Davis Cabell S.

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Davis

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Cabell S.

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Interannual differences in larval haddock survival : hypothesis testing with a 3D biophysical model of Georges Bank

( 2014-06) Petrik, Colleen M. ; Ji, Rubao ; Davis, Cabell S.

The ultimate goal of early life studies of fish over the past century has been to better understand recruitment variability. As evident in the Georges Bank haddock (Melanogrammus aeglefinus) population, there is a strong relationship between recruitment success and processes occurring during the planktonic larval stage. This research sought new insights into the mechanisms controlling the recruitment process in fish populations by using biological-physical modeling methods together with laboratory and field data sets. We created the first three-dimensional model of larval haddock on Georges Bank by coupling models of hydrodynamics, lower trophic levels, a single copepod species, and larval haddock. Interactions between feeding, metabolism, growth, vertical behavior, advection, predation, and the physical environment of larval haddock were quantitatively investigated using the coupled models. Particularly, the model was used to compare survival over the larval period and the sources of mortality in 1995 and 1998, two years of disparate haddock recruitment. The results of model simulations suggest that the increased egg hatching rates and higher food availability, which reduced starvation and predation, in 1998 contributed to its larger year-class. Additionally, the inclusion of temperature-dependent predation rates produced model results that better agreed with observations of the mean hatch date of survivors. The results from this biophysical model imply that food-limitation and its related losses to starvation and predation, especially from hatch to 7 mm, may be responsible for interannual variability in recruitment and larval survival outside of the years studied.
Accurate automatic quantification of taxa-specific plankton abundance using dual classification with correction

(Inter-Research, 2006-01-11) Hu, Qiao ; Davis, Cabell S.

Optical imaging samplers are becoming widely used in plankton ecology, but image analysis methods have lagged behind image acquisition rates. Automated methods for analysis and recognition of plankton images have been developed, which are capable of real-time processing of incoming image data into major taxonomic groups. The limited accuracy of these methods can require significant manual post-processing to correct the automatically generated results, in order to obtain accurate estimates of plankton abundance patterns. We present here a dual-classification method in which each plankton image is first identified using a shaped-based feature set and a neural network classifier, and then a second time using a texture-based feature set and a support vector machine classifier. The plankton image is considered to belong to a given taxon only if the 2 identifications agree; otherwise it is labeled as unknown. This dual-classification method greatly reduces the false positive rate, and thus gives better abundance estimation in regions of low relative abundance. A confusion matrix is computed from a set of training images in order to determine the detection and false positives rates. These rates are used to correct abundances estimated from the automatic classification results. Aside from the manual sorting required to generate the initial training set of images, this dual-classification method is fully automatic and does not require subsequent manual correction of automatically sorted images. The resulting abundances agree closely with those obtained using manually sorted results. A set of images from a Video Plankton Recorder was used to evaluate this method and compare it with previously reported single-classifier results for major taxa.
Habitat usage by the cryptic copepods Pseudocalanus moultoni and P. newmani on Georges Bank (Northwest Atlantic)

( 2015-10-04) Bucklin, Ann ; McGillicuddy, Dennis J. ; Wiebe, Peter H. ; Davis, Cabell S.

The cryptic copepod species, Pseudocalanus moultoni and P. newmani, co-occur on Georges Bank and in the Gulf of Maine (Northwest Atlantic); even recent studies have reported results and conclusions based on examination of the combined species. Species-specific PCR (SS-PCR) based on mitochondrial cytochrome oxidase I (COI) sequence divergence was used in this study to discriminate the species. Species-specific descriptions of habitat usage and predicted patterns of transport and retention on Georges Bank were made by mapping distributions and calculating abundances of each species from January to June, 1999 for four vertical strata (0-15 m, 15-40 m, 40-100 m, and 0-100 m) and five regions (Northern Flank, Bank Crest, Northeast Peak, Southern Flank, and Slope Water) identified on the basis of bathymetry and circulation. Patterns of distribution and abundance for the two species during January to June, 1999 were largely consistent with those described based on vertically integrating mapping and analysis for the same period in 1997 by McGillicuddy and Bucklin (2002). The region-specific and depth-stratified analyses allowed further discrimination in habitat usage by the species and confirmed the distinctive patterns for the two species. The observed differences between the species in abundances among the five regions and three depth strata over Georges Bank impact their transport trajectories. The concentration of P. moultoni in deep layers likely explains the higher rates of retention and lower rates of advective loss of this species from the Bank, compared to P. newmani, which may be more subject to wind-driven transport in the surface layer. Accurate identification and discrimination of even closely-related and cryptic species is needed to ensure full understanding and realistic predictions of changes in diversity of zooplankton and the functioning of pelagic ecosystems.
A simplified age-stage model for copepod population dynamics

(Inter-Research, 2008-05-22) Hu, Qiao ; Davis, Cabell S. ; Petrik, Colleen M.

Complex 3D biological-physical models are becoming widely used in marine and freshwater ecology. These models are highly valued synthesizing tools because they provide insights into complex dynamics that are difficult to understand using purely empirical methods or theoretical analytical models. Of particular interest has been the incorporation of concentration-based copepod population dynamics into 3D physical transport models. These physical models typically have large numbers of grid points and therefore require a simplified biological model. However, concentration-based copepod models have used a fine resolution age-stage structure to prevent artificially short generation times, known as numerical ‘diffusion.’ This increased resolution has precluded use of age-stage structured copepod models in 3D physical models due to computational constraints. In this paper, we describe a new method, which tracks the mean age of each life stage instead of using age classes within each stage. We then compare this model to previous age-stage structured models. A probability model is developed with the molting rate derived from the mean age of the population and the probability density function (PDF) of molting. The effects of temperature and mortality on copepod population dynamics are also discussed. The mean-age method effectively removes the numerical diffusion problem and reproduces observed median development times (MDTs) without the need for a high-resolution age-stage structure. Thus, it is well-suited for finding solutions of concentration-based zooplankton models in complex biological-physical models.
Influence of ocean freshening on shelf phytoplankton dynamics

(American Geophysical Union, 2007-12-28) Ji, Rubao ; Davis, Cabell S. ; Chen, Changsheng ; Townsend, David W. ; Mountain, David G. ; Beardsley, Robert C.

Climate change-induced freshening of the ocean can enhance vertical stratification and alter circulation patterns in ways that influence phytoplankton dynamics. We examined the timing of spring phytoplankton blooms and the magnitude of net primary productivity in the Nova Scotian Shelf (NSS) - Gulf of Maine (GoM) region with respect to seasonal and interannual changes in surface water freshening from 1998 to 2006. The general pattern of temporal westward progression of the phytoplankton bloom corresponds with the gradient of increasing sea surface salinity from the NSS in the east to the western GoM. Increased freshening enhances the spatial gradients in bloom timing by stimulating earlier blooms upstream (NSS), but it has less impact downstream (the western GoM). Strong spatial gradients (increasing westward) of mean chlorophyll concentration and net primary productivity during post-bloom months (May–June) indicate that lower sea surface salinity upstream can likely impede nutrient fluxes from deep water and therefore affect overall productivity.
Wind-induced interannual variability of sea level slope, along-shelf flow, and surface salinity on the Northwest Atlantic shelf

(John Wiley & Sons, 2014-04-16) Li, Yun ; Ji, Rubao ; Fratantoni, Paula S. ; Chen, Changsheng ; Hare, Jonathan A. ; Davis, Cabell S. ; Beardsley, Robert C.

In this study, we examine the importance of regional wind forcing in modulating advective processes and hydrographic properties along the Northwest Atlantic shelf, with a focus on the Nova Scotian Shelf (NSS)-Gulf of Maine (GoM) region. Long-term observational data of alongshore wind stress, sea level slope, and along-shelf flow are analyzed to quantify the relationship between wind forcing and hydrodynamic responses on interannual time scales. Additionally, a simplified momentum balance model is used to examine the underlying mechanisms. Our results show significant correlation among the observed interannual variability of sea level slope, along-shelf flow, and alongshore wind stress in the NSS-GoM region. A mechanism is suggested to elucidate the role of wind in modulating the sea level slope and along-shelf flow: stronger southwesterly (northeastward) winds tend to weaken the prevailing southwestward flow over the shelf, building sea level in the upstream Newfoundland Shelf region, whereas weaker southwesterly winds allow stronger southwestward flow to develop, raising sea level in the GoM region. The wind-induced flow variability can influence the transport of low-salinity water from the Gulf of St. Lawrence to the GoM, explaining interannual variations in surface salinity distributions within the region. Hence, our results offer a viable mechanism, besides the freshening of remote upstream sources, to explain interannual patterns of freshening in the GoM.
WHOI-NEFC fisheries ecology seminar series : a summary

(Woods Hole Oceanographic Institution, 1985-06) Davis, Cabell S. ; Grosslein, Marvin D. ; Wiebe, Peter ; Grice, George D. ; Murawski, Steven A.

This report summarizes the findings of the joint WHOI-NEFC seminar series on recruitment processes in marine fish populations. The seminar series reviewed the status of knowledge of the recruitment process together with on-going research in this field. From the seminars presented it was evident that potentially important biological and physical processes which may control recruitment occur throughout the entire first year of life. It is important to understand the causes of recruitment variability in order to know the degree to which density dependence controls marine fish population dynamics. Future research, therefore, should not focus on a single process or life stage but instead should evaluate all potentially important processes throughout the first year of life.
Biological structure and seasonality in the Japan/East Sea

(Oceanography Society, 2006-09) Ashjian, Carin J. ; Arnone, Robert ; Davis, Cabell S. ; Jones, Burton ; Kahru, Mati ; Lee, Craig M. ; Mitchell, B. Gregory

The Japan/East Sea (JES) contains several oceanic regions separated by dynamic boundaries. These distinct regions, and the physical features that establish and maintain the boundaries between the regions, have significant impacts on its ocean biology. Until recently, most studies of the biology of the JES have focused on nearshore regions, with few detailed studies of the interior of the JES or the dynamic features that define the different regions. In addition, the classic sampling methods used in previous work have not allowed high-resolution studies of biological-physical interactions associated with key dynamic mesoscale frontal zones, quasi-synoptic surveys of water column and biological structure in three dimensions, or broad-scale description of the seasonal cycles in the different biogeographic regions of the JES.
Biological/physical modeling of upper ocean processes

(Woods Hole Oceanographic Institution, 1994-09) Davis, Cabell S. ; Steele, John H.

To enhance collaboration between researchers who model upper ocean biological/physical processes, a workshop was held at WHOI on June 7-12, 1993. The workshop was part of our on-going URIP project entitled "Modeling Biological-Physical Interactions: A Population Biological Approach" sponsored by ONR (Grant N000l4-92-J-1527). The two principal goals of the workshop were to: 1) identify critical problems related to mixed-layer biological-physical models, and 2) develop approaches for solving these problems. The workshop was organized into two parts to address these goals. The first part, held over the first day and a half, included three overview presentations given in plenary followed by working groups, organized along disciplinary lines, to identify critical issues. The second part of the workshop consisted of working groups, organized across disciplines, using "hands-on" modeling to address critical aspects of coupled biological-physical models. Several coupled models were presented and/or developed at the workshop addressing specific aspects of both the biological and physical dynamics. These aspects included the different mixed-layer formulations, a structured grazer population model, and an allometric food-web model including microbial-loop dynamics.
Remote silicate supply regulates spring phytoplankton bloom magnitude in the Gulf of Maine

(Association for the Sciences of Limnology and Oceanography (ASLO), 2022-02-24) Zang, Zhengchen ; Ji, Rubao ; Liu, Zongguang ; Chen, Changsheng ; Li, Yun ; Li, Siqi ; Davis, Cabell S.

Spring phytoplankton blooms in the Gulf of Maine (GoM) are sensitive to climate-related local and remote forcing. Nutrient supply through the slope water intrusion has been viewed as critical in regulating the GoM spring blooms, with an assumption that nitrogen is the primary limiting nutrient. In recent years, this paradigm has been challenged, with silicate being recognized as another potential limiting nutrient, but the source of silicate and its associated water mass remain difficult to be determined. In this study, a time series of spring bloom magnitude was constructed using a self-organizing map algorithm, and then correlated with the fluctuation of water composition in the deep Northeast Channel. The results reveal the importance of silicate supply from previously less-recognized deep Scotian Shelf Water inflow. This study offers a new hypothesis for spring bloom regulation, providing a better understanding of mechanisms controlling the spring bloom magnitude in the GoM.
The depth-distribution of nitrogen fixation by Trichodesmium spp. colonies in the tropical–subtropical North Atlantic

(Elsevier, 2015-07-02) Olson, Elise M. B. ; McGillicuddy, Dennis J. ; Dyhrman, Sonya T. ; Waterbury, John B. ; Davis, Cabell S. ; Solow, Andrew R.

Nitrogen fixation is an important yet still incompletely constrained component of the marine nitrogen cycle, particularly in the subsurface. A Video Plankton Recorder (VPR) survey in the subtropical North Atlantic found higher than expected Trichodesmium colony abundances at depth, leading to the hypothesis that deep nitrogen fixation in the North Atlantic may have been previously underestimated. Here, Trichodesmium colony abundances and modeled nitrogen fixation from VPR transects completed on two cruises in the tropical and subtropical North Atlantic in fall 2010 and spring 2011 were used to evaluate that hypothesis. A bio-optical model was developed based on carbon-normalized nitrogen fixation rates measured on those cruises. Estimates of colony abundance and nitrogen fixation were similar in magnitude and vertical and geographical distribution to conventional estimates in a recently compiled climatology. Thus, in the mean, VPR-based estimates of volume-specific nitrogen fixation rates at depth in the tropical North Atlantic were not inconsistent with estimates derived from conventional sampling methods. Based on this analysis, if Trichodesmium nitrogen fixation by colonies is underestimated, it is unlikely that it is due to underestimation of deep abundances by conventional sampling methods.
Does predation control the diapausing stock of Calanus finmarchicus in the Gulf of Maine?

(Elsevier, 2022-07-29) Wiebe, Peter ; Baumgartner, Mark F. ; Copley, Nancy ; Lawson, Gareth L. ; Davis, Cabell S. ; Ji, Rubao ; Greene, Charles H.

The variability of zooplankton populations is controlled by external and internal forcing, with the former being principally large-scale changes in circulation, and the latter being driven by in situ growth, competition, and predation. Assessing the relative importance of these forcings is challenging and requires analyses of multifaceted observational data. As part of the U.S. GLOBEC Georges Bank program, a series of cruises were conducted in fall 1997, 1998, and 1999 to survey diapausing populations of Calanus finmarchicus and their predators in Wilkinson, Jordan, and Georges Basins of the Gulf of Maine. Station and underway sampling were conducted using net (1 m2 MOCNESS) and bioacoustic (BIOMAPER-II) systems, respectively, to acquire vertically stratified data for zooplankton biomass, taxonomic, size, and life-stage composition, together with associated environmental data. The results show that the autumn diapausing C. finmarchicus abundance was much lower in 1998 than in 1997 or 1999, even though the overall zooplankton biomass levels were comparable between the three years. The size frequency distribution of the diapausing individuals had a bi-modal pattern in 1997 and 1999, but a single mode in 1998, indicating the demise of an early cohort of the diapausing stock. The relative biomass and computed energy demand of potential invertebrate predators (euphausiids, decapods, medusae, and siphonophores) was found to be higher in 1998 and could account for the missing C. finmarchicus cohort. Evidence collected from this study supports the hypothesis that local predation has the potential to control the diapausing stock of C. finmarchicus in the Gulf of Maine.
RAPID : research on automated plankton identification

(Oceanography Society, 2007-06) Benfield, Mark C. ; Grosjean, Philippe ; Culverhouse, Phil F. ; Irigoien, Xabier ; Sieracki, Michael E. ; Lopez-Urrutia, Angel ; Dam, Hans G. ; Hu, Qiao ; Davis, Cabell S. ; Hansen, Allen ; Pilskaln, Cynthia H. ; Riseman, Edward M. ; Schultz, Howard ; Utgoff, Paul E. ; Gorsky, Gabriel

When Victor Hensen deployed the first true plankton1 net in 1887, he and his colleagues were attempting to answer three fundamental questions: What planktonic organisms are present in the ocean? How many of each type are present? How does the plankton’s composition change over time? Although answering these questions has remained a central goal of oceanographers, the sophisticated tools available to enumerate planktonic organisms today offer capabilities that Hensen probably could never have imagined.
Climate impacts on zooplankton population dynamics in coastal marine ecosystems

(The Oceanography Society, 2013-12) Batchelder, Harold P. ; Daly, Kendra L. ; Davis, Cabell S. ; Ji, Rubao ; Ohman, Mark D. ; Peterson, William T. ; Runge, Jeffrey A.

The 20-year US GLOBEC (Global Ocean Ecosystem Dynamics) program examined zooplankton populations and their predators in four coastal marine ecosystems. Program scientists learned that environmental controls on zooplankton vital rates, especially the timing and magnitude of reproduction, growth, life-cycle progression, and mortality, determine species population dynamics, seasonal and spatial distributions, and abundances. Improved knowledge of spatial-temporal abundance and distribution of individual zooplankton taxa coupled with new information linking higher trophic level predators (salmon, cod, haddock, penguins, seals) to their prey yielded mechanistic descriptions of how climate variation impacts regionally important marine resources. Coupled ecological models driven by improved regional-scale climate scenario models developed during GLOBEC enable forecasts of plausible future conditions in coastal ecosystems, and will aid and inform decision makers and communities as they assess, respond, and adapt to the effects of environmental change. Multi-region synthesis revealed that conditions in winter, before upwelling, or seasonal stratification, or ice melt (depending on region) had significant and important effects that primed the systems for greater zooplankton population abundance and productivity the following spring-summer, with effects that propagated to higher trophic levels.
Event logs from the U.S. GLOBEC Georges Bank project, from 10 vessels and 104 cruises in the Gulf of Maine and Georges Bank area from 1994-1999 (GB project)

(Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2019-02-18) Ashjian, Carin J. ; Bollens, Steve M. ; Bucklin, Ann ; Campbell, Robert ; Davis, Cabell S. ; Durbin, Edward ; Gallager, Scott ; Garrahan, Peter ; Gibson, James ; Gifford, Dian J. ; Green, John ; Greene, Charles H ; Hebert, Dave ; Horgan, Erich ; Houghton, Robert W ; Incze, Lewis ; Irish, Jim ; Ledwell, James R. ; Lentz, Steven J. ; Limeburner, Richard ; Lough, Greg ; Madin, Laurence P. ; Miller, Charles B. ; Mountain, David ; Oakey, Neil ; Schlitz, Ronald ; Sibunka, John ; Smith, Peter C. ; Taylor, Maureen ; Weller, Robert A. ; Wiebe, Peter H. ; Williams, Albert J. ; Wishner, Karen ; Lee, Craig

Event logs from the U.S. GLOBEC Georges Bank project, from 10 vessels and 104 cruises in the Gulf of Maine and Georges Bank area from 1994-1999. Event logs provide an overall summary of the sampling activities during a cruise. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/2321
Effects of warming and fishing on Atlantic sea scallop (Placopecten magellanicus) size structure in the Mid-Atlantic rotationally closed areas

(Oxford University Press, 2023-04-17) Zang, Zhengchen ; Ji, Rubao ; Hart, Deborah R. ; Jin, Di ; Chen, Changsheng ; Liu, Yonggang ; Davis, Cabell S.

The Atlantic sea scallop supports one of the most lucrative fisheries on the Northeast U.S. shelf. Understanding the interannual variability of sea scallop size structure and associated drivers is critically important for projecting the response of population dynamics to climate change and designing coherent fishery management strategies. In this study, we constructed time series of sea scallop size structures in three rotationally closed areas in the Mid-Atlantic Bight (MAB) and decomposed their total variances using the variance partitioning method. The results suggested that the interannual variances in sea scallop size structures were associated more with thermal stress in regions shallower than 60 m but more with fishing mortality in regions deeper than 60 m. The percentages of small (large) size groups increased (decreased) with elevated thermal stress and fishing pressure. We adopted a scope for growth model to build a mechanistic link between temperature and sea scallop size. Model results suggested a gradual decrease in maximum shell height and habitat contraction under warming. This study quantified the relative contributions of thermal stress and fishing mortality to the variance of scallop size structure and discussed the need for adaptive management plans to mitigate potential socioeconomic impacts caused by size structure changes.
Mesoscale eddies and Trichodesmium spp. distributions in the southwestern North Atlantic

(John Wiley & Sons, 2015-06-08) Olson, Elise M. B. ; McGillicuddy, Dennis J. ; Flierl, Glenn R. ; Davis, Cabell S. ; Dyhrman, Sonya T. ; Waterbury, John B.

Correlations of Trichodesmium colony abundance with the eddy field emerged in two segments of Video Plankton Recorder observations made in the southwestern North Atlantic during fall 2010 and spring 2011. In fall 2010, local maxima in abundance were observed in cyclones. We hypothesized surface Ekman transport convergence as a mechanism for trapping buoyant colonies in cyclones. Idealized models supported the potential of this process to influence the distribution of buoyant colonies over time scales of several months. In spring 2011, the highest vertically integrated colony abundances were observed in anticyclones. These peaks in abundance correlated with anomalously fresh water, suggesting riverine input as a driver of the relationship. These contrasting results in cyclones and anticyclones highlight distinct mechanisms by which mesoscale eddies can influence the abundance and distribution of Trichodesmium populations of the southwestern North Atlantic.
Focus detection from digital in-line holograms based on spectral l1 norms

( 2007-05-16) Li, Weichang ; Loomis, Nicholas C. ; Hu, Qiao ; Davis, Cabell S.

In this paper a rapid focus detection technique is developed for objects imaged using digital in-line holograms. It differs from previous approaches in that it is based directly on the spectral content of the object images and does not need a full reconstruction of the actual images. It is based on new focus metrics defined as the l1 norms of the object spectral components associated with the real and imaginary parts of the reconstruction kernel. Furthermore, these l1 norms can be computed efficiently in the frequency domain using a polar coordinate system, yielding a drastic speedup of about two orders of magnitude compared with image-based focus detection. The subsequent reconstruction, when done selectively over these detected focus distances, leads to significant computational savings. Focus detection results from holograms of plankton are demonstrated showing that the technique is both accurate and robust.

Davis Cabell S.

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