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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.

Bax, NJ, Appeltans W, Brainard R, Duffy JE, Dunstan P, Hanich Q, Davies HH, Hills J, Miloslavich P, Muller-Karger FE, Simmons S, Aburto-Oropeza O, Batten S, Benedetti-Cecchi L, Checkley D, Chiba S, Fischer A, Garcia MA, Gunn J, Klein E, Kudela RM, Marsac F, Obura D, Shin YJ, Sloyan B, Tanhua T, Wilkin J.  2018.  Linking capacity development to GOOS monitoring networks to achieve sustained ocean observation. Frontiers in Marine Science. 5   10.3389/fmars.2018.00346   AbstractWebsite

Developing enduring capacity to monitor ocean life requires investing in people and their institutions to build infrastructure, ownership, and long-term support networks. International initiatives can enhance access to scientific data, tools and methodologies, and develop local expertise to use them, but without ongoing engagement may fail to have lasting benefit. Linking capacity development and technology transfer to sustained ocean monitoring is a win-win proposition. Trained local experts will benefit from joining global communities of experts who are building the comprehensive Global Ocean Observing System (GOOS). This two-way exchange will benefit scientists and policy makers in developing and developed countries. The first step toward the GOOS is complete: identification of an initial set of biological Essential Ocean Variables (EOVs) that incorporate the Group on Earth Observations (GEO) Essential Biological Variables (EBVs), and link to the physical and biogeochemical EOVs. EOVs provide a globally consistent approach to monitoring where the costs of monitoring oceans can be shared and where capacity and expertise can be transferred globally. Integrating monitoring with existing international reporting and policy development connects ocean observations with agreements underlying many countries' commitments and obligations, including under SDG 14, thus catalyzing progress toward sustained use of the ocean. Combining scientific expertise with international capacity development initiatives can help meet the need of developing countries to engage in the agreed United Nations (UN) initiatives including new negotiations for the conservation and sustainable use of marine biological diversity of areas beyond national jurisdiction, and the needs of the global community to understand how the ocean is changing.

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.

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.

Shen, SG, Thompson AR, Correa J, Fietzek P, Ayon P, Checkley DM.  2017.  Spatial patterns of Anchoveta (Engraulis ringens) eggs and larvae in relation to pCO(2) in the Peruvian upwelling system. Proceedings of the Royal Society B-Biological Sciences. 284   10.1098/rspb.2017.0509   AbstractWebsite

Large and productive fisheries occur in regions experiencing or projected to experience ocean acidification. Anchoveta (Engraulis ringens) constitute the world's largest single-species fishery and live in one of the ocean's highest pCO(2) regions. We investigated the relationship of the distribution and abundance of Anchoveta eggs and larvae to natural gradients in pCO(2) in the Peruvian upwelling system. Eggs and larvae, zooplankton, and data on temperature, salinity, chlorophyll a and pCO(2) were collected during a cruise off Peru in 2013. pCO(2) ranged from 167-1392 atm and explained variability in egg presence, an index of spawning habitat. Zooplankton abundance explained variability in the abundance of small larvae. Within the main spawning and larva habitats (6-10 degrees S), eggs were found in cool, low-salinity, and both extremely low (less than 200 mu atm) and high (more than 900 mu atm) pCO(2) waters, and larvae were collected in warmer, higher salinity, and moderate (400-600 atm) pCO(2) waters. Our data support the hypothesis that Anchoveta preferentially spawned at high pCO(2) and these eggs had lower survival. Enhanced understanding of the influence of pCO(2) on Anchoveta spawning and larva mortality, together with pCO(2) measurements, may enable predictions of ocean acidification effects on Anchoveta and inform adaptive fisheries management.

Tommasi, D, Stock CA, Pegion K, Vecchi GA, Methot RD, Alexander MA, Checkley DM.  2017.  Improved management of small pelagic fisheries through seasonal climate prediction. Ecological Applications. 27:378-388.   10.1002/eap.1458   AbstractWebsite

Populations of small pelagic fish are strongly influenced by climate. The inability of managers to anticipate environment-driven fluctuations in stock productivity or distribution can lead to overfishing and stock collapses, inflexible management regulations inducing shifts in the functional response to human predators, lost opportunities to harvest populations, bankruptcies in the fishing industry, and loss of resilience in the human food supply. Recent advances in dynamical global climate prediction systems allow for sea surface temperature (SST) anomaly predictions at a seasonal scale over many shelf ecosystems. Here we assess the utility of SST predictions at this fishery relevant scale to inform management, using Pacific sardine as a case study. The value of SST anomaly predictions to management was quantified under four harvest guidelines (HGs) differing in their level of integration of SST data and predictions. The HG that incorporated stock biomass forecasts informed by skillful SST predictions led to increases in stock biomass and yield, and reductions in the probability of yield and biomass falling below socioeconomic or ecologically acceptable levels. However, to mitigate the risk of collapse in the event of an erroneous forecast, it was important to combine such forecast-informed harvest controls with additional harvest restrictions at low biomass.

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.

Shen, SG, Chen FY, Schoppik DE, Checkley DM.  2016.  Otolith size and the vestibulo-ocular reflex of larvae of white seabass Atractoscion nobilis at high pCO(2). Marine Ecology Progress Series. 553:173-183.   10.3354/meps11791   AbstractWebsite

We investigated vestibular function and otolith size (OS) in larvae of white seabass Atractoscion nobilis exposed to high partial pressure of CO2 (pCO(2)) The context for our study is the increasing concentration of CO2 in seawater that is causing ocean acidification (OA). The utricular otoliths are aragonitic structures in the inner ear of fish that act to detect orientation and acceleration. Stimulation of the utricular otoliths during head movement results in a behavioral response called the vestibulo-ocular reflex (VOR). The VOR is a compensatory eye rotation that serves to maintain a stable image during movement. VOR is characterized by gain (ratio of eye amplitude to head amplitude) and phase shift (temporal synchrony). We hypothesized that elevated pCO(2) would increase OS and affect the VOR. We found that the sagittae and lapilli of young larvae reared at 2500 mu atm pCO(2) (treatment) were 14 to 20% and 37 to 39% larger in area, respectively, than those of larvae reared at 400 mu atm pCO(2) (control). The mean gain of treatment larvae (0.39 +/- 0.05, n = 28) was not statistically different from that of control larvae (0.30 +/- 0.03, n = 20), although there was a tendency for treatment larvae to have a larger gain. Phase shift was unchanged. Our lack of detection of a significant effect of elevated pCO(2) on the VOR may be a result of the low turbulence conditions of the experiments, large natural variation in otolith size, calibration of the VOR or mechanism of acid-base regulation of white seabass larvae.

Lindegren, M, Checkley DM, Ohman MD, Koslow JA, Goericke R.  2016.  Resilience and stability of a pelagic marine ecosystem. Proceedings of the Royal Society B-Biological Sciences. 283   10.1098/rspb.2015.1931   AbstractWebsite

The accelerating loss of biodiversity and ecosystem services worldwide has accentuated a long-standing debate on the role of diversity in stabilizing ecological communities and has given rise to a field of research on biodiversity and ecosystem functioning (BEF). Although broad consensus has been reached regarding the positive BEF relationship, a number of important challenges remain unanswered. These primarily concern the underlying mechanisms by which diversity increases resilience and community stability, particularly the relative importance of statistical averaging and functional complementarity. Our understanding of these mechanisms relies heavily on theoretical and experimental studies, yet the degree to which theory adequately explains the dynamics and stability of natural ecosystems is largely unknown, especially in marine ecosystems. Using modelling and a unique 60-year dataset covering multiple trophic levels, we show that the pronounced multi-decadal variability of the Southern California Current System (SCCS) does not represent fundamental changes in ecosystem functioning, but a linear response to key environmental drivers channelled through bottom-up and physical control. Furthermore, we show strong temporal asynchrony between key species or functional groups within multiple trophic levels caused by opposite responses to these drivers. We argue that functional complementarity is the primary mechanism reducing community variability and promoting resilience and stability in the SCCS.

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.

Jackson, GA, Checkley DM, Dagg M.  2015.  Settling of particles in the upper 100 m of the ocean detected with autonomous profiling floats off California. Deep-Sea Research Part I-Oceanographic Research Papers. 99:75-86.   10.1016/j.dsr.2015.02.001   AbstractWebsite

We have deployed an autonomous profiling float, the SOLOPC, to sample the concentration of particles larger than 100 mu m off the California coast at approximately hourly intervals down to at least 100 m for periods as long as 12 d. We used the data to estimate total aggregate concentrations hourly at 2-m depth intervals, studying the dynamics of particle sedimentation in this difficult-to-sample region. We find that even over time scales of a week, sedimentation is highly variable, with detectable sedimentation events on about one quarter of the days. Most of these observations were along the southwest coast of the United States, a region known for its coastal upwelling and not necessarily representative of more oligotrophic regions. The aggregate settling rates that we estimate, on the order of 50 m d(-1), are consistent with in situ measurements and with rates calculated from coagulation models. The time interval between observations and their vertical resolution constrain the velocities that can be measured. To capture particle settling with velocities less than the 100 m d(-1) that is usually reported for near surface aggregates requires a sampling interval no more than about 0.25 d with a 2 m vertical resolution. This technique provides a powerful new tool to study the dynamics of particles and their sedimentation near the ocean surface, where export starts. (C) 2015 The Authors. Published by Elsevier Ltd.

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.

Checkley, DM, Lindegren M.  2014.  Sea surface temperature variability at the Scripps Institution of Oceanography Pier. Journal of Physical Oceanography. 44:2877-2892.   10.1175/jpo-d-13-0237.1   AbstractWebsite

Sea surface temperature (SST) has been measured from near the end of the Scripps Institution of Oceanography (SIO) pier daily since 1916. It is one of the world's longest instrumental time series of SST. It is widely used in studies of climate and marine ecosystems and in fisheries management. The authors hypothesized that a discontinuity exists in 1988, when the old pier was replaced with the present pier. A regression of annual-mean SST at SIO (SSTSIO) on the Pacific decadal oscillation index for 1916-87 was used to predict annual-mean SST (SSTSIO,PDO) for 1916-present. The residual (ResSST(SIO) = SSTSIO - SSTSIO,PDO) time series shows a positive discontinuity in 1988, when the present SIO pier was first used to measure SSTSIO. No discontinuity in 1988 was observed for ResSST at 12 other shore stations or in nearby waters. Use of the first principal component of other shore station time series of annual-mean SST as the predictor yields similar results. SSTSIO measured over 3 days shows a diel cycle and short-term variability consistent with rip current transport of warm surf-zone water to the end of the SIO pier. This study hypothesizes that rip current transport increased with the change from the old to the present pier and contributed to the observed discontinuity in SIO pier SST. The authors estimate an artifact of about +0.45 degrees C due to both rapid (1988 pier change) and gradual processes. Adjusting the SIO pier SST time series for this artifact reduces the long-term trend from +1.1 degrees to +0.6 degrees C century(-1), consistent with the global rate of change of SST over the past century.

Lindegren, M, Checkley DM.  2013.  Temperature dependence of Pacific sardine (Sardinops sagax) recruitment in the California Current Ecosystem revisited and revised. Canadian Journal of Fisheries and Aquatic Sciences. 70:245-252.   10.1139/cjfas-2012-0211   AbstractWebsite

Small pelagic fish typically show highly variable population dynamics due, in large part, to climate variability. Despite this sensitivity to climate, few stocks of pelagic species are managed with consideration of the environment. The Pacific sardine (Sardinops sagax) represents a notable exception, for which sea surface temperature (SST) from the Scripps Institution of Oceanography (SIO) pier has been used, until recently, to adjust exploitation pressure under warm (favorable) and cold (unfavorable) climate conditions. Recently, the previously established temperature-recruitment relationship was reassessed using different methods, resulting in abandonment of the temperature-sensitive harvest control rule in 2012. In this study, we revisit the previous temperature-recruitment relationship using the original methodology and an updated data set from 1981 to 2010. In contrast to the recent reassessment, we find temperature explains significant variability in recruitment and recruitment success. We also show that mean annual SST averaged over the present California Cooperative Oceanic Fisheries Investigations area is a better predictor of recruitment variability than SST at the SIO pier. We propose that sustainable management of the Pacific sardine should consider climate variability and that the basis for this be periodically updated and revised to inform management with the best available science.

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.

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–anchovy fluctuations and a knowledge base for sustainable fisheries management in the California Current Ecosystem and beyond.

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.

Petrik, CM, Jackson GA, Checkley JDM.  2013.  Aggregates and their distributions determined from LOPC observations made using an autonomous profiling float. Deep Sea Research Part I: Oceanographic Research Papers.   10.1016/j.dsr.2012.12.009   AbstractWebsite

The vertical flux of particles in the ocean drives the movement of organic carbon to the deep ocean. We have been studying the distribution and flux of these particles using the SOLOPC, a profiling Lagrangian (SOLO) float with a Laser Optical Particle Counter (LOPC). We have been able to distinguish between aggregate-like and zooplankton-like particles with diameters > 2 mm but needed a way to separate the smaller particles into aggregates and zooplankton. Observations included a lognormal-shaped fraction in the normalized volume distribution similar to that observed in results for simulations of particles in the euphotic zone. By fitting a lognormal distribution to the volume spectrum of particles with diameters ≤ 2 mm , we have been successful at making a separation of marine snow material from other, presumably living, particles. The particle volumes derived using the separations are positively correlated with fluorescence, particulate organic carbon, and the volume of larger particles classified as aggregate-like, which supports the conclusion that these particles are truly aggregates, in some cases derived from phytoplankton. The residual volumes (total less the above fit) are highly correlated with the volumes of large, zooplankton-like particles. Downward velocities of the aggregate fraction calculated from time series of particle profiles are consistent with previous estimates of particle settling rates ( 20 – 70 m d − 1 ) . We now have a tool to estimate aggregate distributions, properties, and vertical fluxes in the euphotic zone, including when and where they change.

Song, H, Miller AJ, McClatchie S, Weber ED, Nieto KM, Checkley DM.  2012.  Application of a data-assimilation model to variability of Pacific sardine spawning and survivor habitats with ENSO in the California Current System. Journal of Geophysical Research-Oceans. 117   10.1029/2011jc007302   AbstractWebsite

The Pacific sardine (Sardinops sagax) showed significant differences in spawning habitat area, spawning habitat quality and availability of survivor habitat as the Pacific Ocean went through the La Nina state in April 2002 to a weak El Nino in April 2003. During another El Nino/Southern Oscillation transition period in 2006-2007 when the El Nino state retreated and the La Nina returned, a similar pattern in spawning habitat quality was seen. The coupling between the atmospheric forcing, the physical ocean states and the properties of the sardine egg spawning are investigated using dynamically consistent data-assimilation fits of the available physical oceanographic observations during these months. Fits were executed using the Regional Ocean Modeling System four-dimensional variational assimilation platform along with adjoint model runs using a passive tracer to deduce source waters for the areas of interest. Analysis using the data-assimilation model runs reveals that unusually strong equatorward wind-forcing drives offshore transport during the La Nina conditions, which extends the spawning habitat for sardine further offshore. A statistical model of sardine spawning habitat shows better habitat quality during the El Nino conditions, which is associated with higher egg densities and corresponded to higher daily egg production. Concentration of eggs is also increased by convergence of water. The results of the source waters analysis using the adjoint data assimilation model support the idea that offshore transport extends the spawning habitat, and show that higher levels of nutrient are brought into the spawning habitat with high concentration of sardine eggs.

Takahashi, M, Checkley DM, Litz MNC, Brodeur RD, Peterson WT.  2012.  Responses in growth rate of larval northern anchovy (Engraulis mordax) to anomalous upwelling in the northern California Current. Fisheries Oceanography. 21:393-404.   10.1111/j.1365-2419.2012.00633.x   AbstractWebsite

We examined variability in growth rate during the larval stage of northern anchovy (Engraulis mordax) in response to physical and biological environmental factors in 2005 and 2006. The onset of spring upwelling was anomalously delayed by 23 months until mid-July in 2005; in contrast, spring upwelling in 2006 began as a normal year in the northern California Current. Larval and early juvenile E. mordax were collected in August, September, and October off the coast of Oregon and Washington. Hatch dates ranged from May to September, with peaks in June and August in 2005 and a peak in July in 2006, based on the number of otolith daily increments. Back-calculated body length-at-age in the June 2005 hatch cohort was significantly smaller than in the August 2005 cohort, which had comparable growth to the July 2006 cohort. Standardized otolith daily increment widths as a proxy for seasonal variability in somatic growth rates in 2005 were negative until late July and then changed to positive with intensification of upwelling. The standardized increment width was a positive function of biomass of chlorophyll a concentration, and neritic cold-water and oceanic subarctic copepod species sampled biweekly off Newport, Oregon. Our results suggest that delayed upwelling in 2005 resulted in low food availability and, consequently, reduced E. mordax larval growth rate in early summer, but once upwelling began in July, high food availability enhanced larval growth rate to that typical of a normal upwelling year (e.g., 2006) in the northern California Current.

Jackson, GA, Checkley DM.  2011.  Particle size distributions in the upper 100 m water column and their implications for animal feeding in the plankton. Deep-Sea Research Part I-Oceanographic Research Papers. 58:283-297.   10.1016/j.dsr.2010.12.008   AbstractWebsite

We deployed autonomous particle-sensing SOLOPC floats more than eight times during five cruises, amassing almost 400 profiles of particle size (d > 90 mu m) and abundance between the ocean surface and 100 m. The profiles consistently had subsurface maxima in particle volume. The median (by volume) equivalent spherical diameter for the particle distribution was 0.4-0.8 mm and increased with depth in a manner similar to that observed in coagulation simulations. There was a sharp cutoff at the bottom of the high particle concentration region. Estimation of particle fluxes made using the size distributions show an increasing downward movement through the particle field above the sharp particle cutoff. The increase of particle flux with depth through the euphotic zone implies a partial spatial separation of production and consumption. The sharp drop in particle volume and flux implies that the base of the particle-rich zone is a region of active particle consumption, possibly by zooplankton flux feeding. Our data show greater concentrations of zooplankton-type particles relative to marine snow-type particles below the particle maximum. Such behavior could explain why zooplankton are frequently observed at and immediately below the particle maximum rather than the productivity maximum and suggests an important role for flux feeding in carbon and nutrient cycling at the base of the particle maximum. This implies that zooplankton act as gatekeepers for the movement of organic matter to the mesopelagic. The ability of the SOLOPC to sample hourly with high resolution in the upper 100 m of the ocean provides a powerful complement for the study of particles where it has been difficult to use sediment traps. (C) 2011 Elsevier Ltd. All rights reserved.

Checkley, DM, Barth JA.  2009.  Patterns and processes in the California Current System. Progress in Oceanography. 83:49-64.   10.1016/j.pocean.2009.07.028   AbstractWebsite

The California Current System (CCS) is forced by the distribution of atmospheric pressure and associated winds in relation to the west coast of North America. In this paper, we begin with a simplified case of winds and a linear coast, then consider variability characteristic of the CCS, and conclude by considering future change. The CCS extends from the North Pacific Current (similar to 50 degrees N) to off Baja California, Mexico (similar to 15-25 degrees N) with a major discontinuity at Point Conception (34.5 degrees N). Variation in atmospheric pressure affects winds and thus upwelling. Coastal, wind-driven upwelling results in nutrification and biological production and a southward coastal jet. Offshore, curl-driven upwelling results in a spatially large, productive habitat. The California Current flows equatorward and derives from the North Pacific Current and the coastal jet. Dominant modes of spatial and temporal variability in physical processes and biological responses are discussed. High surface production results in deep and bottom waters depleted in oxygen and enriched in carbon dioxide. Fishing has depleted demersal stocks more than pelagic stocks, and marine mammals, including whales, are recovering. Krill, squid, and micronekton are poorly known and merit study. Future climate change will differ from past change and thus prediction of the CCS requires an understanding of its dynamics. Of particular concern are changes in winds, stratification, and ocean chemistry. (C) 2009 Elsevier Ltd. All rights reserved.

Checkley, DM, Dickson AG, Takahashi M, Radich JA, Eisenkolb N, Asch R.  2009.  Elevated CO2 Enhances Otolith Growth in Young Fish. Science. 324:1683-1683.   10.1126/science.1169806   AbstractWebsite

A large fraction of the carbon dioxide added to the atmosphere by human activity enters the sea, causing ocean acidification. We show that otoliths (aragonite ear bones) of young fish grown under high CO2 (low pH) conditions are larger than normal, contrary to expectation. We hypothesize that CO2 moves freely through the epithelium around the otoliths in young fish, accelerating otolith growth while the local pH is controlled. This is the converse of the effect commonly reported for structural biominerals.

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
Checkley Jr., DM, Ayon P, Baumgartner TR, Bernal M, Coetzee JC, Emmett R, Guevara R, Hutchings L, Ibaibariaga L, Nakata H, Oozeki Y, Planque B, Schweigert J, Stratoudakis Y, Van der Lingen CD.  2009.  Habitats. Climate change and small pelagic fish. ( Checkley Jr. DM, Alheit J, Oozeki Y, Roy C, Eds.).:12-44., Cambridge, UK; New York: Cambridge University Press Abstract