Abt Associates Inc., May 19, 2010 Ecopath Simulations of Chesapeake Bay 1

Environment and Resources

55 Wheeler Street, Cambridge, MA  Tel: 617 492-7100  www.abtassociates.com

Date November 18, 2009

To Tom Born, Josh Hall, and Erik Helm, U.S. Environmental Protection Agency

From James Palardy, David Mitchell, and Elena Besedin, Abt Associates, Inc.

Subject WA 2-09 Task 4: Ecopath simulations of Chesapeake Bay

1 Introduction

The operation of cooling water intake structures (CWIS) results in the impingement and entrainment (I &

E) of aquatic organisms. The effects of these I & E losses may be a substantial decrease in populations of

commercial, recreational, and forage fish species (Blaber et al. 2000). One way to estimate the value of

these losses is to apply traditional single-species fisheries management techniques, such as the Thompson

Bell model of fisheries yield (Ricker 1975), to generate estimates of forgone fish productivity. However,

these single-species approaches, based solely on species-specific demographic parameters, fail to consider

the effects of ecological interactions among species (e.g., predation, competition) that occur within food

webs (May et al. 1979; NMFS 1999). Consequently, such approaches cannot assess community-level

effects of I & E on the overall productivity and community stability of the ecosystem (Link 2002a; Link

2002b; Leslie and McLeod 2007). Thus, attempts to assess the effects of I & E reductions on fish stocks

should not be based solely upon single-species stock estimates (Walters et al. 2005), but should also

include an ecosystem-based approach to help identify nonlinearities and potential non-intuitive effects

that may result from changes to individual populations (Pauly et al. 2000; Christensen and Walters 2004).

This document describes the application of a common ecosystem-based management tool (Ecopath with

Ecosim) to estimate effects of I & E reductions in the Chesapeake Bay. It describes methodology,

parameter estimation, necessary background data, and presents results of the ecosystem response to I & E

reductions on aquatic species. As such, the document contains the following sections:

 The Chesapeake Bay Fisheries Ecosystem Model

 Model Results

 Model Limitations and Future directions

 Key Findings

2 The Chesapeake Bay Fisheries Ecosystem Model

The Chesapeake Bay Fisheries Ecosystem Model (CBFEM) is an Ecopath with Ecosim (EwE) model that

describes the trophic structure and biomass pools of aquatic organisms within Chesapeake Bay. Because

it was constructed using EwE software, the CBFEM allows fisheries managers to quantitatively evaluate

trophic interactions within Chesapeake Bay, thereby allowing modelers to estimate the outcome of

ecosystem-based fisheries management policy options. For this assessment, I & E losses were input into

the CBFEM, and community shifts were examined under various I & E scenarios.

memorandum
Abt Associates Inc., May 19, 2010 Ecopath Simulations of Chesapeake Bay 2

2.1 Model Background

The EwE approach to fisheries models consists of two essential components: 1) Ecopath, which uses

trophically-linked biomass pools to create a static, mass-balanced snapshot of the ecosystem, and 2)

Ecosim, which estimates ecosystem dynamics through time (Christensen and Pauly 1992; Pauly et al.

2000; Christensen and Walters 2004).

2.1.1 Ecopath

Ecopath routines within the model are based upon the trophic interactions of biomass pools. These

biomass pools may represent a single species, an ontogenetic age category within a species, or a group of

species with similar ecological characteristics. To obtain accurate model output, all major components of

biomass and major trophic pathways must be represented within these biomass pools. For each biomass

pool, biomass accumulation, net migration, diet composition, and total fisheries catch must be known.

Additionally, three of the following input parameters must be obtained: biomass, productivity per unit

biomass, consumption per unit biomass, and ecotrophic efficiency (the fraction of production that is

consumed or harvested within the ecosystem). Ecopath then uses these input data to construct a

quantitative network diagram of energy flow for the system for an arbitrary time period (generally 1 year)

(Figure 1). For additional details, see Christensen and Pauly (1992) and Christensen and Walters (2004).

2.1.2 Ecosim

Using inputs from Ecopath, the Ecosim routines describe the interactions among ecosystem biomass

pools through time, thereby facilitating policy exploration at the ecosystem level. Ecosim operates by: 1)

transforming base Ecopath parameters into a system of differential equations that can be varied through

Figure 1: Flow diagram of biomass pools (circles) and trophic interactions (lines) in the

CBFEM. Lines connecting two biomass pools indicate energy flow (i.e., predation/grazing).

Biomass inputs enter the lower half of the circle, while flows exiting do so on the upper half.

The trophic level of each biomass pool is estimated by summing across food sources the

product of food item trophic level and the proportion of the food item to the overall diet. Pools

are arranged along the x-axis to minimize line overlap.
Abt Associates Inc., May 19, 2010 Ecopath Simulations of Chesapeake Bay 3

time, 2) introducing a vulnerability parameter that expresses how predation mortality varies through time

as a function of local carrying capacities, and 3) by parameterizing and ground-truthing these equations

based on time-series analysis using a Monte Carlo optimization algorithm. Following optimization,

Ecosim allows the modeler to vary all parameters through time, either individually, or in groups.

Parameters may be altered gradually (e.g.,, a 10-year phase-out of a particular fishery or fishing

technique) or as one-time forcing functions (e.g.,, a poor recruitment year for a particular species or group

of species) to explore various policy scenarios. For additional details, see Pauly et al. (2000) and

Christensen and Walters (2004).

2.2 Model Construction

The CBFEM was first conceived in October 2001 (Sellner et al. 2001), and has been under continuous

development by the NOAA Chesapeake Bay Office, in collaboration with the Fisheries Center at the

University of British Columbia, since then (Christensen et al. 2008). The current model contains 45

biomass pools, representing all important components of aquatic biomass within the Chesapeake Bay

(Figure 1, Appendix 1). To obtain necessary Ecopath inputs, diet compositions were based upon advice

from local experts (Sellner et al. 2001), retrieved from FishBase (Froese and Pauly 2009), or obtained

from the literature (see Appendix A of Christensen et al. 2008 for a complete list of sources). To tune the

model’s parameters to time-series data, data from 92 time series are included in the model (Christensen et

al. 2008). These time-series include catch monitoring, survey and stock assessment data, and extend from

1950-2002. Consequently, the model has been tuned to more than 50 years of data, and consequently is

able to produce important time-series trends in individual fish biomass stocks (Christensen et al. 2008).

2.3 Model Parameterization for I & E Losses

As designed, the CBFEM does not explicitly include stock reductions due to I & E. To incorporate these

losses into the CBFEM, species-specific estimates of I & E for the Chesapeake Bay were extracted from

regional estimates, then incorporated into the EwE model as a targeted fishery of known size and biomass

pool composition. All I & E fishery losses were treated as bycatch, and biomass was returned to the

ecosystem via the detrital loop. After applying this fishery, Ecopath parameters were re-fit to historical

time-series stock data with a Monte Carlo optimization procedure.

2.3.1 Estimating I & E losses

To incorporate I & E losses into the CBFEM, estimates of lost biomass within the mid-Atlantic region

were obtained from model output (Stratus Consulting, 2009). These regional-scale I & E estimates were

converted to Chesapeake Bay I & E estimates by scaling regional losses by the proportion of regional

CWIS average intake flow (AIF) occurring within Chesapeake Bay (27.75%).

After obtaining species-specific loss estimates due to I & E (67 species/groups), these values were

converted from total losses (in lbs) from the entire bay to kg/km2[using 10,000 km2as the area of the bay,

consistent with estimates used in the construction of the CBFEM (Christensen et al. 2008)] then

apportioned into the 45 biomass pools within the CBFEM (Appendix 1). First, species-level matches

between CBFEM biomass pools and I & E model output (20 pools, 15 species) were identified. For

species with multiple biomass pools, losses were apportioned as the proportion of biomass present in each

pool. As such, young-of-year (YOY) biomass losses always represented less than 1% of total I & E

biomass loss. Next, biomass pools representing multiple species were matched with I & E output from

relevant species (6 pools, 33 species). These matches were identified either according to group identities

stated within CBFEM documentation (Christensen et al. 2008), or by matching trophic interactions

among biomass pools to the known feeding ecology of species with estimated I & E losses (Froese and

Pauly 2009; Sea Around Us 2009). For 17 biomass pools, no equivalent data could be extracted from I &

E model output. Many of these biomass pools, however, represented groups of species for which I & E is
Abt Associates Inc., May 19, 2010 Ecopath Simulations of Chesapeake Bay 4

not ecologically relevant (e.g., sea birds, detritus), unlikely due to natural history (e.g., sandbar shark,

adult oysters), or of little demographic importance due to high reproductive rates and short life-cycles

(e.g., zooplankton, phytoplankton, ctenophores, sea nettles).

Together, the 26 biomass pools with matched I & E losses accounted for 87% of all estimated I & E

losses. To ensure relevant amounts of biomass were removed from the CBFEM at each timestep,

remaining losses were apportioned relative to the size of biomass pools.

2.3.2 Generating the I & E fishery

Estimates of I & E were implemented within the EwE model by creating a new fishery. Within the EwE

framework, fisheries are classified by the biomass of all captures, broken down by target species. This

captured biomass must in turn be distributed between landings (i.e., catch that is kept, taken ashore and

sold) and bycatch (i.e., catch that is returned to the ecosystem) (Christensen and Walters 2004). Finally,

the fate of the bycatch must be specified. The I & E “fishery” was defined as follows: the magnitude of

the fishery was determined according to section 2.3.1, with 100% of the catch classified as bycatch, and

100% of this bycatch returning to the ecosystem via the detrital loop (i.e., all I & E losses were classified

as fatalities). Consequently, I & E biomass was allowed to be recycled within through the ecosystem

rather than being removed.

2.3.3 Reparamaterizing Ecopath

The original CBFEM, tuned to fisheries data from 1950, is able to produce trends in fish biomass stocks

(Christensen et al. 2008). However, because the I & E ‘fishery’ was not included during model

optimization simulations, we re-optimized basic Ecopath parameters to ensure their ability to predict the

consequences of reductions in I & E. To do this, we used a Monte Carlo optimization procedure to search

relevant combinations of Ecopath parameter space (i.e., parameters that meet the assumptions of mass

balance) that produced a better fit of model output to time-series data including I & E. Models were

conditioned on fisheries data from 1950-2002, including I & E data beginning in 1980, when AIF from

CWIS were > 90% current values in the Chesapeake Bay (based on operational dates for power

generating stations). During this time period, we assumed that I & E losses did not vary.

2.4 Simulation Scenarios and Model Output

We simulated four scenarios using the modified CBFEM. For all simulations, parameters remained

constant unless noted, simulation began in 1950 (start of time-series data), and proceeded 40 years

beyond available time-series data. These scenarios included:

 Baseline: I & E remained at current levels throughout the simulation

 Immediate I & E reduction: I & E is set to zero throughout the simulation

 Gradual I & E reduction: I & E decreases at 2% per year

 I & E increase: I & E increases at 2% per year

The value used for I & E reduction and increase (i.e., 2%) does not represent any particular policy

scenario. These I & E treatments were included to provide a useful estimate of the ecological effects of

gradual changes in the magnitude of CWIS AIF in the Chesapeake Bay. Model output represents biomass

within each pool on an annual basis, and was tested for community-level and biomass-pool changes 5, 10,

15, 25, and 40 years following the end of time-series data (i.e., years after 2002). All statistics were

calculated in R (R Development Core Team 2008), and null hypotheses were rejected for  < 0.05.

2.4.1 Community-level changes

Model output was tested for changes to the Chesapeake Bay community by I & E treatment and through

simulated time using two measures. First, the effects of I & E treatment and time on overall community

structure were tested using permutational multivariate analysis of variance (PERMANOVA) on BrayCurtis distances (Anderson 2001; McArdle and Anderson 2001; Oksanen et al. 2008). This procedure
Abt Associates Inc., May 19, 2010 Ecopath Simulations of Chesapeake Bay 5

describes how multivariate variability in data can be attributed to various I & E treatments and the

covariate of simulation time.

Second, biomass pool data were used to generate values of Simpson’s Index of Diversity (D):



 

S

i

D pi

1

2

1

where S is the number of biomass pools, and piis the proportionate biomass of biomass pool i. Values of

D range between 0 and 1, and represent the probability that two individuals sampled at random will be

from different biomass pools (Magurran 2004). Effects of I & E (factor) and time (covariate) on

Simpson’s Index were tested using analysis of covariance (ANCOVA) (Gotelli and Ellison 2004). Prior to

analysis, the assumptions of ANCOVA were tested by visually inspecting plots of model residuals against

predicted values, and testing for significant interaction terms between the covariate and main factor.

2.4.2 Changes in individual biomass pools

To document changes in biomass pools through time, we standardized all reported output to the baseline

simulation (to control for non-equilibrium conditions at the beginning of simulation), and reported

changes as absolute and proportionate increases in biomass. In recognition of model variability and

uncertainty, only differences that exceed an arbitrary (but minimal) threshold are reported. For

proportionate biomass data, this threshold was set as a 0.25% deviation from baseline model runs. For

absolute changes to biomass, the threshold was set at 1 kg/km2. Because the surface area of suitable

habitat for many fish stocks within the Chesapeake Bay is approximately 10,000 km2(Christensen et al.

2008), a change of 1 kg/km2represents a bay-wide change of 10 metric tons, or approximately 22,000 lbs.

3 Results

3.1 Model Inertia

Due to residual model inertia from previous policy choices and fisheries pressure, biomass pools in the

CBFEM were not in equilibrium at the end of time series data (when I & E was altered in the model).

Because ecological systems with major fisheries are highly dynamic, model inertia is not surprising, nor

does it reduce the effectiveness of EwE in estimating average effects of I & E losses within the

Chesapeake Bay. As a consequence of model inertia, biomass pools in the baseline simulation (as well as

all I & E treatment simulations) did not approach equilibrium values for 20 years of simulation (Table 1,

Appendix 2). Although the pool magnitude of plankton did not change appreciably, the magnitude of

many finfish biomass pools at equilibrium was substantially different than the magnitude of these same

pools at the end of time series data. At equilibrium, several biomass pools had increases of >10%,

including young of year and adult bluefish, catfish, and resident striped bass. Pools with decreases of

>10% included alewife & herring, Atlantic croaker, hard clam, sandbar shark, spot, migratory striped bass

and weakfish (Table 1, Appendix 2).

3.2 Community-level changes

The effect of simulation time on Simpson’s Index was statistically significant, explaining 50% of the

variability in the data (Table 2). Conversely, I & E treatment had no detectable effect on Simpson’s Index

(Table 2). Interestingly, despite substantial shifts in individual biomass pools through time, values of

Simpson’s Index only ranged between 0.849 and 0.861. The minimal range observed suggests that the

diversity of the Chesapeake Bay (as represented by the CBFEM) is stable through time (Magurran 2004),

and that the significance of simulation time in the statistical model would not be biologically relevant

(Gotelli and Ellison 2004).
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The stability in community diversity is supported by PERMANOVA analysis of overall community

structure. Total changes within the ecosystem were minimal (Table 3), despite a detectable influence of

simulation time on community structure. This suggests that large-scale shifts in the ecosystem do not

occur, and that the overall ecosystem remains relatively stable.

3.3 Changes to individual biomass pools

Due to the substantial changes in biomass through simulation time attributable to model inertia (Table 1),

all I & E treatment effects were standardized to changes from baseline biomass values. Because all

demographic parameters within the model were identical, these changes can only be attributed to

differences in the I & E treatment proscribed.

3.3.1 Relative biomass changes within pools

Measured as a percent change from baseline data, the effects of reducing I & E on biomass pools within

Chesapeake Bay are relatively small. The magnitude of these changes, however, are in direct proportion

to the reduction of I & E mortality imposed by various simulations (Table 4). However, due to the indirect

nature of food web interactions and time delays due to baseline model inertia, reducing I & E does not

result in an increase in biomass for all species (Table 4).

3.3.1.1 Change with elimination of I & E

When all I & E losses were removed from the CBFEM, 16 of 45 biomass pools showed changes > 0.25%

(relative to baseline data) after 40 years of simulation (Table 4). The fact that these changes are driven

through trophic interaction is affirmed by the fluctuating directionality of change observed in some

biomass pools. For example, 5 years following the cessation of I & E losses, Spot populations were

0.36% higher than expected under baseline data (Table 4). Over time, however, trophic interactions led to

a decline in Spot populations relative to baseline data, with a decrease of 0.31% after 40 years of

simulation. These changes through time appear to be a consequence of time lags in the accumulation of

biomass in other pools which prey upon spot (e.g., bluefish, striped bass and weakfish).

Interestingly, the majority of commercially important fisheries species show population increases of >

0.25% (Table 4). At simulation equilibrium, the largest increases occur for Weakfish, which experience a

population increase of 2% (relative to baseline data) within 5 years of I & E closure, and a population

increase in excess of 5% by 25 years (Table 4). Other commercially important species pools with

detectable increases at model equilibrium include Bluefish (1.4%), Striped Bass [Migratory (1%) and

Resident (0.7%) populations], Atlantic Croaker (0.4%), white perch (0.3%), flatfish (0.7%) and various

reef associated fish [such as smallmouth bass and tautog] (2.2%). These increases in biomass are offset in

the model by decreases in the biomass of sea nettles (-0.3%), littoral forage fish (-0.25%), and bay

anchovy (-0.25%) (Table 4). The directionality of these changes suggests that as I & E decreases, there is

an observable pattern of an increased biomass of fish at higher trophic levels, and a decrease in the

biomass of forage fish.

3.3.1.2 Change with reduced I & E

When simulated I & E losses decreased at a rate of 2% per year, the general direction of change in

biomass pools relative to baseline data was as the same as when I & E losses were ended abruptly.

However, the time required to observe these changes (beyond a threshold of 0.25%) increased

substantially (Table 3). For example, after 5 years simulation, no biomass pools had changes in excess of

0.25% (compared with 14 pools when I & E was abruptly eliminated), and only two pools passed the

threshold after 15 years (15 pools when I & E eliminated). By 40 years of simulation, however, 10

biomass pools had observable differences (Table 3).
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When changes to biomass pools surpassed the threshold of 0.25%, the magnitude of these changes was

substantially smaller in simulations when I & E was gradually reduced than when I & E was stopped

immediately. On average, the magnitude of these proportionate changes were 48.0±5.6% smaller (Table

3).

3.3.1.3 Change with increased I & E

When I & E losses increased at a rate of 2% per year, the direction of change in biomass pools was

exactly opposite of those changes observed when I & E losses decreased. Briefly, the vast majority of

biomass pools showed appreciable losses over 40 years of model simulation (Table 4). In many cases, the

magnitude of proportionate decline exceeds the magnitude of increase that occurs for the same pools

when I & E losses are ended. Not all pools exhibit decreases in mass with increases in I & E. Those pools

that increase include forage fish (0.27%), sea nettles (0.30%) and Non-Reef Associated fish (0.63%).

3.3.2 Absolute biomass change within pools

Although the directionality of changes in absolute and proportional biomasses are (by definition)

identical, an examination of absolute changes from baseline biomass data through time shows a slightly

more nuanced description of changes within the CBFEM as a consequence of I & E. Overall, 30 of 46

biomass pools exhibited changes in excess of 1 kg/km2in one or more I & E treatments. Due to the large

size of Chesapeake Bay, even small changes in absolute biomass pools may reflect substantial changes in

total biomass. Additionally, because most fisheries are managed on the basis of absolute fish population

size, these results may be more immediately applicable to estimates of altered fish harvest as a

consequence of changes in I & E.

Generally, the largest changes in absolute biomass occurred in the largest biomass pools (Table 5). In

some cases, these changes exceeded 100 kg/km2(approximately 2.5 million pounds bay-wide). As with

observed changes to biomass proportions, the magnitude of changes in absolute biomass is not always

straightforward due to the indirect nature of food web interactions and time delays due to baseline model

inertia (Table 5.)

3.3.2.1 Change with elimination of I & E

When I & E losses ended at the beginning of simulated data, changes in biomass relative to baseline data

were rapid, and were clearly representative of some trophic pathways within the CBFEM (Figure 1, Table

5). For example, after I & E losses ceased, substantial, immediate and negative changes occurred within 5

years in the biomass pools of alewife and herring, littoral forage fish, bay anchovy, zooplankton, in- and

epi-fauna, and submerged aquatic vegetation (SAV). All of these pools serve as important food sources

for biomass pools in higher trophic levels (Figure 1).

The largest change in biomass observed in any pool occurred in adult menhaden, which increased in

biomass by a minimum of 85 kg/km2relative to baseline data when I & E was eliminated (Table 5). These

changes represent an increase of nearly 1000 tons in biomass throughout Chesapeake Bay. Although this

increase does not represent a large proportional change in menhaden biomass, it may reflect an

economically important increase at the scale of the Chesapeake. Similarly, substantial decreases were

observed for the biomass pool of in- and epi-fauna, which decreased a minimum of 32 kg/km2below

baseline biomass (Table 5). Other biomass pools with large increases from baseline data include Atlantic

croaker, bluefish, striped bass (both migratory and resident) and adult weakfish. Substantial declines in

biomass were observed in littoral forage fish, zooplankton, and SAV (Table 5).

3.3.2.2 Change with reduced I & E

The effect of reducing I & E losses on biomass pools were qualitatively similar but quantitatively

different than the effects of I & E elimination. These changes include increases in the biomass of high

trophic level predatory fish such as weakfish and striped bass, and decreases in forage fish, zooplankton,
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SAV, as well as in- and epi-fauna. Although the magnitude of these changes increase through time with

respect to baseline data, they never approach the magnitude of changes observed shortly after I & E losses

are eliminated. For example, after 5 years of simulation, the biomass of adult menhaden increase 6.5

kg/km2 when I & E is reduced, but decrease 105.3 kg/km2 when I & E is eliminated (Table 5). Although

the magnitude of difference in biomass between I & E treatments decreases with time, the productivity

differences at higher trophic levels represent hundreds of tons of commercial fish available per year. For

example, increases in striped bass [migratory and resident] and weakfish biomasses (19.54, 27.52 and

20.10 kg/km2, respectively)) observed within 5 years of I & E cessation are not achieved after 40 years of

I & E losses declining 2% per year (13.88, 9.61 and 18.63 kg/km2).

3.3.2.3 Change with increased I & E

When I & E losses slowly increase through time, their effect on the biomass of high trophic-level biomass

pools is substantial. With respect to baseline data, increasing I & E losses led to large decreases in

Weakfish (-32.45 kg/km2), striped bass (-28.21 and -21.18 kg/km2for migratory and resident fish),

bluefish (-13.93 kg/km2) Atlantic croaker (-15.34 kg/km2) and adult menhaden (-104.82 kg/km2) after 40

years of model simulation. Additionally, the biomass pools with substantial increases, namely alewife &

herring (9.76 kg/km2), littoral forage fish (15.61 kg/km2), meso- and micro-zooplankton (19.41 and 13.12

kg/km2, respectively), in- and epi-fauna (48.56 kg/km2) and SAV (15.76 kg/km2), suggest that the system

was moving to a less diverse, lower-trophic level equilibrium (Pauly et al. 1998).

4 Model limitations and future directions

Although EwE provides a very sophisticated modeling approach for estimating ecosystem level impacts

of I & E losses, there are several limitations which must be noted. Some of these limitations are inherent

to the model, and some are data limitations. To address some of these limitations, future work could

explore incorporating spatially-explicit routines and increasing the number of biomass pools with age

structure in the CBFEM.

4.1 Structural Limitations

All models use simplified assumptions to make predictions. One of the largest simplifying assumptions

within the CBFEM is that the model deals with bay-wide averages, and is not spatially explicit. When

dealing with point-source impacts such as I & E, however, such an assumption may underestimate

impacts and/or mask potential nonlinearities within the system. For example, if spawning aggregations

were to occur near high-volume CWIS, averaging the impact throughout the bay would be problematic

because impacts would be highly localized. These spatially-structured effects could be explored in future

work with the spatially-explicit Ecospace routine within the EwE model framework (Christensen et al.

2008).

A second major limitation inherent to the dynamics of biomass pools within the CBFEM is the lack of

population structure for the majority of biomass pools within the model: currently, only 7 biomass pools

incorporate population age structure. This simplifying assumption is likely to lead to underestimates of I

& E impacts within the Chesapeake, because the majority of I & E losses occur early in the life-history of

most species. Due to the nature of the mathematical functions driving EwE, however, the disproportionate

effects of I & E losses on eggs and juvenile fish cannot be accurately portrayed in the implicit population

dynamics of the model. These nonlinear effects of I & E losses on age-structured populations can be seen

in model output of the 7 biomass pools with age structure. These biomass pools, including Bluefish,

Menhaden, Striped Bass, Weakfish, and White Perch, are over-represented among those pools with high

proportionate and absolute changes in biomass (Table 4, Table 5). Consequently, addressing this

limitation should be a key focus of future work on estimating I & E impacts using EwE. Two possible
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routes to investigate would include using estimates of foregone yield to drive I & E losses within the

model, or creating additional age-structured biomass pools within the model.

4.2 Data-based limitations

Like all models, the accuracy of CBFEM output is limited by the accuracy of its input data. In the case of

the model simulations described above, the weakest data source is I & E inputs. First, unlike fish

population estimates, and the catch of other fisheries, they are not bay-specific. Instead, they are derived

from estimated regional-level I & E losses. These regional-level I & E losses are themselves treated as

constant, despite being generated from data that vary in both space and time. As such, although I & E

losses are likely to fluctuate through time with changes in fish populations naturally, they are unable to

fluctuate in the model. Furthermore, there are several biomass pools, including oysters and other shellfish,

that do not have estimates of I & E losses. Consequently, trophic discontinuities may occur within model

simulations that are not present in the actual ecosystem.

Other data-based limitations to CBFEM output include various assumptions about environmental policy.

During simulation, it was assumed that fisheries-related mortality and other environmental forces

(including nutrient availability, climate, water quality, etc.) remained constant. Since these forces can

have substantial impacts on communities and the ecosystem goods and services they provide (Steneck and

Carlton 2001; Ronnback et al. 2007), model predictions should be considered qualitatively.

5 Key findings

The CBFEM provides a tool useful in estimating community-level effects of I & E losses within

Chesapeake Bay, and as a case study for I & E losses more generally. Importantly, varying I & E

treatment within the model did not lead to substantial community-level shifts within Chesapeake Bay.

This suggests that the structure of the marine ecosystem within the bay is not significantly impacted by I

& E losses. This lack of a community-level shift, however, does not suggest that quantitative estimates of

the effects of I & E on the population structure of individual fish stocks are negligible. Indeed, I & E

treatment led to substantial changes in the absolute biomass of several commercially and recreationallyimportant species of fish, including striped bass, weakfish, menhaden, and bluefish. Moreover, changes

were observed through several trophic levels as a consequence of changes in I & E loss rates. However, as

a consequence of incomplete model inputs through time and structural limitations of the model itself, the

magnitude of I & E impacts in CBFEM output are likely to underestimate its true effects within the

Chesapeake, particularly on a local level. Consequently, population and species-specific fisheries models

are likely to provide more accurate quantitative estimates of I & E effects on fish stocks and fisheries

impacts.

6 References

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JH, Walters CJ, Wood RJ, Townsend H (2008) Fisheries ecosystem model of the Chesapeake

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Abt Associates Inc., May 19, 2010 Ecopath Simulations of Chesapeake Bay 11

Table 1 – Changes to biomass pools through time in baseline Ecopath model run.

Biomass Percent Change in Biomass from 0 Years (kg/km2)

Biomass Pool 0 Years 5 Years 10 Years 15 Years 25 Years 40 Years

Alewife & Herring 5446.89 -16.89 -17.88 -17.62 -17.32 -17.24

American Eel 3415.15 -2.59 -4.46 -4.47 -4.49 -4.42

Atlantic Croaker 5309.96 -33.70 -48.38 -52.24 -53.78 -54.03

Bay Anchovy 3625.26 -1.41 -0.91 -1.13 -0.84 -0.92

Benthic Algae 1515.39 -3.01 -4.41 -5.02 -4.83 -5.42

Black Drum 616.64 4.40 3.14 0.77 -2.73 -4.56

Blue Crab (Adult) 2657.88 3.09 8.35 8.24 10.20 6.57

Blue Crab (YOY) 1652.83 6.59 -6.73 -0.13 -4.40 0.77

Bluefish (Adult) 742.85 19.89 30.90 36.04 40.20 41.46

Bluefish (YOY) 44.50 8.21 13.80 16.39 18.50 19.07

Catfish 1024.04 12.90 20.61 23.86 24.92 24.57

Ctenophores 3717.30 0.53 1.49 1.84 2.33 2.31

Detritus 1056.48 0.61 0.96 1.15 1.31 1.27

Gizzard Shad 2250.10 -1.54 -4.92 -8.04 -11.53 -13.09

Hard Clam 4849.21 -11.46 -20.42 -21.72 -23.27 -22.73

Littoral Forage Fish 5557.62 0.33 1.65 2.74 2.70 2.74

Menhaden (0-1) 19894.93 0.75 0.93 0.83 0.87 0.73

Menhaden (Adult) 38970.09 1.95 0.86 0.29 -0.21 -0.53

Mesozooplankton 11117.92 0.43 1.42 1.89 2.41 2.45

Microzooplankton 7081.41 0.97 1.85 2.27 2.68 2.62

Non-piscivorous Seabirds 1477.65 -2.45 -4.92 -3.51 -3.13 -2.90

Non-Reef Associated Fish 138.60 5.27 10.10 13.25 16.11 17.33

Other Elasmobranchs 581.26 -1.88 -3.41 -3.80 -3.10 -1.48

Other Flatfish 178.81 4.17 8.95 11.66 13.06 13.32

Other In- and Epi-fauna 75407.17 2.98 4.94 5.33 5.59 5.89

Other Suspension Feeders 6853.62 -5.08 -6.72 -8.30 -8.25 -7.95

Oyster (Adult) 163.10 -0.77 -2.29 -3.41 -5.82 -9.26

Oyster (YOY) 63.26 -1.16 -2.54 -4.34 -6.70 -9.75

Phytoplankton 27236.39 0.31 0.24 0.35 0.30 0.31

Piscivorous Birds 337.54 0.90 1.62 2.13 2.78 3.17

Reef-Associated Fish 249.58 1.83 -0.52 0.08 0.71 0.99

Sandbar Shark 120.46 -29.32 -50.32 -60.53 -67.83 -69.80

SAV 9997.89 0.85 1.89 1.62 1.98 1.90

Sea Nettles 683.63 0.64 2.76 3.23 4.22 4.30

Spot 1973.11 -23.58 -30.93 -32.57 -34.12 -34.49

Striped Bass (Migratory) 2995.25 -15.99 -14.15 -15.10 -16.25 -16.49

Striped Bass (Resident) 2176.08 14.95 8.68 6.83 7.03 6.77

Striped Bass (YOY) 13.91 2.18 -0.15 -0.07 0.24 0.23

Summer Flounder 414.24 -3.29 -6.75 -7.25 -7.39 -7.34

Weakfish (Adult) 790.75 -3.86 -3.73 -2.94 -3.03 -3.03

Weakfish (YOY) 34.72 -10.91 -15.06 -16.55 -16.78 -16.87

White Perch (Adult) 332.78 0.62 1.47 2.18 2.50 2.69

White Perch (YOY) 3.53 0.68 2.10 2.56 3.07 3.29

Note: Rapid changes from year 0 to year 5 indicates that the CBFEM was not in equilibrium at

the end of time-series data.
Abt Associates Inc., May 19, 2010 Ecopath Simulations of Chesapeake Bay 12

Table 3: Results of PERMANVOA testing the effects of time and I & E treatments on overall

community structure of the Chesapeake Bay ecosystem estimated by Ecopath simulation.

DF=degrees of freedom, MS = mean squares

Factor DF MS (x10-3)

* F p

Time 1 4.422 182.512 0.001

I & E 3 0.015 0.614 0.625

Error 159 0.024

Table 2: Results of ANCOVA testing the effects of time and I & E treatments on values of

Simpson’s Diversity Index estimated from 40 years of annual Ecopath simulation output. DF =

degrees of freedom, MS = mean squares

Factor DF MS F p

Time 1 6.280 165.959 <0.001

I & E 3 0.001 0.026 0.994

Error 159 0.038
Abt Associates Inc., May 19, 2010 Ecopath Simulations of Chesapeake Bay 13

Table 4: Proportionate change to biomass pools (with respect to baseline data) during Ecopath simulation by I & E treatment and time. Changes

> 0.25% from baseline data at each time step are noted.

Simulation Time 5 Years 10 Years 15 Years 25 Years 40 Years

Biomass Pool / I & E Trt None Red. Inc. None Red. Inc. None Red. Inc. None Red. Inc. None Red. Inc.

Init. Biomass

(kg/km2)

American Shad 0.30 0.40 0.56 -0.56 0.01

Atlantic Croaker 1.03 0.87 0.61 0.44 -0.36 0.42 0.28 -0.63 5309.96

Bay Anchovy -0.25 3625.26

Bluefish (Adult) 0.88 1.27 1.39 -0.29 1.41 0.43 -0.64 1.40 0.68 -1.33 742.85

Bluefish (YOY) 0.52 0.60 0.62 0.62 -0.29 0.60 0.30 -0.61 44.50

Littoral Forage Fish -0.28 -0.26 -0.26 -0.25 0.27 5557.62

Menhaden (Adult) 0.27 -0.27 38970.09

Non-Reef Associated Fish -0.45 -0.66 -0.59 -0.60 0.32 -0.60 -0.31 0.63 138.60

Other Flatfish 0.41 0.57 0.65 0.71 -0.33 0.73 0.35 -0.69 178.81

Reef-Associated Fish 1.67 2.02 0.27 -0.31 2.17 0.44 -0.55 2.23 0.76 -1.15 2.22 1.14 -2.28 249.58

Sandbar Shark 0.50 0.63 0.69 -0.28 0.70 0.34 -0.61 120.46

Sea Nettles -0.26 -0.27 -0.28 -0.28 -0.29 0.30 683.63

Spot 0.36 -0.30 -0.31 1973.11

Striped Bass (Migratory) 0.78 1.14 1.11 -0.28 1.05 0.38 -0.57 1.06 0.55 -1.13 2995.25

Striped Bass (Resident) 1.10 0.78 0.64 -0.26 0.74 0.30 -0.49 0.73 0.41 -0.91 2176.08

Striped Bass (YOY) -0.29 -0.27 13.91

Summer Flounder 0.27 414.24

Weakfish (Adult) 2.64 3.53 0.49 -0.56 4.83 0.88 -1.07 5.07 1.56 -2.20 5.18 2.43 -4.23 790.75

Weakfish (YOY) 0.36 34.72

White Perch (Adult) 0.26 0.28 0.31 0.31 0.31 -0.35 332.78

I & E treatments: (1) None: No I & E losses, (2) Reduced: I & E losses decline 2% per year, (3) Increased: I & E losses increase 2% per year
Abt Associates Inc., May 19, 2010 Ecopath Simulations of Chesapeake Bay 14

Table 5: Absolute change (in kg/km2) to biomass pools during Ecopath simulation by I & E treatment and time. Differences > 1 kg/km2from

baseline data are noted.

Simulation Time 5 Years 10 Years 15 Years 25 Years 40 Years Initial Biomass

Biomass Pool / I & E Trt None Red. Inc. None Red. Inc. None Red. Inc. None Red. Inc. None Red. Inc. (kg/km2)

Alewife & Herring -7.81 -9.34 -1.17 1.32 -8.89 -1.94 2.42 -9.01 -3.24 4.93 -9.07 -4.75 9.76 5446.89

American Eel -2.85 -4.82 -4.85 1.08 -4.60 -1.59 2.34 -4.50 -2.37 4.74 3415.15

Atlantic Croaker 36.24 2.00 -2.09 23.93 3.58 -4.12 15.49 4.34 -5.58 10.91 5.46 -8.88 10.23 6.72 -15.34 5309.96

Bay Anchovy -5.23 -7.47 -8.51 -1.42 1.70 -8.91 -2.69 3.86 -9.07 -4.32 8.19 3625.26

Benthic Algae -1.12 -1.52 -1.71 -1.75 1.35 1515.39

Blue Crab (Adult) -3.47 -2.20 -2.42 -2.11 1.42 -2.49 -1.34 2.78 2657.88

Blue Crab (YOY) -1.45 -1.37 -1.04 1.16 1652.83

Bluefish (Adult) 7.82 12.37 1.33 -1.50 14.07 2.42 -2.96 14.72 4.52 -6.63 14.72 7.15 -13.93 742.85

Ctenophores -5.08 -5.34 -5.54 -1.28 1.64 -5.69 -2.06 3.19 -5.91 -3.04 6.22 3717.30

Gizzard Shad 1.04 1.55 1.90 2.49 2.84 1.13 -2.06 2250.10

Hard Clam 2.04 3.34 3.13 2.95 1.04 -1.52 3.21 1.59 -3.11 4849.21

Littoral Forage Fish -13.31 -16.01 -1.95 2.19 -14.70 -3.16 3.93 -14.64 -5.21 7.91 -14.49 -7.63 15.61 5557.62

Menhaden (0-1) -5.01 -6.77 -7.79 -7.51 -1.69 1.91 -7.02 -3.04 4.56 19894.93

Menhaden (Adult) 105.30 6.54 -6.89 89.65 15.34 -17.83 87.81 22.50 -29.03 88.51 34.78 -54.96 91.86 49.36 -104.82 38970.09

Mesozooplankton -15.76 -1.22 1.30 -16.47 -2.64 3.09 -16.94 -4.01 5.16 -17.46 -6.41 9.98 -18.19 -9.40 19.41 11117.92

Microzooplankton -10.84 -11.61 -1.73 2.01 -12.07 -2.68 3.42 -12.32 -4.37 6.70 -12.69 -6.48 13.12 7081.41

Non-Reef Associated Fish -6.54 -9.24 1.11 -8.35 -1.76 2.17 -8.53 -2.98 4.51 -8.57 -4.43 9.09 138.60

Other Elasmobranchs -1.23 581.26

Other Flatfish 1.10 1.29 1.43 1.48 -1.40 178.81

Other In- and Epi-fauna -89.11 -5.58 5.83 -46.05 -11.09 13.00 -36.53 -13.66 18.16 -31.10 -17.46 29.33 -32.02 -20.99 48.56 75407.17

Other Suspension Feeders -1.73 -3.98 -5.10 1.01 -5.89 -1.66 2.42 -5.80 -2.68 5.10 6853.62

Reef-Associated Fish 4.23 5.03 5.43 1.11 -1.38 5.60 1.92 -2.88 5.60 2.88 -5.74 249.58

SAV -13.29 -14.23 -2.06 2.37 -14.93 -3.22 4.08 -15.18 -5.30 8.06 -15.49 -7.87 15.76 9997.89

Sea Nettles -1.80 -1.91 -1.95 -2.01 1.11 -2.07 -1.06 2.17 683.63

Spot 5.47 -2.75 -3.96 -4.07 -1.22 1.21 1973.11

Striped Bass (Migratory) 19.54 1.03 -1.07 29.25 3.46 -3.92 28.32 5.84 -7.23 26.28 9.48 -14.34 26.40 13.88 -28.21 2995.25

Striped Bass (Resident) 27.52 1.73 -1.82 18.42 3.54 -4.13 14.99 4.65 -6.12 17.19 7.03 -11.38 17.02 9.61 -21.18 2176.08

Summer Flounder 1.09 414.24

Weakfish (Adult) 20.10 1.38 -1.45 26.90 3.70 -4.24 37.03 6.72 -8.24 38.90 11.98 -16.87 39.73 18.63 -32.45 790.75

White Perch (Adult) 1.05 1.06 1.05 -1.19 332.78

I & E treatments: (1) None: No I & E losses, (2) Reduced: I & E losses decline 2% per year, (3) Increased: I & E losses increase 2% per year
Abt Associates Inc., May 19, 2010 Ecopath Simulations of Chesapeake Bay 15

Appendix 1: Matched CMFEM Biomass pools and species output from I & E model of biomass losses

CBFEM Biomass Pool Species From I & E Model

Alewife & Herring Alewife, Atlantic Herring,

Blueback Herring, Herrings

American Shad American Shad

Atlantic Croaker Atlantic Croaker

Bay Anchovy Bay Anchovy

Black Drum Black Drum

Blue Crab (YOY)

Blue Crab (Adult)

Blue Crab, Other Commercial

Crabs

Bluefish (YOY)

Bluefish (Adult) Bluefish

Catfish Brown Bullhead, Bullhead spp.,

Channel Catfish

Gizzard Shad Gizzard Shad

Littoral Forage Fish

Atlantic Silversides, Chain

Pipefish, Northern Pipefish,

Rainbow Smelt, Scup, Silver

Perch, Silversides, Striped

Mullet, Striped Killifish,

Threespine Stickleback, Other

Forage Fish

Menhaden (0-1)

Menhaden (Adult) Atlantic Menhaden, Menhaden

Non-Reef Associated Fish

Butterfish, Grubby, Red Drum,

Red Hake, Sea Robin, Silver

Hake, Spotted Sea Trout

Other Flatfish Hogchoker, Windowpane,

Winter Flounder

Reef-Associated Fish

Cunner, Gobies, Seaboard

Goby, Smallmouth Bass,

Tautog

CBFEM Biomass Pool Species From I & E Model

Spot Spot

Striped Bass (YOY)

Striped Bass (Resident)

Striped Bass (Migratory)

Striped Bass

Summer Flounder Summer Flounder

Weakfish (YOY)

Weakfish (Adult)

Weakfish

White Perch (YOY)

White Perch (Adult) White Perch

American Eel

Benthic Algae

Ctenophores

Detritus

Hard Clam

Mesozooplankton

Microzooplankton

Non-piscivorous Seabirds

Other Elasmobranches

Other In- and Epi-fauna

Other Suspension Feeders

Oyster (Adult)

Oyster (YOY)

Phytoplankton

Piscivorous Birds

Sandbar Shark

SAV

Sea Nettles

Soft Clam

No relevant I & E model

output.
Abt Associates Inc., May 19, 2010 Ecopath Simulations of Chesapeake Bay 16

Appendix 2: Baseline Ecopath output.

Absolute Biomass (kg/km2)

Biomass Pool 0 Years 5 Years 10 Years 15 Years 25 Years 40 Years

Alewife & Herring 5446.89 4526.87 4473.24 4487.02 4503.71 4507.75

American Eel 3415.15 3326.62 3262.68 3262.61 3261.68 3264.27

American Shad 0.00 0.00 0.00 0.00 0.00 0.00

Atlantic Croaker 5309.96 3520.60 2741.02 2535.91 2454.10 2441.05

Bay Anchovy 3625.26 3574.18 3592.37 3584.37 3594.96 3591.79

Benthic Algae 1515.39 1469.84 1448.52 1439.36 1442.15 1433.24

Black Drum 616.64 643.80 635.99 621.38 599.81 588.49

Blue Crab (Adult) 2657.88 2739.96 2879.70 2876.88 2928.86 2832.46

Blue Crab (YOY) 1652.83 1761.68 1541.56 1650.66 1580.06 1665.51

Bluefish (Adult) 742.85 890.59 972.38 1010.60 1041.50 1050.86

Bluefish (YOY) 44.50 48.15 50.64 51.79 52.73 52.98

Catfish 1024.04 1156.16 1235.12 1268.37 1279.26 1275.61

Ctenophores 3717.30 3736.93 3772.70 3785.87 3803.91 3803.28

Detritus 1056.48 1062.95 1066.63 1068.61 1070.33 1069.87

Gizzard Shad 2250.10 2215.43 2139.31 2069.10 1990.76 1955.54

Hard Clam 4849.21 4293.37 3859.02 3795.84 3720.58 3746.86

Littoral Forage Fish 5557.62 5576.21 5649.10 5709.64 5707.93 5709.68

Menhaden (0-1) 19894.93 20044.79 20080.77 20059.32 20067.64 20039.34

Menhaden (Adult) 38970.09 39730.51 39306.90 39081.75 38887.85 38762.45

Mesozooplankton 11117.92 11166.12 11275.82 11327.80 11385.95 11390.08

Microzooplankton 7081.41 7150.41 7212.41 7242.27 7271.47 7266.76

Non-piscivorous Seabirds 1477.65 1441.46 1404.92 1425.80 1431.34 1434.84

Non-Reef Associated Fish 138.60 145.91 152.60 156.96 160.93 162.63

Other Elasmobranchs 581.26 570.31 561.46 559.18 563.27 572.69

Other Flatfish 178.81 186.27 194.82 199.67 202.17 202.63

Other In- and Epi-fauna 75407.17 77657.32 79135.06 79427.64 79620.69 79848.76

Other Suspension Feeders 6853.62 6505.20 6392.79 6284.79 6288.08 6308.75

Oyster (Adult) 163.10 161.84 159.36 157.53 153.60 148.00

Oyster (YOY) 63.26 62.53 61.65 60.52 59.03 57.10

Phytoplankton 27236.39 27320.23 27301.19 27330.57 27318.10 27320.53

Piscivorous Birds 337.54 340.57 343.00 344.72 346.91 348.25

Reef-Associated Fish 249.58 254.15 248.29 249.78 251.36 252.06

Sandbar Shark 120.46 85.14 59.85 47.55 38.76 36.38

SAV 9997.89 10083.33 10187.23 10160.17 10196.33 10187.70

Sea Nettles 683.63 688.00 702.47 705.67 712.44 713.04

Soft Clam 0.00 0.00 0.00 0.00 0.00 0.00

Spot 1973.11 1507.87 1362.81 1330.41 1299.89 1292.58

Striped Bass (Migratory) 2995.25 2516.26 2571.57 2542.93 2508.47 2501.19

Striped Bass (Resident) 2176.08 2501.35 2364.94 2324.80 2328.97 2323.41

Striped Bass (YOY) 13.91 14.21 13.89 13.90 13.94 13.94

Summer Flounder 414.24 400.62 386.27 384.19 383.63 383.83

Weakfish (Adult) 790.75 760.20 761.26 767.50 766.78 766.77

Weakfish (YOY) 34.72 30.93 29.49 28.98 28.90 28.87

White Perch (Adult) 332.78 334.83 337.67 340.05 341.09 341.74

White Perch (YOY) 3.53 3.55 3.60 3.62 3.63 3.64

Note: Values for American Shad and Soft Clams are not errors. These stocks crashed in timeseries data, and although not formally extinct, are of minimal biomass during model simulation.