dynamics in the Northeast Pacific have been suggested to be predominately bottom-up regulated. However, it remains unknown to what extent top-down regulation occurs, or whether the relative importance of bottom-up and top-down forcing may shift in response to climate change. In this study, we investigate the effects and relative importance of bottom-up, top-down, and physical forcing during changing climate conditions on ecosystem regulation in the Southern California Current System (SCCS) using a generalized food web model. This statistical approach is based on nonlinear threshold models and a long-term data set (similar to 60years) covering multiple trophic levels from phytoplankton to predatory fish. We found bottom-up control to be the primary mode of ecosystem regulation. However, our results also demonstrate an alternative mode of regulation represented by interacting bottom-up and top-down forcing, analogous to wasp-waist dynamics, but occurring across multiple trophic levels and only during periods of reduced bottom-up forcing (i.e., weak upwelling, low nutrient concentrations, and primary production). The shifts in ecosystem regulation are caused by changes in ocean-atmosphere forcing and triggered by highly variable climate conditions associated with El Nino. Furthermore, we show that biota respond differently to major El Nino events during positive or negative phases of the Pacific Decadal Oscillation (PDO), as well as highlight potential concerns for marine and fisheries management by demonstrating increased sensitivity of pelagic fish to exploitation during El Nino.

Bird, JL, Eppler DT, Checkley DM.  1986.  Comparisons of herring otoliths using Fourier series shape analysis. Canadian Journal of Fisheries and Aquatic Sciences. 43:1228-1234.   10.1139/f86-152   AbstractWebsite

Numeric analysis of otolith morphology provides vital information to commercial fisheries concerning the age distribution, racial origin, and, to some extent, the environmental history of fish stocks. Conventional methods used to retrieve these data, though proven to be effective, are time consuming, susceptible to ambiguous interpretations, and only semiquantitative. Fourier shape descriptors, when used to analyze outlines of otolith silhouettes, represent a rapid, objective, semiautomated means of obtaining much of this information. Analysis of Fourier shape information derived from otoliths of juvenile and adult Alaskan herring and adult Northwest Atlantic herring show that otolith shape reflects differences in fish age and fish race. The shape of otoliths of juvenile fish are significantly different from those of adult fish. Few shape differences can be found, though, between otoliths from adult fish of different age within the same stock. Distinct differences exist between Atlantic and Alaskan adult otolith shapes. For some stocks, minor shape differences occur between left and right otoliths. Differences in otolith shape arising from sexual dimorphism are not apparent.

Osgood, KE, Checkley Jr. DM.  1996.  Concentration of Calanus pacificus in the Santa Barbara Basin. EOS Trans. AGU. 76:36. Abstract
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Checkley, DM, Ortner PB, Settle LR, Cummings SR.  1997.  A continuous, underway fish egg sampler. Fisheries Oceanography. 6:58-73.   10.1046/j.1365-2419.1997.00030.x   AbstractWebsite

We describe a method to sample the highly contagious distribution of pelagic fish eggs. CUFES, the continuous, underway fish egg sampler, consists of a submersible pump, concentrator, electronics and sample collector. This system operates continuously and under nearly all sea conditions, providing a real-time estimate of the volumetric abundance of pelagic fish eggs at pump depth, usually 3 m. CUFES-derived estimates of volumetric abundance agree well with those from nets towed at pump depth and with areal abundance estimated from vertically integrated plankton tows. CUFES has been used successfully to sample the eggs of menhaden, pinfish, sardine, and anchovy off the coasts of the eastern and western United States and South Africa. Two large patches of eggs of the Atlantic menhaden were sampled off North Carolina in winter 1993-94, had a linear scale of 5-10 km, and were found in waters between the Gulf Stream and mid-shelf front. Spawning location may he related to bathymetry. CUFES is now being used to estimate spawner biomass by the daily egg production method. An optical plankton counter provided accurate estimates of the number of Atlantic menhaden eggs sample by CUFES.

Checkley, DM, Dotson RC, Griffith DA.  2000.  Continuous, underway sampling of eggs of Pacific sardine (Sardinops sagax) and northern anchovy (Engraulis mordax) in spring 1996 and 1997 off southern and central California. Deep-Sea Research Part Ii-Topical Studies in Oceanography. 47:1139-1155. AbstractWebsite

Eggs of the northern anchovy and Pacific sardine were sampled at 3 m depth using the Continuous, Underway Fish Egg Sampler (CUFES) during two cruises off southern and central California in March and April 1996 and 1997. Simultaneous measurements were made of seawater temperature and salinity. Real-time AVHRR satellite images of sea surface temperature were processed onshore and transmitted to the ship at sea. Sardine and anchovy eggs were identified and counted live, at sea, and again ashore, preserved. A total of 2129 CUFES samples were collected during 41 d at sea and contained 62,409 sardine and 15,123 anchovy eggs. Sardine eggs were widespread and abundant in both cruises (mean concentrations: 5.2 and 5.1 eggs m(-3)) at and shoreward of the eastern boundary of the California Current. Anchovy eggs were found primarily inshore in the Southern California Eight and were less abundant (0.4 and 1.0 eggs m(-3), respectively, for the two cruises). Temperature-salinity plots indicated distinct separation of the spawning habitat of these two species and consistency in habitat between cruises in successive years. The distributions of sardine eggs and euphausiids collected by CUFES were complementary in space and time. (C) 2000 Elsevier Science Ltd. All rights reserved.