Processes
controlling abundance of dominant copepod species on Georges Bank:

Local
dynamics and large-scale forcing

PIs:  Cabell
Davis (WHOI), Robert Beardsley (WHOI), Changsheng
Chen (UMassD),

Rubao Ji
(WHOI), Edward Durbin (URI), David Townsend (UMaine),

Jeffrey Runge (UNH), Charles Flagg (SUNY), Richard
Limeburner (WHOI)

Project
Summary

A fundamental goal of
Biological Oceanography is to understand how underlying biological-physical
interactions determine abundance of marine organisms.  For animal populations, it is well known
that factors controlling survival during early life stages (i.e., recruitment)
are strong determinants of adult population size, but understanding these
processes has been difficult due to model and data limitations.   Recent advances in numerical
modeling, together with new 3D data sets, provide a unique opportunity to study
in detail biological-physical processes controlling zooplankton population
size.  We propose to use an existing
state-of-the-art biological/physical numerical model (FVCOM) together with the
recently-processed large 3D data set from the Georges Bank GLOBEC program to
conduct idealized and realistic numerical experiments that explore the detailed
mechanisms controlling seasonal evolution of spatial patterns in dominant
zooplankton species on Georges
Bank.  We will examine a series of hypotheses
that address how dominant copepod species populations are maintained on the
bank, including local dynamics and large-scale forcing.  Specifically we will determine whether
the observed characteristic seasonal-spatial
pattern of each species (long-term and inter-annual) is predictable from the
interaction between its characteristic
life-history traits and physical transport.  The extent to which the copepod
populations are controlled by food-availability (bottom-up) or predation
(top-down) processes will be examined, including the influence of Warm Slope
Water versus Labrador Slope Water (NAO-dependent) on nutrient influx through
the Northeast Channel and subsequent upwelling and biological enhancement on
the bank.  Self-sustainability of
each species population on the bank itself and in the Gulf of Maine will be studied by controlling immigration from
specific source regions.
Large-scale forcing including NAO and catastrophic global warming (e.g.
complete polar ice melt) will be examined explicitly by forcing the model at
the boundaries, using scenarios based on basin-scale data and from concurrent
basin-scale modeling efforts.  Intellectual
Merits:  The proposed modeling study will provide
new insights into the role of local and large-scale processes controlling
zooplankton abundance in the ocean.
The dominant copepod species to be studied include small species that
are the dominant prey for larval cod and haddock in this region, thus providing
critical information for concurrent larval fish modeling studies.  This detailed, process-oriented,
regional-scale modeling with boundary forcing will lay the groundwork for
integration with models of the entire ocean basin.  The resulting model will be a legacy of
the GLOBEC Georges Bank program by providing a powerful new tool for
understanding how local and large-scale forcing interact to control plankton
production in the sea.  Broader
Impacts:  Results of the
proposed work will be broadly disseminated to the general oceanographic
community, the fishing industry, K-12 institutions, and to the population at
large, through web-based servers using existing infrastructure at the proposers’ institutions.  Web-based users will be able to access
model results and run the model using chosen parameter settings to obtain
predictions of currents, hydrography, and plankton abundance patterns given
selected climate forcing scenarios.
Collaboration with the WHOI/UMASS COSEE program will foster
communication with K12 students and the public both nationally and
internationally.

1.      Background

The
GLOBEC approach — Understanding
complex marine ecosystems requires use of simplifying assumptions, which
historically has involved trophodynamic analysis of energy or mass flow by measurement
and modeling (Lindeman, 1942; Teal, 1962; Odum, 1957; Steele, 1974).  In regions of high diversity such as the
oligotrophic ocean this approach remains the only feasible method of analysis (e.g.,
Sarmiento et al., 1993).  As an
alternative in low diversity regions, it is possible to model the population
dynamics of a few dominant species to understand processes controlling their
abundance and to obtain information about system level functioning (e.g., Davis, 1987a).
The trophodynamic concept has been used to relate primary and secondary
production to fish production (e.g., Clarke, 1946; Cushing, 1975; Sissenwine et
al., 1984; Cohen and Grosslein, 1987; Nixon, 1988), but this method is of
limited utility in predicting abundance of particular fish species.  It is well known that adult fish
populations are dominated by a few strong year classes that are set by
recruitment from early life stages (Hjort, 1914; Grosslein and Hennemuth, 1973).  The GLOBEC program recognizes
recruitment as the dominant factor controlling population abundance in marine animal
species (GLOBEC, 1991a).  The regional
GLOBEC programs focus on target species and their dominant prey, with emphasis
on individual organisms, population dynamics, and interactions with the
physical environment, especially as it relates to global climate change (GLOBEC,
1991b, 1992, 1996, 1997, 2000).

Georges
Bank GLOBEC: dominant zooplankton species —
Georges Bank was chosen as the first GLOBEC study site due to its sensitivity
to climate change, definable populations, importance as a fishing ground, and
significant historical database (GLOBEC, 1992).  The goal of this program is to
understand the biological and physical processes controlling abundance of cod
and haddock larvae and their dominant prey species.  In the program implementation plan we emphasized
the copepods Calanus finmarchicus and
Pseudocalanus spp.
as target species, since these are dominant prey items for larval cod and
haddock.  Subsequent studies have
found that small copepods (Pseudocalanus spp., Oithona
similis, Centropages
spp., Temora longicornis) are dominant prey items for
cod and haddock larvae on Georges and Western Banks (Lough and Mountain, 1996;
Lough et al, 1996; McLaren and Avendano. 1995; McLaren
et al., 1997).  This contrasts sharply
with the situation in the eastern Atlantic (North Sea and Norwegian Sea) where cod larvae feed almost solely on Calanus finmarchicus (Sundby, 1999), and decadal shifts in C. finmarchicus abundance affect larval cod survival (Beaugrand et al., 2003).  This difference in larval fish prey
preference appears due to prey availability since the larval fish diets reflect
ambient copepod species composition, and the shallow banks have high
concentrations of small copepod species (Davis, 1987; Sherman et al., 1987; Meise,
and O’Reilly, 1996., McLaren et al. 2001; Reiss et al, 2003).  In the shallow Baltic Sea, cod larvae also feed on small copepod species (Hinrichsen et al, 2002).  In general, small copepods are an
important component of marine ecosystems (e.g., Davis, 1987b; Turner, 2004). The
present proposal focuses on understanding the biological-physical processes
controlling the abundance of dominant copepod species in the Georges Bank/ Gulf of
Maine region, including Calanus finmarchicus and the smaller
species, Pseudocalanus spp. (moultoni and
newmani),  Oithona
similis, Temora longicornis, Centropages spp. (typicus and hamatus).

1.1.
The Georges Bank Physical Environment

Local dynamics — Georges
Bank (GB), the Gulf of Maine (GOM), and Scotian Shelf (SS) are part of a single
regional coastal current system, driven in large part by upstream mass and
buoyancy forcing (Fig. 1). The bank itself is a quasi-flow-through system, with water from offshore and upstream sources arriving on
the bank, being modified locally by surface forcing and tidal mixing before
moving off-bank to the Mid-Atlantic Bight or re-circulated northward along the
Great South Channel.

The strongest currents over
the bank are of tidal origin, and turbulent mixing associated with the tidal
bottom boundary layer is most intense over the shallow cap of the bank,
effectively eliminating local vertical temperature and salinity stratification
throughout the year.  As seasonal
stratification increases on the flanks of the bank, the tidal mixing front
forms with associated secondary flow. The clockwise around-bank residual flow
increases with seasonal stratification, becoming partially closed from June
through

Figure 1. Circulation: 1 flow across GSC into the north flank jet, 2
tidal-pumping of deep water onto GB, 3 wind-driven near-surface flow, 4  small-scale cross-frontal processes, 5 SS
cross-over

Figure 2. Schematic of the western North Atlantic shelf-break current system in summer,

(Fratantoni and Pickart, 2005)

September until fall storms
and surface cooling destroy the local stratification.  Surface heating drives the development
of the seasonal thermocline.  Salinity
on the bank is controlled by advective and mixing processes along the northern
and southern flanks.  On the
southern flank salinity is influenced by on-bank intrusions of saline shelf-break
frontal water and very saline warm-core ring water (Fig. 1).  Along the northern flank salinity is
controlled by advection from the western Gulf across the northern Great South
Channel (Fig. 1, 1), tidally-driven near-bottom residual flow (the “tidal
pump”, Fig. 1, 2), wind-driven near-surface flow (Fig. 1, 3), small-scale
cross-frontal processes (Fig. 1, 4), and intermittent cross-over of low salinity SS
surface water (Fig. 1, 5).
The tidal pump in particular provides a strong mechanism for bringing
deep water from Georges Basin up onto the bank (Chen
and Beardsley, 1998; Chen et al., 2003).

Figure 3. Schematic showing the strong westward
penetration of LSW and northward position of the Gulf Stream following low winter North Atlantic Oscillation
(NAO) index (left) and weak penetration of LSW and more southward position of
Gulf Stream following high winter NAO index.  (Drinkwater et al, 2003)

Large-scale forcing — Water enters the GOM via two primary
paths:  (1) the flow of relatively fresh
water above 100m from the SS and (2) warmer, more saline Slope Water (SW) at
depths greater than 100m through the Northeast Channel (NEC). The primary
source of SS water is the West Greenland/Labrador Current system, with
additional input from the St. Lawrence system (Fig. 2). As the Labrador Current
flows around the Grand Banks, the large shoaling in shelf-break depth from
~300m in the north to ~100m to the southwest helps force the deeper Labrador
Current water to flow along the upper slope, thus forming Labrador Slope Water
(LSW), which flows west into the Laurentian Channel
and along the Scotian upper slope. The westward extent of LSW depends on its
source strength, thought to depend on basin-scale forcing (NAO) (Fig 3), and
degree of mixing with ambient Warm Slope Water (WSW) of Gulf Stream origin. Since WSW
is warmer, more saline, and nutrient rich than LSW, the relative mix of these
two end members entering the NEC, and its transport relative to the inflow of SS
water, strongly influences circulation, water property distributions, and nutrient
content in the GOM/GB system.

Fig. 4.  GB salinity
anomaly (Mountain, 2005)

Fig. 5.  Percent LSW in bottom water (150-

200 m) in 1998.  (Drinkwater et al, 2003)

Data from the 1995-1999 GB
GLOBEC field study provide an excellent example of the flow-through nature of
the GB/GOM system and its linkage to larger basin-scale forcing. The salinity
on GB exhibited two significant freshening events between early 1996 to early
1997 and between late 1997 through 1998, with a net drop of ~1 psu (Fig. 4). These two events also were observed in
surface (0-30m) GOM waters, suggesting significant increases in freshwater
influx from the SS (Smith et al., 2001).  In the NEC, WSW was replaced by cooler,
fresher LSW in January 1998 as the leading edge of LSW flow extended west due
to an increase in the Labrador Current associated with a low NAO. As LSW
entered the GOM during early 1998, it mixed with resident GOM water (Fig
5).  By early 1999, WSW was again
flowing into the GOM through the NEC.
Since the tidal pump mechanism can carry deep water up on the northern flank
of GB, advection of LSW in Georges Basin onto the bank can occur on relative
short time scales (>=1 month), suggesting that part of the freshening on GB
observed during 1998 was due  to the
influx of LSW into the GOM.
Clearly, variations in the primary upstream sources (the SS Water, the
mix of WSW versus LSW) linked to basin-scale forcing strongly control the water
properties (including heat, salt and nutrients) through the GOM and onto GB.

Fig. 5a.
Scenario of nutrient input onto GB from the NEC (Townsend et al., 2004).

1.2.
Connection
between NAO and plankton productivity on GB

NAO-dependent
intrusions of LSW and WSW through the NEC greatly influence the nutrient (N, Si) input into the GOM.  It is
believed that the tidal pumping mechanism along the northern edge of the bank
can quickly transport nutrients from Georges Basin up onto the NE peak of GB, impacting the productivity of the bank very rapidly
(Fig. 5a).  The ratio of N and Si in the inflow water can influence the duration of the
diatom bloom.  In general, the NEC inflow
can affect the total salt and nutrient budget of the GB/GOM, determining the
thermohaline circulation and influencing upwelling along the western GOM and
subsequent nutrient transport to western GB.  The potential impact of this inflow will
be modeled in the proposed study.

1.3.   Characteristics of GB zooplankton

GB
zooplankton is dominated by Calanus
finmarchicus, Pseudocalanus spp., Oithona similis, Centropages
spp., and Temora longicornis, and Paracalanus
parvus (Bigelow, 1926; Davis, 1984, 1987b; Sherman et al, 1987; Durbin et
al., 2003; Durbin and Casas, submitted).  Each
species exhibits a characteristic
life cycle and seasonal/spatial pattern in the GB/GOM region.  Calanus
finmarchicus and Pseudocalanus spp. are cold-water species that avoid the warm surface
layer (>10-12oC) during summer and fall and produce large spring
populations.  Centropages spp,
Temora, and
Paracalanus are warm water species
and are most abundant during late summer and fall.  Oithona
is plentiful throughout the GB/GOM region year round.

Fig. 6. Calanus
finmarchicus abundance (log10(#/10m2)
in the GB/GOM, mean 1977-1987, (MARMAP data redrawn from Meise and OReilly, 1998).

Calanus
finmarchicus— This
species spends the warmer months in a state of diapause as stage CV in cooler
waters (5-7 oC) at depth in the GOM (Fig. 6). During late December,
it emerges from diapause (mechanism unknown), swims to the surface and molts to
adult.  Subsequent egg production depends
on availability of phytoplankton (Durbin et al., 2003), with the first
generation born in late December-early January (Durbin et al., 1997).  Generation time is ~2 months at the cold
winter/spring temperatures (~5 oC), so G1 adults appear in March,
and there is time for a total of 3 generations by the end of its growing season
in July.  Overwintering females produce eggs for a
prolonged period, smearing out cohorts
(Durbin and Casas, submitted).   This
annual cycle in the GB/GOM appears stable, having
persisted for many decades (Bigelow, 1926; Clarke et al, 1946; Meise-Munns et al., 1991), but the extent to which this
population is self-sustaining is unknown.

Fig. 7. Calanus finmarchicus abundance in the N Atlantic from CPR data (Spears 2005) and nets/OPC (Heath et
al. 2004).  Note high densities in
the Labrador and Norwegian Seas.

Calanus  finmarchicus is an open ocean species, occurring throughout the
northern North Atlantic from the eastern US to the Barents Sea, with centers of population abundance in the Norwegian and Labrador seas (Fig. 7).  Immigration
into the GB/GOM population from upstream sources may contribute to the apparent
stability of the population.  C. finmarchicus enters the GOM from the SS
and possibly from the SW through the NEC.
C. finmarchicus in the SW
originate from the Labrador
Sea and to an unknown extent
from spill-over of the productive shelf populations.  Scotian Shelf C. finmarchicus originate from Labrador Sea via the SW (Head et al., 1999) and to some degree from
the productive Gulf of St. Lawrence population (Zakardjian et
al. 2003).  It is unlikely that immigration
directly determines the large spring abundance peak in C. finmarchicus in the GB/GOM, since the water mass turnover time
is long relative to the generation time, but a seeding type of immigration
during the “off-season” could be important in determining the size
of the startup population of CVs in December (Saumweber and Durbin, submitted).  Since
the diapausing SW population resides at a depth of 500m (below the NEC sill
depth), and high concentrations are not observed in the upper water column
until April (Miller et al., 1991), well-after initiation of the GB/GOM
population growth, it is unlikely that a SW population entering through the NEC
contributes significantly to the GB/GOM C.
finmarchicus population.

It
may well be that the resident diapausing GOM population is sufficient to
produce the large spring GOM/GB population.  At the end of the growing season,
downward migrating diapausing CVs cannot reach their normal open ocean depths
of 500-2000m, and they become trapped in the GOM basins.  A similar effect has been observed on
the SS basins (Sameoto and Herman, 1990) and for C. pacificus
in the Santa Barbara basin (Osgood and Checkley,
1997).  Lagrangian modeling studies
have found retention of diapausing CVs in the GOM to be high, especially if the
animals stay below 150 m (Johnson et al., submitted).  Thus it appears possible that the GB/GOM
population could be self-sustaining, but further 3D modeling work is needed,
using a concentration-based approach to quantify population dynamics and
transport continuously throughout this region during the year.  This self-sustainability is in sharp
contrast with the situation in the North Sea, which has
no deep basins and is dependent on annual input from offshore waters (e.g.
Heath et al., 1999).

Fig. 8. GLOBEC monthly mean Calanus abundance

on GB, showing abundance “hole”

Fig. 9.  Pseudocalanus
abundance in the GB/GOM. MARMAP bi-monthly means 1977-1987 (from McGillicuddy et al., 1998).

Although
C. finmarchicus may be able to
sustain itself in the GB/GOM system, it does not maintain itself on GB, since
the bulk of the population disappears from the bank during the off-season (Fig.
6) and even during the growing season its abundance appears to be driven by GOM
concentrations, with a well-defined “hole” in abundance in the
center of the bank (Fig. 8, Durbin and Casas,
submitted).  This hole results from
a combination of advection around the bank of the large GOM population and
possibly high predation over the crest.
A huge literature exists for C.
finmarchicus egg production, development and growth as a function of food
and temperature including several studies done as part of the GLOBEC GB process
work (Campbell and Head, 2000; Campbell et al., 2001a,b; Runge et al. submitted).  Such data can be incorporated into the
population model for this species and used together with the large field data
base to conduct targeted forward modeling to examine biological/physical
processes controlling observed patterns.

Pseudocalanus spp.— Like Calanus, the growth season for Pseudocalanus is winter/spring (Fig. 9,
10).  Its abundance is higher in
shallower areas (<100m) and is highest in the crest region of the bank in
June.  Pseudocalanus does not
overwinter in the GOM as does Calanus and is
not normally present in the central Gulf during winter.  This genus is an egg carrier and
consequently has lower egg production and egg mortality rates (Corkett and McLaren, 1978; Ohman
et al., 2002).  Pseudocalanus in the GB/GOM

Fig. 10. GLOBEC data for Pseudocalanus

Fig.
11.  A) Temora, B) Centropages
hamatus C) Centropages typicus,
D) Oithona similis.  Mean
monthly GLOBEC data for 1995-1999, A,B,D May; C January; log10(#/m3+1)

region comprises
two species: P. newmani and P. moultoni (Frost, 1989; McLaren et
al., 1989a; Bucklin et al., 1998, 2001; McGillicuddy
and Bucklin, 2002).   P. moultoni appears to be a colder water
species and more abundant during winter/spring, while P. newmani is more plentiful during spring/summer (McLaren et al.,
1989a,b).  P. moultoni is a coastal species and P. newmani an offshore one (Frost,
1989).  Thus P. moultoni may be carried onto the bank from western GOM coastal
waters (e.g., Cape
Cod Bay), while P.
newmani may have a source from SS water, either crossing over the NEC, or
indirectly through the central GOM (McGillicuddy and
Bucklin, 2002).  Inverse modeling,
representing the biology by a single source/sink term, revealed that the two
species are likely to have different source locations on the bank but
intermingle by June (McGillicuddy and Bucklin, 2002).
The use of a simple cost function instead of a population model, however, meant
that the independent species-specific life history information could not be
included in the model.  Substantial
information on development, growth and egg production as a function of food and
temperature is available for Pseudocalanus
(e.g. Corkett and McLaren, 1978; Vidal, 1980; Davis, 1983,
1984a,b; McLaren et al., 1989b; Ban et al., 2000; Lee et al., 2003; Dzierzbicka-Glowacka, 2004).  Use of these laboratory and shipboard derived
rates together with field data on distributional patterns of the combined
species (plus a subset of species-specific data, Bucklin et al., 2001) can be
used in numerical models to explore the biological/physical processes controlling
seasonal development of the spatial distribution patterns.  Targeted forward modeling experiments
are required to determine the potential source locations and interactions
controlling subsequent spatial patterns of each population, given their
distinctive temperature-food dependent growth and reproductive rates.

Other
Dominant Copepod Species — Each dominant copepod species on GB has its own
characteristic temporal-spatial patterns and life histories (e.g., Davis, 1987a).
Copepods that lay bottom resting eggs, including Centropages hamatus and Temora longicornis, have well defined
populations on the crest of the bank (Fig. 11A, B) (Davis, 1987; Sherman et
al., 1987).  It has been suggested
that these species use resting eggs as a strategy for “gluing”
their populations to regions that are favorable for growth (Davis, 1987; Lindley
and Hunt, 1989; Lindley, 1990; Marcus, 1996; Marcus and Lutz, 1998), but the
necessary biological/physical dynamics have yet to be verified via modeling. Centropages typicus
abundance is highest during late summer and fall and decreases markedly during
winter and spring.  It is most
abundant in the warm surface layer above the thermocline and not restricted to the
crest of GB like C. hamatus.  Oithona
similis is abundant year round and is not restricted to GB but has a pattern
similar to C. finmarchicus, with a
large off-bank population.   A substantial
literature on life history information is available for these species,
including egg production, development and growth rates as functions of food and
temperature (e.g., Davis and Alatalo, 1992; Klein Breteler and
Gonzalez, 1986; Klein Breteler et al., 1982, 1996; Sabatini
and Kiørboe, 1994; Maps et al. 2005).

Fig. 12.
Abundance trends in GB copepod, GLOBEC 1995-1999.

Abundance
trends during the GLOBEC years —
Abundance of the dominant copepod species, except Calanus, increased significantly during the five-year GLOBEC GB
field program (Fig. 12.).  While
this trend may reflect a change toward smaller species, indicative of a warming
trend, no concomitant increase in temperature was observed.  These changes were
negatively correlated with salinity (Durbin and Casas,
submitted.). High abundances in 1999 appear to be related to a phytoplankton
bloom that took place during winter in the central
GOM, leading to high reproductive rates and abundances (Durbin et al 2003). The
elevated abundances may have been advected onto GB.  It is possible that low surface salinity
during winter increased stability of the water column and led to the bloom. A
negative correlation between salinity and chlorophyll on GB also was found at
this time (Durbin and Casas, submitted), the reason
for which is unknown.  The proposed
modeling work will examine the potential causes
of the zooplankton increase and its relationship to large-scale forcing and climate
change.

1.4.
Available
Data Sets

GLOBEC GB
— The GLOBEC GB field program was conducted from 1995-1999 and included a
combination of monthly broadscale and process-oriented cruises (GLOBEC, 1992;
Wiebe et al, 2002).
Broadscale cruises provided 3D maps of the plankton species based on net
tows (1-m2 MOCNESS, Wiebe et al., 1985) at a set of 41 standard
stations covering the bank and adjacent waters, and plankton pump sampling
(Durbin et al 1997, 2000) at ~18 of the standard stations. CTD bottle casts were
made at all stations.  MOCNESS (0.15
mm mesh nets) zooplankton samples were collected from 0-15, 15-40 m, and 40-100
m or the bottom (if shallower than 100 m) and 100 m to the bottom or 450 m (if
>100 m).  Pump (0.035-mm nets)
samples were collected over the same depth ranges as the MOCNESS in the upper
water column but the maximum depth it was deployed to was 70-100 m depending on
wind and tides, or to the bottom on shallower parts of the bank.  For complete description of collection
and processing methods see (Durbin et al. 1997; 2000).  Samples were sorted, and processed data
now are available for all life stages of Calanus finmarchicus and Pseudocalanus
spp. (N1-N6, C1-Adult).  For other copepod
species life stages were sorted as adult males and females, copepodids,
and nauplii. These data are stored in an Oracle
database together with all of the CTD and chlorophyll data (http://globec.gso.uri.edu).  The complete GLOBEC GB data set for
broadscale zooplankton includes >3500 net samples (41 stations, 3 depths, 30
cruises), plus >1500 pump samples (18 stations, 3 depths, 30 cruises).  In addition, vertically stratified data
from several other cruises have been collected in deeper regions of the GOM.

Other Data Sets —  Data from the bimonthly cruises of the
MARMAP program 1977-87 and its follow-on program, ECOMON (1992-present),
include shelf-wide distributions of hydrography and zooplankton (0.333mm
bongos).  The complete data set is
available to us via an NMFS Oracle database (D. Mountain, pers.
comm.)  Although the zooplankton
data are from integrated hauls, these data cover a broader area than the GLOBEC
GB data, and, together with GLOBEC vertical data from deeper GOM, will allow us
to approximate 3D spatial patterns of each species throughout the GOM
region.  Further data from the GOM CPR
transect, transatlantic CPR, UNH Coastal Observing Center, the 1939-41 GB study, and Canadian AZMP (see Head
letter), allows the 1995-1999 GLOBEC data to be viewed in a larger context.

1.5.   Previous modeling

Several
previous biological/physical models of the GB/GOM region have been
developed.  Davis (1984) showed that the interaction between around-bank
advection/diffusion and temperature-dependent development of the copepod Pseudocalanus could explain observed
spatial patterns in population structure.
Subsequent studies have shown that this scenario is most likely for P. moultoni, with an admixture of P. newmani later in the season (McGillicuddy and Bucklin, 2002).  McGillicuddy
et al. (1998) had used the same inverse approach to locate source/sink areas
for the Pseudocalanus
population.   Klein (1987)
modeled the 2D NPZD-advection-diffusion on the bank and found that
phytoplankton production was removed from the bank via detritus rather than
grazing.  Lewis et al., (1994, 1991)
used 3D modeling to show that strong wind forcing can cause a partial washout
of plankton from the bank, increasing the phytoplankton/zooplankton ratio (NPZ
model), and causing spatially-temporally sensitive larval populations
(particle-based) to be lost from the bank, affecting recruitment.  The Calanus
finmarchicus population in the GB/GOM has been modeled using the Dartmouth model to show that the deep basins and SS can contribute
to the bank population; these models used 2D transport of concentration-based
(Lynch et al. 1998), individual-based (Miller et al., 1998), and particle
trajectories (Hannah et al 1998).  The
C. finmarchicus population throughout
the Gulf of  St. Lawrence/SS/GOM
region was modeled to examine local dynamics and exchange between regions
within the model interior (Zakardjian et al.,
2003).  The latter model was a 3D
concentration-based 13-stage population model with temperature-dependent
development and was run for a full-annual cycle.  The results indicated that horizontal
transport was dominant on the SS, but that the population is self-sustaining in
the Gulf of St. Lawrence.  Food-dependence
effects on population dynamics during the active season were not examined,
however.

1.6.   Combining existing models and data

Over
the past decade, the GLOBEC GB program has acquired and processed an
exceptional 5-year 3D data set of plankton and physical variables, while at the
same time developing a high-resolution state-of-the-art prognostic 3D biological/physical
model of this region (FVCOM).  Data
processing and model development recently have reached the point where they can
be effectively combined.  By the
start of the proposed study, the FVCOM model will have been ported to a
massively-parallel supercomputer. We now have the unique opportunity to use the
data and model together to study the detailed mechanisms controlling zooplankton
abundance patterns on GB, explicitly including boundary forcing determined by
basin-scale dynamics.

We
have assembled a team of PIs who are leading experts on the plankton and
physical dynamics of this area.
Beardsley and Flagg are physical oceanographers with a long background
in this region. Chen is a physical oceanographer and developer of the FVCOM
model. Durbin is the scientist in charge of the broadscale data acquisition and
processing.  Runge is an expert in
copepod biology specializing in Calanus
fertility and population dynamics.
Townsend is the lead scientist studying nutrient-plankton production in
the GB/GOM region.  Davis is a zooplankton biologist who has done field,
laboratory, and biological-physical modeling studies of copepod population
dynamics in the GB/GOM region.
Davis and Beardsley helped formulate the theoretical underpinnings and
approach for the GLOBEC GB program (GLOBEC, 1992).

2.      Proposed
Research

2.1.   Hypotheses

Working  Hypothesis – The seasonal evolution of characteristic mean spatial abundance
patterns of each dominant copepod species on GB is predictable from the
interaction between its characteristic
life-history traits and physical transport.  These life-history traits include egg
production, development, and growth rates (temperature/food dependent) as well
as other traits such as vertical migration and diapause.  Both the long-term, multi-year, mean and
year-to-year variations in seasonal-spatial patterns are predictable by these
interactions.  Within this working
hypothesis, we will address three specific null hypotheses:

H10:  The abundance
of copepod species on the bank is controlled by food availability (bottom-up
control).  Here we will examine the
scenario that GB productivity, and thus food availability for the dominant
copepod species, is controlled by nutrient input into the GOM through the NEC, which
is determined by the intrusions of Labrador Slope Water versus Warm Slope
Water.  Alternative hypotheses
include:  1) predatory control of
copepod seasonal cycles (top-down control), 2) a combination of food-limitation
and predation (time-space dependent), and 3) purely physical control by direct
effects of temperature on vital rates or advection.  In 3), we will examine causes of the observed
increase in warm-water copepod species during the GLOBEC years (1995-1999).

H20:
Copepod populations on GB and/or the GOM region are not self-sustaining.  We will examine the need for immigration
from different sources to maintain the copepod populations over multiple years.
Key source regions will be examined
including the SS and SW.  For
self-sustainability on GB itself, we will examine potential sources from the
coastal regions (e.g., Cape Cod Bay, Penobscot Bay), the GOM, and from bottom resting eggs.

H30:
Catastrophic global warming (e.g., total polar ice melt), parameterized
as a lack of Labrador Sea water at the NEC, causes a regime shift on GB from cold-water
copepod species to warm-water ones.

2.2.   Objectives

The
overall goal of the proposed study is to understand the underlying
biological-physical mechanisms controlling the seasonal development of spatial
patterns of dominant copepod species on GB.  Our specific objectives are: 1) to
examine how local-dynamics and external forcing control the abundance of these species
on GB, 2) to determine the degree to which top-down versus bottom up processes
control the dominant copepod species on GB, and 3) to use existing
state-of-the-art 3D physical/biological numerical models together with existing
high-quality 3D data sets from the GLOBEC GB field program (and other
historical data sets), to conduct targeted numerical experiments that explore
the likelihood of the hypotheses listed above.

2.3.   Methods

2.3.1.      The Integrated Model System

The UMASSD-WHOI research
team has developed an integrated model system for the GOM/GB region (Fig. 13).
The major components of this system include: (1) the modified fifth-generation
community mesoscale atmospheric model (MM5), (2) the unstructured grid Finite-Volume Coastal Ocean circulation Model
(FVCOM), (3) a generalized lower trophic level food web model, and (4)
multi-stage zooplankton models. The 4-D optimal interpolation (OI) and nudging
data assimilation methods are used with FVCOM to incorporate satellite-derived
sea-surface height (altimeter), insolation, SST, and
remote sensing reflectance (RSR) as well as in-situ oceanographic data (moored
and shipboard hydrographic and current data) in model simulations conducted
with realistic forcing and boundary conditions and observed ocean response for
specific periods of time. The integrated model system can be run with idealized
forcing and boundary conditions to investigate specific processes.  A brief description of the integrated
model system is given below.

MM5— The current version of the meteorological model
utilizes the fifth-generation mesoscale regional weather model (MM5) developed
by NCAR/Penn State (Dudhia et al., 2003; Grell et al., 1994) for community use. MM5 uses NCAR/NCEP
or ETA weather model fields as initial and boundary conditions with two-way
nesting capability, and can provide continuous hindcasts and three-day
forecasts. We have used MM5 to construct the surface weather hindcast and
forecast system for fishery studies in the GOM/GB (Chen et al., 2004). This
model (called GOM-MM5) is configured with a regional domain (covering the Northeast U.S.) and a local domain (covering the SS, GOM, and New
England Shelf) with horizontal grid spacing of 30 and 10 km, respectively, and
31 sigma levels in the vertical with finer resolution in the PBL. To improve
the model-based surface wind field, wind stress and heat flux estimates over
the ocean, GOM-MM5 uses the COARE 2.6 bulk algorithm (Fairall
et al, 2003) for the air-sea fluxes, satellite-based insolation,
cloud cover, and SST data (International Satellite Cloud Climatology Project)
for the radiative fluxes, and all coastal NDBC and
C-MAN surface weather data available in the local domain are incorporated
through 4D data assimilation.

GOM-MM5
is presently in operational use, with 3-day forecasts of the surface
conditions, (including wind stress, heat flux, P-E) over the GOM/GB region
posted on the SMAST website (http://www.smast.umassd.edu/research_projects/GB/mm5/mm5_eta/)
for research, education, and public use.  By this summer, we will complete the
hindcast of the surface forcing fields with mesoscale (10-km) resolution covering
the FVCOM domain for the 1995-1999 GLOBEC field period.
This is the first calibrated mesoscale meteorological database built in the
GLOBEC GB Phase 4 program.

FVCOM— FVCOM
is a prognostic, unstructured grid, finite-volume, free-surface, 3D primitive
equation coastal ocean circulation model (Chen et al., 2003; Chen et al.
2004a). In common with other coastal models, FVCOM uses the modified Mellor and
Yamada level 2.5 (MY-2.5) and Smagorinsky turbulent
closure schemes for vertical and horizontal mixing, respectively (Mellor and
Yamada, 1982; Galperin et al., 1988; Smagorinsky, 1963), and a sigma coordinate to follow bottom
topography. The General Ocean Turbulent Model (GOTM) developed by Burchard’s research group in Germany (Burchard, 2002) has been
added to FVCOM to provide optional vertical turbulent closure schemes. Unlike
existing coastal finite-difference and finite-element models, FVCOM is solved
numerically by flux calculation in the integral form of the governing equations
over an unstructured triangular grid. This approach combines the best features
of finite-element methods (grid flexibility) and finite-difference methods
(numerical efficiency and code simplicity) and provides a better numerical
representation of momentum, mass, salt, heat, and tracer conservation.  The ability of FVCOM to accurately solve
scalar conservation equations in addition to the geometrical flexibility
provided by unstructured meshes (Fig. 14) and the simplicity of the coding
structure makes FVCOM ideally suited for interdisciplinary applications (Chen
et al., 2005b-c; Ji 2003; Ji et al., 2005). Examples can be viewed on
Chen’s research group website at http://codfish.smast.umassd.edu).

FVCOM
has been validated through direct comparison with analytical solutions for
idealized cases (Chen et al., 2005b; Huang et al., 2005a-c) and other models
for application in estuaries (Chen et al., 2005d-e; Huang et al., 2005d),
inter-bays (Zhao et al., 2005) and the GOM/GB region (Chen et al, 2003b; Chen et
al., 2005c).  These studies show
that different physical processes controlling currents and stratification in
the coastal ocean have inherent time and space scales that must be carefully
considered when determining model grid resolution for accurate simulation. This
is particularly important with freshwater discharge, buoyancy-driven coastal
plumes and currents, tidally-forced flows and upwelling, and fronts in the GOM/GB
region (Chen et al 2005a).  For
example, model dye experiments made to simulate Houghton’s May/June 1999
dye dispersion observations on GB suggest that the horizontal resolution needed
to resolve the diffusive flux is 500 m (Chen et al., 2005c).  This resolution is also required to have
a convergence solution of the tidal-induced residual current and
buoyancy-induced current at the shelfbreak on GB
(Chen et al., 2005b).  These
requirements will be used to refine the final FVCOM grid used in the proposed
work. FVCOM has been used to hindcast currents
and hydrography in the GOM/GB region for 1995 and 1999 using GOM-MM5 surface
forcing, 4D data assimilation of 5-day averaged satellite SST and available
moored current data, and open boundary conditions (Chen et al., 2003b).  The model tidal currents compare very
well with available surface elevation and current data, with overall
uncertainties for the dominant M2 component of less than 3 cm in amplitude,
5° in phase, and 3 cm/s in the tidal current major axis (Chen et al.,
2005c).  The model subtidal currents and stratification also compare well with
existing in-situ measurements, capturing the seasonal cycle in vertical
stratification and increased around-bank circulation during
June-September.  These two hindcasts
clearly illustrate significant short-term (daily to weekly) and long-term
(seasonal and interannual) variability in the subtidal currents on GB.  For example, surface winds in March 1999
were stronger and more variable than in 1995, resulting in stronger
monthly-mean offbank near-surface flow in 1999 than
in 1995 (Fig 15).

FVCOM Biological Module— Various ecosystem models have been implemented in FVCOM,
including NPZ, NPZD, NPZDB, and water quality models. To make FVCOM more
flexible for ecosystem studies, we have built a generalized biological module
into FVCOM to allow users to select either a pre-built biological model (such
as NPZ, NPZD, etc) or construct their own biological model using the
pre-defined pool of biological variables and parameterization functions,
including zooplankton life-stage models.
This module acts like a platform that allows us to examine the relative
importance of different physical and biological processes under well-calibrated
physical fields.

Upstream
Boundary Conditions—   For this study, we plan to move the
“upstream” boundary of the GOM/GB FVCOM domain eastward to cut
across the SS and upper slope through Banquereau Bank.
This choice simplifies the cross-shelf bathymetry and separation of along-shelf
flow into inner-shelf and shelfbreak components (Han
et al, 1997), and was used in the Hannah et al (2001) model simulations of the
seasonal circulation on the western and central SS.  They used the Dartmouth circulation model (QUODDY4) to produce
dynamically-consistent seasonal-mean solutions based on historical
hydrographic, wind stress, and M2 tidal elevation data.  The model solutions show generally good
agreement with moored current data and capture the strong seasonality of the
major currents, indicating that the seasonal-mean barotropic
and baroclinic pressure gradients specified along the
upstream boundary were realistic.
We plan to use the Hannah et al (2001) seasonal-mean boundary
conditions, a statistical method to compute the along-shelf wind-driven
time-dependent transport over the inner-shelf (Schwing,
1992), recent hydrographic and moored data, and the new shelfbreak
current system climatology (Fratantoni and Pickart, 2005a,b) to construct the best set of upstream
boundary conditions for both process and long-term hindcast simulations.  In addition to the extensive
hydrographic data set collected in GLOBEC GB, additional data have been
collected in the GB/GOM by the ongoing NMFS ECOMON program and on the SS by the
Canadian Atlantic Zone Monitoring Program (AZMP) (see letter from Dr. Erica
Head).  Starting in 1997, a
comprehensive suite of hydrographic, nutrient, and biological data is being
collected 3-4 times a year along transects through Browns Bank, off Halifax,
through Banquereau Bank (the “Louisbourg Line”), across Cabot Strait,
and others further upstream.  The
overlap of AZMP with GLOBEC GB field effort begins in 1997, the collocation of
our upstream boundary with the AZMP Louisbourg Line
will allow us to compute a climatology of physical and
biological properties (1997-2005) which will help determine realistic boundary
conditions and their interannual variability.  In formulating boundary conditions we
will collaborate with Haidvogel (Rutgers) who is modeling basin-scale dynamics and with McGillicuddy
et al. who have proposed a concurrent basin-scale adjoint modeling study of Calanus.[1]

We
will not include the potential influence of warm core rings (eg., Flierl and Wroblewski,
1985) and other eddy features originating in the Gulf Stream (Fig. 1),
because the larger regional and basin-scale models do not yet produce these
features accurately enough in this region for us to use them to construct the
boundary conditions along the open ocean part of FVCOM.  The influence of rings may be minor
(e.g., Churchill et al., 2003), however,
and we will be able to infer their potential importance by their omission.  As the larger-scale models mature in
this respect, follow-on studies of these processes can be developed.

FVCOM
Computational Aspects— With GLOBEC
GB Phase 4 support, FVCOM has been converted into a FORTRAN 95/2K parallelized
program to take advantage of multi-processor computing (Cowles et al.,
2003).  This implementation uses a
SPMD (Single Program Multiple Data) approach with a message-passing model to
perform the necessary inter-processor communication and synchronization. The
physical domain is decomposed into sub-domains using the METIS graph
partitioning libraries.  Each
sub-domain is assigned to a processor for integration of the model equations.
The exchange subroutines utilize non-blocking sends and receive from the MPI
(Message Passing Interface) 2.0 library.  The efficiency of the code can be
measured in terms of its speedup and/or scalability on a multiprocessor
computer. Chen’s modeling lab will install a new high-performance
256-processor super-cluster computer this summer. With this computer, 1-yr
model run with data assimilation and the existing GOM/GB FVCOM grid should take
less than 1-day clocktime. We plan to use this
computer with attached mass storage for the proposed Phase 4B model experiments
(1995-1999 hindcasts and process studies), model/data comparisons, model result
analysis and visualization, and archiving model output and results.

2.3.2.
Biological
Models

We
will incorporate a copepod population model and a simple food web model (NPZ) into
the plug-in modules of FVCOM.  We will
draw from our previous modeling work involving Calanus, Pseudocalanus,
and other copepod species (Davis, 1984a,c, 1987; Lynch
et al., 1998; McGillicuddy et al., 1998; Zakardjian et al., 2003), as well as our food web
modeling (Davis, 1987b; Flierl and Davis, 1993; Lewis et al., 1994; Davis and
Steele, 1994; Zeldis et al., 1995; Dadou et al. 1996; Ji, 2003, submitted a,b,c).

Population
model —
Copepod dynamics will be modeled using a stage-structured population model
containing 15 life stages (egg, N1-6, C1-3, C4M-F, C5M-F, Adult) plus
additional diapause stages (e.g. eggs or CV) as needed.  A standard formulation for the
stage-based model will be used (e.g., Zakardjian et al., 2003).   A potential problem with using only 15
life stages is artificial diffusion of individuals through the life stages,
and, to prevent this, age-within-stage models have been developed (Davis 1984c).
If necessary we will use a 150-age-stage class model (e.g., Davis 1984c) which will still run efficiently given the
supercomputing power available.  Egg
production, molting, and growth rate parameters as functions of temperature and
food will be taken from the vital rate measurements made during the GLOBEC
process cruises and from the large body of available literature (see citations
in Background section). The model will be initialized and validated using
observed patterns of copepod abundance according to the numerical experiments
described below.  The copepod
population then will grow based on ambient temperature and food levels.  Mortality rates will be inferred by
adjusting them to match model and field abundances (Hall, 1964; Davis,
1984a).  Mortality is stage-specific
and typically higher for younger stages (e.g., Davis, 1984a).  Mortality
rates as a function of life-stage have been found for Calanus and Pseudocalanus
as part of the GLOBEC GB studies (Ohman et al.,
2002).  We will use relative
stage-dependent mortality curves, from this and other studies, when inferring
mortality rates.  We also will
explore the possibility of conducting targeted inverse modeling to obtain the
stage-dependent mortality rates (e.g. Li et al, in prep).  Vertical migration behavior observed
from the GLOBEC data sets during process and broadscale cruises will be incorporated
into the model using a simple biological advection term.  The temperature fields are given by the
physical model.  For the food-fields
we will use two approaches as described in the next section:  1) empirically-forced 3D static
phytoplankton fields derived from 3D chlorophyll measurements and ocean color
data, and 2) a dynamic 3D prey field based on a simple NPZ-type of food web
model.  In the former case the
copepods will be transported through static prey fields, and in the latter case
the copepods and prey field will be transported together.

Lower trophic level food web
model — We will explore the possibility of generating
temporally evolving 3D phytoplankton fields from a lower trophic level food web
model (e.g. NPZ or NPZD) to provide food for the copepod population model.  We will use one-way coupling whereby the
copepods depend on the food field but do not affect it (e.g. Carlotti, 1998; Batchelder et
al., 2002).  In this case, the Z
will represent microzooplankton grazers used solely as a closure term.  We can generate realistic 3D
phytoplankton fields using a simple NPZ model (Ji, 2003).  It may also be possible to allow the
copepods to graze the P and Z (e.g., Carlotti, 1996),
but this approach may not be necessary or feasible in 3D.  The NPZ model will be adjusted so that
the resulting fields approximate the 3D chlorophyll and satellite data.  The concept of using an NPZ model to
generate spatially explicit prey fields has been used with an IBM of larval
pollock in the Gulf of Alaska (Hermann et al., 2001), where the Z represented
copepod prey.  Here we propose to
use the NPZ to generate the P fields for spatially explicit population models
of dominant copepod species.  The
resulting copepod distributions will be used in a concurrent modeling study of
Werner et al. who are proposing to develop an IBM of larval cod (see Werner
letter).

Plankton
food web models are variously complex, ranging from simple NPZ to models with
multiple subcomponents. In the GOM/GB a simple NPZ (Klein, 1987; Lewis et al.,
1994; Franks and Chen, 1996; Franks and Chen, 2001) and a nine-compartment
model (Ji, 2003) have been used.  The NPZ model coupled with a 3-D
nonlinear, primitive equation, finite-difference ocean circulation model (ECOM-si, Blumberg and Mellor, 1987) can successfully approximate
3D phytoplankton fields observed on GB from summer cruises and satellite data.  Robust features, such as the subsurface
maximum and mixing-front induced productivity were produced with this model
(Franks and Chen, 2001). More recently, a nine-compartment model (Ji, 2003),
coupled to ECOM_si and FVCOM, captured the basic seasonal
and spatial patterns of nutrients and phytoplankton on GB.  This model includes 3-N (nitrate,
ammonia and silicate), 2-P (large and small), 2-Z (large and small), and two detrital pools (N and Si). Silicate
can limit the spring diatom bloom on GB (Townsend and Thomas, 2001; Townsend
and Thomas, 2002, Ji, 2003).

In
the proposed study, the simple NPZ model will be used due to its capability and
robustness, as well as the availability of observation data for the initial and
boundary conditions. We also will explore the use of separate pools in the
model for Si and N and for P (diatom, non-diatom).  The model will run continuously for 3
years from January 1997 to December 1999, a period when we have both nutrient
and phytoplankton data from the GLOBEC GB program.  Initial horizontal distributions of
nitrogen, phytoplankton and zooplankton during winter will be derived from
climatological data (e.g. Petrie and Yeats, 2003), satellite imagery and MARMAP
data, respectively.  An initial
homogenous vertical distribution also will be specified (as observed in winter).
While the NPZ model is being tested
against the observed data, these same data will be used to generate spatially
and temporally interpolated 3D static prey fields for the copepod population
model.  This empirical approach is
complementary to the model-based approach.

Upstream
data – Biological
data for the SS and SW will be obtained from our Canadian colleagues, who
have been actively involved in the GB and Canadian GLOBEC programs as well as
in other studies of the SS and Labrador
Sea including the AZMP (see
Head letter).  To the extent
available we will use interpolated data from 1995-1999 in the SS and SW.  We also will use idealized boundary
scenarios based on observed data from other years and larger scales (eg. CPR data).

Biological
transport — We will use concentration-based (Eulerian) rather than
individual-based (Lagrangian) transport for the copepod and food web models. While
we have used both types of models in the past, the use of concentration-based
models allow us to compute fluxes and mass balances directly and more
accurately.  This approach is
necessary for quantifying such factors as sustainability of populations in
particular areas.  The
concentration-based approach lends itself easily to stage-structured population
models.  This straightforward method
avoids the necessity of using super-individual particles or spawning and
removing particles at each time step.

2.3.3.
Numerical
experiments

We
will conduct a series of targeted numerical experiments using prognostic forward
model runs (rather than inverse methods) to address each of the above
hypotheses.  Data and model will be
compared using a maximum-likelihood method (Stock, 2005; Stock et al.,
submitted). These process studies will help interpret the basic behavior and
inter-annual variability shown in the 1995-99 hindcast.  Detailed tasks and time table for this
work are given in the required supplement on project management and data
exchange.

Working hypothesis— We will initialize
the model with the mean winter concentrations of each copepod species (in
separate model runs).  The same
model structure will be used for all species, changing only the parameter
values (temperature/food/life-stage dependent egg production rate, development
rate, growth rate, and normalized stage-dependent mortality) and behaviors, and
thus expediting the model runs.  The
inputs of characteristic life history traits of each species together with its
initial abundance patterns should generate its observed characteristic
seasonal/spatial patterns. The model will be run for a complete annual cycle
and compared with the 5-year monthly mean abundance patterns.  To examine inter-annual variation we will
model each copepod species during the complete 5-year GLOBEC period 1995-1999,
first year by year, then continuously over the 5 years.  The result will be a complete 5-year
biological/physical hindcast.

Food versus Predation— We will examine the degree of food-dependence and
mortality with regard to inter-annual variability for each species.  First we will confirm that the NPZ model
can be used to approximate the 3D distribution of phytoplankton for the
multi-year monthly mean and year-to-year changes.  In parallel, we will use fixed 3D
phytoplankton fields approximated from monthly averaged satellite and in situ
data.  We will interpolate the
phytoplankton fields between monthly values to avoid discontinuities.  We will use the NPZ model together with scenarios
of salinity and nutrient (N, Si) input through the NEC,
to determine the extent to which phytoplankton biomass/production on GB is
determined by this forcing and the extent to which the copepod species are
affected by it.  We will examine
possible effects of temperature and transport during 1995-1999 on the trends in
mean abundances of each species.

Self-sustainabilty— We will initialize the
model with the observed distribution of each species and exclude input from
other regions, to determine whether the local population is self-sustaining.  In particular we will examine the
importance of Calanus input from SW
and/or SS to the GOM/GB population, the input of Pseudocalanus from western GOM to the GB population, the key source
regions for Oithona similis, and
whether Centropages typicus
depends on immigration to sustain its population on GB.  We will further examine whether resting
eggs can explain high abundance of Centropages hamatus and Temora longicornis on the crest of GB.  We will initialize the population as
resting eggs on the crest and determine whether the resulting plume of nauplii and subsequent copepodids
matches the observed distributions.
We will examine the formation of the Calanus
“hole” on GB by initializing with CVs in the GOM during December
and determining the extent to which the hole forms as a result of gradient
advection versus high crest mortality.

Catastrophic global warming— Finally we will use
boundary forcing that represents a scenario of catastrophic warming (see FVCOM
section).  We will run the model for
single and multiple years to determine the impact on the NPZ fields and on each
dominant copepod species.

2.3.4.
Work schedule— The schedule for the proposed modeling work together
with a description of individual tasks, project management, dissemination, and
timeline are described in the required supplemental documents.

3.      Significance
of Proposed Research– Intellectual Merit

The
proposed work will provide new insights into the role of local dynamics and
large-scale forcing in controlling population dynamics of marine copepods.  We believe that the physical/biological
model resulting from the proposed work will be a legacy of the Georges Bank
GLOBEC program by providing a valuable tool that subsequent researchers can use
to study the dynamics of this system in hindcast, nowcast, and forecast modes. The
results of the targeted experiments will provide insights into the degree of
bottom-up and top-down control and the degree of sustainability of copepod
populations under different conditions of external forcing.  The work will provide a new
understanding of the impact of basin-scale forcing, including catastrophic
change, on local-scale plankton dynamics.
The resulting spatially explicit model of small and large copepod
species will provide dynamic prey fields for concurrent and subsequent larval
fish modeling studies, leading to a better understanding of recruitment in fish
populations.

4.      Broader
Impacts

The New England Regional Center for Ocean Science Education Excellence (NER-COSEE) at WHOI will work with us to facilitate
development of the education and outreach component of this project. COSEE is a
national program, with regional centers, designed to facilitate K-12, college,
and public education and outreach.  The
proposed work will provide a state-of-the art coupled biological/physical model
of an important marine area.  We
envision a broad user-base for this final product, which will be served via the
web to our scientific colleagues as well as to fishermen, K-12 educators, and
the general public.  The main
web-page will be located at WHOI with links to the other institutions.  Chen’s group at UMD will create a
website specifically for this work, expanding their existing FVCOM site, which
now has user-friendly point-and-click modeling capacity.  Users will be able to examine 4D model
data from the hindcast for the GLOBEC years as well as from pre-run nowcasts
and forecasts.  Users will be able
to change model parameters and create new model runs, with the level of
sophistication depending on skill level. Further discussion of these broader impacts is given in the required
supplementary section on this topic.

References

Ban, S., H.
Lee, A. Shinada, and T. Toda. 2000. In situ egg production and hatching success of the
marine copepod Pseudocalanus newmani in Funka Bay and adjacent waters off
southwestern Hokkaido, Japan: associated to diatom
bloom.  J. Plankton Res. 22, 907-922.

Batchelder, H.P., C.A. Edwards and T.M. Powell, 2002. Individual-based models of copepod populations in coastal upwelling
regions: implications of physiologically and environmentally influenced diel
vertical migration on demographic success and nearshore
retention. Prog. Oceanogr., 53,
307-333.

Bigelow,
H. B. 1926. Plankton of the offshore waters of the Gulf of Maine. Bull. US Bur. Fish., 40, 1–507.

Bucklin, A., A. M. Bentley and S. P. Franzen. 1998.
Distribution and relative abundance of the copepods Pseudocalanus
moultoni and P. newmani
on Georges Bank based on molecular identification of sibling species.
Mar. Biol., 132, 97–106.

Bucklin,
A., M. Guarnieri, D. J. McGillicuddy
and R. S. Hill. 2001. Spring-summer evolution of Pseudocalanusspp.
abundance of Georges Bank based onmolecular discrimination of P. moultoni
and P. newmani. Deep-Sea Res. II., 48, 589–608.

Burchard,
H., 2002. Applied turbulence modeling in marine waters.
Springer:Berlin-Heidelberg-New York-Barcelona-Hong
Kong-London-Milan Paris-Tokyo, 215pp.

Campbell
R W, Head E J H
2000  Egg production
rates of Calanus finmarchicus in the
western North Atlantic: effect of gonad maturity, female size, chlorophyll
concentration, and temperature. Can J
Fish Aquat Sci
57:518–529

Campbell, R.G., M.W. Wagner, G.J. Teegarden, C.A. Boudreau and E.G. Durbin. 2001b Growth and development rates of the copepod Calanus
finmarchicus reared in the laboratory. Mar. Ecol. Prog.
Ser., 221, 161–183.

Campbell, R.G., Runge, J. A., Durbin, E.G., 2001a. Evidence for food limitation of Calanus finmarchicus production
rates on the southern bank of Georges Bank during April 1997. Deep-Sea Research II 48, 531-549.

Carlotti, F. and G. Radach, 1996. Seasonal dynamics of phytoplankton
and Calanus finmarchicus in the
North
Sea
as revealed by a coupled one dimensional model. Limnol. Oceanogr., 41, 522-539.

Carlotti, F. and K.U. Wolf, 1998. A Lagrangian ensemble model of Calanus finmarchicus coupled with a 1-D ecosystem model. Fish. Oceanogr., 7, 191-204.

Chen, C, G. Cowles and R. C. Beardsley, 2004a.  An
unstructured grid, finite-volume coastal ocean model: FVCOM User Manual.  SMAST/UMASSD Technical Report-04-0601,
pp183.

Chen, C. and R. C. Beardsley. 1998. Tidal mixing over finite-amplitude banks: a
model study with application to Georges
Bank. Journal of Marine
Research, 56 (6), 1163-1203.

Chen, C., H. Liu, and R. Beardsley, 2003a. An unstructured grid, finite-volume,
three-dimensional, primitive equations ocean model: Application to coastal
ocean and estuaries. Journal of Atmospheric
and Ocean Technology, 20 (1),
159–186.

Chen,
C., H. Liu, R. C. Beardsley, G. Cowles, J. Pringle, R. Schlitz, and B.
Rothschild, 2003b. Application of FVCOM to the Gulf of Maine/Georges Bank:
Simulated and assimilated modeling studies of stratification and subtidal circulation.
EOS Trans, AGU, 84(52), Ocean Science Meeting Suppl.,
Abstract OS51G-08.

Chen,
C., J. Qi, H. Liu, C. Li, H. Lin, R. Walker and K.
Gates, 2005d. Tidal Flushing Dynamics in the Satilla
River, Georgia: A Comparison between FVCOM and ECOM-si.
Journal of Geophysical Research, to
be submitted.

Chen, C., Q. Xu, R. C.
Beardsley, and P. J. S. Franks., 2003. Modeling Studies of the Cross-Frontal Water Exchange on Georges Bank: A 3D Lagrangian Experiment, Journal of Geophysical
Research, 108(C5), 3142, 10.1029/2000JC000390 .

Chen, C., R. C. Beardsley, H. Huang, H. Liu, and Q. Xu, 2005b. A finite-volume numerical approach for coastal ocean
studies: Comparisons with the finite-difference models. Journal of Geophysical Research, in revision.

Chen,
C., R. C. Beardsley, Q. Xu, G. Cowles, and R.
Limeburner, 2005c. Tidal Dynamics in the Gulf of Maine and New
England Shelf: An
Application of FVCOM. Deep Sea Research
II-GLOBEC/GB special issue, submitted.

Chen,
C., R. Houghton, R. C. Beardsley, Q. Xu, and H. Liu,
2003c. Preliminary results of model dye experiments on Georges Bank. EOS Transactions, AGU, 84(52), Ocean Science Meeting Suppl., Abstract OS32C-13.

Chen, C., Wang, T, L. Wang, J. Blanton, C. Li, H. Huang
and H. Lin, 2005e. Tidal-induced flushing
process over the estuarine-tidal creek-salt marsh complex of the Okatee/Collection River in South Carolina: An application of FVCOM. Journal of Geophysical Research. To be submitted.

Chen, C., Z. Wu, R. C. Beardsley, S. Shu, and C. Xu, 2005a. Using MM5 to hindcast the ocean
surface forcing fields over the Gulf of Maine and Georges Bank region. Journal of
Atmospheric and Oceanic Technology,
22(2): 131-145.

Churchill, J. H., J. P.
Manning, and R. C. Beardsley, 2003.  Slope
water intrusions onto Georges Bank. Journal of Geophysical Research, (GLOBEC special section),
108(C11), 8012, doi:10.1029/2002JC001400.

Clarke, G.L.,
1946. Dynamics of production
in a marine area. Ecol. Monogr.
16, 321–337.

Cohen, E. B., and M. D. Grosslein. 1987. Production on Georges
Bank Compared with other shelf ecosystems. Pp. 383–391, In R.H.
Backus and D.W. Bourne (eds.) Georges Bank. MIT Press. Cambridge, MA. 593 pp.

Corkett C
J, and I. A. McLaren. 1978. The biology of Pseudocalanus.
Adv. Mar Biol., 15, 1-231.

Cushing.
D. H. and J. J. Walsh. 1976. The Ecology of the Seas. London: Blackwell. 467 pp.

Dadou, I.
V. Garcon, V. Anderson, G. Flierl, and C. Davis. 1996. Impact of the north
equatorial current meandering on a pelagic ecosystem:  A modeling approach.  J. Mar. Res.,  54, 311–342.

Davis,
C. S. 1983. Laboratory rearing of marine calanoid
copepods.  J. Exp. Mar. Biol.
Ecol., 71, 119-133.

Davis,
C. S. 1984a. Predatory control of copepod seasonal cycles on Georges Bank.   Mar.  Biol., 82,
31-40.

Davis,
C. S. 1984b. Food concentrations on Georges Bank:
Non-limiting effect on growth and survival of laboratory reared Pseudocalanus sp.
and
Paracalanus parvus.
Mar.
Biol., 82, 42-46.

Davis,
C. S. 1984c. Interaction of a copepod population with the
mean circulation on Georges Bank.   J. Mar. Res., 42, 573-590.

Davis,
C. S. 1987a. Components of the zooplankton production cycle in the temperate
ocean.   J. Mar. Res.,  45, 947-983.

Davis,
C. S. 1987b. Zooplankton Life Cycles.  pp. 256-267.  In: Georges Bank.  R. H.
Backus (ed.), MIT Press.

Davis, C. S. and J. H. Steele. 1994. Modeling upper ocean biological-physical
processes. URIP Workshop Report, WHOI TECH RPT 94-32, 65 pp.

Davis, C.S. and P. Alatalo.  1992.
Effects of constant and intermittent food supply on life history parameters in
a marine copepod.   Limnol.  Oceanogr.,  37,
1618–1639.

Drinkwater, K. F., D. B. Mountain, and A. Herman.  2003.
Variability in the Slope Water Properties off Eastern North America and their Effects on the Adjacent Shelves.  J. Geophys.
Res. (submitted)

Dudhia,
J., D. Gill, K. Manning, W. Wang, C. Bruyere, J.
Wilson, and S. Kelly, 2003: PSU/NCAR mesoscale modeling system tutorial class
notes and user’s guide, MM5 modeling system version 3, Mesoscale and Microscale Meteorology Division, National Center for Atmospheric Research.

Durbin,
E. G., J. A. Runge, R. G. Campbell, P. R. Garrahan,
M. C. Cascas and S. Plourde.
1997. Late fall-early winter recruitment of Calanus finmarchicus on
Georges Bank., Mar. Ecol. Prog. Ser.,
151, 103-14.

Durbin, E.G., Garrahan,
P.R., Casas, M.C. 2000. Abundance and distribution of Calanus
finmarchicus on Georges Bank during 1995 and 1996. ICES Journal of Marine Science 57, 1664-1685.

Durbin, E.G., M.C. Casas. Abundance, spatial distribution, and interannual variability of copepods on Georges Bank during the winter spring period. Deep-Sea Research (Submitted)

Durbin, E.G., R. Campbell, M. Casas,
B. Niehoff, J. Runge, M. Wagner. 2003. Interannual Variation
in phytoplankton blooms and zooplankton productivity and abundance in the Gulf of Maine during winter. Mar
Ecol Progr Ser. 254:81-100

Dzierzbicka-Glowacka, L.  2004. Growth and development of copepodite stages of  Pseudocalanus spp., J. Plankton Res., 26, 49-60.

Fairall,
C. W., E. F. Bradley, D. P. Rogers, J. B. Edson, and
G. S. Young, 1996. Bulk parameterization of air-sea fluxes for tropic ocean
global atmosphere coupled-ocean atmosphere response experiment. Journal of Geophysical Research, 101 (C2), 3747-3764.

Fairall,
C. W., E. F. Bradley, J.E. Hare, A.A. Grachev, and J.
B. Edson, 2003. Bulk parameterization of air-sea
fluxes:  updates and verification
for the COARE algorithm. J. Climate, 16, 571-590.

Flierl, G. R. and C. S. Davis.  1993.
Biological effects of Gulf
Stream meandering.  J. Mar. Res.,  51, 529–560.

Flierl, G.R.
and Wroblewski, J.S. 1985. The
possible influence of warm core Gulf
Stream rings upon shelf
water larval fish distribution. Fish. Bull.,
83: 313-330

Franks, P.J.S. and C. Chen, 1996.  Plankton
production in tidal fronts: A model of Georges Bank in summer. Journal
of Marine Research 54, 631-651.

Franks, P.J.S. and C. Chen, 2001.  A 3-D prognostic numerical model study of the Georges Bank ecosystem. Part II: biological-physical model. Deep Sea Research II 48, 457-482.

Fratantoni, P. S.
and R. S. Pickart, 2005a. The
western North Atlantic shelfbreak current system in summer. J. Phys. Oceanography,
submitted.

Fratantoni, P. S.
and R. S. Pickart, 2005b. Structure
and alongstream evolution of the shelfbreak
jet in the western North Atlantic.  J. Phys. Oceanography,
submitted.

Frost B
W. 1989. A taxonomy of the marine calanoic
copepod genus Pseudocalanus.
Can J Zool
67: 525±551

Galperin, B., L. H. Kantha, S.
Hassid, and A. Rosati, 1988. A quasi-equilibrium turbulent
energy model for geophysical flows. Journal
of the Atmospheric Sciences, 45,
55–62.

GLOBEC, 1991a. U. S. GLOBEC: Initial Science Plan, Report Number 1.

GLOBEC, 1991b. U. S. GLOBEC: Northwest
Atlantic Program, GLOBEC
Canada/U.S. Meeting on N.W. Atlantic Fisheries and Climate, Report Number 2.

GLOBEC, 1992. U. S. GLOBEC: Northwest
Atlantic Implementation
Plan, Report No. 6,

GLOBEC, 1996. U. S. GLOBEC: Northeast
Pacific Implementation Plan, Report No. 17.

GLOBEC, 1997. U. S. GLOBEC: Workshop on
Modeling the Southern Ocean Ecosystem, Report No. 18.

GLOBEC, 2000. GLOBEC in the Gulf of
Mexico: Large Rivers and
Marine Populations, Report No. 19.

Grell, G.
A., J. Dudhia, and D. R. Stauffer, 1994: A
description of the Fifth-Generation Penn State/NCAR Mesoscale Model (MM5). NCAR Technical Note, NCAR/TN 398+STR, 117pp.

Grosslein, M. S., and R. C. Hennemuth,
1973.  Spawning stock and other factors related
to recruitment of haddock on Georges
Bank. Rapp. P.-v. Réun. Cons.
Int. Explor. Mer, 163, 77–88.

Hall, D. J. 1964. An experimental approach to
the dynamics of a natural population of Daphnia galeata
mendotae . Ecology 45 (1), 94-112.

Han, G., C. E. Hannah, J. W.
Loder, and P. C. Smith, 1997.  Seasonal variation of
the three-dimensional mean circulation over the Scotian Shelf. J.
Geophysical Research, 102(C1), 1011-1025.

Hannah, C. G., J. A. Shore, J. W. Loder, and C. E. Naimie,
2001.  Seasonal
circulation on the western and central Scotian Shelf. J. Phys.
Oceanography, 31(2), 591-615.

Hannah,
C.G., Naimie, C.E., Loder,
J.W., Werner, F.E. 1998 Upper-ocean transport mechanisms from the Gulf of Maine to Georges
Bank, with implications for Calanus
supply. Cont. Shelf Res., 7, 18871911.

Head,
E.J.H., Harris, L.R., Petrie, B., 1999. Distribution of Calanus spp. on and around the Nova Scotia Shelf in April: evidence
for an offshore source of Calanus finmarchicus to the central and
western regions. Canadian Journal of Aquatic Sciences 56,
2463-2476.

Heath,
M.R., Backhaus, J.O., Richardson, K., McKenzie, E., Slagstad,
D., Beare, D., Dunn, J., Fraser, J.G., Gallego, A., Hainbucher, D., Hay,
S., Jónasdóttir, S., Madden, H., Mardaljevic, J., Schacht, A., 1999. Climate
fluctuations and the spring invasion of the North Sea by Calanus finmarchicus. Fisheries Oceanography 8 (Suppl.
1), 163-176.

Hermann, A. J., S. Hinckley, B. A. Megrey
and J. M. Napp. 2001 Applied and
theoretical considerations for constructing spatially explicit individual-based
models of marine larval fish that include multiple trophic levels, ICES
J. Mar. Sci. 58:1030-1041

Hinrichsen, H.H., C.
Möllmann, R. Voss, F.W. Köster, and G. Kornilovs. 2002. Biophysical modeling
of larval Baltic cod (Gadus morhua) growth and survival. Can.
J. Fish. Aquat. Sci., 59,
1858–1873.

Hjort, J . 1914. Fluctuations in the great fisheries of Europe
viewed in the light of biological research. Rapp . P.-v . Reun . Cons. int. Explor.
Mer, 20, 1-228.

Huang, H., C. Chen, G. Cowles, R. C. Beardsley, and K.
Hedstrom, 2005a. Sensitivity of the numerical solution to unstructured triangular
grids: A validation experiment of FVCOM for the Rossby
equatorial soliton.  Deep Sea Research II-GLOBEC/GB special issue, to be submitted.

Huang, H., C. Chen, J. O. Blanton, and F. A. Andrade,
2005d. Tidal current asymmetry and
implication to variability of the dissolved oxygen over shallow tidal creeks:
an application of FVCOM to the Okatee River, South
Carolina. Journal of Geophysical Reseqarch, to be
submitted.

Huang, H., C. Chen, R. C. Beardsley, and K. Hedstrom, 2005c.
Validation experiments of FVCOM for the wind-driven flow in an elongated
rotating basin: A comparison with analytical solution. Deep Sea Research II-GLOBEC/GB special
issue, to be submitted.

Huang, H., C. Chen, R. C. Beardsley, and K. Hedstrom.
2005b. Capability and Accuracy of the unstructured grid model to simulate the
coastal hydraulic jump: A validation experiment of FVCOM via horizontal
advection schemes. Deep Sea Research II-GLOBEC/GB special issue, to be submitted.

Ji, R., 2003. Biological and physical processes controlling the
spring phytoplankton bloom dynamics on Georges Bank. Ph.D.
Dissertation, University of Georgia, Athens, Georgia.

Ji, R., C. Chen, P. J. S. Franks, D.W. Townsend, E.G.
Durbin, R. C. Beardsley, R.G. Lough, and R.W. Houghton, 2004. Spring bloom and associated lower trophic level food
web dynamics on Georges Bank: from observation to model. Submitted to Deep-Sea
Research II

Ji, R., C. Chen, P. J. S. Franks, D.W. Townsend, E.G.
Durbin, R. C. Beardsley, R.G. Lough, and R.W. Houghton, 2004. Effects of topography and tidal mixing front on the
spring phytoplankton bloom on Georges
Bank: 2-D model experiments.
Submitted to Deep-Sea Research II.

Ji, R., C. Chen, P. J. S. Franks, D.W. Townsend, E.G.
Durbin, R. C. Beardsley, R.G. Lough, and R.W. Houghton, 2004. The impact of Scotian Shelf Water
“cross-over” on the plankton dynamics on Georges Bank: A 3-D experiment for the 1999 spring bloom.
Submitted to Deep-Sea Research II

Johnson, C., J. Pringle, and C. Chen.  Transport and retention of dormant copepods in the Gulf of Maine. (submitted to DSRII).

Klein Breteler WCM, Fransz HG, Gonzalez SR (1982) Growth and development of
four calanoid copepod species under experimental and
natural conditions. Neth J Sea Res
16: 195–207

Klein Breteler WCM,
Gonzalez SR (1986) Culture and development of Temora
longicornis (Copepoda, Calanoida) at different conditions of temperature and food.
Syllogeus 58:71–84

Klein Breteler WCM,
Gonzalez SR, Schogt N (1995) Development of Pseudocalanus elongatus
(Copepoda, Calanoida)
cultured at different temperature and food conditions. Mar Ecol Prog Ser 119:99–110

Klein,
P., 1987.  A
simulation of some physical and biological interactions. Georges Bank (eds. by R.H.Backus and D.W.Bourne), pp. 395-402.  MIT Press, Cambridge, Massachusetts.

Lee, H., S.
Ban, T. Ikeda and T. Matsuishi.  2003. Effect of temperature on development, growth and reproduction in the
marine copepod Pseudocalanus newmani at satiating food condition. J. Plankton Res.
25, 261-271.

Lewis, C. V. W., C. Chen, and C. S. Davis. 2001. Variability in wind forcing and its effect on
circulation and plankton transport over Georges Bank.  Deep-Sea
Research II, 48, 137–158.

Lewis, C. V., C. S. Davis, and G. Gawarkiewcz. 1994. Wind-forced biological-physical dynamics on an
isolated off-shore bank.  Deep-Sea Res.
41, 51–73.

Li, X., D. J. McGillicuddy,
E. G. Durbin, P. H. Wiebe.
Biological control of the vernal population increase of Calanus finmarchicus on Georges Bank. In prep for Deep Sea Research II.

Lindeman,
R. L. 1942. The trophic-dynamic aspect of ecology. Ecology, 23, 399-418.

Lindley
J A, and  H
G Hunt. 1989. The distribution of Labidocera wollastoni and Centropages hamatus in the North Atlantic Ocean and the North Sea in
relation to the role of resting eggs in the sediment. In: Ryland
JS, Tyler PA (eds)
Reproduction, genetics and distributions of marine organisms. Olsen and Olsen, Fredensborg, pp 407–413

Lindley
JA 1990 Distribution of overwintering calanoid copepods eggs in sea bed sediments around southern
Britain. Mar Biol 104:209–217

Lough, R. G., and D. G. Mountain. 1996. Effect of small-scale turbulence on feeding
rates of larval cod and haddock in stratified water on Georges Bank.  Deep Sea Res. II, 43, 1745-1772.

Lough,
R.G., E. M. Caldarone, L. J. Buckley, E. A.
Broughton, M. E. Kiladis, and B. R. Burns, 1996.
Vertical distribution of cod and haddock eggs and larvae feeding and condition
in stratified and mixed waters on southern Georges Bank, May 1992. Deep Sea Res., 43, 18751904.

Lynch,
D. R., Gentleman, W. C., McGillicuddy, D. J. and C.
S. Davis, 1998. Biological/ physical simulations of Calanus finmarchicus population dynamics
in the Gulf of Maine.  Marine
Ecology Progress Series, 169, 189–210.

Maps, F., J.A. Runge, B. Zakardjian
and P. Joly. 2005. Egg production and hatching success of Temora longicornis (Copepoda,
Calanoida) in the southern Gulf of St. Lawrence. Mar.-Ecol. Prog. Ser.285:117-128

Marcus, N. 1996. Ecological and evolutionary significance of resting eggs in marine
copepods: past, present, and future studies. Hydrobiologia, 320: 141–152.

Marcus, N. H. and R. V. Lutz. 1998. Longevity of subitaneous
and diapause eggs of Centropages hamatus (Copepoda: Calanoida) from the
northern Gulf of Mexico, Marine Biology,
131, 249-257.

McGillicuddy, D. J. Jr. and A. Bucklin. 2002. Intermingling of two Pseudocalanus
species on Georges Bank. J. Mar. Res. 60: 583–604.

McGillicuddy,
D. J., D. R. Lynch, A. M. Moore, W. C. Gentleman, C. S. Davis, and C. J. Meise. 1998. An adjoint data assimilation approach to the
diagnosis of physical and biological controls on Pseudocalanus spp.
populations in the Gulf of Maine - Georges Bank Region.  Fisheries Oceanogr.,  7,
205–218.

McLaren
IA, Laberge E, Corkett CJ, Sevigny J-M 1989a Life cycles of four species of Pseudocalanus in Nova Scotia. Can J Zool
67: 552-558

McLaren IA, Sevigny
J-M, Corkett CJ 1989b Temperature-dependent
development in Pseudocalanus species. Can J Zool 67: 559-564

McLaren, I. A., and P. Avendano. 1995. Prey field and diet of larval cod on Western
Bank, Scotian Shelf. Can. J. Fish. Aquat. Sci., 52, 448–463.

McLaren, I. A., E. Head, and D. Sameoto. 2001. Life cycles and seasonal distributions of Calanus
finmarchicus on the central Scotian Shelf.  Can.
J. Fish. Aquat. Sci., 58,
659–670.

McLaren, I. A., P. Avendaño, C.
T. Taggart, and S. E. Lochmann, 1998. Feeding by larval cod in different
water-masses on Western Bank, Scotian Shelf.  Fish. Oceanogr., 6, 250-265.

Meise, C.J. and J. E. O'Reilly, 1996. Spatial and seasonal patterns in abundance and
age-composition of Calanus finmarchicus in the Gulf of Maine and on Georges
Bank, 19771987,
Deep-Sea Res. II, 7, 14731501

Meise-Munns, C., J. Green, M. Ingham, and D. Mountain, 1990.  Interannual
variability in the copepod populations of Georges Bank and the western Gulf of Maine, Mar. Ecol. Progr. Ser., 65,
225-232,

Mellor, G. L. and T. Yamada, 1982. Development of a turbulence closure
model for geophysical fluid problem. Reviews of Geophysics and Space. Physics, 20, 851–875.

Miller,
C. B., T. J. Cowles, P. H. Wiebe, N. J. Copley, and
H. Grigg, 1991. Phenology
in Calanus finmarchicus: Hypotheses about control mechanisms, Mar.
Ecol. Progr. Ser., 72, 79-91,.

Miller,
C.B., Lynch, D.R., Carlotti, F., Gentleman,W., Lewis,V.W., 1998. Coupling of an individual-based population dynamic model of Calanus
finmarchicus to a circulation model for the Georges Bank region. Fisheries Oceanography, 7, 3/4,
219-234.

Nixon,
S. W. 1988. Physical energy inputs and the comparative
ecology of lake and marine ecosystems.  Limnol. Oceanogr., 33, 1005-1025

Odum, H.
T. 1957. Trophic structure and productivity of Silver Springs, Florida. Ecological
Monographs, 27, 55-112.

Ohman, M. D., J. A. Runge, E. G. Durbin, D. B. Field and B.
Niehoff.
2002. On birth and death in the sea. Hydrobiol., 480, 55-68.

Osgood, K. E. and D. M. Checkley. 1997. Seasonal variations in a deep aggregation of Calanus
pacificus in the Santa Barbara Basin. Mar. Ecol. Prog. Ser., 148,
5969.

Petrie,
B.  and P.
Yeats, 2000. Annual and interannual
variability of nutrients and their estimated fluxes in the Scotian Shelf-Gulf
of Maine region. Can. J. Fish. Aquat. Sci. 57, 2536–2546.

Plourde, S., and J. A. Runge. 1993. Reproduction of the planktonic copepod, Calanus
finmarchicus, in the Lower St. Lawrence Estuary: Relation to the cycle of
phytoplankton production and evidence for a Calanus pump, Mar.\ Ecol. Progr. Ser., 102, 217-227.

Reiss, C. S., I. A. McLaren, and P. Avendaño. 2003. Horizontal and vertical distribution patterns,
retention rates, and population dynamics of zooplankton on Western Bank,
Scotian Shelf. Canadian Journal of Fisheries and Aquatic Sciences, 60,12291244.

Runge,
J.A.,  S. Plourde, P. Joly, E. Durbin and
B. Niehoff.
Characteristics of egg production of the planktonic copepod, Calanus finmarchicus, on Georges Bank: 1994-1999. Submitted.to Deep-Sea Res. II.

Sabatini,
M. and Kiørboe,T.
1994. Egg production, growth and development of the cyclopoid copepod Oithona similis. J.
Plankton Res., 16,
1329–1351.

Sameoto, D. D., and A. W. Herman. 1990. Life cycle and distribution of Calanus
finmarchicus in deep basins on the Nova Scotia shelf and seasonal changes in Calanus spp., Mar. Ecol. Progr. Ser.,
66, 225-237,.

Sarmiento,
J. L., R. Slater, M. J. R. Fasham, H. W. Ducklow, J. R. Toggeweiler and G.
T. Evans, 1993. A seasonal three-dimensional ecosystem model
of nitrogen cycling in the North Atlantic euphotic
zone. Global Biogeochemical Cycles, 7, 417-450.

Saumweber, W. J. and E. G. Durbin.  The
implications of energetic limitation for diapausing Calanus finmarchicus: Towards a Gulf of Maine Calanus budget. submitted to Deep Sea
Res. II

Sissenwine, M. P., E. B. Cohen, and M. D. Grosslein,
1984. Structure
of the Georges
Bank
ecosystem. Rapp. P.-v. Reun. Cons. int. Explor. Mer, 183, 243-254

Smagorinsky, J., 1963. General circulation experiments
with the primitive equations, I. The basic experi-ment. Monthly Weather
Review, 91, 99–164.

Smith, P.C., R.W. Houghton, R.G. Fairbanks, and D.G. Mountain. 2001. Interannual
variability of boundary fluxes and water mass properties in the Gulf of Maine and on Georges
Bank: 1993-1997. Deep Sea Res. II, 48, 37-70.

Steele,
J. H., 1974. The Structure of Marine Ecosystems.
Harvard Univ. Press, Cambridge, MA.

Stock, C. A., 2005. Testing hypotheses concerning the
Initiation and development of blooms of the toxic dinoflagellate
Alexandrium fundyense
in the western Gulf of Maine using a coupled physical-biological
model, PhD Thesis, WHOI.

Stock,
C.A., McGillicuddy, D.J.,
Solow, A.R. and Anderson, D.M.  Evaluating hypotheses for initiation and
development of Alexandrium fundyense blooms in the western Gulf of Maine using coupled physical-biological model. Submitted, Deep Sea Research II

Sundby,
S. 2000. Recruitment of Atlantic cod stocks in relation to temperature and
advection of copepod populations. Sarsia, 85, 277-298.

Teal, J. M. 1962. Energy Flow in the Salt Marsh Ecosystem of Georgia. Ecology, 43, 614-624.

Townsend, D.W. and A.C. Thomas, 2001. Winter-spring transition of
phytoplankton chlorophyll and inorganic nutrients on Georges Bank. Deep Sea Research II 48, 199-214.

Townsend, D.W. and M. Thomas, 2002.  Springtime nutrient and phytoplankton dynamics on Georges Bank. Marine Ecology
Progress Series 228, 57-74.

Townsend, D.W. and N.R. Pettigrew.
1997.  Nitrogen limitation of
secondary production on Georges
Bank.  J. Plankton Res. 19: 221-235.

Townsend, D.W.,A.C. Thomas,
L.M. Mayer, M. Thomas and J. Quinlan. 2004. Oceanography of the Northwest Atlantic Continental Shelf.  pp. 119-168.  In:  Robinson, A.R. and K.H. Brink (eds).  The Sea, Volume 14, Harvard University Press.

Turner,
J. T. 2004. The importance
of small planktonic copepods
and their

roles in pelagic marine food webs. Zoological
Studies, 43, 255-266.

Wiebe, P. H., R. Beardsley, D. Mountain, and A. Bucklin. 2002. U.S. GLOBEC Northwest Atlantic/Georges Bank
Program, Oceanography, 15,
12-29.

Wiebe,
P.H., A.W. Morton, A.M. Bradley, R.H. Backus, J.E. Craddock, T.J. Cowles, V.A.Barber, and G.R. Flierl. 1985. New developments in the
MOCNESS, an apparatus for sampling zooplankton and micronekton.
Mar. Biol. 87: 313-323.

Zakardjian, Bruno. A., J. Sheng, J. A. Runge, I. McLaren, S. Plourde,
K. R. Thompson, and Y. Gratton . 2003. Effects of
temperature and circulation on the population dynamics of Calanus
finmarchicus in the Gulf of St. Lawrence and Scotian Shelf: Study
with a coupled, three-dimensional hydrodynamic, stage-based life history model,
J. Geophys. Res., 108(C11), 8016, doi:10.1029/2002JC001410.

Zeldis,
J. R., C. S. Davis, M. R. James, S. L. Ballara, W. E.
Booth, and F. H.  Chang.  1995. Salp grazing
in a larval fish habitat: effects on phytoplankton abundance, vertical
distribution, and species composition.
Mar. Ecol. Prog. Ser.,  126, 267–283.

Zhao, L., C. Chen, and B. Rothschild, 2005. Tidal dynamics and eddy shedding in the Mount Hope Bay and Narragansett
Bay: An application of
FVCOM.  Journal of Geophysical
Research, to be submitted.

[1] We note
that several groups of other investigators (e.g., J. Wilkens
and D. Haidvogel at Rutgers and D. Wright, C. Hannah,
and others at BIO) are examining how well existing North Atlantic large
regional (the Rutgers Northeast North Atlantic ROMs) and basin-scale (e.g.,
HYCOM, MERCATOR, OPA, POP3) models can hindcast observed physical conditions
over the Northeast America continental margin between Cape Hatteras
and the Grand Banks.  In particular,
Loder and co-workers at BIO have just completed a
long-term moored array study over the Scotian slope and the ongoing
physical/biological transect data being collected in AZMP both provide an
extensive data set for detailed comparison with large-scale model
hindcasts.  We will follow their
work closely during Phase 4B to help determine to what extent these
larger-scale models can provide accurate boundary conditions along the North
American Atlantic margin, including the shelfbreak/slope
current system and the influence of Gulf Stream eddies and warm-core rings as
they move along the margin, with the idea of using this capability when proven
to drive our regional FVCOM integrated model system in future studies.