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Iwamoto, I, Trivedi MM, Checkley Jr. DM.  1998.  Real-time detection and classification of objects in flowing water. Machine vision systems for inspection and metrology VII : 4-5 November, 1998, Boston, Massachusetts . 3521( Batchelor BG, Miller JWV, Solomon S, Eds.).:214-220., Bellingham, Wash.: SPIE (International Society for Optical Engineering) Abstract
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Iwamoto, S, Checkley DM, Trivedi MM.  2001.  REFLICS: Real-time flow imaging and classification system. Machine Vision and Applications. 13:1-13.   10.1007/pl00013270   AbstractWebsite

An accurate analysis of a large dynamic system like our oceans requires spatially fine and temporally matched data collection methods. Current methods to estimate fish stock size from pelagic (marine) fish egg abundance by using ships to take point samples of fish eggs have large margins of error due to spatial and temporal undersampling. The real-time flow imaging and classification system (REFLICS) enhances fish egg sampling by obtaining continuous, accurate information on fish egg abundance as the ship cruises along in the area of interest. REFLICS images the dynamic flow with a progressive-scan area camera (60 frames/s) and a synchronized strobe in backlighting configuration. Digitization and processing occur on a dual-processor Pentium II PC and a pipeline-based image-processing board. REFLICS uses a segmentation algorithm to locate fish-egg-like objects in the image and then a classifier to determine fish egg, species, and development stage (age). We present an integrated system design of REFLICS and performance results. REFLICS can perform in real time (60 Hz), classify fish eggs with low false negative rates on real data collected from a cruise, and work in harsh conditions aboard ships at sea. REFLICS enables cost-effective, real-time assessment of pelagic fish eggs for research and management.

Checkley, DM.  1984.  Relation of growth to ingestion for larvae of Atlantic herring Clupea harengus and other fish. Marine Ecology-Progress Series. 18:215-224.   10.3354/meps018215   AbstractWebsite

Larvae of Atlantic herring Clupea harengus were reared on wild plankton and Artemia salina nauplii in the laboratory at 7 to 9°C for 95 d. Between ages of 20 and 38 d, larvae were fed only Artemia nauplii and the specific rates of ingestion and growth were measured and compared. Relations of rate and efficiency of growth to ingestion were similar in terms of carbon and nitrogen. Growth was linearly related to ingestion (r2= 0.89, n = 9). Starved larvae lost mass at a specific rate of 0.03 d^-1 (3% d^-1) until death at 14 d. A specific ingestion rate of 0.04 d^-1 was required to balance defecation and metabolism. Gross growth efficiency (growth rate/ingestion rate) rose from -1.2 at a low ingestion rate (0.015 d^-1) to 0.4 at the greatest observed ingestion rate (0.11 d^-1) . Condition factor (dry weight length^-3) was significantly related to both ingestion rate and length (r2 = 0.69, n = 20).These results, combined with those for other fish larvae, indicate an asymptotic relation between rates of growth and ingestion such that gross growth efficiency is maximal (0.4) at intermediate ingestion rate. Fish larvae surviving in the sea appear to maximize their ingestion rate and thus grow rapidly but with a reduced efficiency.

Reiss, CS, Checkley DM, Bograd SJ.  2008.  Remotely sensed spawning habitat of Pacific sardine (Sardinops sagax) and Northern anchovy (Engraulis mordax) within the California Current. Fisheries Oceanography. 17:126-136.   10.1111/j.1365-2419.2008.00469.x   AbstractWebsite

We use trivariate kernel density estimation to define spawning habitat of northern anchovy (Engraulis mordax) and Pacific sardine (Sardinops sagax) in the California Current using satellite data and in situ egg samples from the Continuous Underway Fish Egg Sampler (CUFES) deployed during surveys in April by the California Cooperative Oceanic Fisheries Investigations (CalCOFI). Observed egg distributions were compared with monthly composite satellite sea surface temperature (SST) and surface chlorophyll a (chl a) data. Based on the preferred spawning habitat, as defined in SST and chl a space, the satellite data were used to predict potential spawning habitat along two areas of the west coast of North America. Data from the southern area (21.5 to 39 degrees N) were compared to observations from the CUFES data for the period 1998-2005. Northern anchovy and Pacific sardine exhibited distinctly different spawning habitat distributions. A significant relationship was found between satellite-based spawning area and that measured during surveys for sardine. CUFES area estimated for sardine was similar in magnitude to that estimated from satellite data (similar to 60 000 km(2)). In contrast, spawning habitat of anchovy averaged between 1000 and 200 000 km(2) for the period 1998-2005, for CUFES and satellite estimates, respectively. Interannual variability in the area (km(2)) and duration (months) of estimates of suitable habitat varied between species and between the northern (39 to 50.5 degrees N) and southern portions of the California Current. Long-term monitoring of habitat variability using remote sensing data is possible in the southern portion of the California Current, and could be improved upon in the northern area with the addition of surveys better timed to describe relationships between observed and estimated spawning habitats.

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.

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.